Biology I Notes Packet
Biology I Notes Packet
Competency: Inquiry
Lab Equipment, Procedures and Safety Symbols
Use a graduated cylinder to accurately measure liquids in milliliters (ml). You always want to choose the graduated cylinder that holds the smallest amount possible while not being smaller than the amount you are measuring-this allows it to be the most accurate. When measuring, we look at the bottom of the curve in the surface of the liquid (the meniscus). Beakers and Erlenmeyer flasks can be used for storage and mixing, but are not as precise.
Graduated cylinder Meniscus Triple-beam balance Spring scale Erlenmeyer Flask
Use a triple-beam balance to measure mass in grams (g).
Use a meter stick to measure length in meters (m) or centimeters (cm).
Use a thermometer to measure temperature in degrees Celsius (°C).
Use a spring scale to measure force in Newtons (N).
Microscopes allow us to see object that are much smaller than we can see with our eyes. When carrying a microscope, carry it with one hand on the base and the other on the arm of the microscope. To find the total magnification, multiple the magnification of the first lens by the magnification of the second lens.
|Light Microscope |Electron Microscope |
|Can view living things |Specimens must be dead |
|Can see color and movement |Black and white, no movement |
|Not very good magnification |Really good magnification |
|Easy to use, not expensive |Hard to use, really expensive |
Bunsen burners are used to heat up objects in the lab. When using a Bunsen burner, make sure that you keep your hair and cloths tied back so they don’t start on fire. When heating a substance in a test tube, make sure you don’t fill it all the way to the top and you point the top of the test tube away from you so chemicals don’t splatter onto you. Also make sure nothing flammable is around the flame.
The eye wash station is available to clean out your eyes if chemicals get into them. The safety shower is available if you get chemicals on your skin or clothing. Make sure that you wear safely goggles when working with chemicals to protect your eyes.
• If you break glass, there is a special container for broken glass-make sure you sweep it up and don’t touch it with your hands-the edges are sharp and can cut you.
• If a fire breaks out, use the fire extinguisher and PASS (Pull the pin, Aim the nozzle, Squeeze the handles and Sweep the nozzle side to side).
• If you need to dispose of living tissues, use the biohazard container.
• If you ever find something that you can’t identify, spill something, break something, or hurt yourself in any way, let the teacher know!
Safety Symbols:
[pic] Radiation
[pic]Biohazard
[pic]Poisonous/Toxic
[pic]Flammable
[pic]Corrosive
[pic] No food or drink
Hypothesis and Scientific Method
A hypothesis is an educated prediction of what we think will happen. Hypotheses are often written as an If…then…. statement. If..then…statements always make a prediction about what will happen if we change something. The most important thing to remember is that a hypothesis needs to be something I can test. Saying rap music is better than pop music is not a hypothesis because we cannot test that. Saying more people prefer rap music in this room than country music is a hypothesis because we can test that by taking a poll.
The scientific method is a systematic way to figure out the answer to a problem.
1. Make an observation or ask a question
2. Gather information
3. Create a hypothesis: an educated prediction of what is going to happen
4. Design and conduct an experiment
5. Analyze the data
6. Draw a conclusion
If the data supports our hypothesis, then we can keep it and perform another experiment to see if it still holds true. If the data does not support our hypothesis, then we will reject the hypothesis. If many experiments support our hypothesis, then we call it a theory. Theories have support from many different experiments and many trials of each of those experiments. If something in science seems to always be true, we call it a law.
Experiments
Experiments are how scientists determine relationships in the world around them.
Independent Variable: The variable that we change or vary to see what happens. If our hypothesis was an if…then… statement, the IV would be the if.
Dependent variable: The variable we measure to see what change has taken place. This will be the then of our if..then…statement.
Constant: Something that does not change or remains the same. Everything in an experiment other than the independent variable should be constant.
Control is the group you are going to compare everything to. It is the group where you don’t change anything-it is the normal state of the IV.
Replicability: Doing an experiment multiple times to make sure that you get the same results over and over
Common pitfalls of experiment designs:
• Forgetting to have a control. A control is needed in order to tell if a change has taken place. If you don’t have a control, you don’t know if changing the IV has caused a change in the DV (you have nothing to compare the experimental group to!).
• Having more than one IV. If we manipulate more than one thing, it is impossible to know which manipulation caused the differences we see in the DV. This is why you only have one IV and everything else is kept constant.
• Not replicating the experiment. If you only do it once, you cannot tell if that is the result you will always get. Replicability allows you to prove that this will always happen. Part of replicability is having a large sample size when we do experiments-if your sample is small, it is difficult to conclude that something happens all the time.
Graphs
Parts of a graph:
Title-goes across the top. Tells you what the graph is about. Usually is written to explain the variables you are comparing.
Axes labels or legend- gives you information on what they represent and how they are measured.
X-axis: the horizontal one (side-to-side). Always has the independent variable.
Y-axis: the vertical one (up and down). Always has the dependent variable.
Types of graphs:
Bar Graph: Used to compare data between groups.
Line Graph: Used to compare data for an independent variable that is continuous (can get larger and smaller like time or temperature)
Pie Chart: Used to show parts of a whole. The information is given as percentages.
Creating Scales:
When you are deciding what value to make each division along an axes, you need to take the largest value you have for each axes and then divide that value by the number of divisions you have on that axes. You will then round up to the nearest value that makes sense for the graphs (nearest whole number, nearest multiple of 5, 10, 100, ect.)
Comptency-Biochemical Basis of Life
Atoms
Atoms are the building blocks for all matter
Atoms are made of protons (positive), neutrons (neutral or no charge), and electrons (negative)
Protons and neutrons are in the nucleus at the center of an atom, electrons are in shells around the nucleus. The number of protons and electrons are equal so the atom has no charge.
Atomic number: the number of protons in an atom. Tells you what element it is.
Mass number: the number of protons and neutrons in an atom. Tells you its mass.
Ions: Formed when an atom gains or losses an electron and becomes charged (positive if it lost an electron, negative if it gained an electron).
Importance of ions: Almost all reactions and processes in the body involve ions including the sending of message from the brain to the rest of the body and the movement of substances into and out of cells.
