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Biology
Cytology (study of the cells)
Basic characteristics of the cells:
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1. Ingestion – Intake of nutrients
2. Digestion – Enzymatic breakdown, hydrolysis, of food so it is small enough to be assimilated by the body.
3. Respiration – Metabolic process that produce energy for all the life processes.
4. Transport – Distribution of molecules from one part of a cell to another or from one cell to another.
5. Regulation – ability to maintain internal stability, homeostasis
6. Synthesis – Combining of small molecules or substances into larger, more complex ones.
7. Excretion -- Removal of metabolic waste.
8. Egestion – removal of undigested waste.
9. Reproduction – Ability to generate offspring.
10. Irritability – Ability to respond to stimuli
11. Locomotion – Moving from place to place
12. Metabolism – Sum total of all the life functions
Prokaryotic and eukaryotic cell - principal differences.
Similarities: Both have membranes, both use DNA as genetic material, similar basic metabolism.
Prokaryotic
- do not have nucleus or organelles
- bacteria and archaea
Eukaryotic
- have nucleus
- contain organelles
- ten times as large as prokaryotic cells
- more complex DNA that is formed into chromosomes
- Plant cells (eukaryotic) have cell wall of cellulose, animal cells (eukaryotic) do not.
The cell as an open system.
Open system exchange energy with its surroundings. The total energy content of the system plus its surroundings is always the same according to the first law of thermodynamics (energy cannot be created or destroyed).
Organic and inorganic components in the cell.
Micromolecules (Inorganic):
- water (60%)
- minerals; macronutrients: Ca, S, P, Mg, Fe, K. Micronutrients: Co, Mn, Mo, Zn, Cl. Some may act as buffers.
- gases: O2, Na, CO2, NH3. Soluble in water.
Macromolecules (Organic):
- Carbohydrates (C, H, O)
- Lipids (C, H, O, but poorer in O)
- Amino acids (C, H, O and sometimes S)
- Nucleotides (DNA, RNA)
Carbohydrates in the cell - basic structure and function.
- Sugars, starches, cellulose
- C, H, O in the ratio CH2O.
Monosaccharides: 3-7 carbon atoms.
- OH group attached to each C atom except one; this last forms a carbonyl group. Carbonyl group at the end of the chain = aldehyde. Any other position = ketone.
- OH groups makes it hydrophilic.
- Glyceraldehyde, dihydroxyacetone, ribose, glucose(aldehyde), fructose(ketone), galactose(aldehyde).
- Glucose(aldehyde) and fructose(ketone) = structural isomers (identical formula).
- ring form: alfa-glucose = OH opposite side of CH2OH
- ring form: beta-glucose = OH same side of CH2OH
Disaccharides: two sugars:
- Glycosidic linkage between carbon 1 and 4.
- Maltose = glucose + glucose
- Sucrose = glucose + fructose
- Lactose = glucose + galactose
Polysaccharide: starches, glycogen, cellulose
- Starch: alfa-glucose. Consists of amylose and amylopectin. Stored in amyloplasts.
- Glycogen: alfa-glucose. More extensively branched than starch. Stored mainly in muscle and liver cells.
- Cellulose: beta-glucose. Structural carbohydrate that make up plant walls.
Proteins in the cell - basic structure and function.
Amino acid consist of an amino group (-NH2), and a carboxyl group (-COOH) bonded to the alpha carbon.
- Dipolar. NH2 accepts protons, and COOH donates protons. This way, amino acids function as buffers.
- 9 of the standard 20 = Essential amino acids (must obtain from diet): isoluecine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine, histidine. + ariginine in children.
- Amino acids combine through peptide bonds, bonding the carboxyl carbon of one, and the amino nitrogen of another.
- Globular proteins are folded, compact, spherical shape. ex, enzymes, hormones.
- Primary structure: beads on a string.
- Secondary structure: alfa-helix(fibrous proteins that make up wool, hair, skin, nails. The coil allows the fibers to stretch under tension) and beta-pleated sheet (strong, but NOT elastic).
-> stabilized by hydrogen bonds.
- Tertiary structure: 3D structure.
- Quaternary structure: multiple polypeptides into a single, larger protein. Hemoglobin has quaternary structure due to association of two alpha globin and two beta globin polyproteins.
Enzymes and enzymatic reactions.
- Enzymes speeds up a reaction by lowering its activation energy.
- Some enzymes consist of only a protein. Others have two components: a protein, apoenzyme + a cofactor. The two components only gives catalytic activity when combined.
- Inorganic cofactor: Mg ion, Ca ion, iron, copper, zinc and Mn).
- Organic, nonpolypeptide functioning as a cofactor = coenzyme. ex; NADH, NADPH, FADH2, ATP, coenzyme A.
- Temperature for enzymes in the human body is 35-40 degrees. Even short exposure to high temperature denature the enzymes. Optimal pH to most enzymes is 6-8.
- Enzymes follows a series of reactions called metabolic pathway.
Functional and substrate specificity of enzymes.
Kinase is an enzyme that transfers a P from ATP to a substrate (specific substance it acts on) -> process called phosphorylation.
A regulatory protein(ex inhibitor) can bind to the receptor site / allosteric site on the enzyme protein kinase and thus change its shape, making the substrates unable to combine with the enzyme. However, when cAMP removes the allosteric inhibitor, the enzyme change to active shape, and the substrates fit into the active receptor site. This is called an Enzyme-Substrate (ES) complex.
Competitive: bind to active site. inhibitor competes with the normal substrate for the active site of the enzyme.
Non-competitive: changing shape of "key hole". inhibitor binds with the enzyme at a site other than the active site, altering the shape of the enzyme, and thereby inactiviting it.
Nucleic acids in the cell - structure and function.
Polymers of nucleotides, molecular units that consist of: a 5-carbon sugar (deoxyribose OR ribose), one or more phosphate groups (makes the molecule acidic), a nitrogenous base (double ring purine(A, G) or single ring pyrimidine (C, T. U replace T in RNA).
Some types of RNA have catalytic activity similar to that of enzymes.
Types of nucleic acids.
- In cells: Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).
RNA has one more OH group (actually only one more O, which forms OH), and are thus more reactive than DNA.
Nucleotides important in energy transfers:
- Adenosine triphosphate (ATP) and Guanosine triphosphate (GTP)
-> ATP can be converted to cyclic adenosine monophosphate (cAMP) by the enzyme adenylyl cyclase. GTP can be converted to cGMP. --> Cell signaling processes.
- NADH
Lipids in the cell - their structural and storage function.
- Hydrophobic because of small amount of oxygen.
- Fats, phospholipides, carotenoids, steroids, waxes.
Fats/triglyceride:
- one glycerol + 3 fatty acids. Hydroxyl(-OH) from glycerol bonds with carboxyl(-COOH) on fatty acid. Forms ester linkage.
- about 30 different fatty acids; ex, butyric acid, and oleic acid.
- Saturated fatty acid: contain maximum number of Hydrogen atoms. Animal fat. Solid, because linear hydrocarbon chain. Van der waals interaction limiting motion.
- Unsaturated fatty acid: double bonds. Liquid, because double bond produces a bend in the hydrocarbon chain, and thus limiting van der waals interactions -> freer molecular motion.
-ex; oleic acid and linoleic acid (unsaturated) are cis configurated. When fatty acids are artifically hydrogenated (ex when making margarine), the double bonds can become rearranged resulting in trans configuration. Because trans configuration does NOT produce a bend at the site of double bond, they are more solid. Like saturated fatty acids, they increase the risk of cardiovascular disease.
Phosphilipids:
- amphipathic lipids; components of cell membranes.
- consists of glycerol: + two fatty acids at one end, + P group linked to an organic compound (ex N) at the other end.
Carotenoids:
- orange and yellow plant pigments.
- ex; beta-carotene (-> converted to vitamin A -> converted to retinal)
- consist of isoprene units.
Steroids:
- 4 attached rings: 3 x six carbon rings, 1 x five carbon ring.
- ex; cholesterol, bile salt, reproductive hormones, cortisol.
Biomembranes:
Composition:
- consists of a phospholipid bilayer with embedded proteins that may constitute close to 50% of membrane content.
- Cholesterol is very abundant and necessary in membranes of eukaryotic cells.
- double bonds in fatty acid chains creates a bend and "loosen up" membrane packing, and thus are responsible for membrane permeability.
- High electrical resistance, Impermeable to ions, Permeable to gases and small lipid soluble molecules, Slightly permeable to water, Ability to self seal (always form closed compartments
Orientation of membrane macromolecules:
- Carbs: receptors, structure of plants cell wall
- Proteins: receptors
- Lipids: Membrane structure, insulation
Characteristics of the cytoplasm membrane:
- Allow cells to store energy, analogous to a dam on a river making a electrochemical gradient.
- membrane fluidity allows molecules in the membrane to move laterally on the same side of the bilayer.
- Low temperature = motion of fatty acid chain is slowed. Cholesterol is put into the membrane as a buffer to lower the temperature at which the membrane lipids solidify, and stabilize fluidity. Cholesterol act as "spacers", restricting van der waals interactions that would promote solidifying. Cholesterol also prevent the membrane from becoming weakened at higher temperature.
Transport of molecules across membranes by diffusion and osmosis:
- Oxygen and carbon, and water are small enough to pass through the bilayer.
- Carrier proteins, transporters, bind the ion or molecule and undergo changes in shape, resulting in movement of the molecule across the membrane.
- Channel proteins forms tunnels.
- Porins are beta-shaped barrels (aka water gates).
Diffusion = from region of higher concentration to region of lower concentration.
Osmosis = special kind of diffusion. A solution with high solute concentration has low effective water concentration and a high osmotic pressure; low solute concentration has high effective water concentration and low osmotic pressure.
- the force that must be exerted by the piston to prevent the rise in fluid level is equal to the osmotic pressure of the solution.
The role of transport proteins in the transfer of metabolites across cell membranes.
Endocytosis and exocytosis - the process of phagocytosis and pinocytosis, the role of Golgi complex in exocytosis, the role of cytoskeleton in these processes.
- Phagocytosis = cell eating. Cell ingests large solid particles such as food or bacteria.
- Pinocytosis = cell drinking.
- The Golgi apparatus is modifying, sorting, and packaging macromolecules for exocytosis.
- Cytoskeleton use motor proteins and microtubules(tracks) for movement of molecules. Motor protein kinesin (+), dynein (-).
Osmosis - transport of the water across semipermeable membrane, hypertonic and hypotonic solutions, plant and animal cell in hypertonic and hypotonic environments.
- Isotonic solution = cell neither shrink or swell. Water pass in and out.
- Hypertonic solution = cell dehydrates and shrinks. Water diffuse out because higher concentration of dissolved substances outside the cell.
- Hypotonic solution = cell swell or burst. Water diffuse into the cell.
- An example of an animal cell showing the affects of hypertonicity is when your fingers wrinkle.
- Plants get their rigid cell walls when they are placed in hypotonic surroundings; water moves into the cell, filling their central vacuoles and distending the cell, building up turgor pressure. In hypertonic medium, the plant shrinks, aka plasmolysis.
Structure of the prokaryotic cell:
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Organisation of DNA, membranous and non-membranous structures, composition of the cell wall, ribosome characteristics.
- Nucleiod Region - They have no true nucleus as the DNA is not contained within a membrane or separated from the rest of the cell, but is coiled up in a region of the cytoplasm called the nucleoid or nuclear area.
- Capsule - Found in some bacterial cells, this additional outer covering protects the cell when it is engulfed by other organisms, assists in retaining moisture, and helps the cell adhere to surfaces and nutrients.
- Cell Wall - Outer covering of most cells that protects the bacterial cell and gives it shape
- Cytoplasm
- Cell Membrane
- Pili - Hair-like structures on the surface of the cell that attach to other bacterial cells. Shorter pili called fimbriae help bacteria attach to surfaces
- Flagella
- Ribosomes
- Plasmids - Gene carrying, circular DNA structures that are not involved in reproduction.
Structure of the eukaryotic cell
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Membranous structures of the cell
Nucleus, Golgi Apparatus, mitochondria, Lysosomes, ER, vacuoles, vesicles, peroxisomes and plastids
Characteristics and function, one- and two-membranous organelles, non-membranous structures of the cell
Non-membranous organelles: ribosomes, cytoskeleton.
- Ribosomes: Granules composed of rRNA and protein. Some attached to ER, and some free in cytosol. Synthesize polypeptides, by using an enzyme to join amino acids. Ribosomes have 4 binding sites: one for mRNA + E(xit), P(eptidyl), and A(minoacyl) binding sites for tRNA.
- Cytoskeleton:
- Microtubules: serve as tracks, used for movement. Kinesin (+), Dynein (-).
- Microfilaments: aka actin filaments: mechanical support, determine shape. Cannot contract, but can generate movement by rapidly assembling and disassembling. Myosin, actin and ATP is needed for this process.
- Intermediate filaments: mechanical strength, stabilize shape. ex, in keratin.
One-membranous organelles: golgi, ER, vesicles, vacuoles, lysosomes, peroxisomes.
- Golgi: Modifies proteins; packages secreted proteins; sorts other proteins to vacuoles and other organelles; manufactures lysosomes.
- ER: Synthesize lipids and modifies many proteins; origin of intracellular transport vesicles that carry proteins.
- Smooth ER: Lipid(phosphilipids and cholesterol, steroid hormones, including reproductive hormones) synthesis; drug detoxification; break down glycogen in liver; calcium ion storage.
---> alcohol stimulate liver to produce more Smooth ER, so as to detox better.
- Rough ER: Manufactures proteins.
- Vesicles: Small bubble within a cell, enclosed by lipid bilayer
- Vacuoles: Larger than vesicles, often a merging of many vesicles. Up to 80% of the volume of a plant cell may be occupied by a large central vacuole that contains water, stored food, salts, pigments, metabolic waste and compounds that are noxious to herbivores as a means of defense.
- Lysosomes: contains enzymes that break down ingested materials; break down damaged or unneeded organelles and proteins. Perform phagocytosis.
- Peroxisomes: contain the enzyme catalase which splits excess hydrogen peroxide to water and oxygen, rendering it harmless. Break down fatty acid molecules. Also detoxify toxic compounds, ex alcohol.
Two-membranous organelles: Nucleus, Mitochondria, Chloroplasts.
- Nucleus: DNA transcribes its information in mRNA, which moves into the cytoplasm to produce proteins. DNA are packed in chromosomes in the nucleus.
- Nucleolus: granular body within nucleus; consists of RNA and protein. Site of ribosomal RNA synthesis; ribosome subunit assembly. (Ribosome subunits are not put together until just outside the nucleus, in the cytoplasm).
- Mitochondria: Cellular aerobic respiration; transformation of energy originating from glucose or lipids into ATP energy. Important in programmed cell death (apoptosis) by releasing cytochrome c which activates caspases that cut up vital compounds in the cell.
- Chloroplast: contain chlorophyll; site of photosynthesis; Enzymes in the inner membrane(stroma) are used to convert CO2 and water to carbohydrate, by using energy trapped from sunlight. Disclike sacs, thylakoids is suspended in the stroma, and they are arranged in stacks called grana.
Characteristics and function, composition and function of the cytoskeleton, proteinous cellular structures
Characteristics of the nucleus, chromatine - composition, nuclear chromosomes structure and shape, extranuclear DNA in the cell - characteristics and function.
- Chromatin = DNA + structural proteins (ex histones). Chromosome = is only present during cell dividing, when the chromatin needs to be bundled up. When two chromosome come together to form a X, the whole complex is still called a chromosome, but each side of the X is referred to as a chromatid.
- Small circular chromosomes, called extranuclear, or cytoplasmic, DNA, are located in two types of organelles found in the cytoplasm of the cell. These organelles are the mitochondria in animal and plant cells and the chloroplasts in plant cells. Mitochondrial DNA (mtDNA) contains some of the genes that participate in the conversion of the energy of chemical
bonds into the energy currency of the cell—a chemical called adenosine triphosphate (ATP)—as well as genes for mitochondrial protein synthesis.
Metabolism: sum of all chemical activities.
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Catabolic and anabolic processes
- common anabolic hormones; growth hormone, IGF1, insulin, testosterone, estrogen
Energy exchange in the cell
Cells are open systems.
Primary source of energy in the cell
ATP: Adenine, Ribose(five carbon sugar), 3 x phosphate groups.
Aerobic and anaerobic metabolism
Aerobic:
Requiring O2. Electrons associated with the H atoms in glucose are transferred to O in a series of steps. Free energy of the electrons is coupled to ATP synthesis.
- Glucose is oxidized, Oxygen is reduced.
1) Glycolysis: Occur in cytosol.
Six-carbon glucose -> 2 x three-carbon of pyruvate. + 2ATP and NADH
2) Formation of acetyl coenzyme A: Occurs in mitochondria.
Pyruvate oxidized to acetate (two-carbon group) and combines with coenzyme A. + NADH. CO2 released as waste.
3) Citric acid cycle: mitochondria
Acetate group combines with oxaloacetate(four-carbon molecule), forming citrate(six-carbon molecule). Citrate recycled to oxaloacetate: CO2 released as waste. 2ATP+NADH and FADH2.
4) Electron transport and chemiosmosis:
Electrons removed from glucose preceding steps -> NADH and FADH2 -> electron chain. Energy used to transport H ions (protons) across the inner mitochondrial membrane, forming a proton gradient. H2O produced as well.
-> Chemiosmosis use proton gradient to produce ATP through Complex V: ATP Synthase.
Lipids are rich in energy because many H and few O:
- Six-carbon fatty acid -> 44 ATPs
- Glucose -> 36-38 ATPs
Anaerobic:
Inorganic substance; ex nitrate (NO3-) or sulfate (SO42-) instead of oxygen as terminal electron acceptor.
- Ex fermentation: does not involve electron transport chain. 2 ATP per glucose.
Oxidative phosphorylation in the eukaryotic and prokaryotic cells
Eukaryotes;
- These redox reactions carried out by electron transport chains within the cell's intermembrane wall mitochondria.
- Enzymes here use energy released from oxidation of NADH to pump protons across the inner membrane of the mitochondrion -> protons build up in the intermembrane space, and generates an electrochemical gradient across the membrane. Energy stored in this potential is then used by ATP synthase to produce ATP.
Prokaryotes;
- Electron transport chains are located in the cells' intermembrane space.
- Main difference; bacteria and archaea use many different substances to donate or accept electrons. Thus, they can grow under a wide variety of environments.
Anaerobic glycolysis in eukaryotic and prokaryotic cells,
- Prokaryotic: Alcohol- and lactate fermentation (toxic for the cell), when not enough O2.
- Eukaryotic: Lactic acid during short, strenuous activity, when not enough O2 present.
The use of energy released by oxidative phosphorylation,
The use of energy released during anaerobic glycolysis.
The cell as an energetically autonomous unit.
Autotrophy and its different types. Heterotrophy and its different types Autotrophs(producers): plants, algae, certain bacteria.
- carbon dioxide + water + light energy -> glucose + oxygen
Types:
Chemoautotrophs: make their own food by chemical means, ie. without light. Literally chemical-self-nutrition (Lithotrophs make use of inorganic compounds)
Photoautotrophs: use light as an energy source.
Heterothrophs(consumers/decomposers): animals and fungi. Depend on producers for food, energy and oxygen. Primary consumers eat producers, secondary consumers eat primary consumers.
- glucose + oxygen -> carbon dioxide + water + energy
Types:
Herbivores, such as cows, obtain energy by eating only plants.
Carnivores, such as snakes, eat only animals.
Omnivores, such as humans, eat both plants and animals.
Detritivores, such as earthworms, feed on dead matter.
Decomposers, such as fungi, break down organic matter.
Scavengers, such as vultures, consume the carcasses of other animals.
Characteristics of photosystem I and photosystem II
Photons hit PS II and splits H2O. Electrons are passed along the electron transport chain and donated to PS I.
=== Similarities ===
* Both photosystems consist of a complex of molecules embedded in thylakoid membranes of the chloroplast.
* Both contain chlorophyll molecules, which can convert light energy into chemical energy.
* In both photosystems, a photon causes an electron to reach a high energy level.
* In both photosystems, the energized electron must be passed to a chlorophyll molecule in the reaction center before it can leave the photosystem.
* Both contain carotenoid molecules.
=== Differences ===
* The chlorophyll molecules in the reaction center of photosystem II are P680 (sensitive to wavelengths up to about 680 nm), whereas those in photosystem I are P700, which can therefore respond to slighter longer wavelengths.
* Photosystem II contains plastoquinone, which passes the energetic electron to cytochromes b6 and f, but photosystem I passes the electron to ferredoxin.
* In non-cyclic photophosphorylation, photosystem II is associated with the photolysis of water and subsequent synthesis of ATP; photosystem I is associated with the conversion of NADP+ to NADPH.
* In cyclic photophosphorylation, only photosystem I produces an energized electron on receipt of a photon. Instead of producing NADPH, this electron travels to plastoquinone, and then to cytochromes b6 and f, as in the non-cyclic proceess
Genetic material and protein synthesis:
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Replication of DNA, transcription, translation, localisation of transcription and translation in prokaryotic and eukaryotic cells,
Semiconservative replication:
(1) Replication begins at specific sites called origin of replication.
(2) Here, DNA helicases break hydrogen bonds, thereby separating the two strands of DNA. Both strands replicate at the same time at the Y-shaped junction called the replication fork.
(3) As the DNA helicases separates the strands, Single-strand binding (SSB) proteins bind to single DNA strands and prevents the double helix from re-forming until the strands are replicated.
(4) As the strands are uncoiled, the enzyme topoisomerase breaks and rejoin the DNA strands in a more relaxed configuration to prevent excessive coiling during replication.
(5) DNA primase synthesizes short RNA primers at the point where replication begins. DNA polymerase then links nucleotide subunits to form a new DNA strand from a DNA template. It always proceed in a 5' -> 3' direction.
- The leading strand is synthesized toward the replication fork.
- The lagging strand is synthesized away from the replication fork.
(6) Only short pieces called Okazaki fragments can be synthesized. These fragments are joined by DNA ligase that links the 3' hydroxyl of one fragment to the 5' phosphate of the DNA next to it, forming phosphodiester linkage.
In bacteria: Plasmids are small, circular DNA molecules that carry genes separate from those on a bacterial chromosome.
Eukaryotic chromosome DNA contains multiple origins of replication; making bubbles that eventually merges.
Prokaryotic usually have only one origin of replication; the ends eventually meets.
Telomeres are protective end caps on chromosomes that retains important genetic information. These caps are short, noncoding, guanine-rich DNA sequences that repeat many times. Telomerase can lengthen this by adding repeating sequences. Telomerase is typically present in cancer cells and other cells that rapidly divide unlimited number of times.
Transcription and translation;
Transcription: Happen in nucleus in eukaryotic.
- Transcription is the general term for the synthesis of any kind of RNA on a DNA template
- From DNA to RNA. Uracil substitutes thymine.
- Three kinds of RNA are transcribed: mRNA, tRNA, rRNA.
- MessengerRNA carries the information for making a protein.
- TransferRNA; bonds with a specific kind of amino acid, and carries it to the ribosome. It can also recognize the appropriate mRNA codon for that particular amino acid because of tRNA's anticodon.
- RibosomalRNA is in globular form and is an important part of the structure of ribosomes. Also have catalytic functions needed during protein synthesis.
- Three RNA polymerases:
- RNA polymerase I catalyzes synthesis of several kinds of rRNA molecules that are components of the ribosome.
- RNA polymerase II catalyzes production of protein-coding mRNA
- RNA polymerase III catalyzes synthesis of tRNA and one of the rRNA molecules.
- Like DNA polymerases, RNA polymerases carry out synthesis in the 5'->3' direction. As RNA is synthesized in the 5'->3' direction, the DNA template is read in its 3'->5' direction.
- Promoter; the nucleotide sequence in DNA to which RNA polymerase initially bind.
- Termination RNA polymerase recognizes termination sequence, and thus RNA transcript and RNA polymerase are released. Stop codons; UAA, UGA, UAG.
- Bacterial mRNA are used immediately after transcription, without further processing. In eukaryotes, the original transcript, called precursor mRNA, is modified while still in the nucleus. These are posttranscriptional modification and processing activities that produce mature mRNA for transport and translation.
- At about 20-30 nucleotides long, enzymes add a 5' cap to the 5' end of the mRNA chain. This cap is 7-methylguanosine. Eukaryotic ribosomes cannot bind to an uncapped message. Capping also protects mRNA of degradation and explains why eukaryotic mRNA are much more stable than bacterial mRNA.
- Polyadenylation: may occur at the 3' end of the molecule. Here it usually lies a sequence of bases that serves as a signal for adding many adenine-containing nucleotides, known as poly-A tail. Longer the tail, longer the molecule persists in the cytosol.
- Intron = noncoding, intervening sequences. Much greater in combined length than exons.
- Exons = coding, expressed sequences.
Summary: For pre-mRNA to be made into a functional message:
(1) Must be capped and have a poly-A tail added
(2) introns must be removed and the exons spliced together to form a continuous protein-coding message.
Splicing exons involves association of several small nuclear ribonucleoprotein complexes (snRNPs) to form large ribonucleoprotein complex called spliceosome. Spliceosomes catalyze reactions that remove introns from pre-mRNA.
Translation:
- Conversion of nucleic acid language in mRNA into amino acid language of protein.
- Amino acids are covalently linked to their respective tRNA by enzymes called aminoacyl-tRNA synthetases, which use ATP.
- A codon is a triplet code that specifies one amino acid.
- Codons for amino acids and for start and stop signal are collectively named genetic code.
- Ribosomes, the site of translation, attach to the 5' end of the mRNA and travel along it, allowing the tRNAs to attach sequentially to the codons of the mRNA.
- The proteins free ribosomes makes are free to go wherever within the cell.
- The proteins made from bound ribosomes on RER stay in the ER and usually get trapped in a vesicle for transport.
- Ribosome has four binding sites, one for mRNA and three for tRNA (A, P, E)
- The tRNA that bears the first amino acid is called initiator tRNA. It carries the peptide methionine which is often removed later. Bacteria use fMet as the initiator tRNA.
- Peptide bond forms between the amino group of the new amino acid(5') and the carboxyl group of the preceding amino acid(3'). The formation also require the enzyme peptidyl transferase (RNA component).
5' NH2 -----------translation----------> COOH 3'
- Translocation: ribosome moves down the mRNA by one codon (toward the 3' end).
- Chaperones: ribosome-associated proteins that assist in the folding of the newly synthesized polypeptide chain into its 3D active shape.
The role of polymerases in replication and transcription, regulation of proteosynthesis
- Replication is controlled by the Watson-Crick pairing of the bases in the template strand with incoming deoxynucleotide triphosphates, and is directed by DNA polymerase enzymes
- Transcription ends when the RNA polymerase enzyme reaches a triplet of bases that is read as a "stop" signal. The DNA molecule re-winds to re-form the double helix.
- RNA polymerase I catalyzes synthesis of several kinds of rRNA molecules that are components of the ribosome.
- RNA polymerase II catalyzes production of protein-coding mRNA
- RNA polymerase III catalyzes synthesis of tRNA and one of the rRNA molecules.
Cell division:
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Haploid and diploid cells, the process of amitosis and mitosis, the origin and the role of the spindle and centromere of chromosomes
- Two sets of chromosomes = diploid chromosome number - diploid cell
- Single set of chromosomes = haploid chromosome number - haploid cell
- Three or more sets = polyploid cell
Humans have 2 sets of 23 chromosomes for a total of 46 chromosomes:
Autosomal chromosomes (non-sex chromosomes) - 22 sets of 2.
Sex chromosomes - 1 set of 2.
-> In humans, examples include having a single extra chromosome (such as Down syndrome), or missing a chromosome (such as Turner syndrome).
- Amitosis divides relatively simply, as the nucleus and cytoplasm are directly cut in two. Unlike regular mitosis, no spindles or the formation and appearance of chromosomes are involved in amitosis.
-> Mitosis a cell create an exact copy of itself. Amitosis a cell's nucleus splits into two.
- Each chromatid includes a constricted region called the centromere. Sister chromatids are tightly associated in the vicinity of their centromeres.
- Sister chromatids are physically linked by cohesins, which are particularly concentrated at the centromere.
- Attached to each centromere is a kinetochore, a multiprotein to which microtubules can bind.
- Microtubules radiate from each pole, and some of these protein fibers elongate toward chromosomes, forming the mitotic spindle, a structure which separates the duplicated chromosomes during anaphase.
Cell cycle and its phases, processes occurring during individual phases of the cell cycle, regulation of the cell cycle, cells during the phase GO, cells with the failure in the main control point.
G0 phase:
Cells that are not dividing usually become arrested in the G1 phase, and are said to be in a state called G0. Cell is neither dividing nor preparing to divide. Some cell types in mature organisms, such as parenchymal cells of the liver and kidney, enter the G0 phase semi-permanently and can be induced to begin dividing again only under very specific circumstances.
Cell cycle:
- Interphase (G1 phase, S phase, G2 phase) -> M phase (mitosis and cytokinesis)
-> Chromosomes duplicate during interphase.
G1 phase: growth and normal metabolism. (longest phase)
S phase: synthesis; DNA replicates, histones are synthesized so to duplicate copies of its chromosomes.
G2 phase: increased protein synthesis, final preparation for division. (short phase)
M phase: Mitosis and cytokinesis;
Mitosis: the nuclear division that produces two nuclei.
prophase -> prometaphase -> metaphase -> anaphase -> telophase.
Prophase:
(1) Chromatin condense as compact chromosomes. 2 sister chromatids connected at the centromere; the protein complex cohesin makes the link.
(2) Cytoskeleton is disassembled, and mitotic spindle forms between centrioles at the poles.
(3) Nuclear envelope begins to disassemble.
Prometaphase:
(1) Nuclear envelope fragments.
(2) Mitotic spindle assemble. Spindle microtubules attach to kinetochores(multiprotein attached to each centromere, to which microtubules can bind) of chromosomes. Chromosomes begin to move toward cell's midplane.
Metaphase:
(1) Chromosomes line up along cell's midplane. The chromosomes are more obvious at metaphase, so this is when the karyotype (chromosome composition) is checked for abnormalities.
(2) Spindle microtubules attach each chromosome to both poles.
Mitotic spindle 3 types of microtubules:
- Polar microtubules: aka nonkinetochore. extend from each pole to equatorial region, where they overlap and interact with the nonkinetochore from the opposite side.
- Kinetochore microtubules: extend from each pole, attach to chromosomes at kinetochore.
- Astral microtubules: short microtubules that form asters at each pole.
Anaphase:
(1) Sister chromatids separate at their centromeres. One group of chromosomes moves toward each pole of cell.
(2) Spindle poles move farther apart.
Telophase:
(1) Chromosomes are grouped at poles.
(2) Chromosomes decondense, spindle microtubules disappear, and nuclear envelopes begin to form.
(3) Cytokinesis produces two daughter cells.
Cytokinesis: begins before mitosis is complete; the division of the cell cytoplasm to form two cells.
Regulation of the cell cycle;
- Control mechanisms in the genetic program, cell-cycle check-points ensure that all the events of a particular stage have been completed before the next stage begins.
- ex; if metaphase-anaphase checkpoint molecules fails; anaphase might be initiated too early, before all chromosomes were properly attached to spindle fibers. The resulting daughter cells might have too few or too many chromosomes -> may cause Down syndrome.
- Protein kinases, enzymes that activate or inactivate other proteins by phosphorylating (adding P) them. Protein kinase involved in controlling the cell cycle are cyclin-dependent kinases (Cdks). Various Cdks increases and then decreases as the cell moves through the cell cycle. Cdks are active only when they bind to regulatory proteins called cyclins. Cyclin levels are often higher than normal in human cancer cell.
- ex; p27 is a major inhibitor of cell division, initiate degradation of the protein.
- G1-S checkpoint: ensures necessary growth factors, nutrients, and enzymes to synthesize DNA. Without this, DNA synthesis will not start.
- G2-M checkpoint: ensures that DNA replication is finished before cell begins mitosis. If damaged or unreplicated DNA, the checkpoint will not let mitosis to start.
- Metaphase-anaphase checkpoint: spindle checkpoint; prevents anaphase from occurring until all kinetochores are properly attached to spindle fibers along the cell's midplane.
- In plants, cytokinins (group of hormones) promote mitosis both in normal growth and in wound healing. Similarly, animal hormones such as certain steroids, and growth factors stimulate growth and mitosis. Many cancer cells divide in the absence of growth factors.
Multicellular organisms:
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Cell differentiation, tissue types, association of cells in plants, division and characteristics of tissues, regulation of processes in organism.
Types of reproduction in multicellular organisms: vegetative reproduction, sexual reproduction, the origin and types of gametes, isogamy and anisogamy.
Vegetative reproduction = form of asexual reproduction in plants. Process by which new individuals arise without production of seeds or spores. It can occur naturally or be induced by horticulturists. Not really a "reproduction" but survival and expansion of biomass of the individual. When an individual organism increases in size via cell multiplication and remains intact, the process is called "vegetative growth". However, in vegetative reproduction, the new plants that result are new individuals in almost every respect except genetic. Of considerable interest is how this process appears to reset the aging clock.
Anisogamy = sexual reproduction, different size of gametes. Small = sperm, big = egg
Isogamy = sexual reproduction, similar morphology gametes. Differ only in allele expression in one or more mating-type regions. Both look alike, so cannot be classified as "male" or "female.", but instead + and - .
Oogamy = large nonmotile female gamete, motile male gamete.
Meiotic division:
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Characteristics of phase I. and II. of meiotic division,
synapsis, tetrad, crossing-over
Difference between meiotic and mitosis:
1. Meiosis involves two nuclear and cytoplasmic divisions, producing up to four cells.
2. Despite two nuclear divisions, DNA and other chromosome components duplicate once - during interphase preceding the first meiotic division.
3. Each of the four cells contains haploid chromosome number.
4. During meiosis, each homologous (two partners similar in size, shape and position of centromere) chromosome pair is shuffled, so the resulting haploid cells each have virtually unique combination of genes.
- Meiosis I separates homologous chromosomes, producing two haploid cells
(N chromosomes, 23 in humans), and thus meiosis I is referred to as a reductional division.
- Meiosis 2 is similar to mitosis. However, there is no "S" phase. The chromatids of each chromosome are no longer identical because of recombination. The end result is production of four haploid cells (23 chromosomes, N in humans) from the two haploid cells (23 chromosomes, N * each of the chromosomes consisting of two sister chromatids) produced in meiosis I. Equational division.
Meiotic divison:
Both phase 1 and 2 includes prophase, metaphase, anaphase, and telophase stages.
Phase 1:
- Interphase:
preceding meiosis; DNA replicates.
- Prophase:
Chromatids are still elongated and thin, the homologous(one paternal and one maternal) chromosomes synapse and exchange segments by crossing over; nuclear envelope breaks down.
Synapse = chromosomes come to lie lengthwise side by side - fastening together. Ex; animal cell with diploid number of four, synapsis results in two homologous pairs
Tetrad = because each chromosome duplicated during interphase and now consists of two chromatids, synapsis result in the association of four chromatids.
- A tetrad is a group of four chromosomes (2 sets of sister chromatids) that come together during sexual reproduction. Crossing-over occurs at the level of the tetrad.
- In animal cell with diploid number of 4, there are 2 tetrads (8 chromatids). In human cell at prophase 1, there are 23 tetrads (92 chromatids).
Crossing over = process in which enzymes break and rejoin DNA molecules, allowing paired homologous chromsomes to exchange genetic material.
Chiasmata = In late prophase 1, the homologous chromosomes (maternal and paternal) are held together only at these specific regions.
- Metaphase:
Tetrads align on the midplane.
- Anaphase:
Homologous chromosomes separate and move to opposite poles. Sister chromatids remain attached at their centromeres. This differs from mitotic anaphase, in which the sister chromatids separate and move to opposite poles.
- Telophase:
One of each pair of homologous chromosomes at each pole (in humans; 23 chromosomes at each pole). Cytokinesis occurs. Nuclear envelope may reorganize.
Phase 2:
- Prophase:
Chromosomes condense again following brief period of interkinesis. DNA does NOT replicate again. There is no pairing of homologous chromosomes, and no crossing-over.
- Metaphase:
Chromosomes line up along midplane in groups of two (as in mitotic metaphase, contrary to meiotic metaphase 1 where they are bundles of four).
- Anaphase:
Sister chromatids separate, chromosomes move to opposite poles. The chromatids are now referred to as chromosomes.
- Telophase:
Nuclei form at opposite poles of each cell. Cytokinesis occurs. One representative for each homologous pair at each pole. Each is a single chromosome. The two divisions of meiosis yield four haploid nuclei.
homologous chromosomes:
Two partners, known as homologous chromosomes, are similar in size, shape, and the position of their centromeres. Humans; 23 homologous pairs. Homologous chromosomes carry information about the same genetic traits,although this information may not be identical.
Genetic recombination, spermatogenesis, oogenesis, ploidity of gametogonia and of gametes.
Genetic recombination is the production of new combinations of alleles, encoding a novel set of genetic information, e.g., by the pairing of homologous chromosomes in meiosis, or by the breaking and rejoining of DNA strands, which forms new molecules of DNA. This last type of recombination can occur between similar molecules of DNA, as in the homologous recombination of chromosomal crossover, or dissimilar molecules, as in non-homologous end joining. Genetic recombination can occur without the breaking and rejoining of DNA strands, in meiosis, with the random pairing of homologous chromosomes (synapsis).
Genetic recombination: Principle of independent assortment, states that members of any gene pair segregate from one another independently of the members of the other gene pairs. This mechanism occurs in a regular way to ensure that each gamete contains one allele for each locus, but the alleles of different loci are assorted at random with respect to each other in the gametes. The independent assortment of these alleles can result in genetic recombination, the process of assorting and passing alleles to offspring in new combinations that are different from those in the parents. It occurs because two pairs of homologous chromosomes can be arranged in two different ways at metaphase 1 of meiosis. Two different pairs of homologous chromosomes can line up two different ways at metaphase 1 and be subsequently distributed.
spermatogenesis:
Spermatogenesis produces mature male gametes, commonly called sperm but specifically known as spermatozoa, which are able to fertilize the counterpart female gamete, the oocyte. Start out as spermatogonia cells and mature in the seminiferous tubules (in the testes). Spermatogensis starts with spermatogonia (diploid) cells in the walls of the tubules.
Spermatogonium (diploid) -> primary spermatocyte (diploid) -> two secondary spermatocytes (haploid) -> four spermatids (haploid) -> four mature sperm (haploid).
The head of the sperm consists of the nucleus, and is covered by the acrosome, a large vesicle that contain an enzyme that help the sperm to penetrate the egg.
Oogenesis:
the creation of an ovum (egg cell). The first part of oogenesis starts in the germinal epithelium, which gives rise to the development of ovarian follicles, the functional unit of the ovary.
Oogonium (diploid) -> primary occyte (diploid) -> secondary occyte + first polar body (both diploid) -> (after fertilization) ovum + second polar body (both haploid).
Gametogonia are usually seen as the initial stage of gametogenesis. From gametogonia, male and female gametes develop differently - males by spermatogenesis and females by oogenesis.
Though the ovum development is slightly different from the sprem development but the both are formed from " GERMINAL CELLS " /germ cells. The testis and ovary are lined from inside by the epithelium called the germinal epithelium.
Men; Four functioning, small (head 4 mm), motile spermatozoids at the end of the meiosis.
Women; One large, immotile oocyte (diameter 120 mm) and three shriveled polar bodies are left at the end of the meiosis. Each time the oocyte divides, most of the cytoplasm goes into one product and the other one (the polar body) just gets a set of chromosomes.
Copulation(sexual intercourse), fertilization and origin of the zygote, cleveage, gastrulation, ontogenetic development phases, hermaphroditism and gonochorism, determination of primary and of secondary sex traits, the role of gonosomes in sex determinations.
Time of ovulation, the high estrogen level causes the cervical mucus to become thin, allowing sperm to permit passage from vagina to uterus. During the rest of the cycle, the mucus is too thick for sperm to penetrate. Both high estrogen level and the prostaglandins from the sperm contribute to uterine and oviduct muscle contractions to help move sperm toward the egg.
Cleavage is the division of cells in the early embryo. Shortly after fertilization, zygote undergoes cleavage, a series of rapid mitotic divisions. Repeated divisions increase the number of cells, called blastomeres. At about 32-cell stage, the embryo is a solid ball of blastomeres called a morula. From 64 to several hundred blastomeres form the blastula.
- Radical cleavage = first division (vertical)
- Spiral cleavage = diagonal
- Cleavage can be holoblastic (total or entire cleavage) or meroblastic (partial cleavage).
- Cleavage differs from other forms of cell division in that it increases the number of cells without increasing the mass.
Gastrulation
Process by which the blastula becomes a three-layered embryo, or gastrula.
Zygote -> early cleavage stages -> morula -> blastula -> gastrula.
In gastrulation, the embryo begins to approximate its body plan as cells arrange into three distinct germ layers;
- ectoderm
- mesoderm
- endoderm
Ontogenetic development phases
The origin and the development of an organism – for example: from the fertilized egg to mature form.
Gametogenesis, fertilization, cleavage, blastula, gastrula, organogenesis
Organogenesis; organ formation.
- Ectoderm -> skin, nervous system, sense organs.
- Mesoderm -> Skeletal tissue, muscle, circulatory, excretory, reproductive system.
- Endoderm -> tissue lining digestive tract, liver, pancreas and lungs.
Hermaphrodite is an organism that has reproductive organs normally associated with both male and female sexes
Gonochorism; unisexualism describes the state of having just one of at least two distinct sexes
Primary characteristics involve the organs for reproduction. Males have testicles, females uterus. Secondary characteristics involve traits characterized by hormonal changes such as the differences due to puberty. Examples include breasts, facial hair, the growth of pubic hair and underarm hair.
- In males, testosterone directly increases size and mass of muscles, vocal cords, and bones, deepening the voice, and changing the shape of the face and skeleton. Converted into DHT in the skin, it accelerates growth of androgen-responsive facial and body hair, but may slow and eventually stop the growth of head hair. Taller stature is largely a result of later puberty and slower epiphyseal fusion
- In females, breasts are a manifestation of higher levels of estrogen; estrogen also widens the pelvis and increases the amount of body fat in hips, thighs, buttocks, and breasts. Estrogen also induces growth of the uterus, proliferation of the endometrium, and menses.
Gonosomes are sex chromosomes (autosomes = the other chromosomes).
XX = female, XY = male.
Haploid and diploid parthenogenesis, metagenesis, heterogony.
- Ploidy is the number of sets of chromosomes in the nucleus of a biological cell.
- The haploid number (n) is the number of chromosomes in a gamete. Two gametes form a diploid zygote with twice this number (2n) and two copies of autosomal genes.
- Parthenogenesis is a form of asexual reproduction in which growth and development of embryos occur without fertilization. It is therefore maternal in origin.
Parthenogenesis occurs during meiosis and can result in a haploid or double haploid embryo. If somatic doubling occurs (chromosomes in the egg double but do not divide) then the embryo will be diploid, if not, then the resulting embryo will be haploid.
Two different ways.
1) apospory where the embryo can be produced by a cell from the female parent.
2) diplospory, where an embryo can develop from a diploid spore from the megaspore mother cell.
In general, diploids are identical to the parent, but haploids are not.
- Plants and some algae and fungi have complicated life cycles. Alternation of generations, also called Metagenesis, or Heterogenesis; the alternation of a sexual phase and an asexual phase in the life cycle of an organism.
1) Sporophyte generation (asexual): a multiceullular diploid stage.
- Undergo meiosis to form haploid spores -> divide through mitosis -> multicellular haploid gametophyte.
2) Gametophyte generation (sexual): a multicellular haploid stage.
- Produce haploid gametes by mitosis. Female and male gametes form a diploid zygote that divides mitotically to form multicellular sporophyte. When two gametes fuse, the diploid portion of the life cycle, sporophyte generation, begins.
Sex organs, gametangia (Male: antheridia. Female: archegonia), of most plants are multicellular, whereas the gametangia of algae are unicellular.
Plants have clearly defined alternation of generations in which they spend part of their lives in a multicellular haploid stage and part in a multicellular diploid stage.
1) Gametophyte produces gametes by mitosis.
2) Two haploid gametes fuse to form a zygote.
3) The zygote develops by mitosis into sporophyte.
4) Special cells of the sporophyte undergo meiosis to form spores.
5) Each spore has the potential to undergo mitosis and develop into a gametophyte.
All plants produce spores by meiosis, in contrast with algae and fungi, which may produce spores by meiosis or mitosis.
Heterogony: having females of two different kinds, one sexual and the other abortive or neuter, as ants. Two or more kinds occurring on different individuals of the same species, the kinds differing in the relative length of stamens and pistils
Reproduction of unicellular organisms: conjugation of prokaryotic and eukaryotic organisms, hologamy.
Budding is one method unicellular organisms use to reproduce. A small part of the parents body separates from the rest and develops into a new individual. Both parent and daughter have identical DNA. Yeasts, sponges and cnidarians use this method
Hologamy: It is the sexual fusion of the mature organisms, which do not differ morphologically from the ordinary individuals but are recognized as gametes only by their behavior as in certain Rizopods and Flagellates.
Hologamy : mature individual directly acting as gamete.
Systematic nomenclature of living systems.
Viruses:
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division of viruses depending on nucleic acids, characteristics of viruses depending on external coats, shape of virions, reproduction of viruses, (+)RNA viruses and retroviruses, provirus, the process of virogeny, viruses and diseases.
- Viruses contain either DNA or RNA, not both.
- Nucleic acid can be single-stranded or double-stranded; ssDNA, dsDNA, ssRNA, ds RNA
DNA viruses:
( single-stranded linear DNA
( single-stranded circular DNA
( double-stranded linear DNA
( double-stranded circular DNA
RNA viruses:
( single-stranded RNA (+ssRNA, -ssRNA)
( double-stranded RNA
- Viruses can be classified based on their host range, the types of organisms they infect.
-> plant-, animal-, bacterial viruses and so on.
- Virus family names; suffix -viridae.
- Virus are classified using the Baltimore system based on the type of nucleic acid the virus contains, whether its single-stranded or double-stranded, and how mRNA is produced.
- Virus are coated by a capsid (which can be helical or polyhedral). Capsids are built up of capsomers to give the capsid its shape.
- Polyhedral: adenovirus (respiratory infections) -> appear as spherical.
- Helical: tobacco mosaic virus (TMV) -> appear as rods or thread.
Capsid can be of various shapes.
← regular polyhedron made of 20 triangular faces and 12 vertices (icosahedron) (spherical viruses)
← helical cylinder (rod-shaped viruses)
← specific shape of bacteriophages (head, tail with filaments)
- In some virions the capsid is further enveloped by a fatty membrane, in which case the virion can be inactivated by exposure to fat solvents such as ether and chloroform
Replication of viruses:
- Viruses replicate inside host cells.
- Two types of viral reproductive cycles are lytic and lysogenic cycles:
- Lytic cycle: viruses lyses(destroys) the host cell. Once inside, the virus degrades the host-cells nucleic acid and uses the molecular machinery of the host cell to replicate its own nucleic acid and to produce viral proteins. Then it destroys the host plasma membrane and release its viruses to infect other cells.
- Lysogenic cycle: Viral genome becomes integrated into the host bacterial DNA. The integrated virus = prophage or provirus. When the bacterial DNA replicates, so does the prophage. Bacterial cells carrying prophages = lysogenic cells. UV light and X- rays can cause the temperate viruses to revert to a lytic cycle and destroy their host.
Retroviruses are RNA viruses that have a DNA polymerase called reverse transcriptase, which transcribe the RNA genome into a DNA intermediate. Then becomes integrated into host DNA. Copies of the viral RNA are synthesized as the incorporated DNA is transcribed by host RNA polymerases. ex; HIV.
Positive strand RNA viruses: Also known as a sense-strand RNA virus, a virus whose genetic information consists of a single strand of RNA that is the positive (or sense) strand which encodes mRNA (messenger RNA) and protein. Replication in positive-strand RNA viruses is via a negative-strand intermediate. Ex; polio virus, Coxsackie virus, and echovirus.
The process of virogeny: Viral genom is incorporated into the genom of host cell and thus viral genom is replicated together with the genom of host cell. This phenomenon is known as virogeny (lysogeny in the case of bacteriophages).
Virogeny: viral DNA is replicated within host cell but virions are not formed and released. Viral DNA (1) is replicated within host cell independently, i.e. it functions as a plasmid, or (2) is incorporated into a chromosome of host cell and is replicated together with the chromosome. Such viral DNA is referred to as provirus. In the case of bacteriophages, virogeny is known as lysogeny.
Bacteria:
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The structure of bacterial cell, shape of bacteria, forms of autotrophic nutrition, bacterial plasmids, transformation, conjugation and transduction, the role of prophylaxy.
- Shape:
- Spherical (cocci)
- Grouped in two; diplococci
- Long chains; streptococci
- Rod-shaped (bacilli)
- Spiral: spirochete(flexible), spirillum (rigid). Vibrio: Spirrilum shaped like a comma.
- Some archae can be triangular or square
- Structure:
- No nucleus, but have nuclear area (nucleoid) which contains DNA. In addition, they have plasmids (smaller circular fragments of DNA).
- Ribosomes (smaller than in eukaryote)
- Storage granules; glycogen, lipid, phosphate.
- Cell wall: rigid framework that supports and maintain shape of the cell. Keeps the cell from bursting under hypotonic solutions, as the bacteria have high concentration of dissolved solutes.
- Wall includes peptidoglycan; Gram-positive = thick wall of peptidoglycan. Gram-negative = thin layer of peptidoglycan + a thick outer membrane. Penicillin works best against gram-positive bacteria.
- Capsule / slime layer: protection against phagocytosis (ex by white blood cells).
- Fimbriae (short), pili (long): attachment.
- Flagellum
- Gene transfer
- Horisontal gene transfer; genetic material to another organism that is not its offspring. (Transfer TO the offspring = vertical gene transfer).
1) Transformation; bacteria takes up fragments of foreign DNA (or RNA) released by another dead bacterium. Foreign DNA is incorporated into the host's own genome. It can also be taken up as plasmids.
2) Transduction; a phage carries bacterial genes from one bacterial cell into another.
3) Conjugation; two cells of different mating types come together, and genetic material is transferred from one to the other. Involves contact! in contrast to 1) and 2).
- Forms of autotrophic nutrition
- Most prokaryotes are heterotrophs.
- Autotrophs use inorganic compounds (ex CO2) for manufacturing their organic molecules.
- Two forms of autotrophs;
- Chemotrophs; obtain energy from chemical compounds.
- Phototrophs; capture energy from light.
- Furthermore, we can classify prokaryotes into four groups;
1) Photoautotrophs; use energy from sunlight to synthesize organic compounds from CO2 and other inorganic compounds.
- Cyanobacteria.
2) Chemoautotrophs; use CO2 as carbon source, but obtain energy by oxidizing inorganic chemical substances such as ammonia (NH3) and hydrogen sulfide (H2S).
- Most archaea are in this group.
3) Photoheterotrophs; obtain carbon from other organisms but use chlorophyll and other pigments to trap energy from sunlight.
4) Chemoheterotrophs; Majority of prokaryotes are in this group. Depend on organic molecules for both carbon and energy.
- Many of these (= saprotrophs) are decomposers that feeds of dead organic matter.
- Some are pathogens that feeds of the organism they infect.
- Others benefit their host.
- The role of prophylaxy: (active treatment)
- Some microorganisms (ex; actinomycetes, Bacillus, molds) produce antibiotics.
- Genetically engineered bacteria to produce vaccines, human growth hormone, insulin etc.
- Botulism exotoxin (Botox) paralyzes muscles and are used for relaxing wrinkles.
Plants:[pic]
Plant cell and its cellular organelles,
- Either herbaceous (aerial part die at the end of the season) or woody (aerial part persist).
- Annuals Herbaceous: (corn, geranium, marigold) die in one year or less.
- Biennials Herbaceous: (carrot, cabbage) grow in two years before dying.
- Perennials Herbaceous and Woody plants: (onion, asparagus) die back each winter. The roots live in dormancy with minimum metabolic state through the winter.
- All woody plants are perennials.
- Deciduous: shed their leaves in a short period, and produce new stems the following spring.
- Evergreen: shed their leaves over a long period, so some leaves are always present.
1) Large central vacuole enclosed by a membrane(tonoplast) that maintains the cell's turgor, stores useful material and digests waste proteins and organelles.
2) Cell wall of cellulose and hemicellulose, pectin and in many cases lignin, is secreted by the protoplast on the outside of the cell membrane. This contrasts with the cell walls of fungi (which are made of chitin), and of bacteria, which are made of peptidoglycan.
3) Cell-to-cell communication pathways; plasmodesmata.
4) Plastids: As in mitochondria, encoding 37 genes, plastids have their own genomes of about 100–120 unique genes.
- Chloroplast(with chlorophyll).
- Amyloplasts; starch storage.
- Elaioplasts; fat storage
- Chromoplasts; synthesis and storage of pigments.
5) Cell division by construction of a phragmoplast as a template for building a cell plate late in cytokinesis is characteristic of land plants and a few groups of algae.
6) Sperm of bryophytes and pteridophytes have flagellae similar to those in animals, but higher plants, (including Gymnosperms and flowering plants) lack the flagellae and centrioles that are present in animal cells.
types of chlorophyles in plant cells,
Chlorophyll A and B. A most important:
- Chlorophyll A: Green; absorbs wavelength of 450 nm and at 650-700 nm.
- Chlorophyll B: Green, but more yellowish; 450-500nm and at 640nm.
characteristics of plant tissues,
In vascular plants, tissues are organized into three tissue systems. All systems extends through the whole plant: roots, stems, leaves, flower.
1) Ground tissue system: support
Parenchyma tissue: photosynthesis, storage, secretion.
Collenchyma -: support.
Sclerenchyma -: support, strength.
2) Vascular tissue system:
Xylem -: conduction of water and nutrient minerals, support, storage, strength.
Phloem -: transport sugars from the root to other parts of the plant, support, storage, strength.
3) Dermal tissue system: protective covering over surface of plant body.
Epidermis -:
Periderm -:
Cell walls may contain cellulose, hemicelluloses, pectin and lignin.
active and passive intake of the water,
water activity inside the cells,
- Xylen conducts water and dissolved minerals.
- Phloem conducts dissolved sugars.
the process of transpiration ("sweating"):
Loss of water vapor by evaporation from aerial plant parts is called transpiration. The stomatal pores that are effective in gas exchange for photosynthesis also provide openings for water vapor to escape.
- Light increases its transpiration rate.
- Transpiration cools the leaves and stems.
- Transpiration is responsible for water movement in plants, and without it water would not reach the leaves from the soil. Also distributes minerals throughout the plant.
- Important part of the hydrologic cycle (water from ocean and land to atmosphere and back).
Guttation,
Guttation is loss of water, drops of xylem sap, through the tips or edges of leaves of some vascular plants. Typically occurs at night when stomatas are closed, but water continues to move into the roots by osmosis. Guttation is not to be confused as dew.
The main characteristics of photosynthesis,
1) Light splits the water molecule into hydrogen and oxygen atoms.
2) Hydrogen combines with carbon dioxide to make glucose. (Carbon comes into the plant through stomata)
3) Oxygen is released as a waste product.
Saprophytism, semiparasitism and parasitism,
Saprothrophs = decomposers. Most bacteria and fungi.
Parasitsm = a symbiotic relationship where one partner lives on or in the other. Parasit benefits and the host is harmed.
- Ectoparasites lives outside the host.
- Endoparasites lives inside the host.
Semiparasitsm = commonly parasitic but also capable of living on dead or decaying animal matter.
mixotrophic nutrition, breathing in plants, divisional and prolongational growth, regulation of tissue differentiation, plant development, plant movement and plant reproduction.
Mixotroph: mix of different sources of energy and carbon. Ex; between photo- and chemotrophy, between litho-(inorganic) and organotrophy(organic), between auto- and heterotrophy or a combination of it.
- Plants take in CO2 and give out O2. At night, they take in O2, because of no sunlight; but this amount of exhaled CO2 is far less than the amount of O2 released during photosynthesis.
- The fusion of male and female gametes (fertilization) produces a diploid zygote, which develops by mitotic cell divisions into a multicellular sporophyte.
Algae:
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Division depending on the type of chlorophyl, body structure and main characteristics, representatives of different classes and their characteristics.
Most are photosynthetic.
Brown Algae, golden brown algae, and diatoms: Chlorophylls A(green) and C(red-brown)
The Red Line: only Chlorophyll A(green)
The Green Line: Plants and green algae: Chlorophylls A(green) and B(green).
Classes:
- Red algae
- Diatoms (golden-brown algae)
- Kelps (brown algae)
- Dinoflagellates
- Green algae
Land plants:
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Dermal tissue system - epidermal cells, guard cells, hair cells - their description and function.
Epidermal cells:
- Transparent, so light can shine through to photosynthetic tissue.
- One cell thick; Outer wall covered by cutile (waxy layer).
- Protective covering over surface of plant; helps reduce water loss.
- Dispersed among epidermal cells, we find Guard cells and Trichome.
Guard cells:
- Chloroplast-containing cells; occur in pairs, and surrounds stomata.
- Pair changes shape to open and close stomatal pore.
- Stomata open during day when photosynthetic is occurring; also provides some evaporative cooling.
- CO2 diffuse through stomatal pores.
- Located at epidermis of stems and leaves.
Trichome:
- Hair or outgrowth on the epidermis.
- Absorption, secretion, excretion, protection, reduction of water loss.
- Ex removes excessive salts accumulating in the plant.
- Protective; stinging nettle leaves.
Ground tissue system- parenchyma cells, collenchyma cells, sclerenchyma cells - their description and function.
Parenchyma cells:
- Thin primary cell walls
- Most common type of cell and tissue. Soft parts of the plant.
- Photosynthetic(green chloroplasts), or non-photosynthetic(colorless)
- Storage (starch, grains, oil droplets, water, salts)
- Secretion (resins, tannins, hormones, enzymes, nectar)
Collenchyma cells:
- Unevenly thickened primary cell walls
- Flexible structural tissue; support in soft, nonwoody plants.
Sclerenchyma cells:
- Thick secondary cell walls
- May be living or dead at maturity
- Pits through which substances can exchange between living sclerenchyma cells.
- Strength; hard and flexible tissue.
Vascular tissue system - xylem and phloem - description and function.
Xylem:
- Conducts water and dissolved minerals.
- Composed of four cell types: tracheids, vessel elements, parenchyma cells, and fibers.
Phloem:
- Conducts food materials; carbs formed in photosynthesis.
- Composed of four cell types: sieve tube elements, companion cells, fibers, and phloem parenchyma cells.
The basic plant life cycle - alteration of generation, gametophyte and sporophyte.
Bryophyta - body structure, alteration of generation, classes and representatives.
- Nonvascular and lack xylem and phloem; and no true roots, stems or leaves.
- Only plant with dominant gametophyte generation. Sporophytes remain permanently attached and nutritionally dependent on the gametophytes.
Three phyla:
- Mosses (Bryophyta); have leafy plant gametophytes.
- Representatives; Polytrichum, Sphagnum, Physcomitrella
- Liverworts (Hepatophyta); have thalloid(lobelike/flattened) or leafy plant gametophytes.
- Repr; Marchantia
- Hornworts (Anthocerophyta); have thalloid plant gametophytes.
- Repr; Anthoceros
General characteristics of Pteridophyta (ferns), Coniferophyta and Anthophyta (flowerig plants).
Fungi:
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Characteristics of fungi: hyphae, haustoria, mycelium, mycorrhizae, saprobes.
- All fungi are eukaryotes and heterotrophs.
- Hyphae: long, branched, threadlike filaments that the body consists of.
- Mycelium: Hyphae that have grown and formed a tangled mass or tissue-like network. Fungi that form mycelia are called molds.
- Mycorrhizae: the symbiotic associations between the hyphae of certain fungi and the roots of plants.