Types of Bonds
Molecule: When two or more atoms are bonded together.
Chemical bond: a process where the electrons furthest from the center of the atom are shared or transferred to another atom so that all the atoms have a full outer shell.
Ionic bonds: electrons are transferred between atoms to form ions. The ions are attracted to each other to form the bond. They both fill their own outer shells. They can be identified because of the labeled charges on each of the ions.
Covalent bonds: electrons are shared between atoms and this forms the bond. They both share their outer shells. The can be identified by the overlap or sharing of the electrons.
Hydrogen bonds: Formed between the partial positive charge of hydrogen in a polar compound and the partial negative charge in another atom it is bonded to. Especially important in water.
Chemistry of Water
Water is made of 2 hydrogen atoms and 1 oxygen atom bonding through a polar covalent bond.
This makes it polar (one + end and one – end)( see picture above.
When 2 water molecules stick together they form a Hydrogen bond
Special Properties of Water because of its polar nature:
Universal solvent: because of its polarity, other polar and ionic compounds dissolve in it easily
Adhesion: water “sticking” to another surface
Cohesion: water “sticking” to water
High heat capacity: it takes a lot of heat/energy to change the temperature of water
Surface tension: caused by cohesion of water; makes it have a “surface”, bugs can walk on it
Expands when freezing: unlike most substances which shrink when they freeze, water expands
pH
Acids are compounds that form H+ ions in a solution. Bases are compounds that form OH- ions in a solution
The pH scale measures the concentration of H+ ions in solution
1-6=acidic 7.0= neutral (pure water) 8-14= basic
[pic]
Importance of acids/bases in the body-
You must have a strong acid (pH 1.5) in the stomach to break down food into smaller pieces
The pH of the blood must be 7.4. If you get too much CO2 in the blood, the blood will become too acidic
All organisms are designed to work at a specific pH-when they are put into environments with different pHs, they will no longer be able to function because the enzymes in their body would no longer work!
Neutralization: when an acid and base mix, they will neutralize and create water.
Buffer: a system that prevents change. When acid is added, it will create a base to neutralize it. When base is added, it will create an acid to neutralize it.
Four Major Organic Compounds
Organic compounds: compounds that are built around CARBON that is covalently bonded to other carbon atoms and to other elements (hydrogen, oxygen, nitrogen). Chemistry of LIFE.
A. Carbohydrates:
Structure: Made of C, H, and O
Monosaccharides: simple sugars. Ex) glucose, fructose
Polysaccharides: chains of many sugars. Ex)Glycogen, Starch and Cellulose
Examples: bread, rice, pasta
Function: Provide short-term energy
B. Lipids:
Structure: triglycerides (glycerol backbone and 3 fatty acid chains)
Saturated: no double bonds in the fatty acids
Unsaturated: one or more double bonds in the fatty acid chains
Cholesterol: rings Phospholipids: two fatty acids and a phosphate group
Examples: fats & oils
Function: give lots of energy (long-term energy)
C. Proteins:
Structure=chain of amino acids (carbon, hydrogen, oxygen, nitrogen)
Examples=meat, beans, and nuts
Function=structural (bone & muscle), enzymes
D. Nucleic acids:
Structure: chain of nucleotides (sugar, phosphate group, nitrogenous base)
Examples: DNA & RNA
Function: Store genetic information
Enzymes
Made of proteins. Lowers the activation energy to increase the rate of a reaction.
Enzymes do not change in the course of the reaction-it gets reused over and over.
Activation energy: the energy required to make a reaction go
Substrate: the material that the enzyme acts on
Product: the results of the reaction, what the substrate turns into
Active site: this is the place the reaction occurs on the enzyme
Enzymes are incredibly specific. Their shape determines what types of compounds they react with. An enzyme and its substrate are like a lock and key-only the specific key will work for each lock.
Enzymes work best at specific pH, temperatures, and concentrations.
When it gets too cold, the enzyme does not interact with the substrates fast enough to help the reaction. When it gets too hot for an enzyme, it will denature (fall apart like melting).
If it gets too high or too low in pH, the enzyme will be destroyed.
The concentration of the enzyme and substrate is a balance-not enough of either and there will either be enzyme that is not interacting with a substrate or there will be substrate that will not be reacting.
ATP Structure and Function
ATP (Adenosine Triphosphate): It stores energy needed for cells to undergo life processes. It is made of adenine, ribose sugar, and three phosphates groups. The energy is stored in the bonds between the phosphates-when you break the bonds, you release energy. When you add a bond, you store energy.
ADP (Adenosine Diphosphate): Is like ATP but is only has two phosphates which means less bonds and thus it stores less energy. ADP is what we create when we use ATP by removing a phosphate.
ATP is the energy source for all cellular processes. Whenever you are asked how a cell gets energy, it is using ATP and breaking the bonds to release the energy. This is how it gets energy to build things in the cell and move things into and out of the cell.
Competency-Biological Organization (Cell)
Cellular Organization
Cell-basic unit of life
Tissue-group of cells that work together to perform a certain function (blood, bone, nerves)
Organ-several different types of tissues work together to carry out a function (eye, heart, lungs)
Organ System-many organs working together (digestive system, nervous system)
Organism-the complete living thing (person, plant, animal)
Types of Tissues
Epithelial tissue:
Covers the body surface for protection as skin
Covers the internal organs to keep them in place
Makes up glands which help the body secrete (make) different things (sweat, oils, ect.)
Connective tissue:
Helps make ligaments and tendons which hold bones together and attach muscle to them
Helps store fat which acts as insulation (keeps us warm), energy storage, and cushioning
Provides protection for joints as cartilage (stuff that makes your nose and ears)
Helps build bones and blood
Muscle tissue:
Attaches to bones to provide movement and heat. Also makes up the heart so it can pump blood.
Nervous tissue:
Makes the brain, spinal cord, and nerve cells (called neurons). They receive, process, and regulate sensory information from the environment.