- Haustoria: Special hyphal branches produced by parasitic fungi that penetrate the host cells and obtain nourishment from the cytoplasm.
- Saprobe: an organism that derives its nutrition from the dead remains of other organisms; a scavenger, if you will. Saprobic fungi usually live on dead vegetable matter (sticks, leaves, logs...), as they are the only multi-celled organisms that can digest the structural proteins cellulose and lignin, the two major components of wood (and plants' cell wall). Fungi handle the really tough organic molecules that nobody else wants to bother with (hair, nails, hooves, shells, insects exoskeleton).
Chytridiomycota - general characterisation, type of reproductions, representative members
- aka chytrids
- small, simple, inhabit ponds and damp soil.
- ex Allomyces
- the only fungi with flagellate cells.
- Sexual reproduction: haploid gametes in some species
1) Haploid thallus produces two types of gametes which can fuse, and plasmogamy (fusing of cytoplasm) and karyogamy (fusing of the two haploid nuclei in the same cell, resulting in a diploid nucleus/zygote nucleus) occur.
2) Each zygote can develop into a diploid thallus (thallus = the few cells that form the simple body of chytrids). The thallus bears two kinds of spore cases, zoosporangia and resting sporangia.
3) Meiosis occurs within resting sporangia, producing haploid zoospores.
4) Haploid zoospore grows into haploid thallus, and the haploid thallus produces two types of gametes by mitosis which again can fuse together.
- Asexual reproduction: Through mitosis, zoosporangia produce flagellate diploid zoospores that develop into new diploid thalli.
(sexual -> haploid zoospores produced in resting sporangia; form haploid thallus)
Endomycota --?? / Glomeromycetes - general characteristics, taxonomic division, representatives and their life cycle.
- Form mycorrhizae. They penetrate the cell wall of the root cells, and are therefore called endomycorrhizal fungi.
- Arbuscular mycorrhizae the most widespread endomycorrhizae.
- Previously considered zygomycetes, but now form a separate monophyletic group.
- Reproduce asexually: with large, multinucleate spores called blastospores.
- Sexual reproduction not observed.
Zygomycota - general characteristics, type of reproduction, representatives
- ex; black bread mold.
- Heterothallic; mates only with opposite mating type.
- Important decomposers.
- most closely related to chytrids.
- Sexual reproduction: in spore sacs, zygosporangia, they produce sexual spores, zygospores.
- Asexual reproduction: haploid spores produced in sporangia.
- Only the zygote and zygospore of a black bread mold are diploid; all the hyphae and the asexual spores are haploid.
Ascomycota - general characteristics representative members
- include most yeasts, powdery midews, blue-green, pink and brown molds on food, edible morels and truffles.
- used to bake bread, ferment alcohol, flavor cheese, enjoyed as morels and truffles, and to produce antibiotics.
- cause the most fungal disease of plants and animals, including humans.
- Candida
- Sexual reproduction:
1) Hyphae of two mating types fuse and nuclei are exchanged.
2) Dikaryotic hyphae form and produce sacs called asci which evolve to ascocarp (fruiting body).
3) Karyogamy occurs in each ascus.
4) The diploid zygote nucleus now undergoes meiosis to form four haploid nuclei with different genotypes.
5) Each of the four haploid nuclei follows a mitosis before they become incorporated into an ascospore.
6) When the ascospore are released it can germinate and form a new haploid mycelia.
- Asexual reproduction: spores called conidia pinch off from the tips of certain hyphae known as conidiophores.
Basidiomycota - general characteristics representative members
- Largest and most familiar of the fungi; the mushrooms(basidiocarp).
- Sexual reproduction:
1) Each basidium produces four basidiospores through meiosis. Basidiospores develop outside the basidium, contrary to ascospores which develop within an ascus.
2) Basidiospores germinate and form primary mycelia.
3) Plasomogamy of primary mycelia occurs with the fusion of two hyphae of different mating types.
4) Fast-growing secondary mycelium is produced, composed of dikaryotic hyphae.
5) Basidiocarps(mushrooms) periodically develop from secondary mycelium.
6) Karyogamy takes place within the young basidia on the gills (underside) of the mushroom.
7) Meiosis occurs producing four haploid nuclei that become basidiospores.
- Asexual reproduction uncommon.
Animal kingdom
[pic]
Unicellulars: general characteristics, taxonomic division, representatives of individual classes with respect to the diseases which they determine, their life cycle and type of reproduction.
- Protists are unicellular, colonial, or simple multicellular organisms that have a eukaryotic cell organization. First eukaryotes to evolve.
- Domain Eukarya (other two domains being Bacteria and Archaea).
- Most protists are unicellular. Some form colonies. Some are coenocytic (multinucleate mass of cytoplasm), some are multicellular composed of many cells.
- Some move by pseudopodia; pushing out cytoplasmic extensions and retracting the cytoplasm that trails behind. Others glide over the surface by waving cilia, or by lashing flagella.
- Some parasitic protists are important pathogens of plants or animals.
- Most protists are aquatic.
- Protists are a paraphyletic group - contain some, but not all, of the descendants of a common eukaryote ancestor.
- Almost all reproduce asexually, and many also reproduce sexually.
- All eukaryotes supergroups are bikonts (common ancestor with two flagella), except Unikonts which are unikonts.
Supergroup Eukaryote:
Excavates: Live in oxygen-less environment; glycolysis for energy.
- Diplomonads: can be parasitic. Giardia Inestinalis: water-borne diarrhea (contaminated water). Trichomonas vaginalis: STD.
- Euglenoids(some photosynthetic. Can be parasitic. Trypanosoma brucei: African sleeping sickness; fever, lethargic, difficulty speaking and walking. (bite of infected tsetse flies).
Chromalveolates: Most are photosynthetic.
- Dinoflagellates: Toxin attacks nervous system in fish and birds that eat fish.
- Apicomplexans: Parasitic; spend most of their life cycle in one host species, and part in a different host by sporozoites (infective agents). Malaria (by Plasmodium).
- Ciliates: Conjugation (sexual process); two come together and exchange genetic material, results in two "new" cells genetically identical.
- Water Molds: Asexually when good conditions. Sexually when not. Can attack Oaks, potatoes, redwoods, maples etc.
- Diatoms: asexually by mitosis. When reaching a fraction of size it reproduce sexually to restore to original size. Shellfish poisonings.
- Brown Algae: aka seaweed, ex kelp. Exhibit alternation of generations; part of life as haploid, and part as diploid.
- Golden Algae: Asexual.
Rhizarians: slender pseudopodia
- Foraminiferans (forams): Dead transform to chalk.
- Actinopods:
Archaeplastids: (in this group we also find Land Plants(but different kingdom))
- Red Algae: No flagellates. Alteration of sexual and asexual stages. Build coral reefs.
- Green Algae: Produce flagellate cells, but some are nonmotile. Both sexual and asexual. Alterations of haploid and diploid generations.
Unikonts: (in this group we also find Fungi and Animals(but different kingdoms)).
Amoebozoa: Most move by lobose (rounded) pseudopodia. In contrast to Rhizarians slender pseudopodia.
- Amoebas: Move by pseudopodia. Asexually. Entamoeba histolytica (contaminated water) causes amoebic dysentry: human intestinal disease (diarrhea, bloody stools, ulcers). Can cause abscesses in liver, lungs or brain. Acanthamoeba: eye infections.
- Plasmodial slime molds:
- Cellular slime molds: Primarily asexual. Usually lack a flagellate stage.
Opisthokonts:
- Choanoflagellates: No flagella or single posterior flagellum. Closest living non-animal relative of animals.
Multicellulars: Origins of multicellularity, taxonomic division - phylum, class, order, family, genus and species.
- Animals are multicellular eukaryotes. They lack cell walls, and depends on collagen for structural support.
Multicellular:
All have choanoflagellates (group of protists) as common ancestor.
- Sponges/poriferans
- flagellated
- Cnidarians
- hydras, jellyfish, corals, sea anemones.
- radial symmetry, stinging cells, tentacles surround mouth.
- Ctenophores
- comb jellies.
- biradial symmetry, tentacles with glue cells.
- Lohotrochozoa (protostomia) : bileteral
- flatworms, nemerteans, mollusks, annelids, lophophorates, rotifers.
- Ecdysozoa (protostomia) : bilateral
- nematodes, tardigrades, onychophorans, arthropods.
- Deuterostomia : bilateral
- echinoderms, hemichordates, chordates.
Difference between protostomes and deuterostomes:
- Protostomes:
- spiral cleavage.
- determinate cleavage: first four cells separated, each cell develop only a fixed quarter of the larva.
- Blastospore develops into the mouth.
- schizocoely: mesoderm splits and widens into a cavity called coelom.
- Deuterostomes:
- radial cleavage.
- indeterminate cleavage: first four cells separated, each cell can form a complete, though small, larva.
- Blastospore develops into the anus. Second opening forms the mouth.
- enterocoely: mesoderm forms outpocketings which pinch off and form pouches. The cavity within the pouches becomes the coelom.
Protostomes -
- The most abundant animals in the world, in terms of species diversity.
- All triploblastic bilaterians animals
Wormlike body plans
- they have well developed coelom that provides space for fluids to circulate and hydrostatic skeleton for movement.
- Echiurans (spoon worms)
- segmented worms
- extended structure (proboscis) leading to mouth (star wars monster)
- Pripulids (penis worms)
- toothed throat can turn inside out and then retracted (movie; aliens)
- Nemerteans (ribbon worms)
- barbed-tipped proboscis entangling prey
Arthropod body plans (insects)
- Segmented bodies (head, thorax, abdomen)
- Jointed limbs
- Chitinous exoskeleton
- Locomotion from muscles instead of hydrostatically
Mollusc body plans (snails and slugs)
- Foot: Move with a large muscle at base
- On top of the foot they have a visceral mass which contains the internal organs
- Mantel covers visceral mass. Snails secretes calcium carbonate shells.
- Squids use the mantle for jet propulsion -> movement.
Reproduction:
Asexual:
- splits in two
- budding
- parthenogenesis: unfertilized eggs develop and grow to adults.
Sexual:
- Sessile organisms use external fertilization. Randomly fertilization.
- Motile organisms use internal fertilization.
taxonomic division,
Protostomes:
Lophotrochozoa
- Grow by extending size of skeletons
- Suspension feeding: Rings their mouth for filterfeeding: pulls water and food particles into mouth.
- Rotifera: (wheel animals) Important components of plancton. Cluster of cilia called corona(crown) that is used for swimming and suspension feeding.
- anterior nervous system
- eyespots
- excretory: protonephridia, flame cells
- digestive: complete gut, corona and mastax (pharynx)
- no respiratory systems
- reproductive: parthenogenesis (growth and development of embryos occur without fertilization)
- Platyhelminthes: (flatworms). broad and flattened body shape; no coelom. One opening for ingestion and elimination of waste.
- Turbellarians: inhabit coral reef ecosystems
- Cestodes (tapeworms): no mouth or digestive system. They diffuse nutrients across body.
- Trematodes: have digestive tract, gulp host tissue.
Characteristics:
- brain and nerve cords
- light sensitive eyespots
- excretory: flame cells and protonephridia
- digestive: shits through the mouth
- no respiratory or circulation systems
- reproductive: sexual, hermaphroditic
- Annelids (segmented worms)
- Polychaeta (sandworms, tubeworms): have parapodia (many appendages / many feet). Have chaetae (bristlelike extensions from parapodia)
- Oligochaeta (earthworms): few bristlelike feet. Lost parapodia, but have reduced chaetae.
- Hirundinea (leeches): lost parapodia and chaetae.
Characteristics:
- brain and ganglia
- closed or open circulatory system with hemoglobin
- respiration by diffusion
- metanephridia (excretory)
- complete gut
- reproductive: sexual/asexual
- Molluscs: 4 groups
- Bivalves: two hinged shells. Suspension feeders.
- Clams burrow and filterfeed with only mouth part exposed to water.
- Oysters and mussels attach themselves to a substrate and filterfeed.
- Scallops move around.
- Gastropods: Marine snails and slugs. Large, muscular foot for gliding movement. Mouth on the foot. Garden snails are pulmonate ("having a lung").
- Chitons: 8 shell plates for protection. Muscular foot and mouth on the foot.
- Cephalopods: nautilus, cuttlefish, squid and octopus. Beak are the only hard part. Foot modified as tentacles. Large brain and eyes. Intelligent.
Characteristics:
- nerve cords, brain
- heart (open circulatory system), pumps blood into a single aorta, which branch into other vessels. Network of large spaces called sinuses (hemocoel). Vessels conduct the blood to the gills where it is recharged with oxygen.
-> in faster moving squids and octopods the circulatory system is closed, in which blood flows through a complete circuit of blood vessels making the blood pressure higher.
- gills
- nepridia (aka kidneys that remove waste)
- complete gut
- Nemerteans (ribbon worms): barbed-tipped proboscis entangling prey.
Characteristics:
-nervous: brain and nerve cord
-cardiovascular: closed. Have no heart, but blood circulate by movement and contractions of muscular blood vessels.
-respiratory: diffusion
-excretory: protonephridia, flame cells
-digestive: complete gut with rhyncocoel
- Lophophorates: ring of ciliated tentacles around mouth used for feeding and respiration. Sessile.
Ecdysozoa
- Shed exoskeleton to expand bodies (molting). Ex; insects
- Nematoda (roundworms): Lives in virtually every habitat. 80% of individual of animals. Unsegmented worms and hydrostatic motion. Some are plant and animal(+human) parasites.
- Tardigrada ("slowwalker"/waterbears): segmented body and 8 limbs. Can survive in very extreme environment: from absolute 0, to 150 degrees, to very radiating environment, some can live a decade without any water, and others have survived in outer space for a few days in orbit.
- Onychophora (velvet worms): looks like caterpillars; antennas, segmented body, multiple pair of legs.
- Arthropodia: most successful and diverse and species rich members on earth. segmented body, jointed exoskeletons, distinct head and trunk. One of two animal groups that are very successful on dry environment; the other being the human group.
- Myriapoda: millipedes(detrivores) and centipedes(predators)
- Insecta/hexapods: (insectum = cut into sections): 3 part body. Compound eyes, antennae. 90% of diversity on Earth.
- Chelicerata: Spiders, ticks, mites, horseshoe crabs, scorpions.
- Crustacea: Lobster, shrimp, crab.
Deuterostomes:
Radial, indeterminate cleavage, pharyngeal slits.
Echinoderms:
- water vascular system; endoskeleton with spines.
- Crinoids (sea lilies, feather stars)
- Asteroids (sea stars)
- Ophiuroids (basket stars, brittle stars)
- Echinoids (sea urchins, sand dollars)
- Holothuroids (sea cucumbers)
Hemichordates: acorn worms
- Proboscis, collar and trunk.
Chordates:
- tubular nerve cord, postanal tail, segmented body.
- Urochordates (tunicates)
- Cephalochordates (lanceletes)
- Vertebrates (hagfishes, lampreys, cartilaginous fishes, ray-finned fishes, coelacanths, lungfishes, amphibians, reptiles, mammals).
Characteristics of phyla, classes and families:
ex;
Kangaroos Play Cellos, Orangutans Fiddle, Gorillas Sing.
Kingdom = the animal
Phylum = chordates (or vertebrae)
Class = mammal
Order = primate
Family = lemuridae
Genus = lemur
Species = ring-tailed lemur
Phyla of protostomes:
Acoelomate: no cavity. ex flatworms
Pseudocoelom: body cavity not completely lined with mesoderm. ex roundworms and rotifers
True coelomate: body cavity completely lined with tissue that develops from mesoderm.
- important step to larger, more complex animals.
- makes up the digestive system
- can serve as a hydrostatic skeleton
Body cavities of protostomes and their characteristics, types of nervous, sensory, excretory reproductive, circulatory and respiratory systems, types of blood pigments,
Lophotrochozoa:
- Bilateral symmetry
- cephalization:
- sensory organs concentrated in the head.
- concentration of nerve cells in the head form a brain, and a nerve cord.
- Protostomes have ventral nervous systems
- Triploblastic (three definite tissue layers
- A true coelom and a tube-within-a-tube body plan
- Most annelids do not have either of these respiratory pigments (hemoglobin:red or chlorocruorin:green) and have colorless blood (plasma).
- Hemocyanin is a bluish-colored copper-containing pigment found in many mollusks and arthropods.
- Roundworms have no circulatory or respiratory systems so use diffusion to breathe and for circulation of substances around their body.
- Most arthropods breathe through a tracheal system. Aquatic arthropods use gills to exchange gases.
- Flatworms:
- brain and nerve cords,
- light sensitive eyespots,
- excretory: flame cells and protonephridia (cilia that propel out waste)
- digestive; incomplete gut
-reproductive: sexual, hermaphroditic
-no respiratory system
ectoparasites and endoparasites of plants, animals and human beings, diseases which are caused by hosts and intermediate hosts of parasites.
Endoparasites live inside the body of its host.
Ectoparasites live outside the body of the host.
Parasitic flatworms - flukes and tapeworms - have suckers or hooks for holding on to their hosts. Some live in digestive tracts resistant to digestive enzymes. Produce large number of eggs. Tapeworms have lost their own digestive system.
Flukes include blood flukes, ex Schistosoma (tropical), and liver flukes (Asia where they use feces for fertilizing crops). They thrive in ponds and use aquatic snails as intermediate hosts. Blood fluke (Schistosoma); larvae burrow through the skin of a foot in a pond. They reproduce in the veins and their eggs pass into the intestine of the human body. Eggs containing embryos are excreted with feces and hatch releasing free-swimming larvae (miracidia). Then they use a snail as a second host where they reproduce asexually. Finally the fork-tailed larvae (cercariae) develop and leave the snail.
Beef tapeworm (Taenia saginata): Cattle ingest zygotes with grass and larvae hatch in the muscle of a cow. When human eats poorly cooked infected beef, digestive juice frees the larvae. The larvae attach itself to the lining of human small intestine and matures into adult tapeworm. Mature proglottids (a segment of the tapeworm, each its own reproductive machine) leave the body with feces and release the zygote in the grass that a cattle can eat.
Many Nematodes (roundworms) are parasites in plants and animals.
- Ascaris are human parasites, living in the human intestine; ingests partly digested food. May produce 200,000 eggs per day!
- Hookworms attach to the intestine and suck blood causing tissue damage and blood loss.
- Pinworms are most common worm found in children. The eggs often ingested by eating with hands contaminated with them.
- Trichina worm lives in pigs, rats and bears. Humans become infected by eating undercooked, infected meat. Larvae encyst in skeletal muscle.
Deuterostomes - characteristics of individual phyla, taxonomic division of Chordata, main characteristics of individual classes of Vertebrates: types of circulatory and transport, respiratory,immune, hormonal, nervous, sensory, excretory and reproductive systems, ontogenetic development,
Characteristics of Deuterostomia, the third major branch of the animal kingdom:
- Indeterminate cleavage (fate of their cells is fixed later in development).
- radial, rather than spiral, cleavage.
- Blastospore becomes anus. A second opening becomes the mouth.
- Pharyngeal slits (openings in the pharynx): hemichordates and chordates.
- True coelom
Phyla:
Echinoderms
- sea stars, sea urchins, and sand dollars.
- Characteristics:
- bilaterally symmetrical, ciliated, free-swimming. In adults; pentaradial symmetry; five parts around a central axis.
- Water vascular system, network of fluid-filled canals and chambers. Functions in feeding and gas exchange, and as a hydrostatic skeleton for locomotion.
- Endoskeleton.
- Pedicellariae, pincerlike spines on the body surface; found only in echinoderms.
- Complete digestive system: well-developed coelom containing fluid that transports materials.
- No excretory organs.
- Simple nervous system; nerve ring with nerves that extends out from it.
- No brain
- Separate sexes; eggs and sperm released into the water for fertilization.
- All echinoderms inhabit marine environment at all depths.
- Five groups:
- Crinoidea (sea lilies and feather stars)
- Asteroidea (sea stars)
- Ophiuroidea (basket stars and brittle stars)
- Echinoidea (sea urchins and sand dollars)
- Holothuroidea (sea cucumbers)
Chordates
- Vertebrata (fishes, amphibians, reptiles (including birds) and mammals).
- Characteristics:
- Bilateral symmetry
- Tube-within-a-tube body plan
- Three well-developed germ layers
- Coelomates
- Notochord; a dorsal rod of cartilage(brusk) which is firm but flexible. Supports the body.
- Dorsal, rather than ventral, nerve cord. It is hollow rather than solid, and is single rather than double.
- Postanal tail.
- Endostyle; a groove in the floor of the pharynx that secretes mucus and traps food particles in the sea water.
- Pharyngeal (gill) slits. Water flows into the mouth and out of the gill slits in the pharynx.
- Endoskeleton
- Closed circulatory system with a ventral heart.
- Segmented bodies (not very apparent).
- Three subphyla:
- Urochordates (tunicates)
- Sea squirts (ascidians) and relatives.
- Develop a protective covering called a tunic. Two openings; for food and water, and for water, waste and gametes. Forcefully expels a stream of water from their "anus" when irritated.
- Cephalochordates (lancelets or amphioxus)
- fish-shaped; long and pointed at both ends.
- Notochord extends from the head (cephalon).
- No fins, jaws, sense organs, heart or well-defined head or brain.
- Vertebrae
- Vertebral column around their notochord, or replaces it completely.
- Cranium
-> Vertabrae and cranium are part of the living endoskeleton that grows with the animal, in contrast to non-living exoskeleton.
-> Bone, instead of cartilage, that produce collagen.
- Neural crest cells; give rise to nerves, head muscles, cranium and jaws.
- Four duplicated hox gene clusters (determine the fate of cells in the anterior- posterior axis), in contrast with one hox gene cluster in invertabraes.
- Pronounced cephalization with 10 or 12 pairs of cranial nerves.
- Two pairs of appendages; ex fins in fishes.
- Closed circulatory system with ventral heart and hemoglobin in blood.
- Complete digestive system with large digestive glands (liver and pancreas).
- Several endocrine glands.
- Paired kidneys to regulate fluid balance.
- Sexes are typically separate.
- Use muscles for feeding, in contrast to filtering.
- Pisces (fishes) and tetrapod (amphibia, reptilia, and mammalia).
- Reptiles and mammals form a clade known as amniotes.
Vertebrate classes:
Infraphylum incertae sedis
Superclass 'Agnatha' (jawless vertebrates)
- Myxini (hagfishes)
- Petromyzontida (Lampreys)
- † Conodonta (extinct chordates resembling eels)
Infraphylum Gnathostomata (jawed vertebrates)
Superclass incertae sedis
- † Placodermi (extinct class of armoured prehistoric fish)
- Chondrichthyes (sharks, rays, skates, chimaeras)
- † Acanthodii (spiny sharks; is a class of extinct fishes)
Superclass Osteichthyes (bony fish)
- Actinopterygii (ray-finned fishes: perch, salmon, tuna, trout)
- Actinistia / Sarcopterygii (lobe-finned fishes: coelacanths)
Superclass Tetrapoda (four-limbed vertebrates
(- Dipnoi (lungfishes) ) - sister group Tetrapodomorpha.
- † Synapsida
- Aves (birds)
- Amphibia (salamanders, frogs, toads)
- Reptilia (turtles, lizards, snakes, alligators. Robins, eagles, pelicans, ducks, penguins, ostriches).
- Mammalia: monotremes(protheria: lay eggs), marsupials(metatheria: young carried in bags), eutheria(mammals with well-developed placentas(morkake).
Hemichordates
- wormlike marine animals. Three-part body: proboscis, collar, and trunk. Ring of cilia surrounding the mouth. Ex; acorn worms that live buried in mud or sand.
Anamniotes, Amniotes, ectothermy, endothermy, taxonomic division of Mammalia, their characteristics and representatives.
The anamniotes are an informal group comprising the fishes and the amphibians, the so-called "lower vertebrates", which lay their eggs in water
The amniotes, the "higher vertebrates" (reptiles, birds and mammals), which lay their eggs on land or retain the fertilized egg within the mother.
- Do not have gills
Ectothermy is the ability of an organism maintain their body temperature by absorbing heat from their environment. Depend on their environment for body heat. Most animals are ectotherms. Lower daily energy expenditure than endotherms. Survive on less food and convert more energy in their food to growth and reproduction. However, daily and seasonal temperature conditions may limit activity.
Endothermy is the ability to generate heat from metabolic processes to maintain its body temperature, typically above the temperature of its surroundings; a homeotherm. Ex; dinosaurs. Up to six times higher metabolic rate than ectotherms. This enables them to be active even in low winter temperature; however, they must spend energy even when inactive. Feathers, hairs and fat reduce the heat loss from the body. Behavioral adaptations; ex elephants spray themselves with cool water. Heat can be increased by action of hormones, such as thyroid hormones, that increase metabolic rate. It can also be increased by contracting muscles; shivering in the cold. When too hot, they pant or sweat.
Regulatory mechanisms in animal kingdom: interrelationships between neural and chemical regulation, biorhytms, homeostasis in organisms.
- Homeostasis: balanced internal environment; keep a steady state of pH, temperature, concentration of nutrients, oxygen, other gases, ions, and compounds needed for metabolism.
- Stressors are what challenges homeostasis.
- Biofeedback systems;
- negative feedback system triggers a response that counteracts, or reverse the change in the steady state.
- positive feedback system; response that intensifies the changing condition. Do NOT maintain homeostasis.
- Body temperature increases above normal, specialized nerve cells signal the temperature-regulating center in the hypothalamus: hypothalamus sends messages to smooth muscle in the walls of blood vessels in the skin that cause them to dilate.
- Body temperature decreases below normal, the hypothalamus signals the pituitary gland to release a hormone that signal the thyroid gland; thyroid hormones increases the metabolic rate and thus increase body temperature. Hypothalamus also sends neural signals that cause blood vessels in the skin to constrict. In addition, nerves signal muscles to shiver.
- Biorhythms: an attempt to predict various aspects of a person's life through simple mathematical cycles. Biorhythm charts illustrate the principle that we are influenced by physical, emotional, and intellectual cycles.
Metabolism and energy flow in the organism: mechanisms of nutrition and processes of digestion.
- Aka bioenergetics in humans.
- Anabolic and catabolic.
- Anaerobic energy metabolism occurs in two forms, the ATP-creatine phosphate system and fast glycolysis. The ATP-creatine phosphate system uses stored creatine phosphate molecules to regenerate ATP that has been depleted and degraded to its low-energy form, adenosine diphosphate (ADP). The creatine phosphate donates a high-energy phosphate molecule to the ADP, thereby replacing spent ATP and re-energizing the cell. Muscle cells typically contain enough free-floating ATP and creatine phosphate to power approximately ten seconds of intense activity, after which the cell must switch to the fast glycolysis process.
- Fast glycolysis synthesizes ATP from glucose in the blood and glycogen in the muscle, with lactic acid produced as a byproduct. This form of energy metabolism is associated with brief, intense bursts of activity &mash; such as power lifting or sprinting — when the cardio-respiratory system does not have time to deliver adequate oxygen to the working cells
- Aerobic metabolism takes place in one of two ways, fast glycolysis or fatty acid oxidation. Fast glycolysis, like slow glycolysis, breaks down glucose and glycogen to produce ATP. Since it does so in the presence of oxygen, however, the process is a complete chemical reaction. While fast gycolysis produces two molecules of ATP for every glucose molecule metabolized, slow gycolysis is able to produce 38 ATP molecules from the same amount of fuel. As there is no lactic acid accumulation during the reaction, fast glycolysis has no associated muscle burn or fatigue.
- Finally, the slowest and most efficient form of energy metabolism is fatty acid oxidation. This is the process used to power activities such as digestion and cellular repair and growth, as well as long-duration exercise activities, such as marathon running or swimming. Rather than using glucose or glycogen as fuel, this process burns fatty acids that are stored in the body, and is capable of producing as many as 100 ATP molecules per unit of fatty acids. While this is a highly efficient, high-energy process, it requires large amounts of oxygen and only occurs after 30 to 45 minutes of low-intensity activity.
- Food is chewed into a bolus. Three pairs of saliva glands secrete the enzymes salivary amylase which digest starch into sugar. This digestion process continues until the bolus reach the stomach, where acidic gastric juice inactivates salivary amylase. Instead, pepsin hydrolyzes proteins to polypeptides.
- Duodenum: the chyme(partially digested food) is acted upon by the enzymes and salts present in pancreatic and bile juice. The starch is converted into maltose by the pancreatic amylase and the remaining proteins, proteoses and peptones into peptides and amino acids by trypsin. The bile juice emulsifies the fats and then converts them into fatty acids and glycerol by the action of lipase.
- In jejunum, there is no digestion. In ileum, the food is completely broken down into the simplest of forms - proteins into amino acids and carbohydrates into monosaccharides. This digested mass is now called the chyle and it is in a liquid form..
Phylogenesis of digestion system.
Gas exchange between tissues and the environment.
- Some epithelial cells are sensory receptors that receive information from the environment. Ex; taste buds and epithelial cells in the nose that specialize as chemical receptors.
- In many animals, including vertebrates, respiratory and circulatory systems are functionally connected. Such systems provide sufficient oxygen to support high metabolic rates.
Water vs air:
- Air contains more than 20 times more oxygen than in water. Oxygen also diffuses about 10,000 times faster through air than through water. Air is less viscous and dense, and thus require less energy for moving air over a gas exchange surface.
- Mammal use 2% energy to breathe.
- Fish use 20% energy to breathe.
- Animals that respire in air continuously struggle with water loss.
Respiratory surfaces must be kept moist.
Four main types of respiratory surfaces in animals:
Except of insect tracheal tubes, respiratory structures are richly supplies with blood vessels that facilitate exchange and transport of respiratory gases.
- animal's own body surface (small, multicellular animals such as earthworms)
- terrestial animals keep a moist surface by secreting fluids. For low metabolic rate.
- tracheal tubes (insects)
- air enters through a series of about 20 tiny spiracles along the body surface, and deliver air directly to the cells. Supports high metabolic rate.
- gills
- Internal gills in chordates. Countercurrent exchange system to efficiently charge the blood with oxygen.
- lungs
- Lungs enables to exchange gas without losing too much water.