Body Systems
Integumentary System
Organs/tissue: Skin, sweat gland/hair, nails
Purpose: Protect the outside of the body, regulate body temperature
Skeletal System
Organs/tissues: Bones/ligaments, cartilage
Purpose: Framework for the body, move with muscles, produce blood
Muscular System
Organs: Muscles
Purpose: Movement, main source of body heat
Nervous System
Organs/cells: Brain, spinal cord, sense organs (eyes, ears, nose, tongue)/neurons (nerve cells)
Purpose: Take in, process, and react to the environment
Endocrine System
Organs: Thyroid gland, pancreas
Purpose: Produce chemical messengers of the body (hormones)
Digestive System
Organs: Stomach, intestines, liver
Purpose: Take in, process, and absorb nutrients from food
Cardiovascular System
Organs: Heart, veins and arteries
Purpose: Circulate blood around the body
Respiratory System
Organs: lungs
Purpose: Take in oxygen, remove carbon dioxide (gas exchange)
Urinary System
Organs: Kidney, bladder
Purpose: Remove waste from the blood
Immune System/Lymphatic System
Organs/cells: Lymph nodes, spleen/white blood cells
Purpose: Defend the body from infections, remove unwanted bacteria and viruses
Reproductive System
Organs: Male: Penis, testes Female: Vagina, uterus, ovaries
Purpose: Produce gametes (eggs and sperm) and facilitate the creation of new life
Prokaryotic and Eukaryotic Cells
Prokaryotic Cells: bacterial Cells. Prokaryotic cells have no nucleus or membrane enclosed organelles
Prokaryotic cells are usually smaller in size. They have a flagella and a cell wall
[pic]
Eukaryotic Cells: Larger, have membrane enclosed organelles, have a nucleus/nuclear membrane, Found in fungi, protists, plants, and animals. Plant/fungus cells have a cell wall and cell membrane while animal cells only have a cell membrane and no Cell Wall!
Cell Organelles
Nucleus: control center of the cell. Contains the DNA of the cell. Surrounded by a nuclear membrane.
Cell membrane: phospholipid bilayer. It is selectively permeable (some things can get through and some cannot); Water can get through very easily.
Endoplasmic Reticulum: transport proteins to other parts of the cell.
Smooth does not have ribosomes while rough has ribosomes on it.
Golgi Bodies: package up proteins and ship them off so they can go out of the cell
Ribosomes: Assemble proteins by joining amino acids with peptide bonds
Cytoplasm: Cell Jelly: fills the space between the cell membrane and nucleus
Mitochondria: powerhouse; produce energy for the cell in the form of ATP (2 membranes)
Vacuole: Large in plants, small in animals: Stores water and waste
Cytoskeleton: thin protein fibers that give the cell its shape. Only in animals.
Lysosomes: Clean up trash in the cell. Digests the waste-like the cells stomach. Only in animals.
Cell wall: Rigid, protective barrier around the outside of the cell. Made of cellulose. Only in plants.
Chloroplasts: Produce sugars from sunlight (2 membranes), site of photosynthesis. Only in plants.
Plant vs. Animal Cells
| |Plant Cells |Animal Cells |
|Cell Membrane |Yes |Yes |
|Cell Wall |Yes |No |
|Nucleus |Yes |Yes |
|Lysosomes |No |Yes |
|Vacuoles |Large |Small |
|Chloroplast |Yes |No |
Cellular Transport
Concentration: the number of particles you have
Concentration gradient: High end and low end
Equilibrium: when the forward and backwards reactions equal out (no net movement)
[pic]
Passive Transport: does not require energy (ATP), goes with diffusion
Diffusion: Movement of particles from high concentration to low concentration
Facilitated Diffusion: Movement of particles from high concentration to low concentration with the use of transport proteins
Osmosis: Movement of water from high concentration of water to low concentration of water
Hypotonic: More concentrated particles on the inside, water moves in to the party. The cell swells
Hypertonic: More concentrated particles on the outside, water moves out. The cell shrinks
Isotonic: Same concentration of particles on both sides; no change
[pic]
Active Transport: requires (ATP) energy, go against diffusion
The energy powers transport proteins: channel proteins, carrier proteins, gate proteins
Endocytosis: materials move inside the cell (Endo means inside)
Pinocytosis: Cell drinking Phagocytosis: Cell eating
Exocytosis: materials move out of the cell (Exo mean outside)
Photosynthesis
Photo (light) + Synthesis (put things together) = use light to put sugar together
Autotrophs: can produce their own food
Photosynthesis: 6CO2 + 6H2O + light energy ( C6H12O6 + 6O2
Light Dependent Reactions: must have light for the reaction to occur. Takes place in the chloroplast.
Electrons in Chlorophyll (green pigment) absorb light energy. The energy is used to make ATP from ADP and to split water molecules to form oxygen (released into the air) and hydrogen ions (attached to the carrier NADP to make NADPH to be used later).
Light Independent Reactions/ Calvin Cycle: Light is not needed
CO2 from the atmosphere and Hydrogen ions that were stored on the HAPPD are combined to form glucose (C6H12O6) using the energy from the ATP that was made during the light-dependent stage.
If too much sugar is produced, it is stored as polysaccharides (Cellulose & Starch)
[pic]
Aerobic Respiration
General Equation:
C6H12O6 + 602( 6H2O + 6C02
Three Main steps:
Glycolysis- 2 ATP
Krebs cycle- 2 ATP
Electron transport chain (ETC) – 32 ATP
Respiration: The process of breaking down sugars to release energy.
Glycolysis: Tales place in the cytoplasm of the cell. This step always takes place with or without oxygen. The glucose (6-carbon) is split in pyruvate (3-carbon) to make 2 ATP.
Krebs cycle: Takes place in the matrix of the mitochondria (the space in the middle). The pyruvate is turned into CO2 (which we exhale) and in the process we strip away High-Energy electrons which go to NAD and FAD to make NADH and FADH2. This step only creates 2 ATP-its main job it to steal all the electrons for the ETC. This step only takes place when there is oxygen.
ETC: Takes place in the cristae of the mitochondria. The electrons are removed from the NADH and FADH2 and move down a series of complexes. As the electrons move, the complexes use the energy to push H+ ions into the inner membrane space. This creates a gradient (lots on one side, few on the other) and the force of diffusion moves the H+ ions back into the matrix through ATP synthase which uses the movement to turn ADP into ATP. The H+ ion and electron are received by O2 which turns into H2O.