- Book lungs in spiders; plates of tissue separated by air spaces that receive oxygen from environment through spiracles.
- Snails and slugs perform gas exchange through a vascular region of the mantle.
- Most amphibians have (rather simple) lungs, but most of their gas exchange takes place across body surface.
- Reptiles have better lungs than amphibians; surface is divided into large sacs to increase surface for gas exchange.
- Birds have the most efficient respiratory system of any living vertebrate. Their lungs have (nine) extensions called air sacs which reach into all parts of the body. Crosscurrent gas exchange (kind of like countercurrent).
- Bird's breathing requires two cycles of inhalation and exhalation:
1) First inhalation: air flows into posterior air sacs.
2) First exhalation: air from posterior air sacs is forced out into the lungs.
3) Second inhalation: air from first inhalation flows into anterior air sacs. Air from second inhalation flows into the posterior air sacs.
4) Second exhalation: air from first inhalation leaves body, air from the second inhalation flows into lungs. Thus, birds get fresh air across its lungs through both inhalation and exhalation.
- Mammals have complex lungs with huge surface area. Mucus in nostrils provide a filter for bacteria. Each bronchiole ends in a cluster of tiny sacs; alveoli (200 million in human lungs). Right lung is divided into three lobes, the left into two lobes. Each lung is covered by a pleural membrane that encloses the lung and give rise to the pleural cavity which contains fluid for lubrication between the lungs and chest wall.
- Oxygen flows from alveoli to the blood, and carbon dioxide flows from the blood to the alveoli. Inhaled air contains about 21% oxygen, and exhaled air contains 14% oxygen. Carbon dioxide is produced during aerobic respiration and thus exhaled air contains about 100 times more carbon dioxide than in inhaled air.
- Partial pressure of air at sea level is 760 mm Hg. Thus 21% of oxygen in air makes up 160 mm Hg. Partial pressure of oxygen in cells in tissue is 40 mm Hg versus 100 mm Hg in blood. Oxygen is more concentrated in blood than in cells, and thus diffuse into cells. Carbon dioxide is more concentrated in cells and thus diffuse out of cells.
- Hemoglobin(heme = iron-porphyrin) is found in annelids, nematode, mollusks, and arthropods. Plasma can take up only 0.25 mL of oxygen per 100 mL. However, oxygen diffuses into red blood cells and combines with hemoglobin which permit whole blood to carry some 20 mL of oxygen per 100 mL.
- Myoglobin stores oxygen in muscle cells.
- Breathing is controlled by respiratory centers in the brain stem.
Phylogenesis of respiratory system.
Types of body fluids in animals and in humans, composition and function.
- Bile: produced by liver. Aids in digestion of lipids in small intestine; thus also important part of the absorption of the fat-soluble substances, such as the vitamins D, E, K and A. Bile also destroy many microbes.
- Bile salt anions are hydrophilic on one side and hydrophobic on the other side; consequently, they tend to aggregate around droplets of fat (triglycerides and phospholipids) to form micelles, with the hydrophobic sides towards the fat and hydrophilic sides facing outwards
- Serum: blood plasma with the fibrinogens removed. Serum includes all proteins not used in blood clotting (coagulation) and all the electrolytes, antibodies, antigens, hormones, and any exogenous substances (e.g., drugs and microorganisms).
- Breast milk: During the first few days after delivery, the mother produces colostrum.It is rich in protein and antibodies that provide passive immunity to the baby (the baby's immune system is not fully developed at birth). Colostrum also helps the newborn's digestive system to grow and function properly.
- Cerebrospinal fluid (CSF): produced in the brain.
Functions:
1) The brain exists in neutral buoyancy, which allows the brain to maintain its density without being impaired by its own weight.
2) protects the brain tissue from injury when jolted or hit.
3) flows throughout the inner ventricular system in the brain and is absorbed back into the bloodstream, rinsing the metabolic waste from the central nervous system through the blood–brain barrier. This allows for homeostatic regulation of the distribution of neuroendocrine factors, to which slight changes can cause problems or damage to the nervous system.
4) The prevention of brain ischemia is made by decreasing the amount of CSF in the limited space inside the skull. This decreases total intracranial pressure and facilitates blood perfusion.
Composition: CSF is a weak salt solution with similar inorganic ion concentrations to plasma, but with small and significant differences, whereas the protein content is about 100 times less than that of plasma
- Chyle is a milky bodily fluid consisting of lymph and emulsified fats, or free fatty acids. It is formed in the small intestine during digestion of fatty foods, and taken up by lymph vessels specifically known as lacteals.
- Feces: Its brown coloration comes from a combination of bile and bilirubin, which comes from dead red blood cells. The distinctive odor of feces is due to bacterial action. Gut flora produce compounds such as indole, skatole, and thiols (sulfur-containing compounds), as well as the inorganic gas hydrogen sulfide.
- Gastric acid has a pH of 1.5 to 3.5 and is composed of hydrochloric acid (HCl) and large quantities of potassium chloride (KCl) and sodium chloride (NaCl). he acid plays a key role in digestion of proteins, by activating digestive enzymes, and making ingested proteins unravel so that digestive enzymes break down the long chains of amino acids.
- Lymph is formed when the interstitial fluid (the fluid around all cells/tissues) is collected through lymph capillaries. As the blood and the surrounding cells continually add and remove substances from the interstitial fluid, its composition continually changes and it changes into lymph fluid. It is then transported through lymph vessels to lymph nodes before emptying ultimately into the right or the left subclavian vein, where it mixes back with blood.
If excessive hydrostatic pressure develops within the lymph vessels, though, some fluid can leak back into the interstitial space and contribute to formation of edema.
Composition: Lymph is comparable to blood plasma, but contains white blood cells. In particular the lymph that leaves a lymph node is richer in lymphocytes. Likewise, the lymph formed in the digestive system called chyle is rich in triglycerides (fat), and looks milky white.
- Rheum is formed by a combination of mucus (in the case of the eyes, consisting of mucin discharged from the cornea or conjunctiva), nasal mucus, blood cells, skin cells, or dust.
- Human saliva is 99.5% water, while the other 0.5% consists of electrolytes, mucus, glycoproteins, enzymes, and antibacterial compounds such as secretory IgA and lysozyme. The enzymes found in saliva are essential in beginning the process of digestion of dietary starches and fats. These enzymes also play a role in breaking down food particles entrapped within dental crevices, protecting teeth from bacterial decay.
- Sebaceous glands are microscopic glands in the skin that secrete an oily/waxy matter, called sebum, to lubricate and waterproof the skin and hair of mammals
- Semen: Besides containing sperm, normal semen contains a number of other substances. These substances include water; simple sugars like fructose that serve as nourishment for the sperm; alkaline chemicals that "buffer" the sperm against the acidic environment of the urethra and vagina; prostaglandins which are fatty acid compounds that spur contractions in the muscles of the uterus and fallopian tubes and are believed to aid the sperm's journey to the uterus/womb; vitamin C; zinc; cholesterol; and a few additional compounds.
- Sweat contains water, minerals, lactate, and urea. Sweating allows the body to regulate its temperature.
- Synovial fluid: Lubricant to reduce friction and shock absorber. Synovial tissue: Type A is derived from blood monocytes, and it removes the wear-and-tear debris from the synovial fluid. Type B produces synovial fluid. Synovial fluid is made of hyaluronic acid and lubricin, proteinases, and collagenases. Synovial fluid has thixotropic characteristics; viscosity decreases and the fluid thins over a period of continued stress. It also contains phagocytic cells that remove microbes and the debris that results from normal wear and tear in the joint.
- Urine: water 95 - 96%, urea 2%, other wastes like chloride, sodium, potassium, creatinine. It also contains non-nitrogenous organic compounds like vitamin C, oxalic acid and phenolic substances.
Systems of open and closed blood circulation , flow of the blood in blood vessels, blood groups and blood clotting in animals and in humans.
Open circulatory system: blood not confined to vessels. For example, in arthropods blood flows freely over tissues in spaces known as haemocoel. Blood flow is slow and low pressure.
Closed circulatory system: heart, arteries, arterioles, capillaries, venules and veins. Higher pressure, more control over distribution as vessels can be dilated or constricted. For example, blood from intestines to skeletal muscles during exercise.
Atrium receives blood from veins, ventricle pumps blood into arteries.
Systole = contraction, diastole = relaxation.
Valves in the vessels ensure that blood flows in one direction only. Pressure gradient from high-pressure areas to low-pressure areas are produced by pumping of the heart, contraction of skeletal muscles squeeze blood along veins, and inspiratory movements of the thorax to reduce the pressure inside the thoracic cavity (helps draw blood to heart).
Red blood cells (erythorcytes).
White blood cells (leukocytes): phagocytes on bacteria etc.
Platelets are fragments of cells broken off from large cells in the bone marrow: blood clotting.
Blood clotting minimizes blood loss following injuries. Clotting factors thromboplastins (released by platelets) together with calcium and vitamin K, convert prothrombin to thrombin which catalyze conversion of fibronogen into fibrin which forms a network that traps blood cells and debris to form a clot. Anticoagulants such as heparin circulates in bloodstream, and endothelium also produces molecules that inhibit clotting in the blood vessels. Thus, blood clots quickly when exposed to air because of the absence of these anticoagulants.
Four blood types:
A, B, AB, O.
- A individual can receive blood only from individuals of groups A or O (with A being preferable), and can donate blood to individuals with type A or AB
- B individual can receive blood only from individuals of groups B or O (with B being preferable), and can donate blood to individuals with type B or AB.
- AB blood can receive blood from any group (with AB being preferable), but cannot donate blood to either A or B group. Universal recipients.
- O individual can receive blood only from a group O individual, but can donate blood to individuals of any ABO blood group. Universal donors.
The heart in vertebrates and in invertebrates, functional characteristics, phylogenesis of the circulatory system.
- No circulatory structures in sponges, cnidarians (hydras, jellyfish), ctenophores (comb jellies), flatworms, or nematodes (roundworms). Body movement move the fluid.
- Flatworms; branched gastrovascular cavity allows nutrients to come close to most body cells.
- Cnidarians; nutrients diffuse a short distance from inner layer of gastrovascular cavity to outer layer of cells.
Open system:
- arthropods and most mollusks.
- their blood and interstitial fluid referred to as hemolymph. This fluid spills out into spaces called sinuses. Sinuses makes up blood cavity hemocoel. Hemolymph bathes the cells directly. Hemolymph then re-enters the circulatory system through openings in the heart (arthropods) or through open-ended vessels that lead to the gills (mollusks).
- In most mollusks, the heart receive hemolymph and conduct it to hemocoel. After bathing the body, hemolymph passes into vessels that lead to the gills where it is recharged with oxygen, and then back to the heart.
- Some mollusks and arthropods have blue blood because of hemocyanin that contains copper.
Some invertebrates have closed circulatory system:
- Annelids, some mollusks and echinoderms.
- Proboscis worms have a closed network of vessels, but no heart. Blood flow depends on movement.
- Earthworms and other annelids have closed circulatory system where two main blood vessels extend lengthwise in the body. Ventral vessel conduct blood posteriorly, and dorsal vessels conduct blood anteriorly. Five pairs of "hearts" in the anterior connects the two vessels. Earthworms have hemoglobin dissolved in blood plasma, not within red blood cells.
Invertebrates;
- Instead of a heart there are blood vessels that act as pumps to force the blood along.
- Instead of capillaries, blood vessels join directly with open sinuses.
- "Blood," actually a combination of blood and interstitial fluid called 'hemolymph', is forced from the blood vessels into large sinuses,
Phylogenesis of the excretory system, structure and function of the nephron, secretion and composition of the urine.
- Excretory systems rid the body of excess water, ions, metabolic waste(carbon dioxide and nitrogenous wastes), and harmful substances.
- Nitrogenous waste: ammonia, uric acid and urea. During the metabolism of amino acids, the nitrogen-containing amino group is removed and converted to ammonia. Humans convert the highly toxic ammonia to uric acid or urea.
- Uric acid produced from ammonia and by breakdown of nucleic acids.
- Urea synthesized in liver from ammonia and carbon dioxide.
- Flatworms and nemerteans; metabolic waste diffuse through body surface. They also have protonephridia with enlarged blind ends consisting of flame cells of cilia. Interstitial fluid enters flame cells and cilia propels fluid through tubules. Excess fluid leaves through nephridiopores.
- Most annelids and mollusks have more complex metanephridia; a tubule open at both ends. Inner end opens into the coelom and outer opens to the outside through nephridiopore. As fluid moves through the tubules, needed materials are reabsorbed into capillaries surrounding the tubules, leaving the waste in the tubules.
- Insects and spiders have several hundred Malpighian tubules; slender extensions of the gut wall. Their blind ends lie in the hemocoel and are bathed in hemolymph. Tubules transport and empty uric acid, potassium ions etc into the gut. Water, some salts and other solutes are reabsorbed in the rectum. Uric acid is thus excreted as a paste with minimum water loss.
Vertebrates:
- Primarily kidney, but also skin, lungs or gills, and digestive system help maintain fluid balance and dispose metabolic wastes. Most carbon dioxide is excreted by the lungs. Sweat glands excrete 5-10% of all metabolic wastes.
- Freshwater fish have large glomeruli, capillary clusters that filter the blood and produce urine. Their kidneys excrete large amounts of dilute urine as water keeps entering their body through gills and mouth. Special gills actively transport salts from water into the body to compensate for the loss through large amounts of excretion.
Mammalian:
- Kidney, urinary bladder, associated ducts.
- Kidney: renal cortex (outer), renal medulla (inner); medulla contains 8-10 renal pyramids. Tip of each pyramid is renal papilla which has several pores, the openings of collecting ducts. Urine produced flows from collecting ducts into the renal pelvis, and into one of the paired ureters that connects kidney to bladder. Urine flows from bladder and out through urethra.
- Kidneys produce:
- Enzyme Renin, which helps regulate fluid balance and blood pressure.
- Hormone Erythropoietin, which stimulates red blood cell production.
- Hormone 1,25-dihydroxy-vitamin D3 which stimulates calcium absorption by the intestine.
Nephron: The nephron carries out nearly all of the kidney's functions. A nephron eliminates wastes from the body, regulate blood volume and blood pressure, controls levels of electrolytes and metabolites, and regulates blood pH.
Kidney consists of one million of these functional units. Nephron consists of Bowman's capsule connected to a long renal tubule. Within Bowman's capsule is a cluster of capillaries called a glomerulus.
- Renal tubule consists of:
1) proximal convoluted tubule which conducts filtrate from Bowman's capsule.
2) Loop of Henle
3) distal convoluted tubule which conducts filtrate to a collecting duct.
Filtrate => Bowman's capsule -> proximale convoluted tubule -> loop of Henle -> distal convoluted tubule -> collecting duct.
- Two types of nephrons:
- Numerous (85%) cortical nephrons:
- Internal juxtamedullary nephrons:
Healthy urine is sterile and used on battlefield wounds.
Hormonal regulations: mechanisms of direct and indirect effect of hormones, regulation of hormone level in body fluids, hormonal regulation in invertebrates and in vertebrates, species specific regulatory odours.
The structure and the function of the neurone.
Transfer of neural signal by neurone and on synapses, action potential of neurite, phylogenesis of nervous system, central nervous system in vertebrates.
- Afferent neurons / sensory neurons
- Efferent neurons / motor neurons
- Negative electric charge inside the cell. The voltage measured across the plasma membrane is called the membrane potential. The resting potential is about -70 mV. 10 times more K+ inside, 10 times more Na+ outside. More Cl- inside.
- K+ easily diffuse out of the neuron, but Na+ cannot easily pass back into the cell. However, K+ diffuse back in.
- Na-K pump pumps 3 Na+ out of the cell, and 2 K+ in.
- When stimulus causes the membrane potential to become less negative than the resting potential, the membrane is depolarized. If it gets to the threshold level (less than -55 mV), an action potential is released. Na+ in, and K+ out results in action potential. It further depends on positive feedback system to intensify the change; Na+ channels open, and diffuse into the cell.
- In contrast, when the membrane potential becomes more negative, the membrane is hyperpolarized: it decreases the ability to generate a neural impulse.
- Electrical synapses are close together and pass ions from one cell to another.
- Chemical synapses convert the electrical signal to a chemical neurotransmitter signal.
- Acetylcholine; Released by cholinergic neurons.From motor neurons; triggers muscle contraction.
- Biogenic amines; Norepinephrine(released by adrenergic neurons), epinephrine and dopamine are catecholamines. The catecholamines and serotonin and histamin belong to biogenic amines, which affect mood.
- Amino acids: Glutamate. Glycine and GABA inhibit neurons in the spinal cord and brain. Aspartate is excitatory in learning and memory.
- Neuropeptides: Endorphines and enkephalins (long term changes that inhibit or enhance synaptic function). Opioids: Inhibit release of substance P. Substance P activities pathways that transmit pain signals from sensory neurons to CNS.
- Gaseous neurotransmitters: Nitric oxide (NO) transmit information from postsynaptic to presynaptic. Carbon monoxide (CO) may be neuromodulator.
- Neurite refers to any projection from the cell body of a neuron, ex dendrites or axon.
Neural impulse transmitted across a synapse:
1) Action potential reaches synaptic terminals at end of presynaptic neuron.
2) Calcium channels open in membrane, letting Ca2+ from extracellular fluid enter the synaptic terminal.
3) Ca2+ cause synaptic vesicles to fuse with plasma membrane and release neurotransmitter into synaptic cleft.
4) Neurotransmitter binds with receptors on membrane of postsynaptic neuron.
5) In response, specific ion channels open or close, resulting in either depolarization or hyperpolarization.
CNS:
- Cerebrum, cerebellum, brainstem (diencefalon, mesencefalon, pons, medulla oblangata), and medulla spinalis.
- 12 brain nerves.
- Medulla spinalis C1 - L2 (31 segments). Then we have cauda equina.
- I grå substans, forhornet, ligger cellekroppen til de motoriske forhorncellene.
- I grå substans, bakhornet, kommer sensoriske nerver fra hud, ledd og muskler inn.
Medulla: contains vital centers that control heartbeat, respiration, and blood pressure; and swallowing, coughing, vomiting.
Pons: Connects various parts of brain together. contains respiratory and sleep centers.
Midbrain: Above pons. Center for visual and auditory reflexes(pupil reflex, blinking etc).
Thalamus: At top of brain stem. Main sensory center for conducting information between spinal cord and cerebrum. Sort and interpret all incoming sensory information before relaying messages to appropriate neurons in cerebrum.
Hypothalamus: Just below thalamus. Pituitary gland connected to hypothalamus. Centers for control of body temperature, appetite, fat metabolism. Regulates pituitary gland. Important in emotional and sexual responses, and in sleep-wake cycle.
Cerebellum: Muscle coordination, refinement of movements, muscle tone, posture, helps plan and initiate voluntary activity. Stores implicit memories.
Cerebrum: Divided into left and right each with divided lobes; frontal, parietal, temporal and occipital lobes. Center of intellect, memory, consciousness, and language. Also controls sensation and motor functions.
- Cerebral cortex (outer gray matter): Arranged into folds. Motor areas, sensory areas and association areas. Control movement of voluntary muscles, receive incoming information from eyes, ears, pressure, touch receptors. Sites of intellect, memory, language and emotion; interpret incoming sensory information.
- White matter: Myelinated axons that connects various regions of the brain; neurons within same hemisphere, right and left hemisphere(corpus callosum), cerebrum with other parts of brain and spinal cord.
Evolution:
- Cnidirians: nerve net with no central control organ. Responds effectively to predator or prey from any direction.
- Echinoderms: radial nervous system is a modified nerve net.
- Flatworms: cerebral ganglia, concentration of nerve cells in the head region. Two nerve cords extend toward the posterior.
- Annelids and arthropods: solid ventral nerve cord connected to a ganglia. Arthropods cerebral ganglia even have specific functional regions.
- Mollusks: two nerve cords; one extends each side of the body. Several pairs of ganglia located along the cords. Squids and octopods have complex nervous systems and well-developed sense organs. Their brain have lobes and intricate folds and specialized areas. Considered the most intelligent invertebrates.
Trends in evolution: 1) increased number of nerve cells. 2) Concentration of nerve cells. 3) Specialization of function. 4) Increased number of interneurons and more complex synaptic contacts. Provide greater range and precision of repsonses. 5) Cephalization.
- Synaptic terminals release neurotransmitters.
- Outside CNS, the cell bodies of neurons are grouped to masses called ganglia. Inside CNS they are called nuclei.
- Four types of glial cells:
- Astrocytes: Physically support neurons, provide nutrients to neurons, remove excess K+, induce blood vessels to form blood-brain barrier, communicate with one another and with neurons, strengthen activity of synapses, help regulate neurotransmitter reuptake, important in memory and learning.
- Oligodendrocytes: form myelin sheaths around neurons in CNS. Schwann cells, form myelin sheaths around neurons in PNS.
- Ependymal cells: line cavities of CNS, help produce and circulate cerebrospinal fluid, may function as neural stem cells.
- Microglia: phagocytosis of bacteria and debris, release signaling molecules that mediate inflammation.
Instincts, conditioned and unconditioned reflexes, origin and stability of conditioned reflexes, memory and memory traces, learning and thinking.
Sense organs: chemoreceptors, mechanoreceptors and radioreceptors, their sensitivity and function, phylogenetic development.
Muscles: structure and function of muscle fibres, smooth muscle - its characteristics, striated muscle - its characteristics, characteristics of heart muscle and regulation of heart activity, classification of muscles according the content of myoglobine, energy sources for muscle activity, muscle fatigue.
Immune reactions of organism: antigens, non-specific and specific immunity, cellular and antibody immunity reaction, response of B and T lymphocytes to antigen, allergy, passive and active immunisation.
Genetics
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Basic genetic terminology: codon, gene, allele, interrelationship between alleles, genotype, phenotype, homozygous and heterozygous individuals, autosomes and sex chromosomes, genome, karyotype, genofond.
Regulatory genes, structural genes and genes for RNAs - their transcription and translation.
Comparison of organisation of structural genes in prokaryotes and eukaryotes. Genetic information in prokaryotic and eukaryotic cell and its expression.
Autosomal heredity: monohybrid and dihybrid crossing with complete and incomplete dominance, heredity of blood groups in human.
Gene linkage.
Genetic determination of sex: homogametic and heterogametic sex, gonosomal heredity in invertebrates, in birds, in mammals and in human, human diseases caused by gonosomes and their heredity.
Modifications, mutations and their classification, gene and genomic mutations in human and their heredity.
Heredity of quantitative and qualitative characteristics.
Definition of the population, autogamic and panmictic populations and their development, validity and limits of validity of the law of population equilibrium, practical application of this law.
Methods used in human genetics, genetic diseases and dispositions, genetic counselling, eugenics and its aim.
Human biology
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Bones: structure, function, connection, scull, permanent and milk teeth, skeleton.
- Echinoderms and chordates have endoskeleton of calcium-impregnated tissue (cartilage or bone) that grows with the animal as a whole.
- Vertebrate skeleton have two main divisions: axial skeleton and the appendicular skeleton.
- 24 vertebrae in humans, and 2 bones composed of fused vertebrae, sacrum (5 fused vertebrae) and coccyx.
- 12 pairs of ribs. 7 first attached to sternum, next 3 attached by cartilage, the last 2 are floating.
- Long bones have bone marrow: yellow; fat. Red; blood cells.
- Bone cells: osteocytes. Substantial blood supply.
- Compact bone consist of osteons. Within osteons, osteocytes lie in small cavities called lacunae.
- Osteblasts are bone-building cells.
- Osteoclasts break down bone. In osteoporosis, bone replacement takes place more rapidly than bone formation.
- Bones support and protect the various organs of the body, produce red and white blood cells and store minerals.
- Skull consist of 8 cranial bones and 14 facial bones.
Teeth:
- primary teeth are small compare to permanent teeth
- primary number of teeth: 20, permanent number of teeth: 32.
- primary teeth are white colour because of less mineralized enamel, permanent teeth are yellowish because of more mineralizes enamel.
- mamelons means three bulges on the incisal edges of the newly erupted central incisor:
- no mamelons for primary teeth and have mamelons for permanent teeth.
- thinner enamel for primary teeth, thicker enamel for permanent teeth
- cervical ridge means ridge at cervix region. Cervix means where crown meet root. - cervical edge is more prominent for primary teeth compare to permanent teeth.
- second molar(jeksel) larger than first molar in primary teeth, second molar smaller than first molar
Muscles: types of muscles, muscle systems, muscle innervation.
- Muscle fiber contains many myofibrils. Myofibrils consists of myosin and actin. Animals with very simple body plans do not have muscle tissue, but still have the contractile protein actin.
Skeletal-, cardiac-, smooth muscles.
- Skeletal: Voluntary control. Striatons (alternating light and dark stripes). Very long, each fiber has many nuclei.
- Cardiac: Unvoluntary control. Striatons. One or two nuclei in each fiber. Intercalated discs (specialized junctions where the fibers join). Heart muscles are controlled by the sinus node influenced by the autonomic nervous system.
- Smooth: Unvoluntary control. Digestive tract, uterus, blood vessels, many internal organs. Each fiber contains a single, central nucleus.
Three types of skeletal muscle fibers:
- Slow-oxidative: slow contraction, endurance and maintaining posture(slow rate of fatigue), require steady supply of oxygen, rich in mitochondria, rich in myoglobin which stores oxygen in red blood cells -> red fibers.
- Fast-glycolytic: great power and rapid movements (sprinting and weight-lifting), fast rate of fatigue, few mitochondria, glycolysis, low content of myoglobin -> white fibers.
- Fast-oxidative: aka intermediate fibers. Contract rapidly (intermediate rate of fatigue), rich in mitochondria, mostly oxygen dependent, rich in myoglobin -> red fibers.
- Sarcoplasm = the cytoplasm of muscle fiber. Sarcoplasmic reticulum = the endoplasmic reticulum.
- Myofibrils consist of myofilaments: myosin and actin. Myosin and actin are organized into repeating units called sarcomeres. Sarcomeres are joined at their ends to the Z line.
- The filaments overlap lengthwise in the muscle fibers, producing patterns.
- I band consist of parts of actin filaments of two adjacent sarcomers.
- A band is the wide, dark region; overlapping myosin and actin filaments.
- H zone is within the A band, and is exclusively of myosin filaments. Light region.
Muscle innervation:
1) Motor neuron releases the neurotransmitter acetylcholine which depolarize and cause an action potential to be generated in the muscle fiber.
2) Action potential is a wave of depolarization that travels along the sarcolemma (cell membrane) and into the system of T-tubule membranes.
3) Depolarization of T-tubules opens calcium channels in the sarcoplasmic reticulum, and stored calcium ions are released into the myofibrils.
4) Calcium ions bind to the protein troponin on the actin filaments which changes its shape. Active sites on actin filaments are exposed.
6) ATP (attached to myosin) is split. Energized myosin binds to exposed active site on the actin filament, forming a cross bridge linking the myosin and actin filaments.
8) Inorganic phosphate is released from the myosin head.
9) Cross bridge flexes, and actin filament is pulled toward center of sarcomere, shortening the muscle. ADP is released.
10) Actin-myosin complex binds ATP, and myosin detaches from actin. If sufficient calcium ions are present, the cycle begins anew from step 4.
- When the impulses from motor neuron cease, acetylcholine is inactivated and calcium ions are pumped back to sarcoplasmic reticulum by active transport. Without calcium ions, tropomyosin once again covers active sites on the actin filaments.
- ATP is needed for both the pull, but also for the release (bringing calcium ions back). In rigor mortis, when death occurs ATP is used up. However, many muscle fibers are in the process of contraction in the time of death, so the cross bridges remain intact.
- ATP can provide energy for only a few seconds of strenuous activity. However, a backup energy storage compound, creatine phosphate, is transferred to ATP as needed. Muscle fibers store chemical energy as glycogen, which can be broken down to glucose if sufficient oxygen is available, to replenish needed quantities of ATP and creatine phosphate.
- In strenuous exercise, the circulatory system cannot deliver enough oxygen. Under these conditions, muscle fibers break down fuel molecules anaerobically, with lactic acid as waste product. Rapid breathing following the strenuous exercise pays back the oxygen debt by consuming lactic acid.
- The more motor units that are recruited, the stronger are contractions. Each motor neuron is connected with average 150 muscle fibers.
- An impulse from a nerve cell causes calcium release and brings about a single, short muscle contraction called a muscle twitch. If the fiber is stimulated a second time before the first twitch done, the two signals add to each other; summation. Summation results in a smooth, sustained contraction called tetanus.
Invertebrate muscle:
- Varies among groups
- Ex clams have two sets of smooth muscle capable of sustained contraction of their shell.
- Striated muscle, which contracts rapidly, is used to swim and to shut shell quickly. Insects:
- Insects flight muscles contract up to 1000 times per second! Butterflies and some other insects bask in the sun or honeybees "shiver" before they fly to warm up the body temperature needed for increased rate of ATP synthesis.
- Most of flying insects beat their wings too rapidly to be controlled by a single motor neuron. Instead, they have asynchronous, or indirect, muscle contractions that are not synchronized with signals from motor neurons. Instead they automatically flap as the muscles in the wings stretch. However, nerve impulses are needed to maintain the contractions.
Blood: composition, function, volume, blood cells - their origin, shape, function, sedimentation(blodsenkende), types of haemoglobin, ABO system, Rh factor and its role, defence reactions of organism, blood transfusion.
Function:
- Supply of oxygen to tissues (bound to hemoglobin, which is carried in red cells)
- Supply of nutrients such as glucose, amino acids, and fatty acids (dissolved in the blood or bound to plasma proteins (e.g., blood lipids))
- Removal of waste such as carbon dioxide, urea, and lactic acid
- Immunological functions, including circulation of white blood cells, and detection of foreign material by antibodies
- Coagulation
- Messenger functions, including the transport of hormones and the signaling of tissue damage
- Regulation of body pH
- Regulation of core body temperature
- Hydraulic functions
Composition:
- Tissue with 50% more fluid than other tissue.
- By volume, the red blood cells constitute about 45% of whole blood, the plasma about 54.3%, and white cells about 0.7%.
- Human body has about 5 liter.