Anaerobic Respiration
Aerobic respiration: Involves oxygen. Creates 36 ATP. Goes through glycolysis, Krebs cycle and ETC. Ends with water and carbon dioxide. Occurs in the cytoplasm and mitochondria.
Anaerobic respiration: No oxygen. Create 2 ATP. Goes through glycolysis and fermentation. Ends with either ethanol and carbon dioxide or lactic acid. All occurs in the cytoplasm.
Two Types of Fermentation:
Lactic acid fermentation: used by bacteria and our body. Turns the pyruvate into lactic acid. Does not produce new energy. Used to make yogurt and cheese (has a sour taste). Is the reason our muscles get tired-our muscle cells make lactic acid when they run out of oxygen and the lactic acid makes our muscles sore. They only way to get rid of it is by using oxygen so we call this oxygen debt (we owe our muscles oxygen).
Ethanol Fermentation: used by yeast. Turns pyruvate into ethanol and carbon dioxide. Does not produce new energy. Used in making beer, wine, bread. The ethanol is the alcohol in beer and wine. The carbon dioxide is what causes bread to rise when we add yeast to it.
Comparing Respiration and Photosynthesis
General Equation for respiration: C6H12O6 + 602( 6H2O + 6C02
Carried out by all cells (plants and animals). A way of releasing energy.
Catabolic-a way of breaking things down.
General Equation for photosynthesis: 6H2O + 6C02( C6H12O6 + 602
Carried out only by plant cells. A way of storing energy.
Anabolic-a way of building things up.
Photosynthesis and respiration are two sides to the same coin. The products of one and the reactants of the other. Each allows the other to continue. The entire process allows for energy from the sun to be captured, stored in glucose, and then used through respiration.
Cell cycle
Somatic Cells: Cell that make up the body, reproduce by mitosis
Gametes: sex cells of egg and sperm, made through meiosis
Haploid Cells: Have ONE set of chromosomes or HALF of the normal set (ex. Gametes)
Diploid Cells: Have TWO sets of chromosomes of a FULL set
The cell cycle is the sequence of growth and development that a cell goes through
1. Interphase: The longer part of the cell cycle where the cell prepares to divide
a. G1 Stage: First growth stage-make new proteins and things needed for DNA replication
b. S Stage: the DNA in the nucleus is replicated
c. G2 Stage: Growth stage where proteins and RNA are made to prepare for division
2. M phase
a. Mitosis: The nucleus divides into two equal halves with the same number of chromosomes
b. Cytokinesis: When the entire cell divides into two halves
Sexual vs. Asexual reproduction
Asexual Reproduction: an individual organism makes a copy of itself (cloning)
Benefits: pass on ALL your genes, fast, can do it by yourself
Down-side: There is no variation, very easy for a disease to wipe everyone out
Types: Binary fission-cell splits in half
Budding-small section of the organism detaches with a full set of genes
Vegetative Propagation- send our runners that grow into new plants, or they grow from cutting
Regeneration- the ability to re-grow lost body parts, can result in growing a whole new body
Spore- small, pollen-like particles that can grow into a new organism on their own
[pic] [pic] [pic]
Sexual Reproduction: two organisms make haploid gametes that fuse together to make a zygote
Benefits: variation in the genes, allows for variety and for a species to evolve and adapt easier
Down-side: each parent only passes on HALF of their genes (and they might not be the best genes), you have to find a mate, mating itself (it takes energy!!)
Types: External fertilization: make lots of eggs, spend little energy on each egg, chances of offspring survival are low
Internal fertilization: make few eggs, spend more energy on eggs, chances of offspring survival are high
Conjugation: a small tube connects two bacteria allowing them to exchange genetic material
Pollination: sperm (pollen) from one plant is transferred to the egg of another (often in a flower)
Mitosis
Process by which a cell divides into two new cells that are exact copies of each other. This is how all cells in your body other than the sex cells allow the body to grow and heal. You will end with TWO diploid cells.
Remember: This takes place AFTER we have made copies of each chromosome so there are TWO copies of each chromosome! We call these matching copies sister chromatids.
Chromatin: the material that makes up chromosomes. Usually not coiled up-like a soup.
Chromosomes-the condensed or coiled up structures made of chromatin
1. Prophase: Chromatin coils up into chromosomes and sister chromatids are held together by a centromere. Nuclear membrane disintegrates and spindle (what moves chromosomes) starts to form. Tighten up!
2. Metaphase: Spindle attaches to the centromere by spindle fibers and moves them to the middle (equator) of the cell. Line up!
3. Anaphase: The sister chromatids are separated and pulled in opposite directions. Separate!
4. Telophase: Chromatids reach opposite ends of the cell, unwind into chromatin, the spindle disappears and new nuclear membranes appear around the two sets of chromosomes. Relax!
[pic]
Meiosis
Homologous chromosomes: The matching pairs of chromosomes—not an exact copy, but the other version of the chromosome that you have—remember, you got one of each chromosome from your mom and one of each from your dad
Meiosis is the process of making sex cells (sperm and eggs). You will make FOUR haploid cells.
1. Prophase I: Sister chromatids pair up with their homologous chromosomes as tetrads
2. Metaphase I: Tetrads are lined up at the equator by the spindle fibers
3. Anaphase I: Each set of homologous chromosomes moves to the opposite side of the cell
4. Telophase I and Cytokinesis: Cell divides into two cells each with a pair of sister chromatids and a new nuclear membrane forms around them
5. Prophase II: New nuclear membranes disappear
6. Metaphase II: Sister chromatids align at equator of cells
7. Anaphase II: Sister chromatids separate at centromere and move to opposite sides of cells
8. Telophase II: Cells divide into haploid cells each with ONE copy of each gene (4 cells total)
Meiosis is important in sexual reproduction because it create gametes that have completely new combinations of DNA. Remember that these gametes will have half the number of chromosomes of the parent because they are haploid!
[pic]
Crossing Over and Linked Genes
When the chromosomes are formed into tetrads, parts of the homologous chromosomes will wrap around each other to hold them together. This can lead to parts breaking off and getting reattached to a different chromosome. We call this process crossing over and it is really important is mixing up genes between the homologous chromosomes and making completely new chromosomes that aren’t like the ones you got from your parents!
Linked genes: When two genes are close on the same chromosome, they are less likely to get split up during crossing over. The closer they are, the less likely they will get split up. (ex. Red hair and freckles).
Heredity
Introduction to genetics
Mendel: Austrian monk who studied peas and other plants to figure out the basics of genetics. Often called the father of genetics.
Gene: a piece of DNA that gives information about a specific trait. (ex. The gene for eye color)
Alleles: different forms of the same gene (Ex. The gene for eye color has a blue and brown allele)
Genotype: the combination of alleles that an organism has for a trait (shown with two letters)
Capitol letters are the dominant trait: the trait that is always expressed
Lowercase letters are the recessive trait: the trait that can be hidden by the dominant trait
If the letters are the same, we say they are homozygote. (ex. AA or aa)
If they are different, they are heterozygous. (ex. Aa)
Phenotype: The physical characteristics of an organism. The expression of the genes.
Law of Dominance: the trait that is dominant will always be expressed in the phenotype if it is present in the genotype. The recessive trait will only be expressed if the dominant trait is not present.
Ex. BB-Brown hair, Bb-Brown hair, bb-red hair
Law of Segregation: There is an equally likely chance that you will pass on either of the genes you have for a trait.
Punnett Square: a tool used to figure out the results of crosses between organisms.
When we do crosses, the organisms we crossed are called the parent generation (P). The first generation of offspring is called F1, the second generation is called F2.
Incomplete Dominance, Codominance, and Multiple Alleles
Incomplete dominance: When neither of two alleles is dominant or recessive to the other. The heterozygous genotype has a blended (mixed) phenotype of the homozygous phenotypes. We show both traits as capitol letters since neither is recessive.
Ex. RR-red flowers, RW has pink flowers, WW has white flowers
Codominance: Similar to incomplete dominance, but the heterozygous genotype has a phenotype that expresses both the homozygous phenotypes in different parts of the organism (instead of mixing them together). They cooperate and share the organism.
Ex. WW-white hairs, RR-red hairs, RW-a mix of red and white hairs (called a roan coat)
Multiple Alleles: Some traits have multiple alleles. Ex. Blood type has A, B and O. A and B are codominant and O is recessive to both.
Sex Linked Genes and Pedigrees
Sex-Linked genes: Genes that are attached to the sex chromosomes (X and Y)-XX is female, XY is male
When doing sex linked problems, each X will receive a letter that represents the gene it carries while Y will not receive a letter. Because the male only gets one X gene, they are much more likely to express recessive alleles for genes on the X chromosome.
Carrier: someone who has just one copy of a recessive gene (they carry the gene but don’t express it).
Pedigree: A family tree of genetic inheritance. Each line represents the next generation. The key will tell you who is male and female and what the colors represent. Very often they will not show you who the heterozygous individuals are and you will need to use the children to figure it out. The trick is to look at parents that are the same color producing a child that is a different color-that different color is the recessive trait. Remember that if a child has a recessive trait, it had to get the recessive gene from both parents.
Dihybrid Crosses
Law of Independent Assortment: Genes on different chromosomes separate independently of each other. For example, the genes for eye color and hair color are on different chromosomes so the eye color alleles do not affect how the hair color alleles sort. Because of this, we have to figure out all possible combinations of genes that could be passed on to do the punnett square.
When figuring out the possible gametes, use the FOIL method or the box method from math to create all four possible combinations. Example: GgTt could create GT, Gt, gT, and gt. After you have the four gametes from each parent, put one parent across the top and the second across the side of a 4X4 punnett square. Fill in the first letter first and THEN fill in the second letter after.
DNA Structure and Replication
DNA (deoxyribose nucleic acid) is the blue-print for the cell. It contains all of the information that builds our bodies and controls the production of all proteins. These pieces of information are called genes.
DNA is made of nucleic acids. DNA is made of two strands that form a double-helix shape with a sugar-phosphate backbone on the outside and nitrogenous bases on the inside. The nitrogenous bases connect the two strands together. Its shape was discovered by Watson and Crick.
There are four nitrogenous bases in DNA: Adenine (A), Thymine (T), Guanine (G) and Cytosine (C). A always pairs with T, G always pairs with C
DNA replication (copying) takes place during the S phase of Interphase.
1. The two strands of DNA unwind and separate (unzip) from each other
2. DNA polymerase attaches itself to the DNA strands, reads what base it is on, and then attaches the matching base from free-floating nucleotides.
3. As DNA polymerase moves down the strand, the newly attached nucleotides bond together to form a new DNA strand that is attached to the old DNA strand. We call this copy the complimentary copy.
4. At the end, we have two copies of the DNA strand. Each has one old strand and one new strand.
RNA Structure and Transcription
RNA (ribonucleic acid) is a single-stranded chain of nucleic acids. It uses similar nitrogenous bases as DNA except it uses Uracil (U) instead of Thymine(T). A pairs with U, G pairs with C.
There are three types of RNA:
• Messenger RNA (mRNA)-send messages from DNA to the rest of the cell
• Transfer RNA (tRNA)-transport amino acids to the site of protein synthesis
• Ribosomal RNA (rRNA)-helps to build the structure of ribosomes
Transcription: (DNA ( RNA) The process of copying DNA strands into messages the cell can use to make proteins (mRNA). Like in DNA replication, the DNA unzips but this time RNA polymerase attaches to the DNA and makes a complimentary copy of the DNA as mRNA. This mRNA can then be sent out into the cell where it is read and turned into a protein during translation.
Translation and Reading Codons
Translation: (RNA( Protein). Occurs at the ribosome in the cytoplasm. mRNA enters the ribosome and the ribosome reads the code of mRNA 3 bases at a time (codon). tRNA brings amino acids to the ribosome where the anti-codon (3 base pairs) of tRNA connects with the codon of mRNA.