- 90% of blood cells are red.
Three types:
1) Erythrocytes(red blood cells): 45%
Function:
- Transport O2 and CO2.
- Too low values -> reduced ability to transport O2
- Too high values -> higher strain on the heart
Shape:
- Circleround, flat compressed. Extra compressed in the middle.
- No nucleus, mitochondria and other organelles -> do not use any of the oxygen they transport for energy.
Origin:
- Live for approx 120 days because they lack DNA and RNA.
- Production of new erythrocytes happen by mitosis of stem cells.
-> Embryo: Liver and Spleen
-> Older/adult: bone marrow (after puberty; mainly in flat bones)
2) Leukocytes(white blood cells): 0,7%
Types:
- Neutrophil gran.(60-70%): bacteria and fungi
- Eosinophil gran.: parasites, allergic reactions
- Basophil gran.: histamine in inflammatory response
- Lymphocyte(30%):
- B cells: Mature to plasma cells; produce specific antibodies that assist T cells.
- T cells: cell-mediated immunity; soldiers.
- Natural killer cells: virus-infected and tumor cells.
- Monocyte: leave the bloodstream to become tissue macrophages
- Natural killer cells; destroy cells infected with viruses etc or altered cells, ex tumor cells.
- Dendritic cells: release antiviral proteins called interferons(a cytokine)
Function:
- Granulocytes and monocytes take up and kill foreign microorganisms
- Lymphocytes blink out and target microorganisms
Shape:
- Contain nucleus and the normal cell organelles.
- Granulocytes contain many vesicles and are grained.
- Monocytes and lymphocytes are not grained.
- Bigger than erythrocytes.
Origin:
- 10-20 times as many Leukocytes in bone marrow as in blood. Released when needed.
- Stem cells in bone marrow.
- Lymfocytes go to lymph nodules, spleen, tonsil's, thymus, intestines and other organs.
3) Thrombocytes(plates): 54,3%
- No nucleus, but rich in cell organelles and cytoplasmic enzymes.
- produced by megakaryocytes in bone marrow.
- Spleen contains lots of trombocytes which can be released by sympaticus n.
- Contain actin and myosin; explains why they can contract.
Types of haemoglobin:
- Constitute 95% of erythrocytes proteins and 34% of their weight.
- Globin; four chains of polypeptides; two alfa chains, and two beta-, gamma-, delta- or epsilon chains. Four hemgroups: Each hemgroup got one iron atom in the middle.
- 300 million hemoglobin molecules in each erythrocyte.
- Blood is blueish without bounded oxygen.
- Men got higher values of hemoglobin because testosterone stimulates production of erythrocytes.
- Four types of haemoglobin:
1) Embryonic: 2 alfa, 2 epsilon.
2) Fetal: HbF2: alfa, 2 gamma. Binds O2 better. Important because of low volume of blood.
3) Adults
1) HbA: >95%. 2 alfa, 2 beta.
2) HbA2: 1-3%.2 alfa, 2 delta.
ABO system:
Rh factor and its role:
An individual either has, or does not have, the "Rhesus factor" on the surface of their red blood cells (in addition to ABO). This term strictly refers only to the most immunogenic D antigen of the Rh blood group system, or the Rh- blood group system. The status is usually indicated by Rh positive (Rh+ does have the D antigen) or Rh negative (Rh- does not have the D antigen) suffix to the ABO blood type. However, other antigens of this blood group system are also clinically relevant. In contrast to the ABO blood group, immunization against Rh can generally only occur through blood transfusion or placental exposure during pregnancy in women.
Rh system consist of more than 40 kinds of Rh antigens/factors. Most important is antigen D. About 85% of US residents are Rh positive (they have antigen D on the surfaces of their red blood cells).
Rh-negative people are homozygous recessive, and Rh-positive people are heterozygous or homozygous dominant.
Rh incompatibility is the most serious maternal-fetal blood type incompatibilities known. If a woman is Rh negative and the father is Rh positive, the fetus may also be Rh positive. If any maternal blood mixes with fetal blood, fetal red blood cells, bearing antigen D, active the mothers immune system. Mothers B cells then produce antibodies to antigen D. If the woman becomes pregnant again, anti-D antibodies cross the placenta and enter the fetal blood. This causes cell rupture, and hemoglobin damage organs; may kill the fetus.
Defence reactions:
- Cell mediated immunity: specific T cells activated; release proteins that destroy cells infected with viruses etc.
- Antibody-mediated immunity: specific B cells activated; multiply and differentiate into plasma cells, that produce antibodies.
- Specific immune responses target distinct antigens. "Remembers".
- Infection; mast cells release histamine etc that cause vasodilation and increased capillary permeability.
Blood transfusion:
First, ABO and Rh status is determined. The sample is then Screened for any alloantibodies(antibody that occurs naturally against foreign tissues from a person of the same species) that may react with donor blood.
Heart: structure, activity, innervation, blood supply, minute volume of the heart, heart stroke, regulation of heart activity.
Structure:
- Septum between right and left atrium and ventricle.
Activity and innervation:
- Right atrium -> right ventricle -> pulmonary arteries -> pulmonary capillaries -> pulmonary veins -> left atrium.
- Pacemaker in the SA node initiate each beat. SA causes atria to contract. Transmission is briefly delayed by AV node and bundle, before they causes ventricles to contract.
- A cardiac cycle: 0,8 second. About 70 beats per minute.
- Systole = contraction. Diastole = relaxation. ex; 120 (systole) over 80 (diastole).
- Stroke volume = volume of blood one ventricle pumps during one beat.
- Stroke volume + heart rate = Cardiac Output (CO)
- Blood pressure = Blood flow (CO, Blood volume), and blood flow resistance (viscosity, vasoconstriction).
Regulation:
- In response to low blood pressure; KI release renin -> angiotensin II (vasoconstrictor).
renin -> aldosterone (increase retention of Na+ by KI, resulting in greater fluid retention and increased blood volume.)
- In response to high blood pressure; heart release atrial natriuretic peptide (ANP), which increase sodium excretion, and thus also dilute urine. Also, nitric oxide cause vasodilation.
- Sympaticus release norepinephrine; increase heart rate and strength of contraction.
- Parasympaticus release acetylcholine; slows the heart by slowing action potentials.
Arteries, veins, capillaries - their structure and function, blood circulation, blood pressure, regulation of blood circulation, lymph production and function, hemostasis, emboly, trombosis.
Lymph:
1) Collects and returns interstitial fluid to the blood.
2) Launches immune responses that defend the body against disease organisms.
3) Absorbs lipids from the digestive tract.
- Interstitial fluid contains glucose, amino acids, other nutrients, oxygen, and variety of salts. This nourishing fluid bathes all the cells.
- Interstitial fluid forms at the arterial (coming from the heart) end of capillaries because of the higher pressure of blood compared to veins, and most of it returns to its venous ends and venules; the rest (1%) enters the lymph capillaries as lymph.
- Proteins don't easily go through to venous blood, and tends to accumulate in the interstitial fluid instead. Lymphatic system keeps fluid homeostasis by absorbing the interstitial fluid and its proteins, and bringing it back to the blood.
Thrombosis (clotting): stays in one place
Embolus: A mass; an air bubble, a detached blood clot, or a foreign body, that travels through the bloodstream and lodges so as to obstruct or occlude a blood vessel. It has broken free and travels.
Respiration: airways, mechanism of inspiration and expiration, internal and external gase exchange, breathing regulation, respiratory defence reflexes and respiratory diseases.
Inhale: diaphragm contracts: space within LU increase -> air pressure falls below the air pressure outside the body. Air thus rushes into the lungs.
- Inhaled air contains 21% oxygen, 0.04% CO2
Exhale: diaphragm relaxes: raising the pressure above atmospheric pressure.
- Exhaled air contains 14% oxygen, 5,6% CO2
- Neurons in medulla regulate the basic rhythm. Respiratory centers in pons help control transition from inspiration to exhalation. CO2 are the main chemical stimulus for regulating rate of respiration.
- Hypoxia = shallow breathing (in anxiety etc)
- Chronic bronchitis(inflammation) = often develop pulmonary emphysema; alveoli wall are destroyed. The surface of the lungs are thus reduced with seriously impaired gas exchange.
- Lung cancer
Respiratory defences:
- Breathing dirty air causes bronchial constriction. Tubes narrow, increasing the chance that particles will land on the sticky mucous lining.
Digestive system: composition and function, glands of digestive secretion and their products, intestinal juice and its composition, metabolism and energy exchange, digestion of different foods, liver and its function, liver and gall-bladder diseases, defecation reflex, starvation, malnutrition and obesity.
Vitamins: names, their role, deficiency effects, hypovitaminosis(deficient) and avitaminosis(chronic deficient).
Fat-soluble: A, D, E, K. -> not easily excreted and can accumulate to harmful levels.
Water-soluble: B and C. -> overdoses easily excreted
Vitamin A: Retinol
- Converted to retinal; vision.
- For normal growth and differentiation
- reproduction
- immunity
-> blindness, if deficient.
Vitamin D: Calciferol
- promote calcium and phosphorus absorption from digestive tract
- for normal growth and maintenance of bone
-> weak and deformed bones, rickets in children.
Vitamin E: Tocopherols
- Antioxidant
- protects unsaturated fatty acids and cell membranes
-> cell membrane and nerve damage
Vitamin K:
- Synthesis of blood-clotting proteins and proteins important in bone production.
-> prolonged blood-clotting time
Vitamin C: Ascorbic acid
- collagen synthesis
- antioxidant
- for synthesis of some hormones and neurotransmitters
- immune function
-> Scurvy; wounds heal slow, capillaries fragile, bone don't grow or heal properly. Immune system suppressed.
Vitamin B1: Thiamine
- Carbohydrate and amino acid metabolism
-> beriberi; weakened heart muscle, nervous system and digestive tract disorders; common in alcoholics.
Vitamin B2: Riboflavin
- Make coenzymes (ex FAD) in cellular respiration
-> dermatitis, inflammation and cracking of corner of mouth, confusion.
Niacin:
- Component in coenzymes NAD+ and NADP+ in cellular respiration
-> Pellagra (dermatitis, diarrhea, mental symptoms, muscular weakness.)
Vitamin B6: Pyridoxine
- Constituent of CoA in amino acid metabolism
-> dermatitis, digestive tract disturbances
Folate:
- Nucleic acid synthesis
- Maturation of red blood cells
-> anemia, birth defects, risk of cardiovascular
Biotin:
- Metabolism
Vitamin B12:
- Metabolism
- Contains cobalt
-> anemia
Excretion: kidneys - their structure and function, primary and secondary urine - composition and amount, regulation of kidney function. Role of the skin excretion.
Regulation of body functions: neural and chemical regulation, their interrelationship.
Endocrine glands and their hormones, regulation of hormone secretion into blood, most important effects of hormones.
Neural system: neurone, synaptic junction, central nervous system.
Brain - its parts and function, head nerves, spinal cord, spinal nerves, reflex circuit, spinal somatic reflexes, sympatic and parasympatic nervous system, higher nervous activity.
Receptors: stimulus, adaptation to stimuli, exteroreceptors, interoreceptors and proprioceptors, radioreceptors, chemoreceptors, mechanoreceptors and photoreceptors.
Reproductive system of women and menstruation cycle, pregnancy, prenatal ontogenesis, parturition.
Reproductive system in men.
Ecology
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Ecology as a science, basic terminology. The relationship between organism and its environment.
- Ecology is the study of how living organisms and the physical environment interact in an immense and complicated web of relationships.
- Biotic factors are the interactions between organisms.
- Abiotic factors are the interactions between organisms and their nonliving, physical environment. Ex; temperature, pH, wind, chemical nutrients.
- Biotic and abiotic factors in the environment may determine the population density.
- Individuals in a population exhibit patterns of dispersion (spacing) relative to each other. Random(rare: unrelated to the presence of others), clumped(ex schools of fish), or uniform(evenly spaced, ex in nesting colony of seabirds) dispersion.
- Dispersal = movement of individual among populations.
- Organisms cannot reproduce indefinitely at their intrinsic rate because environment set limits. Ex; limited food, water, shelter, competition, disease, predation.
- Density-dependent factors; as population density increase, the density factors tend to slow population growth by causing increase in death and/or decrease in birth rate.
- Density-independent factors; typically abiotic, such as random weather events.
- R strategists: small body, early maturity, early reproduction, short lifespan, little or no parental care, live in unpredictable environments.
- K strategists: large body, long lifespans, slow development, late reproduction, invest in parental care, live in constant and stable environments.
- Type 1 survivorship: young have high probability of surviving.
- Type 2 survivorship: probability of surviving does not change with age.
- Type 3 survivorship: young have high mortality rate, but high surviving probability as they get older.
- Metapopulation: a population divided into several local populations among which individuals occasionally emigrate or immigrate.
- Source habitants: areas where local reproductive success is greater than local mortality.
- Sink habitants: areas where local reproductive success is less than local mortality.
Biotope, biocenosis, ecosystem, biosphere.
- Biotope: Biotope is an area of uniform environmental conditions providing a living place for a specific assemblage of plants and animals. Biotope is almost synonymous with the term habitat.
- Biocoenosis describes the interacting organisms living together in a habitat (biotope);
- Zoocoenosis for the faunal community
- Phytocoenosis for the floral community,
- Microbiocoenosis for the microbial community
- Ecosystem: is a biotic community (or biocoenosis) along with its physical environment (or biotope).
- Biosphere: global sum of all ecosystems.
The Sun and its role for ecosystem.
- Energy flow: energy enters ecosystem as sunlight, which a tiny portion (1%) is trapped by producers during photosynthesis. When the energy stored in glucose is used, heat radiates to its environment as unusable energy.
- Control the hydrologic cycle, carbon cycle, and other biogeochemical cycles.
Athmosphere, hydrosphere, litosphere and pedosphere . Abiotic components of the environment. Biotical components of environment.
- Atmosphere on the Earth consist of, from the ground up; the troposphere, stratosphere (ozone layer), mesophere, thermosphere, exosphere(part of space), and the magnetosphere.
- Hydrosphere (water); 75% of the Earth's surface is water.
- Litosphere; outermost shell of a rocky planet. On Earth, it comprises the crust and the portion of the upper mantle that behaves elastically on time scales of thousands of years or greater.
- Pedosphere: The sum total of all the organisms, soils, water and air is termed as the "pedosphere". The pedosphere is the skin of the Earth and only develops when there is a dynamic interaction between the atmosphere (air in and above the soil), biosphere (living organisms), lithosphere (unconsolidated regolith and consolidated bedrock) and the hydrosphere (water in, on and below the soil). The pedosphere is the foundation of life on this planet.
Population - role, composition rule. Interrelationship between populations.
Parasitism and predation, definitions.
Communities.
- A forest is a community, but so is a rotting log in that forest that is invaded by insects, plants, fungi and termites.
- Facilitation: positive interaction between species that enhances and modifies the local environment for other species.
- Organisms play a role: producer, consumer, or decomposer.
- Interactions among species in a community:
1) competition: within a population (intraspesific), or between different species (interspecific)
2) predation
3) symbiosis
- Mutualism: beneficial for both
- Commensalism: beneficial for one, no effect on the other.
- Parasitism: beneficial for one, harmful for the other.
- Ecological niche: every species ecological role within the community. Totality of adaptations to its environment, its use of resources, and lifestyle. Two species with absolutely identical ecological niches cannot coexist.
- Resource partition: reduced competition among coexisting species as a result of each species' niche differing from the others in one or more ways.
- Character displacement reduces the competition of two species because their differences give them somewhat different ecological niches in the same environment. If the same species live separate, they may have the same ecological niches. Ex; Darwin's finches.
- Keystone species are crucial in determining the nature of the entire community. Often not the most abundant species.
Ecosystem - definition, basic characteristics.
- All interaction between organisms living together in a particular place and among those organisms and their abiotic environment.
- Earths largest ecosystem is the biosphere.
-
Nutritionally chains of the ecosystem and nutrial pyramide.
Flow of foodstuffs and of energy in ecosystem.
Changes in the ecosystem. Influences on the ecosystem equilibrium .
Biosphere - basic characteristics.
Biome - definition and characteristics.
A large, relatively distinct terrestrial region that has similar climate, soil, plants, and animals regardless of where it occurs.
Ecotone; the transition zone where two communities or biomes meet and intergrade.
1) Tundra:
- Extreme north where snow melts seasonally. Although, a layer of permafrost is permanently present in the ground.
- Long, harsh winters, and short summers.
- Young soil (formed after the last Ice Age), with poor nutrients and little organic litter.
- Limited precipitation.
- All this causes a landscape of broad, shallow lakes, sluggish streams, and bogs.
- Low species richness and low primary productivity.
- Tundra regenerates slowly after its been disturbed. Hikers, oil exploration and military use has caused injury for many hundred years to portions of the arctic tundra.
2) Boreal forest / taiga:
- World's largest biome.
- Cold winters, but not harsh as tundra.
- Little precipitation.
- Acidic soil with little minerals.
- Numerous ponds and lakes that grinding ice sheets dug during the last Ice Age.
- Spruces(gran), larch (lerke) and conifers (bartrær) dominates, but deciduous trees (lauvfellende trær) such as aspen(osp) or birch(bjørk) form striking stands. The conifers needlelike leaves reduce water loss to withstand the "drought" of the northern winter months when roots do not absorb water from the frozen ground.
3) Temperate rain forest:
- High precipitation.
- Seasonal fluctuations is narrow with mild winters and cool summers.
- Nutrient-poor soil, although high organic content.
- Large evergreen trees. Rich in epiphytic vegetation; plants that grow nonparasitically on trunks and branches of large trees. Like mosses, lichens(lav), and ferns(bregner), which also carpet the ground.
4) Temperate deciduous forest:
- Seasonality (hot summers, cold winters)
- High precipitation, but lower than rain forest.
- Topsoil rich in organic material, and a deep, clay-rich lower layer. If mineral ions from dead organic matter are not absorbed by trees, they leach into the clay.
- Broad-leaf hardwood trees: oak, hickory, maple(lønn), beech(bøk).
5) Temperate grassland:
- Summers are hot, winters are cold.
- Moderate and uncertain precipitation.
- Soil contains much organic material because grass die off each winter.
- Tallgrass prairies: more precipitation. Tall grass.
- Shortgrass prairies: less precipitation. Short grass.
6) Chaparral:
- Soil is thin and infertile.
- Frequent fires occur naturally.
- Mild winters with abundant rainfall, and extremely dry summers.
- During summer, the plants lie dormant and look dry.
7) Desert:
- Low precipitation
- Sparse vegetation; soil low in organic material, but high in mineral content.
- Low water-vapor content in the atmosphere leads to daily temperature extremes of heat and cold.
- Cacti, yuccas, Joshua trees, sagebrushes.
8) Savanna:
- Tropical grassland with scattered clumps of low trees.
- Precipitation, not temperature, regulate seasons. Seasonal rainfall with prolonged dry periods.
- Soil low in essential minerals, but rich in aluminum.
- Trees and grasses have extensive underground root systems to survive droughts and periodic fires.
9) Tropical rain forest:
Two types;
- tropical dry forest: Wet season, and a shorter dry season.
- tropical rain forest:
- High temperature, moist soil. Thus, trees capture much energy from photosynthesis, even though the soil is mineral-poor.
- Most species rich biome.
- Evergreen flowering plants.
- Distinct stories of vegetation:
- Emergent layer (oldest, tallest trees), canopy, shrub layer, ground layer.
- 90% of organisms here live in the middle and upper canopies.
The human - the active part of the environment. Negative effects of human.
- Humans consume far more of the Earth's resources than do any of the other millions of animal species. Our use of global productivity is competing with other species' needs for energy. This may contribute to the loss, through extinction or genetic impoverishment, of many species that have unique roles in maintaining functional ecosystems.
- The persistence and accumulation of synthetic pesticides and industrial chemicals is due to ways to degrade them have not evolved in natural decomposers such as bacteria.
- When an organism cannot metabolize or excrete a toxin, it gets stored, usually in fatty tissues. The buildup and accumulation of toxin in the body is known as bioaccumulation.
- Disease-causing viruses and bacteria from human sewage contaminate fish.
- Million tons of trash end up in marine ecosystems and entangles and kills these organisms.
- Fertilizers, pesticides, heavy metals, synthetic chemicals from agriculture and industry.
- Offshore mining and oil drilling pollute the coastal ocean with oil and other contaminants.
- Mechanistic fishing swipe entire communities.
- Greenhouse gas cause climate change
- Biotic pollution: Introduction of invasive species that upset the delicate balance of organisms in an area
- Destruction of natural habitats kills species.
- Habitat fragmentation; breakup of large areas into small, isolated segments (islands). Ex; roads around a patch of habitat.
- Pollution and acid precipitation contribute to decline in forest and biological death of freshwater lakes.
Human population - growth, differences in the concentration of inhabitants, effects of human activities and their consequences.
- Increasing by about 83 million people per year because of dramatic decrease in death rate, not in birth rate.
- Human population has reached a turning point where experts think that the growth rate slowly decrease until zero population growth is attained.
- Highly developed countries: lowest birth rates, longer life expectancies. Approaching stabilization.
- Moderately developed countries: birth rates are declining.
- Less developed countries: highest birth rates, lowest life expectancies.
The role of biology - biotechnology, gene engineering. Bionics and biocybernetics.
Theories of the origin of life: Coacervate theory, eobiontes, prokaryotic and eukaryotic cells, Darwins's theory of evolution.
Chemistry
Classification of matter
Whatever occupies space and can be perceived by our senses.
-> Mass is the quantity of matter in a material.
Physical versus chemical change
- A physical change is a change in the form of matter but not in its chemical identity. Ex; Changes of physical state. The process of dissolving one material in another. Distillation.
- A chemical change or reaction is a change in which one or more kinds of matter are transformed into a new kind of matter or several new kinds of matter. Ex; rusting of iron.
Potassium (K):
-> Soft, silvery-colored, melts at 64oC = physical properties.
-> Reacts vigorously with water, oxygen and chlorine = chemical properties.
Elements, compounds, and mixtures
A substance is a kind of matter that cannot be separated into other kinds of matter by any physical process. Ex; sodium chloride (NaCl). Pure water (H2O) is also a substance. A substance always has the same characteristic properties. Ex; Sodium is a solid metal having a melting point of 98oC, and it reacts vigorously with water. No matter how sodium is prepared, it always has these properties.
Element is a substance that cannot be decomposed by any chemical reaction into simpler substances. Matter composed of only one kind of atom.
Compounds is a substance composed of two or more elements chemically combined. Matter composed of atoms of two or more elements chemically combined in fixed proportions.
Mixture is a material that can be separated by physical means into two or more substances. Unlike a pure compound, a mixture has variable composition. When you dissolve sodium chloride (NaCl) in water, you obtain a mixture; its composition depends on the relative amount of sodium chloride dissolved.
Two types of mixtures:
1. Heterogeneous mixture: a mixture that consist of physically distinct parts, each with different properties. Ex; mixture of potassium dichromate and iron filings, or salt and sugar that have been stirred together.
2. Homogeneous mixture (aka solution): a mixture that is uniform in its properties throughout a given samples. When sodium chloride is dissolved in water, you obtain a homogeneous mixture, or solution. Air is a gaseous solution, principally of two elementary substances, nitrogen (N) and oxygen (O), which are physically mixed but not chemically combined.
Materials are either substances or mixtures. Substances can be mixed by physical processes, and other physical processes can be used to separate the mixtures into substances. Substances are either elements or compounds. Elements may react chemically to yield compounds, and compounds may be decomposed by chemical reactions into elements.
Unit conversion
Mega (M) - 10 6
Kilo (k) - 10 3
Deci (d) - 10 -1
Centi (c) - 10 -2
Milli (m) - 10 -3
Micro (µ) - 10 -6
Nano (n) - 10 -9
Pico (p) - 10 -12
-- Angstrom (Å) - 10 -10 m. (A non-SI unit)
1. Kelvin - Celsius, 2. Celsius - Kelvin
1: Kelvin - Celsius
0 K = -273,15 C
2: Celsius - Kelvin
0 C = 273,15 K
K = C + 273,15:
1 K = 274,15 C
1. Celsius - Fahrenheit, 2. Fahrenheit - Celcius
1: Celsius - Fahrenheit
0 C = 32 F
1 C = 9/5(or 1,8) x 1 + 32 = 33,8 F
-> 6 C = 1,8 x 6 + 32 = 42,8 F
2: Fahrenheit - Celcius
0 F = -17,8 C
1 F = 1 - 32 = -31/9 = -3,44 x 5 = -17,2 C
Area - Length squared - m2
Volume - Length cubed - m3
Density - Mass per unit volume - kg/m3
Speed - Distance traveled per unit time - m/s
Acceleration - Speed changed per unit time - m/s2
Force - Mass times acceleration of object - kg x m/s2 (= newton, N)
Pressure - Force per unit area - kg/(m x s2) (= pascal, Pa)
Energy - Force times distance traveled - kg x m2/s2 (= joule, J)
SI unit of speed =
Liter is a unit of volume equal to a cubic decimeter.
1 L = 1 dm3 and 1 mL = 1 cm3
Density
Density of an object is its mass per unit volume.
d = - d = = 1.50 g/cm3
Water has a density of 1.000 g/cm3 at 4oC and density of 0.998 g/cm3 at 20oC.
Because the density is characteristic of a substance, it can be helpful in identifying it.
Density can also be useful in determining whether a substance is pure, for example gold.
Specific gravity
Specific gravity is the density of a substance relative to some reference substance:
Specific gravity = density of substance / density of reference substance.
Specific gravity was defined because it's convenient to have a unitless measure of density. The reference substance for solids and liquids is usually water at 4°C
Temperature
Units of energy
Chemical energy has the normal units of energy that are a part of the metric system. Energy has the units of Joules. It can also be converted to calories, where 1 calorie = 4.184 joules. Normally chemical energy is expressed in terms of moles, so a common unit you might see is kJ/mol, or kilojoules per mole.
Skriv mer?
Atomic theory
Difference between an element and a compound.
Two laws:
1. Law of conservation of mass. The total mass remains constant during a chemical reaction.
2. Law of definite proportions (constant composition). Compounds is a type of matter containing atoms of two or more elements in definite proportions. Because the atoms have definite mass, compounds must have the elements in definite proportions by mass.
The law of multiple proportions states that when two elements form more than one compound, the masses of one element in these compounds for a fixed mass of the other element are in ratios of small whole numbers. If we take a fixed mass of carbon, 1.000 gram, and react it with oxygen, we end up with two compounds: one that contains 1.3321 grams of oxygen for each 1.000 gram of carbon, and one that contains 2.6642 grams of oxygen per 1.000 gram of carbon. Applying atomic theory, if we assume that the compound that has 1.3321 grams of oxygen to 1.000 gram of carbon is CO, then the compound that contains twice as much oxygen per 1.000 gram of carbon must be CO2.
Atomic number(Z) and mass number(A)
We categorize a nucleus by its atomic number(Z) and its mass number(A).
- Atomic number (Z) is the number of protons in the nucleus of an atom. An element is a substance whose atoms all have the same atomic number.
- Mass number(A) is the total number of protons and neutrons in a nucleus.
Atomic number is written as a subscript to the left, while mass number is a superscript to the left. Name of the element, with their respective atomic number and mass number is called a nuclide symbol.
A proton is a nuclear particle having a positive charge equal in magnitude to that of the electron and a mass more than 1800 times that of the electron. A neutron is a nuclear particle having a mass almost identical to that of the proton but no electrical charge.
Isotopes
All nuclei of the atoms of a particular element have the same atomic number, but the nuclei may have different mass numbers. Isotopes are atoms whose nuclei have the same atomic number but different mass numbers; that is, the nuclei have the same number of protons but different number of neutrons.
Charged atoms
Naturally occurring sodium atom nucleus contains 11 protons and 12 neutrons. Thus, the charge on the sodium nucleus is +11e, which we usually write as simply +11, meaning +11 units of electron charge e.
An atom is normally electrically neutral, so it has as many electrons about its nucleus as the nucleus has protons. A sodium atom has a nucleus charge +11, and around this nucleus are 11 electrons (with a charge of -11, giving the atom a charge of 0).
Relative atomic mass
Relative atomic mass (Ar): The average mass of an atom of an element taking into account all of the naturally occurring isotopes of the element (relative to Carbon-12).
Although it may be for example two naturally occurring isotopes of Chlorine have two different masses, and neither of these are the relative atomic mass. That is because the relative atomic mass is a weighted average of the naturally occurring isotopes Cl-35(75%) and Cl-37(25%).
Formula for finding REM of Chlorine:
= = 35.5
One atomic mass unit is a mass unit equal to exactly one-twelfth the mass of a carbon-12 atom.
Average atomic weight
To find the AVERAGE ATOMIC MASS of an atom, we take into account all of the isotopes that exist and the percentage of each type. The calculation of the average atomic mass is a WEIGHTED AVERAGE. .
Electronic versus nuclear changes
Radioactivity
Unstable atomic nuclei will spontaneously decompose to form nuclei with a higher stability. The decomposition process is called radioactivity. The energy and particles which are released during the decomposition process are called radiation.
Properties of (-, (-, and (- radiation
Alpha Radiation Alpha radiation consists of a stream of positively charged particles, called alpha particles, which have an atomic mass of 4 and a charge of +2 (a helium nucleus). When an alpha particle is ejected from a nucleus, the mass number of the nucleus decreases by four units and the atomic number decreases by two units. The helium nucleus is the alpha particle.
Beta Radiation Beta radiation is a stream of electrons, called beta particles. When a beta particle is ejected, a neutron in the nucleus is converted to a proton, so the mass number of the nucleus is unchanged, but the atomic number increases by one unit.
Gamma Radiation Gamma rays are high-energy photons with a very short wavelength (0.0005 to 0.1 nm). The emission of gamma radiation results from an energy change within the atomic nucleus. Gamma emission changes neither the atomic number nor the atomic mass. Alpha and beta emission are often accompanied by gamma emission, as an excited nucleus drops to a lower and more stable energy state.