The ribosome knows where to start reading the mRNA because it contains a start codon. The new amino acid attaches to the chain of amino acids with peptide bonds and the protein is released from the ribosome and folds up to the proper shape on its own when the mRNA reaches a stop codon!
The Central Dogma
The central dogma is the main idea behind all of genetics: DNA(RNA(Protein
This includes the processes of transcription (writing a text) and translation (deciphering the text means)
The central dogma helps explain why we always say you genes control what you look like. You genes are instructions for the building of proteins and proteins are the building blocks for most of your body: you hair, you skin, you eyes, ect. When you get your genes from your parents, you get instructions to build the same proteins that give them their features and this is why we look like our relatives!
Mutations and Genetic Disorders
Mutagen-a chemical, substance, or energy (like the suns UV rays) that causes a mutation.
Gene mutations-just one gene is changed
Point Mutation (substitution)-one nucleotide is replace with another nucleotide
Frame-shift mutation: the adding or removing of one nucleotide causes all of the codons after the mutation to shift and change what they code for
Insertion-one nucleotides is added
Deletion-one nucleotides is removed
These can be especially important if we add or remove a stop codon in the middle of a gene since adding a stop codon will stop the production of the protein and make it short and removing a stop codon will cause the ribosome to keep reading the mRNA and cause it to become longer!
Chromosome mutations-change in the structure or number of chromosomes (usually more severe)
Deletion-losing a part of the chromosome
Duplication-doubling and insertion of a part of a chromosome
Inversion-broken parts of a chromosome reattach backwards (they flip)
Translocation: parts of the chromosome move to other chromosomes
Non-disjunction: the chromosomes don’t separate during meiosis and you end up with one extra
Sickle-cell Anemia: caused by a point mutation that causes the blood cells to become sickle shaped. Being heterozygous for the trait allows people to be less effected by malaria, but being homozygous leads to the different shapes of blood cells which can lead to many problems.
Hemophilia: caused by a mutation that prevents the blot-clotting factor from forming. This means that when the person start bleeding, they often can’t stop and lose large amounts of blood.
Down’s Syndrome: caused by a non-disjunction that leads to an extra chromosome 21. This leads to both physical and mental problems in development.
Color blindness: caused by a mutation that prevents the certain color receptors in the eye from forming. Very often means they cannot see the difference between the colors red and green.
DNA Technology
DNA fingerprinting- each person’s DNA is different, it can be used to identify a person (match the bands)
• DNA extraction-scientists take DNA out of the cell from a sample (blood, hair, nails, ect.)
• Restriction enzymes- cut the DNA into smaller pieces using a restriction enzyme
• Gel Electrophoresis-DNA is separated in a gel that is filled with holes as the negative DNA is attracted to the positive end of the electric current. Smaller parts move further.
Recombinant DNA- taking DNA from 2 different organisms and joining them together
Transformation- process of placing a piece of DNA into a living organism. They use a Plasmid: a small circular piece of DNA in bacteria—often injected into the new cell using a virus
Transgenic-when organisms contain genes from other organisms {cows with extra copies of growth hormone, corn with their own insecticides}
Cloning-transferring genetic material into a donor egg cell to make an exact copy of the original cell
Karyotype- shows all of the chromosomes as they are stained during metaphase. Scientists can identify abnormalities or extra chromosomes.
Diversity and Biological Change
Taxonomy and Dichotomous Keys
Taxonomy: branch of biology that classifies organisms into groups called taxa
Linnaean Classification:
Domain Didn’t Don’t
Kingdom King Kids
Phylum/division Phillip Pay
Class Come Cash
Order Over Only
Family For For
Genus Good Gucci
Species Shoes Swag
Each level groups organisms together based on a set of criteria. Each level is more restrictive (harder to get into, more specific) than the last. If two organisms are in one level, they also share all of the levels above but may not share all of the levels below. The levels allow us to be more and more precise as we go down.
Binomial nomenclature: A system of using TWO names to identify every organism. Each organism is identified by its genus (capitalized) and species (not capitalized) both of which are italicized. Sometimes, a third name (called the subspecies or variety) is used when a species has many distinct groups within it.
These relationships are determined by morphological (what something looks like) similarities as well as genetic similarities (same DNA sequence).
Dichotomous Key: A chart consisting of a series of two choice questions that allow you to identify an object/organism. To use it, you pick the answer choice that is correct and follow the directions for that choice to the next number until you end with your answer.
Viruses
Viruses—NOT considered living organisms because they cannot reproduce on their own, don’t grow, and don’t carry out respiration. Essentially they are nucleic acid (DNA or RNA) surrounded by a protein coat (called a capsid). Some also have an envelope around them which is like a cell membrane.
They attach to receptors on the outside of cells in order to infect them. Only cells with the right receptors can get infected by each virus (think of the proteins on the outside of the virus as keys and the receptors on the cell as locks-the key has to fit the lock). Once the virus attaches, we call the cell it infects the host. The virus will then make copes by going through the lytic cycle: The virus injected its DNA or RNA into the host cell and uses that cells enzymes and organelles to create many copies of itself. Those copies eventually burst out of the cell to go infect new cells and kill the host cell. Notice that the virus can make copies of itself, it just can’t do it on its own-it needs to use the cells it infects. Viruses that affect bacteria are called bacteriophages.
Examples: herpes, HIV, Influenza (flu), rabies, polio, mumps, measles, yellow fever
Kingdom “Monera”
Monera is a kingdom that no longer exists. The entire kingdom in unicellular, microscopic, and prokaryotic. We now have split it into two main groups of bacteria: archaea and eubacteria. They differ in what their cell walls are made of and the enzymes they use.
Archaea: Live all over the globe including in harsh environments: hot sulfur springs, deep-sea vents, Great salt lake. We call the ones in extreme environments extremophiles. All of them are autotrophs (make their own food). They reproduce by binary fission or budding.
Eubacteria: Live all over the globe. Can be heterotrophs (eat others for food ) such as Saprotrophs (feed on dead matter) and parasites (feed on living organisms) OR autotrophs either through photosynthesis or chemosynthesis (get energy from inorganic compounds to make own food). Most famous is cyanobacteria which is a photoautotroph which is very prevalent (common) in the ocean. Reproduce by binary fission or budding. They can also exchange DNA through conjugation-a process where they create a thin tube between the bacteria and swap pieces of DNA.
Pros: Nitrogen-fixing bacteria (plants need nitrogen to grow and bacteria can get it for them), help make foods (cheese, yogurt), help to decompose matter, help to make antibiotics, help in our food digestion, protect our bodies (skin, mouth, other openings).
Cons: They can get you sick. The very nasty ones create endospores which are very tough protective coverings that are REALLY hard to destroy which makes it really hard to get rid of them.
You can fight bacteria with antibiotics (which means against life). Antibiotics only work on living things so they will NOT work on viruses. To fight viruses, you can use an antiviral drug.
Kingdom “Protista”
Kingdom Protista: a diverse collection of what is now many different kingdoms. They are a collection of heterotrophs and autotrophs, single-celled and multi-celled, microscopic or large—the only similarity is they are all eukaryotic. The animal-like ones are called protozoans.
Amoeba-use pseudopods (fake foot) for movement and to capture and eat its prey (endocytosis)
Paramecium- oral groove (an indent where it takes is food), cilia (little hairs on its body used for movement), contractile vacuole (controls the amount of water, counter osmosis)
Euglena- Photoautotroph, flagellum (whip-like structure used for movement), red spot (can sense light)
Algae-Single of multi-celled; no roots, stems or leaves; can be red, green or brown
Diatoms- have an outer shell made of silicon (like glass!)
Slime molds- a decomposer that can move!!
Amoeba Euglena Paramecium
Kingdom Fungi
Mostly multi-cellular (but some single-celled), like moist environments
No chlorophyll—no photosynthesis--- Cell wall made of Chitin (not cellulose)---NOT PLANTS
Heterotrophs: Mostly saprotrophs-important as decomposers. Some parasites (ringworm, athlete’s foot). Includes: Mushrooms, Mold, Yeasts (see pictures)
Digest food through extracellular digestion (outside of the cell). Decompose using thread-like structures called hyphae-they release enzymes to digest the food and also absorb it.
Lichens (algae and fungus)-important in breaking down rocks into soil. A symbiotic relationship where the algae makes food using the sun and the fungus breaks down rocks to get nutrients for the algae.
Reproduction:
A. Sexual: haploid spores (mushroom)-the gametes meet after being dispersed
diploid spores (molds)-the gametes meet before being dispersed
B. Asexual: budding, fission, spores
Kingdom Plantae
Plants: Multi-cellular (so NOT algae), eukaryotic, photoautotrophic, cell walls made of cellulose, chloroplasts with chlorophyll. Divided into twelve division
Have an alternation of generations between gametophyte (haploid) stage that makes gametes that fuse to form the sporophyte (diploid) that makes haploid spores that create the next gametophyte generation. Usually the haploid stage is small (like a flower) and the sporophyte is the larger part
Major Groupings:
Vascular (have tube-like cells to carry materials throughout the plant) vs. Non-vascular
Vascular is divided into: Seedless (reproduce with spores) vs. seed-bearing
Seed-bearing is divided into: Gymnosperms (seeds in cones) vs. Angiosperms (flowering plants, seeds in fruit)
A. Non-vascular plants: No roots, stems, leaves, or vascular tissue
Division Bryophyta: Mosses
Also includes Liverworts and Hornworts. Water moves through the plant by osmosis and minerals by diffusion-the process is slow and prevents them from getting big. Need to live by moisture to reproduce
B. Vascular plants: Have Xylem (move water and minerals from the roots to the rest of the plant) and Phloem (moves food from the leaves to the rest of the plant). The xylem is located towards the center of the root and stems while the phloem is located closer to the outside. The xylem and phloem are what allow a plant to become tall-if you don’t have vascular tissue to carry water and nutrients around, you can’t be a tall plant!
Have true roots, stems and leaves. Leaves are protected by a waxy layer called the cuticle. The cuticle helps protect the plant from water loss. These leaves have holes in them called stoma (pl. stomata) which help the plant take in carbon dioxide and let out oxygen (think of this as how the plant breaths!).
1. Seed-less: reproduce by spores
Division Pterophyta: Ferns. Have thick underground roots (rhizomes) and large leaves (fronds). The baby leaf is called a fiddle-head.
Also includes whisk ferns, club mosses and horsetails.
2. Seed-bearing:
Gymnosperms: seeds in cones or “naked”
Division Cycadophyta: Cycads
Division Ginkophyta: ginko tree
Division Gnetophyta: variety of strange plants
Division Coniferophyta: Conifers, needle-like leaves, cones for their seeds
Angiosperms-flowering plants. Flowers are the reproductive organs of the plant. The sperm (pollen) is transferred to the egg (in another flower or the same) by a process called pollination.
Division Anthophyta: produce flowers, produce fruits around their seeds
Class monocotyledones: 1 seed leaf, parallel veins
Class dicotyledones: 2 seed leaves, netted veins
Invertebrate Animals
Animals: Multicellular, no cell wall or chlorophyll, eukaryotic, heterotrophs
Body Symmetries:
Asymmetrical: bodies do not have any certain shape
Radial symmetry: bodies are arranged around a central point (can cut it any way and the two halves are mirror-images of each other)
Bilateral symmetry: can divide the animal lengthwise into two equal halves
Phylum Porifera: Sponges. Attached to a surface, many holes in their bodies called pores, skim food and oxygen from the water as it moves through their bodies. Asymmetrical.
Phylum Cnidaria: Jellyfish, sea anemone, coral. Radial symmetry. Carnivores-eat zooplankton (little baby animals in the water). Mouths at the center of their bodies surrounded by tentacles that have special stinging cells called cnidocytes. If you touch the stinging cell, a tiny stinger called a nematocyst shoots out and paralysis the victim.
Phylum Platyhelminthes: Flatworms (planarians, tapeworms). Bilateral symmetry. Free living or parasitic. Simple nervous system (can respond to stimuli using eye spots). Regeneration: re-grow damaged body parts.