Ionizing radiation
Ionizing (or ionising) radiation is radiation composed of particles that individually carry enough energy to liberate an electron from an atom or molecule, ionizing it. Ionizing radiation is generated through nuclear reactions, either artificial or natural, by very high temperature (e.g. the corona of the Sun), or via production of high energy particles in particle accelerators, or due to acceleration of charged particles by the electromagnetic fields produced by natural processes, from lightning to supernova explosions.
When ionizing radiation is emitted by or absorbed by an atom, it can liberate a particle (usually an electron, but sometimes an entire nucleus) from the atom. Such an event can alter chemical bonds and produce ions, usually in ion-pairs, that are especially chemically reactive. This greatly magnifies the chemical and biological damage per unit energy of radiation.
Ionizing radiation includes cosmic rays, alpha, beta and gamma rays, X-rays, and in general any charged particle moving at relativistic speeds. Neutrons are considered ionizing radiation at any speed. Ionizing radiation includes some portion of the ultraviolet spectrum, depending on context. Radiowaves, microwaves, infrared light, and visible light are normally considered non-ionizing radiation, although very high intensity beams of these radiations can produce sufficient heat to exhibit some similar properties to ionizing radiation, by altering chemical bonds and removing electrons from atoms.
Medical uses of radioisotopes
Radiotherapy can be used to treat some medical conditions, especially cancer, using radiation to weaken or destroy particular targeted cells.
Nuclear medicine uses radiation to provide diagnostic information about the functioning of a person's specific organs, or to treat them. The thyroid, bones, heart, liver and many other organs can be easily imaged, and disorders in their function revealed. Diagnostic techniques in nuclear medicine use radioactive tracers which emit gamma rays from within the body. The first type are where single photons are detected by a gamma camera which can view organs from many different angles. A more recent development is Positron Emission Tomography (PET) which is a more precise and sophisticated technique using isotopes produced in a cyclotron. PET's most important clinical role is in oncology, with fluorine-18 as the tracer, since it has proven to be the most accurate non-invasive method of detecting and evaluating most cancers. It is also well used in cardiac and brain imaging. New procedures combine PET with computed X-ray tomography (CT) scans to give co-registration of the two images (PETCT), enabling 30% better diagnosis than with traditional gamma camera alone.
Electron structure of the atom
When collections individual atoms (in the gas phase) absorb energy, they emit energy as light with only certain wavelenghts, in a line spectrum, like those displayed by electrically excited hydrogen or neon gas, or by potassium or barium salts in a flame.
The energy of each electron in an atom depends on how strongly the electron is attracted by the positive charge on the nucleus and on how much it is repelled by other electrons.
Electron configuration notation
Electron configuration is the distribution of electrons of an atom or molecule (or other physical structure) in atomic or molecular orbitals. For example, the electron configuration of the neon atom is 1s2 2s2 2p6.
Electronic configurations describe electrons as each moving independently in an orbital, in an average field created by all other orbitals.
According to the laws of quantum mechanics, for systems with only one electron, an energy is associated with each electron configuration and, upon certain conditions, electrons are able to move from one configuration to another by emission or absorption of a quantum of energy, in the form of a photon.
Part of n=4:
Three 4p
One 4s
n=3:
FIve 3d
Three 3p
One 3s
n=2:
Three 2p
One 2s
n=1:
One 1s
Periodic table
Constructed by Dmitri Ivanovich Mendeleev. It is a tabular arrangement of elements in rows and columns, highlighting the regular repetition of properties of the elements.
Periods = horisontal row
Groups = column
- The sixth and seventh period actually consists of 32 elements each, but in order for the row to fit on a page, part of it appears at the bottom of the table. The 14 elements belonging to the sixth period are called Lanthanides, the 14 elements belonging to the seventh period are called Actinides. Together they are called the inner transition metals.
- A group (1-2, 13-18) are called the Main-Group Elements.
- B group (3-12) are called Transition Elements.
Group IA are known as alkali metals; they are soft metals that react easily with water. (Hydrogen being an exception).
Group VIIA are known as halogens; these are also reactive elements.
A metal is a substance that has a characteristic luster, or shine, and is generally a good conductor of heat and electricity. Except for mercury, the metallic elements are solids at room temperature (about 20oC).
A nonmetal is an element that does not exhibit the characteristics of a metal. Most of them are gases or solids. The solid nonmetals are usually hard, brittle substances. Bromine is the only liquid nonmetal.
A metalloid, or semimetal, is an element having both metallic and nonmetallic properties. They are usually good semiconductors, when pure, are poor conductors of electricity at room temperature but become moderately good conductors at higher temperatures.
How can atoms achieve lower-energy states?
- Metals lose electrons
- Nonmetals gain electrons
Metal atoms tend to lose electrons, whereas nonmetals tend to gain electrons. When a metal atom such as sodium(Na) and nonmetal atom such as chlorine(Cl) approach one another, an electron can transfer from the metal atom to the nonmetal atom to produce ions.
An atom that picks up an extra electron becomes a negatively charged ion, called anion. An atom that loses an electron becomes a positively charged ion, called a cation. A sodium atom, for example, can lose an electron to form a sodium cation (denoted Na+). A chlorine atom can gain an electron to form a chloride anion (denoted Cl-). A calcium atom can lose two electrons to form a calcium cation, denoted Ca2+.
Oxidation -reduction
Formulas for ionic compounds
An ionic compound is a compound composed of cations and anions. For example when Na+ bonds with Cl- to form a NaCl crystal. All substances, including ionic compounds, are electrically neutral.
Example:
What is the formula of chromium(III) oxide? It is a compound composed of Cr3+ and O2- ions.
Answer: The unit of charge on the O2- anion is 2, and the unit of charge on the Cr3+ cation is 3. Therefore, we predict that the ratio of Cr3+ to O2- is 2:3. two Cr3+ ions have a total charge of 6+, and three O2- have a total charge of 6-. The simplest ratio of this formula is Cr2O3.
Remember that the final formula must give the simplest ratio of ions.
----- Nomenclature
A monoatomic ion is an ion formed from a single atom.
If there is more than one monatomic cation of an element, you must use Roman numeral in parentheses denoting the charge on the ion.
In older systems of nomenclature, such ions are named by adding the suffixes -ous and -ic to indicate ions of lower og higher charge, respectively. Ex; Fe2+ is called ferrous ion, and Fe3+ is called ferric ion. Cu+ is called cuprous ion; Cu2+ is called cupric ion.
The names of the monoatomic anions are obtained from the suffix -ide. Ex; Br- is called bromide ion.
A polyatomic ion is an ion consisting of two or more atoms chemically bonded together and carrying a new electric charge.
Oxoanions(aka oxyanions) consist of oxygen with another element (called the characteristic or central element). They are named adding the suffixes -ite and -ate to indicate oxoanions lesser and greater number of oxygen atoms. Ex; Sulfite ion( SO32- ), and sulfate ion( SO42- ).
When talking about, for example, the four oxoanions of chlorine: ClO-, ClO2-, ClO3-, and ClO4-, the prefixes, hypo- and per- may also be added. Ex; ClO- = hypochlorite ion, ClO2- = chlorite ion, ClO3- = chlorate ion, ClO4- = perchlorate ion.
Some polyatomic ions are oxoanions bonded to one or more hydrogen ions (H+). They are sometimes referred to as acid anions, because acids are substances that provide H+ ions.
The prefix thio- in thiosulfate ion( S2O32- ) means that an oxygen atom in the root ion name (sulfate, SO42- ) has been replaced by a sulfur atom.
The nature of the ionic bond
It is formed between metals and nonmetals. The atoms bond together by gaining or losing electrons.
- formed by the transfer of electrons
- bond is called electrostatic attraction
- has extremely high melting points
- water solutions conduct electricity
- molten ionic compounds also conduct electricity
- soluble in polar solvents
- the solid phase is hard and easily shatters
. all ionic compounds form crystals ..?
Diatomic molecules
(prof. BrINClHOF)
Br: Bromine
I: Iodine
N: Nitrogen
Cl: Chlorine
H: Hydrogen
O: Oxygen
F: Fluorine
A Diatomic molecule is a molecule consisting of two atoms. An oxygen molecule is a Diatomic molecule, for example.
Diatomic elements are examples of homonuclear molecules, where all of the atoms in the molecule are the same.
The noble gases do not form diatomic molecules.
All diatomic molecules have linear geometry
The nature of the covalent bond
Electron sharing usually occurs so that atoms attain the electron configuration of noble gases - to get a filled outer energy level.
For example: H-H, F-F, or O=O(double covalent bonds).
(In Lewis structure; If there is more than one atom type in the molecule, put the most metallic or least electronegative atom in the center.)
Coordinate covalent bonds
A bond formed when both electrons of the bond are donated by one atom.
A coordinate covalent bond is not essentially different from other covalent bonds; it involves the sharing of a pair of electrons between two atoms.
Electronegativity and polarity
The electron pairs shared between two atoms are not necessarily shared equally
Extreme examples:
1. In Cl2 the shared electron pairs is shared equally
2. In NaCl the 3s electron is stripped from the Na atom and is incorporated into the electronic structure of the Cl atom - and the compound is most accurately described as consisting of individual Na+ and Cl- ions
Bond polarity is a useful concept for describing the sharing of electrons between atoms
- A nonpolar covalent bond is one in which the electrons are shared equally between two atoms.
- A polar covalent bond is one in which one atom has a greater attraction for the electrons than the other atom. If this relative attraction is great enough, then the bond is an ionic bond.
Electronegativity is a function of:
- the atom's ionization energy (how strongly the atom holds on to its own electrons)
- the atom's electron affinity (how strongly the atom attracts other electrons)
Recognizing ionic versus molecular compounds
Binary Molecular Compounds is a compound composed of only two elements. Binary compounds composed of a metal and a nonmetal are usually ionic and are named as ionic compounds.
Binary compounds composed of two nonmetals or metalloids are usually molecular and are named using a prefix system. Using the prefix system, the two elements are named in the order given by the formula of the compound: B, Si, C, Sb, As, P, N, H, Te, Se, S, I, Br, Cl, O, F. The first element is the more metallic, the second the more nonmetallic.
Prefix for naming compounds:
1-10: mono, di, tri, tetra, penta, hexa, hepta, octa, nona, deca.
Molecular shape IPAD
Also known as molecular geometry, is the general shape of a molecule, as determined by the relative positions of the atomic nuclei.
The valence-shell electron-pair repulsion (VSEPR) model predicts the shapes of molecules and ions by assuming that the valence-shell electron pairs are arranged about each atom so that electron pairs are kept as far away from one another as possible, thus minimizing electron-pair repulsion. For example; two electron pairs will tend to be at opposite sides of the nucleus, giving a linear arrangement of electron pairs (180 degrees). Three electron pairs tend to arrange a trigonal planar of 120 degrees angles to one another. Four electron pairs = tetrahedral arrangment (109.5 degrees). Five electron pairs = trigonal bipyramidal(120 and 90 degrees). 6 electron pairs = octahedral (90 and 90 degrees).
SKRIV MER HER
Molecular polarity
Bond polarity is due to a difference in electronegativity between atoms in a bond. This creates a dipole moment, one atom with a partial negative charge and one with a partial positive charge.
Molecules can also be polar or nonpolar. This depends on the sum of the bond dipoles, dependent on the type of bond and molecular geometry.
For example, CO2 is nonpolar because the two dipole moments equal in magnitude and opposite in direction will cancel each other out.
A molecule can have polar bonds and not be a polar molecule.
Molecular weight / mass
Individuals versus "packages"
Relative weights
How many particles is in a mole? IPAD
6.02 x 10^23
Moles of compounds IPAD
A mole of a compound is what you have when you weigh out, in grams, the formula weight of that compound. Moles of compounds are also known as molar formula weight or the mole weight or even molar mass.
Example: the formula weight for HF is 20.0 g. That means that one mole of HF weighs 20.0 grams.
15.0 g HF x 1 mole HF / 20.0 g HF = 0.750 mole HF
Or, for example to find the moles of compounds for methane(CH4):
1 mole of carbon, 4 moles of hydrogen.
Trichloromethane (CHCl3)
1 mole of carbon, 1 mole of hydrogen, 3 mole of chlorine.
Gram-mole-particle conversions IPAD
A mole is defined as the quantity of a given substance that contains as many molecules or formula units as the number of atoms in exactly 12g of carbon-12. The number of atoms in a 12g sample of carbon-12 is called Avogadro's number. This number is 6.02 x 10*23.
For all substances, the molar mass in grams per mole is numerically equal to the formula mass in atomic mass units. Example formula:
= 6.06 x 10-23
Mass of a an ethanol molecule, C2H5OH:
C=12.0107 x 2 = 24,0214
H=1.00794 x 5 = 5.0397
O=15.9994
H=1.00794
= 46.06844 / 6.02 x 10*23 = 7.65 x 10*-23 g.
Example gram to mol:
45.6 g PbCrO4 x 1 mol PbCrO4 / 323 g PbCrO4 = 0.141 mol PbCrO4.
Chemical reactions and equations
A chemical equation is the symbolic representation of a chemical reaction in terms of chemical formulas. The formulas on the left side of the equation(arrow) represent the reactants. Formulas on the right side represent the products.
(g) for gas, (l) for liquid, (s) for solid, (aq) for aqueous(water) solution. If the reactants are heated to make the reaction go, place a ∆ on top of the arrow.
∆
Ex; 2NaNO3(s) ------> 2NaNO2(s) + O2(g)
Balancing equations
Balanced when the numbers of atoms of each element are equal on both sides of the arrow. To balance the equation, you select coefficients that will make the numbers of atoms of each element equal on both sides of the equation. It is preferable to write the coefficients so that they are the smallest whole numbers possible. Balance first the atoms for elements that occur in only one substance on each side of the equation.
Example:
C3H8 + O2 -----> CO2 + H2O
C3H8 + 5O2 -----> 3CO2 + 4H2O
Example 2:
Ca3(PO4)2 + H3PO4 -----> Ca(H2PO4)2
Ca3(PO4)2 + 4H3PO4 -----> 3Ca(H2PO4)2
Types of reactions
1. Combustion: A combustion reaction is when oxygen combines with another compound to form water and carbon dioxide. These reactions are exothermic, meaning they produce heat. An example of this kind of reaction is the burning of napthalene:
C10H8 + 12 O2 ---> 10 CO2 + 4 H2O
2) Synthesis: A synthesis reaction is when two or more simple compounds combine to form a more complicated one. These reactions come in the general form of:
A + B ---> AB
One example of a synthesis reaction is the combination of iron and sulfur to form iron (II) sulfide:
8 Fe + S8 ---> 8 FeS
3) Decomposition: A decomposition reaction is the opposite of a synthesis reaction - a complex molecule breaks down to make simpler ones. These reactions come in the general form:
AB ---> A + B
One example of a decomposition reaction is the electrolysis of water to make oxygen and hydrogen gas:
2 H2O ---> 2 H2 + O2
4) Single displacement: This is when one element trades places with another element in a compound. These reactions come in the general form of:
A + BC ---> AC + B
One example of a single displacement reaction is when magnesium replaces hydrogen in water to make magnesium hydroxide and hydrogen gas:
Mg + 2 H2O ---> Mg(OH)2 + H2
5) Double displacement: This is when the anions and cations of two different molecules switch places, forming two entirely different compounds. These reactions are in the general form:
AB + CD ---> AD + CB
One example of a double displacement reaction is the reaction of lead (II) nitrate with potassium iodide to form lead (II) iodide and potassium nitrate:
Pb(NO3)2 + 2 KI ---> PbI2 + 2 KNO3
6) Acid-base: This is a special kind of double displacement reaction that takes place when an acid and base react with each other. The H+ ion in the acid reacts with the OH- ion in the base, causing the formation of water. Generally, the product of this reaction is some ionic salt and water:
HA + BOH ---> H2O + BA
One example of an acid-base reaction is the reaction of hydrobromic acid (HBr) with sodium hydroxide:
HBr + NaOH ---> NaBr + H2O
Oxidation-reduction reactions
Redox reactions, or oxidation-reduction reactions, have a number of similarities to acid-base reactions. Fundamentally, redox reactions are a family of reactions that are concerned with the transfer of electrons between species. Like acid-base reactions, redox reactions are a matched set -- you don't have an oxidation reaction without a reduction reaction happening at the same time. Oxidation refers to the loss of electrons, while reduction refers to the gain of electrons. Each reaction by itself is called a "half-reaction", simply because we need two (2) half-reactions to form a whole reaction. In notating redox reactions, chemists typically write out the electrons explicitly:
Cu (s) ----> Cu2+ + 2 e-
If a chemical causes another substance to be oxidized, we call it the oxidizing agent.
Molar interpretation of the balanced equation
The mole ratio
Formaldehyde(CH2O): Calculate the mass percentages of the elements in CH2O.
1 mol of CH2O has a mass of 30.0 g and contains 1 mol C (12.0 g), 2 mol H (2x1.01 g), and 1 mol O (16.0 g).
% C = 12.0 g / 30.0 g x 100% = 40.0%
% H = 2 x 1.01 g / 30.0 g x 100% = 6.73%
You can find the percentage of O in the same way, but it can also be found by subtracting the percentages of C and H from 100%:
% O = 100% - (40.0% + 6.73%) = 53.3%
How many grams are there in 83.5 g of formaldehyde (CH2O)?
CH2O is 40.% C, so the mass of carbon in 83.5 g CH2O is:
83.5 g x 0.400 = 33.4 g
Mole-mole, mole-gram, gram-gram conversions
Heat as a reactant or product
Gases, liquids, solids
A solid has a definite shape and volume. Examples of solids include ice (solid water), a bar of steel, and dry ice (solid carbon dioxide). Solid are tightly packed, usually in a regular pattern. Solid vibrate (jiggle) but generally do not move from place to place.
A liquid has a definite volume, but takes the shape of its container. Examples of liquids include water and oil. Liquid are close together with no regular arrangement. Liquid vibrate, move about, and slide past each other.
A gas has neither a definite volume nor a definite shape. Examples of gases are air, oxygen, and helium. Gas are well separated with no regular arrangement. Gas vibrate and move freely at high speeds.
Characteristics of gases
-Easily compressed
-Relate pressure, volume, temperature, and molar amount of substance with fair accuracy by the equation of the ideal law.
-Most substances composed of small molecules are gases under normal conditions.
-
Intermolecular forces
Many of the physical properties of liquids(and certain solids too) can be explained in terms of intermolecular forces, the forces of interaction between molecules. These forces are normally weakly attractive.
Intermolecular forces are forces of attraction or repulsion which act between neighboring particles (atoms, molecules or ions). They are weak compared to the intramolecular forces, the forces which keep a molecule together. For example, the covalent bond present within HCl molecules is much stronger than the forces present between the neighbouring molecules, which exist when the molecules are sufficiently close to each other.
There are three types of attractive forces known to exist between neutral molecules:
Dipole–dipole forces
Polar molecules can attract one another through dipole-dipole forces. This is an attractive intermolecular force resulting from the tendency of polar molecules to align themselves such that the positive end of one molecule is near the negative end of another.
An example of a dipole–dipole interaction can be seen in hydrogen chloride (HCl): the positive end of a polar molecule will attract the negative end of the other molecule and influence their arrangement. Polar molecules have a net attraction between them.
London dispersion forces or Instantaneous dipole-induced dipole forces
Electrons that belong to different molecules start "fleeing" and avoiding each other at the short intermolecular distances, which is frequently described as formation of "instantaneous dipoles" that attract each other.
In nonpolar molecules, there can be no dipole-dipole force. Yet such substances liquefy. The London forces (aka dispersion forces) are the weak attractive forces between molecules resulting from the small, instantaneous dipoles that occur because of the varying positions of the electrons during their motion about nuclei. London forces tend to increase with molecular mass, because these often have more electrons, and London forces increase with the number of electrons.
Hydrogen bonding
Molecules that have the -OH group are subject to an additional attractive force called hydrogen bonding. This is a weak to moderate attractive force that exists between a hydrogen atom covalently bonded to a very electronegative atom, X, and a lone pair of electrons on another small, electronegative atom, Y. Usually, hydrogen bonding is seen in cases where X and Y are the atoms F, O, or N.
Physical properties of liquids
- Tend to escape liquid state and form a vapor. The boiling point is the temperature at which the vapor pressure equals the pressure applied to the liquid. Both vapor pressure and boiling point are important properties of a liquid.
- Surface tension: A molecule at the surface of a liquid experiences a net attraction by other molecules toward the interior of the liquid. Surface tension is the energy required to increase the surface area of a liquid by a unit amount. The tension can be affected by dissolved substances. For example soaps can drastically decrease the surface tension. The tension makes it behave as though it had skin. Water bugs also sink in soapy water.
Capillary rise is related to surface tension. Water molecules happen to be attracted to glass. So when a capillary glass is placed upright in water, a column of liquid rises in the tube.
- Viscosity: is the resistance to flow that is exhibited by all liquids and gases. It can be measured by the time it takes for a given quantity to flow. Syrup has a greater viscosity than water.
All of these properties depends on intermolecular forces, which are related to molecular structure.
Classes of crystalline solids
Crystalline solids are those in which the atoms, ions, or molecules that make up the solid exist in a regular, well-defined arrangement. The smallest repeating pattern of crystalline solids is known as the unit cell, and unit cells are like bricks in a wall—they are all identical and repeating.
There are four types of crystalline solids:
Ionic solids—Made up of positive and negative ions and held together by electrostatic attractions. They’re characterized by very high melting points and brittleness and are poor conductors in the solid state. An example of an ionic solid is table salt, NaCl.
Molecular solids—Made up of atoms or molecules held together by London dispersion forces, dipole-dipole forces, or hydrogen bonds. "..is a solid that consists of positive Characterized by low melting points and flexibility and are poor conductors. An example of a molecular solid is sucrose.
Covalent-network (also called atomic) solids—Made up of atoms connected by covalent bonds; the intermolecular forces are covalent bonds as well. Characterized as being very hard with very high melting points and being poor conductors. Examples of this type of solid are diamond and graphite. Graphite has only 2-D hexagonal structure and therefore is not hard like diamond. The sheets of graphite are held together by only weak London forces!
Metallic solids—Made up of metal atoms that are held together by metallic bonds. Characterized by high melting points, can range from soft and malleable to very hard, and are good conductors of electricity. Iron, copper, silver.
Properties of solids
It is characterized by structural rigidity and resistance to changes of shape or volume. Unlike a liquid, a solid object does not flow to take on the shape of its container, nor does it expand to fill the entire volume available to it like a gas does. The atoms in a solid are tightly bound to each other, either in a regular geometric lattice (crystalline solids, which include metals and ordinary water ice) or irregularly (an amorphous solid such as common window glass).
Molecular: low melting point, rather soft, brittle, non-conducting.
Metallic: variable melting point, variable hardness; malleable, conducting.
Ionic: High to very high melting point, hard and brittle, nonconducting solid(conducting liquid).
Covalent network: very high melting point, very hard, usually nonconducting.
Solution terminology
Some compounds, such as sodium chloride and ethyl alcohol dissolve readily and are said to be soluble.
Others, such as calcium carbonate and benzene have quite limited solubilities and are thus said to be insoluble.
Group IA and ammonium compounds are soluble, acetates and nitrates are soluble, MOST chlorides, bromides, and iodides are soluble, MOST sulfates are soluble.
MOST carbonates, phosphates, sulfides, and hydroxides are insoluble.
Factors influencing solubility
Electrolytes IPAD
An electrolyte is a substance that dissolves in water to give an electrically conducting solution. Sodium chloride, table salt, is an example of an electrolyte. In general, ionic solids that dissolve in water are electrolytes. Not all electrolytes are ionic substances. Certain molecular substances dissolve in water to form ions. An example of this is hydrogen chloride gas ( HCl(g) ), which is a molecular substance. In water it dissolves to produce hydrogen ions(H+), and chloride ions, Cl-: this solution of H+ and Cl- is called hydrochloric acid.
A nonelectrolyte is a substance that dissolves in water to give a nonconducting or very poorly conducting solution. For example sucrose(C12H22O11).
Particles in solution
A homogeneous mixture (aka solution) is a mixture that is uniform in its properties throughout given samples. Example, sodium chloride dissolved in water.
Solutions may exist as gases, liquids, or solids.
The solute in the case of a solution of a gas or solid dissolved in a liquid, is the gas or solid; in other cases, the solute is the component in smaller amount.
The solvent, in a solution of a gas or solid dissolved in a liquid, is the liquid; in other cases, the solvent is the component in greater amount.
-> NaCl in water; NaCl = solute, water = solvent.
Fluids that mix = miscible. Fluids that doesn't mix = immiscible.
A saturated solution = a solution that is in equilibrium with respect to a given dissolved substance. For example NaCl in water; when equilibrium is reached, the rate at which ions leave the crystals equals the rate at which ions return to the crystals.
- Molecules with a -OH group are more soluble in water.
- The energy of attraction between an ion and a water molecule is due to an ion-dipole force. Water molecules are polar, so they orient with respect to nearby ions. Positive ions; water molecules orient with their oxygen atoms (the negative ends of the molecular dipoles). For negative ions; water molecules orient with their hydrogen atoms. The attraction of ions for water molecules is called hydration. However, the solubility of an ionic solid also depends on lattice energy, the energy holding ions together.
- Most gases become less soluble in water at higher temperature. The solubility of gases are also strongly affected by pressure.
Solubility
-Unsaturated means you can add more solute into the solvent.
-Satured means you can not add more solute into the solvent, as it has reach an equilibrium.
- Supersaturated; if we increase the temperature we may get more solute to absorb into the solvent. If we let it cool down, it still holds more solute than it should be able to. If you then add a crystal, you can get it to crystallize.
---> Solubility of gases actually works the opposite way; as you increase the temperature, it is less room for gases. For example; increasing the temperature in a fish tank will make the water to carry less oxygen. We can see this in the world as well; you should think that the most lush and exotic life is near the equator; but this is where we find the hottest water, and thus water with less free oxygen. However, because of the current coming in from the poles into the equator we get the best factors for exotic life; cool water with lots of oxygen, plus hot temperature from the sun.
Concentration expressions
- Molarity of a solution is the moles of solute in a liter of solution.
For example: 0.20 mol ethylene glycol / 2.0 L solution = 0.10 M ethylene glycol.
- Mass percentage of solute is the percentage by mass of solute contained in a solution.
- Molality of a solution is the moles of solute per kilogram of solvent.
For example: 0.20 mol ethylene glycol / 2.0 kg solvent = 0.10 m ethylene glycol.
Note that molality is defined in terms of mass of solvent, and molarity is defined in terms of volume of solution.
- Mole fraction is the moles of component substance divided by the total moles of solution (moles of solute plus solvent).
For example: solution made up of 1 mol ethylene glycol and 9 mol of water = 1/10=0.1 mole fraction of ethylene glycol.
Colligative properties of solutions
Freezing point is a colligative property. Colligative properties of solutions are properties that depend on the concentration of solute molecules or ions in solution but not on the chemical identity of the solute (whether it is ethylene glycol or urea, for instance).
Colligative properties include freezing point depression, boiling point elevation, vapor pressure lowering, and osmotic pressure.
Vapor-pressure lowering of a solvent is a colligative property equal to the vapor pressure of the pure solvent minus the vapor pressure of the solution. It depends on the concentration, but not on the nature, of the solute.
Osmotic pressure of solutions
Osmosis is the phenomenon of solvent flow through a semipermeable membrane to equalize the solute concentrations on both sides of the membrane. The solvent migration is faster from the solution of low solute concentration to the solution of high solute concentration.
Osmotic pressure is a colligative property of a solution equal to the pressure that, when applied to the solution, just stops osmosis.
Osmotic pressure is the basis of reverse osmosis, a process commonly used to purify water. The water to be purified is placed in a chamber and put under an amount of pressure greater than the osmotic pressure exerted by the water and the solutes dissolved in it. Part of the chamber opens to a differentially permeable membrane that lets water molecules through, but not the solute particles. The osmotic pressure of ocean water is about 27 atm. Reverse osmosis desalinators use pressures around 50 atm to produce fresh water from ocean salt water.
Osmotic pressure is necessary for many plant functions. It is the resulting turgor pressure on the cell wall that allows herbaceous plants to stand upright, and how plants regulate the aperture of their stomata. In animal cells which lack a cell wall however, excessive osmotic pressure can result in cytolysis.
Colloids and suspensions
Colloids:
Particles intermediate in size between those found in solutions and suspensions can be mixed such that they remain evenly distributed without settling out.
A colloid is a dispersion of particles of one substance (the dispersed phase) throughout another substance or solution (the continuous phase). Fog is an example of a colloid: it consists of very small water droplets (dispersed phase) in air (continuous phase). The dispersed particles differs in that they are larger than normal molecules, though too small to be seen with a microscope.
Types:
- Fog and smoke are aerosols.
- Emulsions consists of liquid droplets dispersed throughout another liquid.
- A sol consists of solid particles dispersed in liquid.
Colloids in which the continuous phase is water are divided into two major classes:
A hydrophilic colloid there is a strong attraction between the dispersed phase and the continuous phase (water). For example, macromolecules dispersed in water. For example, protein solution, such as gelatin in water.
A hydrophobic colloid there is a lack of attraction between the dispersed phase and the continuous phase (water). They are basically unstable, and over time may separate.
Suspensions:
The particles in suspensions are larger than those found in solutions. Components of a suspension can be evenly distributed by a mechanical means, like by shaking the contents, but the components will settle out.
Example: Oil and Water
Telling them apart:
You can tell suspensions from colloids and solutions because the components of suspensions will eventually separate. Colloids can be distinguished from solutions using the Tyndall effect. A beam of light passing through a true solution, such as air, is not visible. Light passing through a colloidal dispersion, such as smoky or foggy air, will be reflected by the larger particles and the light beam will be visible.
Active transport
Active transport is the mediated transport of biochemicals, and other atomic/molecular substances, across membranes. Unlike passive transport, this process requires chemical energy. In this form of transport, molecules move against either an electrical or concentration gradient (collectively termed an electrochemical gradient). This is achieved by either altering the affinity of the binding site or altering the rate at which the protein changes conformations.
There are two main types, primary and secondary. Primary active transport directly uses energy to transport molecules across a membrane. In secondary active transport, there is no direct coupling of ATP; instead, the electrochemical potential difference created by pumping ions out of cells is used.
Osmotic pressure and fluid transport
The transport of water and other molecules across biological membranes is essential to many processes in living organisms. The energy which drives the process is usually discussed in terms of osmotic pressure.
Kinetics and equilibrium
Firstly, it is important to mention that a chemical reaction has kinetic and thermodynamic aspects. The quantity related to kinetics is the rate constant k; this constant is associated with the activation energy required for the reaction to move forward. The thermodynamic quantity is the energy difference resulting from the free energy (ΔG) given off during a chemical reaction. While kinetics can tell us about the rates of reactions and how fast equilibrium is reached, they don't tell us anything about equilibrium conditions once the reaction equilibrates. In the same measure, thermodynamics only gives us information regarding the equilibrium conditions of products after the reaction takes place, but does not tell us the rate of reaction.
Factors influencing reaction rate
Nature of the reactants:
Depending upon what substances are reacting, the reaction rate varies. Acid/base reactions, the formation of salts, and ion exchange are fast reactions. When covalent bond formation takes place between the molecules and when large molecules are formed, the reactions tend to be very slow. Nature and strength of bonds in reactant molecules greatly influence the rate of its transformation into products.
Physical state:
The physical state (solid, liquid, or gas) of a reactant is also an important factor of the rate of change. When reactants are in the same phase, as in aqueous solution, thermal motion brings them into contact. However, when they are in different phases, the reaction is limited to the interface between the reactants. Reaction can occur only at their area of contact; in the case of a liquid and a gas, at the surface of the liquid. Vigorous shaking and stirring may be needed to bring the reaction to completion. This means that the more finely divided a solid or liquid reactant the greater its surface area per unit volume and the more contact it makes with the other reactant, thus the faster the reaction. To make an analogy, for example, when one starts a fire, one uses wood chips and small branches — one does not start with large logs right away. In organic chemistry, on water reactions are the exception to the rule that homogeneous reactions take place faster than heterogeneous reactions.
Concentration:
The reactions are due to collisions of reactant species. The frequency with which the molecules or ions collide depends upon their concentrations. The more crowded the molecules are, the more likely they are to collide and react with one another. Thus, an increase in the concentrations of the reactants will result in the corresponding increase in the reaction rate, while a decrease in the concentrations will have a reverse effect. For example, combustion that occurs in air (21% oxygen) will occur more rapidly in pure oxygen.
Temperature:
Temperature usually has a major effect on the rate of a chemical reaction. Molecules at a higher temperature have more thermal energy. Although collision frequency is greater at higher temperatures, this alone contributes only a very small proportion to the increase in rate of reaction. Much more important is the fact that the proportion of reactant molecules with sufficient energy to react (energy greater than activation energy: E > Ea) is significantly higher and is explained in detail by the Maxwell–Boltzmann distribution of molecular energies.
Catalyst:
A catalyst is a substance that accelerates the rate of a chemical reaction but remains chemically unchanged afterwards. Proteins that act as catalysts in biochemical reactions are called enzymes.
Agitating or mixing a solution will also accelerate the rate of a chemical reaction, as this gives the particles greater kinetic energy, increasing the number of collisions between reactants and, therefore, the possibility of successful collisions.
Pressure:
Increasing the pressure in a gaseous reaction will increase the number of collisions between reactants, increasing the rate of reaction. This is because the activity of a gas is directly proportional to the partial pressure of the gas. This is similar to the effect of increasing the concentration of a solution.
Equilibrium:
Equilibrium refers to the preferred end state of a chemical reaction. For every reaction, the reverse reaction is also possible. Rust can turn back into shiny metal--the reaction exists, it just isn't very likely.
While chemical kinetics is concerned with the rate of a chemical reaction, thermodynamics determines the extent to which reactions occur.
The origin of heats of reaction ((H)
Heat of Reaction is the heat liberated or absorbed when a chemical reaction takes place.
- An exothermic reaction liberates heat, temperature of the reaction mixture increases.
- An endothermic reaction absorbs heat, temperature of the reaction mixture decreases.
The heat required to raise the temperature of a substance is called its heat capacity. Specific heat capacity is the quantity of heat required to raise the temperature of one gram of a substance by one degree at constant pressure.
You measure the heat of reaction in a calorimeter, measuring the heat absorbed or evolved during a physical or chemical change.
Gibbs free energy (or available energy)
Total energy (Enthalpy = H). This is the total energy of the system. For example, a ball rolling down a slide. The potential energy of the ball is higher on the top, than on the bottom of the slide. Energy decreases.
Entropy (S). Measure of the disorder of the system. For example, diffusion; entropy is increasing.
Temperature (T). For example, a bomb; if you increase the temperature its more likely to explode.
Gibbs free energy: ∆G = ∆H - T∆S
In the ball rolling down. the enthalpy(H) of the system decrease. This, in turn, decreases the G value.
In the diffusion, the entropy(S) is increasing. This, in turn, decreases the G value.
In the bomb, the temperature(T); in increasing the temperature, we make the reaction more spontaneous. This, again, in turn, decreases the G value.
So, if ∆G ever decreases, or becomes less than 0, this is a spontaneous reaction.
∆G < 0 = spontaneous (exergonic reaction). Ex; cellular respiration
∆G > 0 = spontaneous backwards ( endergonic reaction). Ex; photosynthesis
∆G = 0 = Equilibrium
Negative/decrease ∆G = spontanous reaction.
-> decrease in enthalpy and increase in entropy = spontanous reaction.
-> Enthalpy and entropy the same; higher temperature = spontanous reaction.
Activation energy
This is the energy required or put in to make the reaction happen. For example, in cellular respiration when you have glucose, you need certain amount of activation energy to break down the bonds to release the energy. Another example, it is required energy to make the bomb go off, or to make the ball roll down the slide. In photosynthesis, the sun works as activation energy.
Reversible reactions
A reversible reaction is a chemical reaction where the reactants form products that, in turn, react together to give the reactants back.
For example, ATP->ADP->ATP
Equilibrium constant
In equilibrium there will always be the same relative amount of Reaction and Product. Keq is the mathematical term for equilibrium constant.
When all the participants (products and reactions) are of the same state, they are in homogeneous equilibrium. For example; H2(g) + I2(g) ≶ 2HI(g). Opposite is Heterogeneous equilibrium.
Acids and bases
Acids are substances that provide H+ ions. An acid is a molecular compound that yields hydrogen ions and an anion for each acid molecule when the acid dissolves with water. Ex; HNO3: the molecule yields one H+ ion and one nitrate ion, NO3-, in aqueous(water) solution.
Nitric acid(HNO3) is an oxoacid/oxyacid. An oxoacid is an acid containing hydrogen, oxygen, and another element. In water the oxoacid molecule yields one or more hydrogen ions, and an oxoanion.
The Arrhenius definition
Svante Arrhenius proposed that water can dissolve compounds into individual ions. Acids release hydrogen ions (H+) when dissolved in water. Bases release hydroxide ions (OH-). This explains their different properties, but also explained neutralization. When you mix acid and base, the H+ ion combines with the OH- ion to create water (neutral).
Bronsted-Lowry definition
An acid is a molecule or ion that is able to lose, or "donate," a hydrogen cation (proton, H+), and a base is a species with the ability to gain, or "accept," a hydrogen cation (proton). This concept defines a species as an acid or a base according to its function in the acid-base, or proton-transfer, reaction. An amphiprotic species can act as either an acid or a base, depending on other reactants. For example, HCO3- acts as an acid in the presence of OH- but as a base in the presence of HF.
1. A base is a species that accepts protons; OH- is just one example of a base.
2. Acids and bases can be ions as well as molecular substances.
3. Acid-base reactions are not restricted to aqueous solution.
4. Some species can act as either acids or bases, depending on what the other reactant is.
Acid and base strength
The strength does not refer to the pH at all. Instead, it refers to how easily H+ will dissolve in water. Strong acids easily loses H+ in water. Weak bases rarily loses OH-.
It is useful to consider acid-base reactions as a competition between species for protons. Thus, the stronger acids are those that lose their protons more easily. Similarly, the stronger bases are those that hold on to protons more strongly than other bases. Stronger and weaker are used in a comparative sense.
Strong electrolytes are completely dissociated into ions in water. The acid or base molecule does not exist in aqueous solution, only ions.
Acids: Strong acids completely dissociate in water, forming H+ and an anion. There are six strong acids. The others are considered to be weak acids. You should commit the strong acids to memory:
HCl - hydrochloric acid, HNO3 - nitric acid, H2SO4 - sulfuric acid, HBr - hydrobromic acid, HI - hydroiodic acid, HClO4 - perchloric acid.
Ionization of water
The hydronium ion H3O+ (or hydrogen ion, H+) and the hydroxide ion OH- are available in any aqueous solution as a result of the autoionization of water. Autoionization or self-ionization, is a reaction in which two like molecules react to give ions. In the case of water, a proton from one H2O molecule is transferred to another H2O molecule, leaving behind an OH- ion and forming a hydronium ion, H3O+ (aq).
pH, measurement of pH
pH is defined as the negative of the base 10 logarithm of the molar hydronium-ion concentration. pH = -log [H3O+] . Ex; pH = -log(1.0 x 10-3) = 3.00.
pH less than 7 is acidic, more than 7 is basic.
The pH can be measured by a pH meter. A voltage, which depends on the pH, is generated between two electrodes and is read on a meter calibrated directly in pH. Other than that, we have the less precise acid-base indicators which usually change color within a small pH range. Red colour is more acidic, blue is more basic.
Reactions of acids and bases
When an acid and a base are placed together, they react to neutralize the acid and base properties, producing a salt. The H(+) cation of the acid combines with the OH(-) anion of the base to form water. The compound formed by the cation of the base and the anion of the acid is called a salt. The combination of hydrochloric acid and sodium hydroxide produces common table salt, NaCl: HCl (acid) + NaOH (base) --> H2O (water) + NaCl (salt)
Acid-base indicators
pH 2=red, pH 4=purple, pH 6=violet, pH 8=blue, pH 10=blue-green, pH 12 = green-yellow.
Acid - base indicators is a dye used to distinguish between acidic and basic solutions by means of the color changes it undergoes in these solutions. For example, the ambler color of tea, is lightened by the addition of lemon juice (citric acid). Red cabbage juice changes to green and then yellow when a base is added. They are usually weak acids or bases.
Litmus is a common laboratory acid-base indicator, where acidic turns red and basic turns blue. Phenolphtalein, another indicator, is colorless in acidic, and pink in basic.
General properties of organic compounds
Organic compounds is an important class of molecular substances that contain carbon combined with other elements, such as hydrogen, oxygen, and nitrogen. Organic compounds make up the majority of all known compounds(60%).
Hydrocarbons are the simplest organic compound; containing only hydrogen and carbon. They are used extensively as sources of energy for heating our homes, for powering internal combustion engines, and for generating electricity. Examples of hydrocarbons; methane(CH4), ethane(C2H6), propane(C3H8), acetylene(C2H2), and benzene(C6H6).
The chemistry of organic molecules is often determined by groups of atoms in the molecule that have characteristic chemical properties. A functional group is a reactive portion of a molecule that undergoes predictable reactions.
The term ether indicates that an organic molecule contains an oxygen atom between two carbons atoms.
Bonding in carbon compounds
Carbon has four valence electrons, so it needs four additional electrons through four covalent bonds. Carbon forms single, double, and triple bonds to achieve this. It can thus have tetrahedral, trigonal planar, or linear geometry.
The covalent bonding of two or more atoms of the same element to one another is referred to as catenation. Although other elements display catenation, none show it to the same degree as carbon. Most carbon compounds are organic.
Hydrocarbons are the simplest organic compounds. Three groups:
1. saturated hydrocarbons contain only single bonds the carbons atoms. Cyclic hydrocarbons forms rings, and acyclic hydrocarbons does not contains rings.
2. unsaturated hydrocarbons contain double or triple bonds between carbon atoms.
3. aromatic hydrocarbons contain benzene rings or similar features.
Structural formulas for organic molecules
The main types of structural formulae of organic molecules are:
Fully Displayed Formulae
Simplified Displayed Formulae (also called "Semi-Displayed Formulae")
3D Structural Formulae (also called "Sketched 3D Structures")
Modelled 3D Formulae
Skeletal FormulaeW
Condensed structural formulas
The condensed structural formula is simply a shortened version of the complete structural formula. Here, the bonds around each carbon atom in the compound are not explicitly written.
Condensed formulas of the first four alkanes are: CH4(methane), CH3CH3(ethane), CH3CH2CH3(propane), CH3CH2CH2CH3(butane).
Functional-group concept
A functional group is a reactive potion of a molecule that undergoes predictable reactions. When you use the term alcohol when referring to a molecular compound, you actually are indicating a molecule that contains an -OH functional group.
Functional groups consist of one or more atoms, and they can be atoms of identical or different elements. The simplest organic molecule is one carbon bonded covalently to four hydrogens, CH4. This compound, a gas, is called methane and is a major component of natural gas. For any other functional group to attach itself to methane, one hydrogen must be removed and the other functional group must be attached in its place. This process is called substitution of the functional group.
The principle used is that organic compounds are named and generally understood as substituted compounds of carbon and hydrogen, the substitution being that of a functional group for one or more hydrogens. The simplest compounds of carbon and hydrogen are the Alkanes, followed by the Alkenes and Alkynes.
The R-group concept
R Group refers to a side chain. The letter R is used as a placeholder. R usually means a carbon group.
The "action" is at the functional group
Organic halide: R-Cl R-Br
Alcohol: R-O-H
Ether: R-O-R
Aldehyde:
O (dobbeltbinding)
R-C-H
Ketone:
O (dobbeltbinding)
R-C-R
Carboxylic acid:
O (dobbeltbinding)
R-C-O-H
Ester:
O (dobbeltbinding)
R-C-O-R
Amine:
R-N-H R-N-H R-N-R
H R R
Amide:
O
R-C-N-R
H
Isomerism
Compounds with the same molecular formula but different structural formulas. Isomers do not necessarily share similar properties, unless they also have the same functional groups. There are many different classes of isomers, like stereoisomers, enantiomers, geometrical isomers, etc. (see chart below). There are two main forms of isomerism: structural isomerism and stereoisomerism (spatial isomerism).
In structural isomers, sometimes referred to as constitutional isomers, the atoms and functional groups are joined together in different ways. Structural isomers have different IUPAC names and may or may not belong to the same functional group. This group includes chain isomerism whereby hydrocarbon chains have variable amounts of branching; position isomerism which deals with the position of a functional group on a chain; and functional group isomerism in which one functional group is split up into different ones.
In stereoisomers the bond structure is the same, but the geometrical positioning of atoms and functional groups in space differs. This class includes enantiomers where different isomers are non-superimposable mirror-images of each other, and diastereomers when they are not. Diastereomerism is again subdivided into "cis-trans isomers", which have restricted rotation within the molecule (typically isomers containing a double bond) and "conformational isomers" (conformers), which can rotate about one or more single bonds within the molecule.
Structural/constitutional isomers:
Made up out of the same molecules, but NOT the same connections.
Stereoisomers:
Made up out of the same molecules, with same connections.
Enantiomers: mirror images of each other. (mirror behind)
Diastereomers: NOT mirror images of each other. (mirror behind)
Meso compound:
The same molecule; flipped over / mirror (mirror between). Superimposed on the mirror image. It is a meso compound only when top and bottom of the molecule is the same/symmetry.
Geometry around carbon atoms
Bonds with other carbon atoms to form chains and rings. The covalent bonding of two or more atoms of the same element to one another is referred to as catenation.
Rotation about single bonds
Carbon atoms in single bonds rotate freely. Rotation does not change this electron distribution; the bond strength remains constant throughout rotation. Because rotation is possible, the molecule can have an infinite number of conformations, and a sketch of any of them is an accurate representation of the molecule.
Isomerism revisited
Nomenclature
Chemical nomenclature is the systematic naming of chemical compounds.
Common nomenclature
Writing structures from names
Nomenclature and isomerism
Physical properties of hydrocarbons
1. Saturated hydrocarbons (single bonds between carbon atoms)
- Alkanes
2. Unsaturated hydrocarbons (double or triple bonds between carbon atoms)
- Alkenes(double) and Alkynes(triple)
3. Aromatic hydrocarbons/arenes (benzene rings or similar features)
1+2 = aliphatic hydrocarbons.
The physical properties of the unsaturated hydrocarbons are pretty much like those of the saturated hydrocarbons.
- The molecules are essentially nonpolar and thus relatively insoluble in water.
- Their intermolecular bonds are the weak van der Waals bonds.
- Melting points and boiling points for the small molecules are fairly low. The larger and heavier the molecules are, the higher their melting and boiling points are.
Chemical properties of alkanes and Homologous series
1) They combust in oxygen to form carbon dioxide, water and heat. It is this heat which makes them good fuel sources.
2)They undergo substitution reactions with halogens in the presents of UV light. Alkanes react with halogens in a so-called free radical halogenation reaction. The hydrogen atoms of the alkane are progressively replaced by halogen atoms. Free-radicals are the reactive species that participate in the reaction, which usually leads to a mixture of products. The reaction is highly exothermic, and can lead to an explosion.
Combustion, oxidation, addition, and substitution.
- Unlike most other organic compounds, they possess no functional groups.
- They react only very poorly with ionic or other polar substances.
Alkanes (aka paraffins) are acyclic saturated hydrocarbons, and the cycloalkanes are cyclic saturated hydrocarbons. Example, methane. Alkanes constitute a homologous series, in which one compound differs from a preceding one by a fixed group of atoms. Members of a homologous series have similar chemical properties, and their physical properties change throughout the series in a regular way.
Generally, the more carbon atoms, the higher the boiling point of an alkane. The reason for this rise is an increase in the intermolecular forces.
The alkanes are rather unreactive and do not combine readily with other substances. When heated sufficiently, however, they burn in air, a process known as combustion.
Alkanes (paraffins)
-> Saturated
-> It is a hydrocarbon
-> Consists of 4 single bonds
-> Ends with -ane
Alkenes (olefins)
-> Unsaturated
-> It is a hydrocarbon
-> Consists of double bonds
Alcohols:
-> They're like Alkanes but with a -OH attached
Alkynes:
-> Triple bonds between two carbon atoms.
-> Like other hydrocarbons, alkynes are generally hydrophobic but tend to be more reactive.
-> Alkynes are more unsaturated than alkenes
Carboxylic acids:
-> A carbon atom with an =O and a -OH -> COOH
Homologous series:
Similarities:
- Same general formula
- Same functional group
- Similar chemical properties
Differences:
- Chain lengths
- Different physical properties
Same general formula, functional group and chemical properties
|Boiling point |Methane |Ethane |Propane |Butane |Functional |Chemical properties |
|increases down the | | | | |group | |
|rows | | | | | | |
|Alkanes (CnH2n + 2) |CH4 |C2H6 |C3H8 |C4H10 |C-C | |
| | | | | | |Generally unreactive |
|Alkenes (C2H2n) |----- |C2H4 |C3H6 |C4H8 |C=C | |
| | | | | | |React with Bromine |
|Alcohols (CnH2n + 1) |----- |C2H5OH |C3H7OH |C4H9OH |O-H | |
| | | | | | |React with Sodium |
|Carboxylic acid |------ |CH3COOH |C2H5COOH |C3H7COOH |COOH | |
|(C2H2nO2) | | | | | |- Acidic |
| | | | | | |-Neutralized by |
| | | | | | |Sodium hydroxide |
Alkenes
Unsaturated chemical compound containing at least one carbon-to-carbon double bond.
Nomenclature of alkenes
Geometric isomerism
Geometric isomers are isomers in which the atoms are joined to one another in the same way but differ because some atoms occupy different relative positions in space.
[pic]
These structural formulas represent entirely different compounds, as their boiling points clearly demonstrate (cis=60 degrees, trans=48 degrees). The central molecular event in the detection of light by the human eye involves the transformation of a cis compound to its corresponding trans compound after the absorption of a photon of light. The difference in being mirror images can also give it other characteristics such as different flavours. Also, for example D-lactic acid occurs in sour milk, whereas only L-lactic acid forms in muscle tissue after exercising.
Furthermore, they may also be differentiated on the basis of dipole moment. The trans compound has no dipole moment because it is symmetrical (the polar C-Cl bonds point in opposite directions and so cancel).However, the cis compound has a dipole moment.
All unprocessed fats and oils contain only cis isomers. During processing, some of the cis isomers are converted to trans isomers, called trans fatty acids. Trans fatty acids are suspected of raising the amount of serum cholesterol in the blood stream, which can cause health problems.
Trans arrangements = symmetrical = nonpolar
Cis arrangements = polar
---> Thus, the cis compounds are more soluble in water, because it is polar.
-----------------------------------------
[pic]
This is also a stereoisomer and a enantiomer.
Chiral = An object that is not superposable on its mirror image.
Achiral (not chiral) = Objects that are identical to their mirror image.
This next one is achiral(not chiral):
[pic]
As you can see, you can have chiral centers, but without the molecule being chiral as a whole.
Bonding in alkenes - The double bond
Alkene reactions
- Produces carbon dioxide and water when reacting with oxygen at high temperatures. Alkenes are more reactive than alkanes because of the double bond.
- Many reactants add to the double bond (addition reaction -> adding reactant while transforming it to single bonds).
Polymerization
Alkynes
Unsaturated hydrocarbons with triple bond. For example acetylene which is a very reactive gas.
Cyclic hydrocarbons
It is a ring formed carbon skeleton. Five and six membered rings are quite common. The most 'famous' cyclic hydrocarbon is the aromatics-group of benzene.
Aromatic hydrocarbons
Usually contains benzene rings: six-membered rings of carbon atoms with alternating carbon-carbon single and carbon-carbon double bonds.
- They are aromatic; for example flavour and aroma of cinnamon, candies and gum etc.
- Benzene rings is also found in aspirin.
Biologically significant hydrocarbons
- Hydrocarbons makeup the backbones of biologically important compounds such as alcohols, sugars, lipids, and amino acids.
Properties of the halogenated hydrocarbons
Halogenated hydrocarbons are compounds with the general formula R-X where R is any hydrocarbon group and X is a halogen (Cl, Br, F or I). The most significant property of halogenated hydrocarbons is that as you increase the number of halogens on the compound, the flammability of the compound decreases. This property has been used to produce ethers that are nonflammable to be used as general anesthetics
Functional groups, when attached to various hydrocarbons, increase their activity and water solubility of the hydrocarbon.
The alcohol functional group
Because of hydrogen bonding, alcohols tend to have higher boiling points than comparable hydrocarbons and ethers.
In general, the hydroxyl group makes the alcohol molecule polar.
Hydrogen bonding in alcohols
Nomenclature of alcohols
Industrial source and use of some alcohols
- Ethanol for beverages
- Ethanol and methanol for anti-microbial / anti-septic
- Ethanol and methanol as fuel
- Ethylene glycol as anti-freeze
- Preservative
- Ethanol as solvent in drugs, perfumes and vegetable essences.
- Methyl alcohol as windshield washer
Dehydration of alcohols
The general idea behind each dehydration reaction is that the –OH group in the alcohol donates two electrons to H+ from the acid reagent, forming an alkyloxonium ion.
When heated with strong acids catalysts (most commonly H2SO4, H3PO4), alcohols typically undergo a 1,2-elimination reactions to generate an alkene and water.
Alcohol ---------------- hot, concentrated sulfuric acid --------------> Alkene
Dehydration of alkanols (alcohols) is an elimination reaction.
Water is eliminated from the alkanol resulting in an alkene.
Any concentrated strong acid can cause the dehydration of an alkanol, but hot, concentrated sulfuric acid is the most commonly used.
The reagent used to dehydrate the alkanol is known as a dehydrating agent.
The dehydration of a primary alkanol (alcohol) produces the 1-alkene .
The dehydration of a secondary alkanol or a tertiary alkanol (alcohol) may produce a mixture of alkene structural isomers*.
Oxidation of alcohols
Primary alcohols can be oxidised to either aldehydes or carboxylic acids depending on the reaction conditions. In the case of the formation of carboxylic acids, the alcohol is first oxidised to an aldehyde which is then oxidised further to the acid.
Partial oxidation to aldehydes:
[pic]
Full oxidation to aldehydes and then to carboxylic acids:
[pic]
Secondary alcohols are oxidised to ketones - and that's it.
Tertiary alcohols aren't oxidised.
Ethers
Ether indicates that an organic molecule contains an oxygen atom between two carbon atoms, as in diethyl ether (CH3CH2OCH2CH3).
Water: H-O-H. An alcohol: R-O-H. An ether: R-O-R.
The carbonyl group
A carbonyl group is a carbon-oxygen double bond. Oxygen can have only two bonds, so nothing else can be bonded to oxygen, but carbon forms four bonds, so there are two "spaces" left over in which other atoms can be bonded to the carbon.
The simplest carbonyl groups are aldehydes and ketones usually attached to another carbon compound. These structures can be found in many aromatic compounds contributing to smell and taste.
- Benzaldehyde, which gives almonds their odor
- Methyl Ethyl Ketone, a strong, sweet-smelling compound that is sometimes used in paints
- Acetic Acid, the active ingredient in vinegar
- Ethyl Acetate, another sweet-smelling compound which can be used as a flavoring. It is produced in small amounts by the yeast which makes bread rise.
Aldehyde and ketone nomenclature
An aldehyde is a compound containing a carbonyl group with at least one H atom attached to it.
[pic]
A ketone is a compound containing a carbonyl group with two hydrocarbon groups attached to it.
[pic]
Physical properties of aldehydes and ketones
Amines -> smelly, ex, fish smell.
Aldehydes:
- Formaldehyde (methanal)
- Benzelaldehyde
- Cinnamaldehyde
- Acetalaldehyde (ethanal)
(Larger aldehydes tend to have a nice, rosy, sweet, flowery smell. Smaller aldehydes tend to have more pungent smell.)
Carbonyl + hydrogen + something else(R).
An aldehyde differs from a ketone by having a hydrogen atom attached to the carbonyl group. This makes the aldehydes very easy to oxidise.
Ketones don't have that hydrogen atom and are resistant to oxidation. They are only oxidised by powerful oxidising agents which have the ability to break carbon-carbon bonds.
- Aldehydes and ketones with 1 to 4 carbons are very soluble. More than 4 and it becomes insoluble. So, if it contains an Oxygen + 4 or less carbons, it is soluble.
- Aldehydes have higher boiling point than similar sized alkanes, but lower boiling point than similar sized alcohol.
Oxidation and reduction of aldehydes and ketones
- Primary alcohols oxidizes to produce aldehydes. Aldehydes oxidizes to produce carboxylic acids.
- Secondary alcohol oxidizes to produce ketones. Ketones cannot be further oxidized.
- Aldehydes and ketones can be reduced by sodium borohydride, NaBH4, or H2. (Reducing is putting the hydrogen back / removing the double bond).
Alcohol addition to aldehydes and ketones
Aldol addition of aldehydes and ketones
'Aldol' is an abbreviation of aldehyde and alcohol.
Addition of α-carbon of an enolizable aldehyde or ketone to the carbonyl group of another aldehyde or ketone and thus by giving a β-hydroxy carbonyl compound also known as an aldol (indicating both aldehyde and alcohol groups).
Reactions of aldehydes and ketones with nitrogen compounds
Alkaloids are a group of naturally occurring chemical compounds that contain mostly basic nitrogen atoms.
The occurrence and use of a few aldehydes and ketones
- The aldehyde retinal is important to the function of the human eye.
- The aldehyde propenal is a major component of bonfire and barbecue smoke.
- The ketone butanedione gives butter and stale sweat their characteristic smells.
- Zingerone is the active ingredient in ginger.
- Progesterone and testosterone are ketones.
Phenols
- If the -OH group is directly attached to a benzene ring, the compounds are called phenols.
- The acidity of the hydroxyl group in phenols is commonly intermediate between that of aliphatic alcohols and carboxylic acids .
- Low molecular weight phenols are normally liquids or low melting solids.
- Due to hydrogen bonding, most low molecular weight phenols are water-soluble.
- Phenols tend to have higher boiling points than alcohols of similar molecular weight because they have stronger intermolecular hydrogen bonding.
- Because of their high acidity, phenols are often called carbolic acids.
Thiols
- thiol, also called mercaptan, any of a class of organic chemical compounds similar to the alcohols and phenols but containing a sulfur atom in place of the oxygen atom.
- Thiols are among the odorous principles in the scent of skunks and of freshly chopped onions; their presence in petroleum and natural gas is objectionable because they have disagreeable odours
- Thiols show many reactions like those of the hydroxyl compounds, such as formation of thioesters and thioethers (sulfides). Toward oxidation, however, they differ profoundly from alcohols: whereas oxidation of an alcohol usually leads to a product in which the oxidation state of a carbon atom has been changed, oxidation of a thiol affects the sulfur atom. Mild oxidants convert thiols to disulfides, and more vigorous reagents result in the formation of sulfonic acids.
- Examples:
Methanethiol – CH3SH
Ethanethiol – C2H5SH
[pic]
Stereoisomerism
Isomers in which the atoms are bonded to each other in the same order but differ in the precise arrangement of the atoms in space.
- Trans and cis arrangements: Cis are more polar and thus more soluble.
Stereoisomerism and glucose
- The two most common stereoisomers of glucose are L-glucose and D-glucose. There are 4 chiral carbons in glucose so there would be 16 possible stereoisomers(8 D and 8 L).
- L-glucose is hardly found in nature.
- D-glucose, right-handed, exists in nature.
- The other most important stereoisomers would be mannose and galactose
[pic]
Fischer projections
The Fischer projection, devised by Hermann Emil Fischer in 1891, is a two-dimensional representation of a three-dimensional organic molecule by projection.
- A Fischer projection is used to differentiate between L- and D- molecules. On a Fischer projection, the penultimate carbon of D sugars are depicted with hydrogen on the left and hydroxide on the right. L sugars will be shown with the hydrogen on the right and the hydroxide on the left.
- Fischer projections should not be confused with Lewis structures, which do not contain any information about three dimensional geometry.
[pic]
Multiple chiral centers
Classification: D-family versus L-family
A compound whose solution rotates the plane of polarized light to the right (when looking toward the source of light) is called dextrorotatory and is labeled d. A compound whose solution rotates the plane of polarized light to the left (when looking toward the source of light) is called levorotatory and is labeled l.
Intramolecular hemiacetals and hemiketals
- With aldehydes, alcohols give hemiacetals, or compounds in which and -OH group, an -OR group, and an H atom are attached to the same carbon atom.
[pic]
- A ketone and an alcohol give a hemiketal, which is similar to hemiacetal except that the H atom is replaced by an R" group.
[pic]
- The simplest way to know whether something is a ketal or acetal is to see if the protected carbon has a H. If it does, it's an acetal, if not, ketal.
Haworth projections
Haworth Projections are commonly used for cyclic sugars. Haworth Projections are useful for being able to clearly determine whether groups are above or below the ring.
[pic]
The -CH2OH group attached to C5 is written up for D sugars and down for L sugars.
The -OH group attached to C1 is written down for the alfa isomer and up for the beta isomer.
Mutarotation
A phenomenon called mutarotation is exhibited by many sugars. This plays an important role in deciding the structure of a carbohydrate.
Mutarotation has to do with how a molecule rotates the plane of light. For example, alpha glucose has the OH group at a different position than beta glucose.
The cyclic alfa and beta anomers of a sugar in solution are in equilibrium with each other, and can be spontaneously interconverted, a process called mutarotation.
Formation of di- and polysaccharides
Polysaccharides are formed through enzyme-catalysed condensation (joining of two molecules with water being a by-product) reactions between other saccharide units.
The reaction involves the removal of a OH- group from one saccharide and H+ from another. The two units join through a glycosidic bond to form the di/oligo/poly saccharide and the OH- and H+ join to form water.
The linkages between the monosaccharide ring units in disaccharides are acetal linkages. We can envision them as being made by the formation of an acetal from a hemiacetal and an alcohol. For this purpose, the hemiacetal includes the anomeric carbon of a monosaccharide and the alcohol role is played by a specific OH group of a second monosaccharide. The formation of maltose from two molecules of glucose is an example of this:
[pic]
- this process (picture) is catalyzed by the enzyme maltase.
Monosaccharides
Chemically, they are aldehydes or ketones that also have several hydroxyl groups attached to their carbon skeletons. For example, glucose is known as an aldose and has an aldehyde structure at carbon atom number 1 (C1). On the other hand, fructose is known as a ketose and has a ketone structure at carbon C2. However, both glucose and fructose have the formula C6H12O6.
- Monosaccharides dissolve easily in water because the large number of polar hydroxyl groups, which hydrogen-bond with water molecules.
Carbohydrates that cannot be hydroliyzed - they do not react with water.
Carbohydrates are aldehydes and ketones with many OH groups, or substances that form these when hydrolyzed.
- Empirical formula (CH2O)n
- Those with aldehyde groups are called aldoses
- Those with keto groups are called ketoses
- The nutritionally important monosaccharides are glucose, galactose and fructose.
- Glucose, C6H12O6, is a hexose with an aldehyde group; aldohexose.
- Galactose, also an aldohexose, is a stereoisomer of glucose.
- Fructose has a keto group and so is a ketohexose; its a constitutional isomer of glucose and galactose.
Enantiomers:
- Mirror images; D-sugar and L-sugar.
- In the D isomeric form, the -OH group on the assymetric carbon ( a carbon linked to four different atoms or groups) farthest from the carbonyl carbon is on the right, whereas in the L-isomer it is on the left. Enzymes known as racemases are able to interconvert D- and L-isomers.
Classification: Reducing and nonreducing sugars
- All common monosaccharides are reducing sugars (they have free ketone or aldehyde group)
- The disaccharides maltose and lactose are reducing sugars
- The disaccharide sucrose is a non-reducing sugar.
- Common oxidising agents used to test for the presence of a reducing sugar are:
- Benedict's Solution
- Fehling's Solution
- Tollen's Reagent
--> reducing sugar oxidised to carboxylate
Reducing:
1. Possess a free aldehyde(-CHO) or ketone (-C=0) Group.
2. Can reduce the Cu2+ cupric ions (blue)in Fehling’s or Benedict’s Solution to Cu+ cuprous
ions (reddish) that precipitate out as Cu2O(cuprous oxide).
3. Maltose. lactose, melibiose, gentiobiose, cellobiose, mannotriose, rhamnotriose.
- reducing sugars have formed the glycosidic link using a hydroxyl group present in the open-chain structure, and so a carbonyl group remains on one monosaccharide. This can therefore form an anomeric centre, and two forms exist: there is an alfa-maltose and a beta-maltose.
- disaccharides are reducing if a carbonyl group remains on one monosaccharide.
Non-reducing:
1. A free aldehyde or ketonic group is lacking.
2. No such reaction.
3. Sucrose, trehalose,raffinose, gentiarose, melezitose.
- non-reducing sugars have formed the glycosidic link using a hydroxyl group formed on making the ring structure of the molecule, and so no carbonyl group remains. This cannot there form anomers, and only one form exists: sucrose is a unique molecule.
Disaccharides
- Carbohydrates that can be hydrolyzed to two monosaccharides.
- Sucrose(glucose + fructose), maltose(glucose + glucose), lactose(galactose + glucose).
- Two monosaccharides are joined together by a glycosidic link, which is a reaction between the carbonyl group of one molecule and a hydroxyl group of another molecule.
Polysaccharides
- Depend to a great extent on the type of glycosidic link (alfa or beta).
- alfa glycosidic link lies outside the plane of one of the monosaccharide rings that i joins.
- beta glycosidic link lies in the plane of the rings.
- The alfa-glycosidic link in amylose and amylopectin results in a coiled molecule most suited for storage in starch grains. This contrasts with the beta-glycosidic link present in cellulose (structural material of plants).
- Glycogen is stored in the liver. Insulin promotes conversion of glucose to glycogen. Glucagon promotes conversion of glycogen to glucose.
- Humans digest starch by the enzyme amylase, which split the alfa-glycosidic link to produce a mixture of glucose and maltose. However, we can't hydrolyse beta-glycosidic links, and therefore we can't digest cellulose.
Classification of amines
Amines and amino acids are organic compounds that contain one or more nitrogen atoms.
Amines have an amine group -NH2.
Amino acids have an amine group + a carboxylic group -COOH attached to the molecule.
Amines are organic compounds derived from ammonia(NH3) in which alkyl groups substitute for some of the hydrogen atoms of the NH3 molecule. Primary, secondary, tertiary amines correspond to the substitution of one, two and three hydrogen atoms respectively. These different structures depend on the number of alkyl groups attached directly to the nitrogen atom of the functional group.
- Ex; Methylamine(CH3NH2 - primary), ethylamine, and dimethylamine( (CH3)2NH - secondary) (gases)
- Ex; other common amines are liquids.
- Many (confusing) various names; methylamine/methanamine/aminomethane.
- Adrenalin is a secondary amine. (it is also a secondary alcohol).
Primary amine:
[pic]
R = alkyl
Aromatic amines consists of an amine -NH2 group attached to a benzene ring.
- phenylamines/aniline, prototype of aromatic amines, are far less soluble in water than are aliphatic amines (An aliphatic amine is an amine in the molecule of which there are no aromatic rings directly on the nitrogen atom).
Nomenclature
Physical properties of amines
- Among aliphatic amines, the lower members are gases while higher members are liquid. Among arylamines the lower members are liquids while higher members are solids.
- The lower amines have ammoniacal smell whereas higher amines have fishy smell. Aromatic amines are colorless in pure form.
- All amines, except the tertiary amines are capable of forming intermolecular hydrogen bonds due to the presence of polar N – H bonds. As a result of this, amines have higher boiling points than the non-polar compounds of comparable molecular masses.
- Aliphatic amines of lower molecular mass are soluble in water. With increase in molecular mass, the hydrocarbon part of the molecule becomes larger and consequently, the solubility in water gradually decreases; the borderline being reached at about six carbon atoms. Aromatic amines are insoluble in water but soluble in ether, alcohols and benzene.
Amine basicity
Most organic bases are amines, which are compounds that are structurally derived by replacing one or more hydrogen atoms of ammonia with hydrocarbon groups(R). Amines are bases because the nitrogen atom has an unshared electron pair that can accept a proton to form a substituted ammonium ion.
Amines are organic derivatives of ammonia. They react with carboxylic acids to give amides.
Nomenclature of carboxylic acids
[pic]
Physical properties of carboxylic acids
- Weak acids
- Polar
- Strong odor, ex vinegar. However, esters of carboxylic acids tend to have a pleasant/perfume odor.
Acidity and salt formation
When acids and bases react with each other, they can form a salt and (usually) water. This is called a neutralization reaction.
The reverse of the neutralization reaction is called hydrolysis. In a hydrolysis reaction a salt reacts with water to yield the acid or base
- When strong acids and strong bases react, the products are salt and water.
- The reaction between a strong acid and a weak base also produces a salt, but water is not usually formed because weak bases tend not to be hydroxides
- When a weak acid reacts with a strong base the resulting solution will be basic. The salt will be hydrolyzed to form the acid, together with the formation of the hydroxide ion from the hydrolyzed water molecules.
- The pH of the solution formed from the reaction of a weak acid with a weak base depends on the relative strengths of the reactants.
Fatty acid salts as soap
Soap is a mixture of sodium salts of various naturally occurring fatty acids. Soap is produced by a soaponification or basic hydrolysis reaction of a fat or oil.
Esterification
Esters are formed by reaction of an acid and an alcohol. Esters are sweet smelling substances.
A close examination of the ester functional group
Esters from phosphoric acids
Thioesters
Anhydrides of carboxylic acids
Hydrolysis of esters
Amides: Nomenclature
- Contains the functional group -CONH2
Properties of amides
- Amides are extremely weak bases; weaker than amines, but stronger than ammonia.
- Amides don't have as clearly noticeable acid-base properties in water (pH 7).
- The solubilities of amides and esters are roughly comparable. Typically amides are less soluble than comparable amines and carboxylic acids since these compounds can both donate and accept hydrogen bonds.
The three major classes of carboxylic acid derivatives are the acetyl chlorides, the esters, and the amides.
Amide formation
- Amides are formed by reacting acyl chlorides with ammonia, or by heating the ammonium salts of carboxylic acids.
Waxes
-
Fats and oils
Hydrogenation of oils
Hydrolysis of simple lipids and digestion
Compound lipids
Phospholipids
The lipid bilayer of cell membranes
Steroids
Structure of amino acids
Amino acids contain both a basic -NH2 group and an acidic -COOH group.
- Almost all naturally occurring amino acids are alfa-amino acids in which the amine group is attached to the alfa-carbon atom of a carboxylic acid. General formula/structure:
[pic]
With the exception of glycine, all amino acids obtained from proteins are optically active because the alfa-carbon atom is a chiral centre.
Classification of amino acids
There are about 20 naturally occurring amino acids. Almost all are alfa-amino acids with the general formula RCH(NH2)COOH. The only part that varies is the R group. If the R group does contain any acidic or basic group, the amino acid is neutral overall. If there are more acidic groups, the amino acid is acidic (apartic acid, glutamic acid); if there are more basic groups, the amino acid is basic (asparagine, arginine, lysine).
Aliphatic - Glycine, Alanine, Valine, Leucine, Isoleucine
Aromatic - Phenylalanine, Tyrosine, Tryptophan
OH- - Serine, Threonine
Acidic - Aspartic Acid, Glutamic Acid
Acid amide - Aspargine, Glutamine
Basic - Arginine, Lysine, Histidine
Sulphur - Cystine, Methionine
Non polar or Hydrophobic - Glycine, Alanine, Valine, Leucine, Isoleucine, Proline
Polar uncharged - Phenylalanine, Tryptophane, Tyrosine
Polar charged - Serine, Threonine (OH-), Cystine, Methionine (sulphur), Aspargine, Glutamine (acid amide)
Positively charged - Aspartic Acid, Glutamic Acid
Negatively charged - Arginine, Lysine, Histidine
Cyclic - Proline
Non-protein functions:
In humans, non-protein amino acids also have important roles as metabolic intermediates, such as in the biosynthesis of the neurotransmitter gamma-aminobutyric acid. Many amino acids are used to synthesize other molecules, for example:
- Tryptophan is a precursor of the neurotransmitter serotonin.
- Tyrosine (and its precursor phenylalanine) are precursors of the catecholamine neurotransmitters dopamine, epinephrine and norepinephrine.
- Glycine is a precursor of porphyrins such as heme.
- Arginine is a precursor of nitric oxide.
- Ornithine and S-adenosylmethionine are precursors of polyamines.
- Aspartate, glycine, and glutamine are precursors of nucleotides.
- Phenylalanine is a precursor of various phenylpropanoids, which are important in plant metabolism.
[pic]
Stereoisomerism in amino acids
The peptide bond
The C-N bond in the -CONH- peptide link is called the peptide bond.
As both the amine and carboxylic acid groups of amino acids can react to form amide bonds, one amino acid molecule can react with another and become joined through an amide linkage. This polymerization of amino acids is what creates proteins. This condensation reaction yields the newly formed peptide bond and a molecule of water.
A peptide bond (amide bond) is a covalent chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, causing the release of a molecule of water (H2O), hence the process is a dehydration synthesis reaction (also known as a condensation reaction), and usually occurs between amino acids. The resulting C(O)NH bond is called a peptide bond, and the resulting molecule is an amide.
[pic]
Polypeptides
In a dipeptide molecule, it retains an amine group at one end and a carboxylic acid group at the other. Further amino acid molecules may condense with this product to extend the chain length. Up to 20 amino acids are called oligopeptides; longer chain are called polypeptides.
Primary structure of proteins (sequence)
About 20 naturally occurring amino acids. The rest are essential amino acids, which must come from our food.
Four levels of structure: primary, secondary, tertiary, quaternary.
[pic]
Each amino acid is joined to the next via a peptide link, which forms between the carboxyl group of one amino acid and the amine group of the next.
As proteins are polyamides, writing out the full structure for each amino acid in a protein would be very tedious, and so primary structure is usually depicted by a three-letter short-hand notation, e.g. ala for alanine, leu for leucine.
Secondary structure of proteins (folding)
The chain of amino acids that makes up the primary structure of a protein can fold itself in two ways, depending on the sequence of amino acids that are next to each other. Hydrogen bonds hold the folded structures in place.
Two main types of secondary structure, the alpha helix and the beta strand or beta sheets, were suggested in 1951 by Linus Pauling and coworkers.
Tertiary structure of proteins
Tertiary structure refers to three-dimensional structure of a single protein molecule. The alpha-helices and beta-sheets are folded into a compact globule. The folding is driven by the non-specific hydrophobic interactions (the burial of hydrophobic residues from water), but the structure is stable only when the parts of a protein domain are locked into place by specific tertiary interactions, such as salt bridges, hydrogen bonds, and the tight packing of side chains and disulfide bonds.
Quaternary structure of proteins
Some structure results from interaction between separate protein chains, which is called quaternary structure.
Fibrous proteins have long molecules, which are strengthened by many cross-links between the chains. Fibrous proteins form structures such as muscle fibres.
Globular proteins are smaller and are much more round and compact. Ex; enzymes and hormones.
Classification of proteins
Three groups...?
- Fibrous proteins: these proteins have a rod like structure. They are not soluble in water. Collagen is an example of a fibrous protein.
- Globular proteins: these proteins more or less spherical in nature. Due to their distribution of amino acids (hydrophobic inside, hydrophillic outside) they are very soluble in aqueous solution. Myoglobin is an example of a globular protein.
- Membrane proteins: these are protein which are in association with lipid membranes. Those membrane proteins that are embedded in the lipid bilayer have extensive hydrophobic amino acids that interact with the non-polar environment of the bilayer interior. Membrane proteins are not soluble in aqueous solution. Rhodopsin is an example of a membrane protein. Note that rhodopsin is an integral membrane protein and is embedded in the bilayer. The lipid membrane is not shown in the structure presented here.
Classification by solubility:
Albumins are proteins that are soluble in water and in water half-saturated with ammonium sulfate. On the other hand, globulins are salted out (i.e., precipitated) by half-saturation with ammonium sulfate. Globulins that are soluble in salt-free water are called pseudoglobulins; those insoluble in salt-free water are euglobulins.
A large group of proteins has been called conjugated proteins, because they are complex molecules of protein consisting of protein and nonprotein moieties. The nonprotein portion is called the prosthetic group. Conjugated proteins can be subdivided into mucoproteins, which, in addition to protein, contain carbohydrate; lipoproteins, which contain lipids; phosphoproteins, which are rich in phosphate; chromoproteins, which contain pigments such as iron-porphyrins, carotenoids, bile pigments, and melanin; and finally, nucleoproteins, which contain nucleic acid.
The weakness of the above classification lies in the fact that many, if not all, globulins contain small amounts of carbohydrate; thus there is no sharp borderline between globulins and mucoproteins.
Structural proteins
SCLEROPROTEINS:
-> COLLAGEN:
Collagen is the structural protein of bones, tendons, ligaments, and skin. Collagen differs from all other proteins in its high content of proline and hydroxyproline. Hydroxyproline does not occur in significant amounts in any other protein except elastin.
Native collagen resists the action of trypsin but is hydrolyzed by the bacterial enzyme collagenase. When collagen is boiled with water, the triple helix is destroyed, and the subunits are partially hydrolyzed; the product is gelatin.
When collagen is treated with tannic acid or with chromium salts, cross links form between the collagen fibres, and it becomes insoluble; the conversion of hide into leather is based on this tanning process.
Collagen seems to undergo an aging process in living organisms that may be caused by the formation of cross links between collagen fibres. The protein elastin, which occurs in the elastic fibres of connective tissue, contains similar cross links and may result from the combination of collagen fibres with other proteins. When cross-linked collagen or elastin is degraded, products of the cross-linked lysine fragments, called desmosins and isodesmosins, are formed.
-> KERATIN:
Keratin, the structural protein of epithelial cells in the outermost layers of the skin, has been isolated from hair, nails, hoofs, and feathers.
Others:
The most thoroughly investigated scleroprotein has been fibroin, the insoluble material of silk. The raw silk comprising the cocoon of the silkworm consists of two proteins. One, sericin, is soluble in hot water; the other, fibroin, is not. The amino acid composition of the latter differs from that of all other proteins. It contains large amounts of glycine, alanine, tyrosine, and serine; small amounts of the other amino acids; and no sulfur-containing ones.
MUSCLE PROTEINS:
Myosin and actin.
Fibronogen and fibrin:
Fibrinogen, the protein of the blood plasma, is converted into the insoluble protein fibrin during the clotting process. The fibrinogen-free fluid obtained after removal of the clot, called blood serum, is blood plasma minus fibrinogen.The clotting process is initiated by the enzyme thrombin, which catalyzes the breakage of a few peptide bonds of fibrinogen.
Albumins, globulins, and other soluble proteins:
Human blood serum contains about 7 percent protein, two-thirds of which is in the albumin fraction; the other third is in the globulin fraction.
MILK PROTEINS:
Milk contains the following: an albumin, α-lactalbumin; a globulin, beta-lactoglobulin; and a phosphoprotein, casein.
Denaturation
The loss of biochemical activity through structural change is called denaturation. For example when enzymes are destroyed by high temperature because the increased kinetic energy causes the protein structure to break down. Loss of tertiary structure means that the enzyme no longer has the specific shape required for its correct function.
This is why cooking eggs become hard and meat becomes firm.
Hydrolysis of proteins
Chemical composition of DNA
The primary structure of DNA
The secondary structure of DNA
Ribonucleic acids
The genetic code
Protein biosynthesis I: Transcription
Protein biosynthesis II: Translation
Enzyme composition
Enzyme classification and nomenclature
Mechanism of enzyme activity
Substrate specifity and the enzyme-substrate complex
Factors affecting enzyme catalysis
Enzyme inhibition
Coenzymes and vitaminsclassification, relationship
Hormones - classification, target effects
Thermodynamic principles
The role of ATP
The roles of eating and breathing
Chiral centre = an asymmetric carbon atom (joined to four different atoms or groups). A compound containing one chiral centre can exist in two forms that are non-superimposable mirror images of each other. These two isomeric forms are called optical isomers or enantiomers.
-> When chiral molecules of different substances react together, the situation can be likened to a hand trying to fit into a pair of gloves. The right hand fits snugly into a right glove, but not so comfortably into a left glove.
-> The odours of spearmint and caraway seed are caused by the two enantiomers of carvone. Althought infrared and ultraviolet spectrometers cannot distinguish the difference, our noses can!
-> One enantiomer of the amino acid asparagine tastes bitter, whereas the other tastes sweet.
-> Only one of the enantiomers of LSD causes hallucinations.
-> One enantiomer of morphine relieves pain strongly and is not greatly addictive, whereas the other is strongly addictive and not nearly so effective at relieving pain.
Common elements:
Aluminum (Al)
Barium (Ba)
Bromine (Br)
Calcium (Ca)
Carbon (C)
Chlorine (Cl)
Chromium (Cr)
Cobalt (Co)
Copper (Cu) (from cuprum)
Fluorine (F)
Gold (Au) (from aurum)
Helium (He)
Hydrogen (H)
Iodine (I)
Iron (Fe) (from ferrum)
Lead (Pb) (from plumbum)
Magnesium (Mg)
Manganese (Mn)
Mercury (Hg) (from hydrargyrum)
Neon (Ne)
Nickel (Ni)
Nitrogen (N)
Oxygen (O)
Phosphorus (P)
Potassium (K) (from kalium)
Silicon (Si)
Silver (Ag) (from argentum)
Sodium (Na) (from natrium)
Sulfur (S)
Tin (Sn) (from stannum)
Zinc (Zn)
Formulas:
Molecular mass(molecular weight) = the sum of the atomic masses of all the atoms in a molecule of the substance.
Formula mass(formula weight) = the sum of the atomic masses of all atoms in a formula unit of the compound.
Mole (mol) = the quantity of a given substance that contains as many molecules or formula units as the number of atoms in exactly 12g of carbon-12.
Avogadro´s number = the number of atoms in a 12g sample of carbon-12. This number is 6.02 x 10^23. Example: 1 mol of ethanol = 6.02 x 10^23 ethanol molecules.
Molar mass = the mass of one mole of the substance. Carbon-12 has a molar mass of exactly 12 g/mol.
Calculate the formula mass of chloroform (CHCl_3):
1 x atomic mass(AM) of C = 12.0 amu
1 x AM of H = 1.0 amu
3 x AM of Cl = 3 x 35.45 amu
Formula mass(FM) of CHCl_3 = 119.4 amu
Calculate the mass of an atom or molecule:
Mass of an CI atom = 35.5g / 6.02 x 10^23 = 5.90 x 10^-23 g
Mass of an HCl molecule = 35.5g + 1 = 36.5 / 6.02 x 10^23 = 6.06 x 10^-23 g
The unit you are converting FROM is on the bottom of the conversion factor; the unit you are converting TO is on the top.
Converting moles of substance to grams:
Example 1: The molar mass of Zinc iodide (ZnI_2) is 319 g/mol. 0,0654 mol ZnI_2. How many grams is this?
0.0654 mol x 319 g / 1 mol = 20.9 g ZnI_2
Example 2: H_2O_2 contains 0.909 mol in 1.00 L of solution. What is the mass of hydrogen peroxide (H_2O_2) in this volume of solution?
H = 2.01588 + O = 31.9988 = 34.01468 g
0.909 x 34.01468 g / 1 mol = 30.9 g H_2O_2
Converting grams of substance to moles:
How many moles is it in 45.6 g of lead(II) chromate (PbCrO_4)?
Molar mass of lead(II) chromate:
Pb(=207.2) + Cr(51,9961) + O(=15.9994 x 4 = 63.9976) = 323 g
45.6 g x 1 mol / 323 g = 0.141 mol PbCrO_4
Calculate the number of molecules in a given mass:
How many molecules are there in a 3.46 g sample of hydrogen chloride (HCl) ?
3.46 g g x 1 mol / 36.5 g x 6.02 x 10^23 / 1 mol = 5.71 x 10^22 HCl molecules.
Mass percentage of A as the parts of A per hundred parts of the total, by mass:
Mass % A = mass of a in the whole / mass of the whole x 100%
Calculating the percentage composition from the formula:
Calculate the mass percentages of the elements in formaldehyde (CH_2O).
CH_2O has a mass of 30.0 g and contains 1 mol C(12.0g), 2 mol H (2x1.01 g), and 1 mol O (16.0 g). You divide each mass of element by the molar mass, then multiply by 100, to obtain the mass percentage:
% C = 12.0 g / 30.0 g x 100% = 40.0%
% H = 2 x 1.01 g / 30.0 g x 100% = 6.73%
You can calculate the percentage of O in the same way, but it can also be found by subtracting the percentages of C and H from 100%:
% O = 100% - (40% + 6.73%) = 53.3%
Calculating the mass of an element in a given mass of compound:
How many grams of carbon are there in 83.5 g of formaldehyde (CH_2O) ?
CH2O is 40.0% C, so the mass of carbon in 83.5 g CH_2O is:
83.5 g x 0.400 = 33.4 g
Calculating the percentages of C and H by combustion:
Acetic acid contains only C, H and O. A 4.24 mg sample of it is completely burned. It gives 6.21 mg of carbon dioxide and 2.54 mg of water. What is the mass percentage of each element in acetic acid?
Grams of C:
6.21 x 10^-3 g CO_2 x 1 mol CO_2 / 44.0 g CO_2 x 1 mol C / 1 mol CO_2 x 12.0 g C / 1 mol C = 1.69 x 10^-3 g C (or 1.69 mg C)
Grams of H:
2.54 x 10^-3 g H_2O x 1 mol H_2O / 18.0 g H_2O x 2 mol H / 1 mol H_2O x 1.01 g H / 1 mol H = 2.85 x 10^-4 g H (or 0.285 mg H)
Mass percentages of C and H:
Mass % C = 1.69 mg / 4.24 mg x 100% = 39.9%
Mass % H = 0.285 mg / 4.24 mg x 100% = 6.72%
You find the mass percentage of oxygen by subtracting the sum of these percentages from 100%:
Mass % O = 100% - (39.9% + 6.72%) = 53.4%
Determining the empirical formula from masses of elements (binary compound):
A compound of N and O is analyzed, and a sample weighing 1.587 g is found to contain 0.483 g N and 1.104 g O. What is the empirical formula of the compound?
This compound has the formula N_xO_y, where x and y are whole numbers that we need to determine.
You convert the masses to moles:
0.483 g N x 1 mol N / 14.0 g N = 0.0345 mol N
1.104 g O x 1 mol O / 16.00 g O = 0.06900 mol O
In order to obtain the smallest integers, you divide each mole number by the smaller one:
For N, you get 1.00; for O you get 2.00. Hence, the empirical formula is NO_2.
Determining the empirical formula from percentage composition (general):
An analysis of sodium dichromate gives the following mass percentages: 17.5% Na, 39.7% Cr, and 42.8% O. What is the empirical formula of this compound?
Here we need to find x, y and z in Na_xCr_yO_2. The first task is to use the percent composition data to determine the moles of the elements in the compound. Then we use the mole ratios to determine the empierical formula.
17.5 g Na x 1 mol Na / 23.0 g Na = 0.761 mol Na
39.7 g Cr x 1 mol Cr / 52.0 g Cr = 0.763 mol Cr
42.8 g I x 1 mol O / 16.0 g O = 2.68 mol O
Now you divide the mole numbers by the smallest one:
Na: 0.761 mol / 0.761 mol = 1.00
Cr: 0.763 mol / 0.761 mol = 1.00
O: 2.68 mol / 0.761 mol = 3.52
3.52 must be converted into a whole number integers by multiplying each of the numbers by 2: you get Na_2Cr_2O_7.
Determining the molecular formula from percentage composition and molecular mass:
Acetic acid have the composition 39.9% C, 6.7% H, and 53.4% O. The molecular mass was determined to be 60.0 amu. What is its molecular formula?
First, find the empirical formula of the compound. Then you calculate the empirical formula mass.
Converting the masses (%) gives 3.33 mol C, 6.6 mol H, and 3.34 mol O. Dividing the mole numbers by the smallest one gives 1.00 for C, 2.0 for H, 1.00 for O. The empirical formula of acetic acid is CH_2O. The empirical formula mass is 30.0 amu.
Now divide the empirical formula mass into the molecular mass to give the number by which the subscripts in CH_2O must be multiplied.
n = molecular mass / empirical formula mass = 60.0 amu / 30.0 amu = 2.00
The molecular formula of acetic acid is, therefore: (CH_2O)_2 or C_2H_4O_2.
Relating the quantity of reactant to quantity of product:
How many grams of iron be produced from 1.00 kg Fe_2O_3?
g Fe_2O_3 -> mol Fe_2O_3 -> mol Fe -> g Fe
1.00 x 10^3 g Fe_2O_3 x 1 mol Fe_2O_3 / 160 g Fe_2O_3 x 2 mol Fe / 1 mol Fe_2O_3 x 55.8 g Fe / 1 mol Fe
= 698 g Fe
Limiting reactant:
2 slices of bread + 1 slice cheese -> 1 sandwich. What you will find is that the cheese will go out before the bread. Cheese is thus the limiting reactant.
Suppose you put 1 mol H_2 and 1 mol O_2 into a reaction vessel. How many moles of H_2O will be produced?
1 mol H_2 x 2 mol H_2O / 2 mol H_2 = 1 mol H_2O
1 mol O_2 x 2 mol H_2O / 1 mol O_2 = 2 mol H_2O
Thus, hydrogen is the limiting reactant.
Calculating with a limiting reactant (involving moles):
Zn(s) + 2HCl(aq) -> ZnCl_2(aq) + H_2(g)
If 0.30 mol Zn is added to hydrochloric acid containing 0.52 mol HCl, how many moles of H_2 are produced?
0.30 mol Zn x 1 mol H_2 / 1 mol Zn = 0.30 mol H_2
0.52 mol HCl x 1 mol H_2 / 2 mol HCl = 0.26 mol H_2
Zinc is the limiting reactant, so the amount of H_2 produced must be 0.26 mol.
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