Phylum Nematoda: Roundworms (heartworm, hookworm). Free living or parasitic (mostly parasitic). Complete digestive system. Bilateral symmetry.
Phylum Annelida: Segmented worms (earthworm, leach). Bilateral symmetry. Body divided into ring-like segments. Blood contained in blood vessels, good nervous system. Can be filter-feeders or carnivores.
Phylum Echinodermata: Sea stars, sea urchins, sand dollars, sea cucumbers. Spiny-skinned. Radial symmetry. Move by using tube feet. Have a water vascular system they use to power movement, respiration (breathing) and circulation (moving things through the body).
Phylum Mollusca: soft body and muscular foot. Gastropods: snails and slugs. May or may not have a shell. Use their file-like tongue (radula) to scrape food. Move on slime trail they produce. Bivalves: clams and oysters. Two shells, use their foot to help them dig into the ground. Filter feeders. Cephalopods: Squids and octopus. Well developed brain, squid have an internal shell (pen), many can change color to blend in or communicate with each other and squirt ink to run away from predators.
Phylum Arthropoda: segmented bodies, exoskeleton made of chitin, jointed appendages. Must molt(shed their old skeleton) to grow-leaves them vulnerable until the new shell hardens because it starts off soft. Crustaceans: lobster, crabs, crayfish, shrimp, barnacles. Often have ten legs. Have two sets of antennae and set of chewing mouthparts called mandibles. Arachnids: Eight legs. Spiders can’t chew food so they liquefy it and then drink it. Scorpions have a venomous stinger and their claws are modified mouth parts. Millipedes and centipedes: Lots of legs. Centipedes are carnivores and have one set of legs per body segment. Millipedes are herbivores and have two sets of legs per body segment. Insects: six legs. Three body segments (head, thorax, abdomen). Go through metamorphosis to grow.
Phylum Chordata: At some point in their lives, they have 1) a spinal cord 2) a notochord (usually turns into a backbone) 3) Gills 4) a tail
The non-vertebrate chordates are called tunicates and sea squirts
Vertebrate chordates are defined by having a backbone that contains the spinal cord. All have bilateral symmetry.
Vertebrate Animals
Body temperatures: Ectotherms-body temperature is determines by the temperature of the environment
Endotherm-body temperature is constant no matter the temperature of the environment
Fish: Ectotherms, get their oxygen from the water through gills. Three classes:
1. Class Agnatha: jawless fish. Have skeletons made of cartilage. Are parasites. Hagfish and lampreys.
2. Class Chondrichthyes: Cartilaginous fish-have jaws! Both predators and filter feeders. Have stream-lined bodies covered in tooth-like scales. Can sense the movement of water (and thus other fish around them) through a special sense organ called the lateral line. Float because of the large amounts of oil in their livers. Sharks, skates and rays.
3. Class Osteichthyes: Bony fish (have skeletons made of calcified bone). Float using a swim bladder (like a pocket of air in their bodies). Also have lateral lines. Mostly external fertilizers.
Class Amphibia: Ectotherms, carnivores, their name means double-life because they spend part of their lives in the water (called tadpoles, breath using gills) and part on land (breath using lungs). They need to return to the water to lay their eggs because their eggs don’t have protective coverings and their babies need water in order to breath. Frogs and toads (can live in wet or dry locations), salamanders (need to stay moist) and caecilians (live underground in the rainforest).
Class Reptilia: Ectotherms, carnivores and herbivores, have dry, scaly skin which prevents water loss which helps them live in dry environments. Their skin doesn’t grow with them, so they must shed it periodically. Their eggs have tough, leathery shells that keep in water so they can lay them on land. They can live in wet or dry environments and can handle hot, but they cannot handle cold (because they are Ectotherms). Crocodiles, alligators, squamates (snakes and lizards), turtles.
Class Aves (birds): Endotherms. Have hollow bones for flight, feathers which are used for insulation (warmth) and for flight, digest food really fast so they don’t have to fly with food in their stomachs.
Class Mammalia: Endotherms, have hair or fur, have a four-chambered heart, make milk for their young from the mammary gland. Monotremes (the egg-laying mammals like platypus and echidna), marsupials (give birth to their young very early and the baby crawls into the mothers pouch to finish growing—kangaroo, koala, wombat, opossum), and placentals (have a placenta which is a structure in the womb where air, nutrients, and wastes are exchanged—humans and most of the other mammals including whales and dolphins).
Spontaneous Generation
Spontaneous generation-the theory that life could appear at random from non-living things.
REDI- A scientists who tried to disprove spontaneous generation by showing that when you let meat rot open to the air, maggots will appear on them but if you put cloth over the jar the meat is in, the maggots will NOT appear on the meat and if you put a lid on the jar, no maggots will appear!
Needham- A scientists who tried to prove spontaneous generation was true by boiling broths (to kill all life in the broth) and letting them cool and the covering them to see if life appeared. While he did show that life would appear in the broth (which he took to mean that life had appeared from nowhere), he was later criticized for not covering the broths while the cooled which allowed them to become contaminated from microorganisms in the air.
Spallanzani- Tried to disprove Needham. He boiled broths for a longer period and capped them right after boiling proving that nothing would grow. If he left them open to the air, then bacteria would grow. However, people argued that the air was needed for life so the debate wasn’t over.
Pasteur- A scientist who developed the swan-necked flask (a flask with a long neck to the side that dips down and then up). This flask allowed him to boil the broth while keeping it open to the air, but the bend in the neck allowed him to trap any microorganisms and prevent them from getting to the broth. Nothing grew in the broth until he bent the flask and allowed the broth to touch the bend where all the microorganisms were trapped. His experiments were the final proof that disproved spontaneous generation.
History of Evolution and Famous Evolutionary Scientists
Uniformitarianism: The idea that all of the natural laws of Earth (gravity, positive and negative attracting) existed in the past and that all processes that take place today (erosion, uplift of the earth, volcanic eruptions) took place on the same time scale in the past Put forth by the geologists Hutton and Lyell. Was later used to date the Earth by using radioactive isotopes in rocks.
Lamarck: Theory of Acquired Characteristics-organisms change to meet the needs of their environments and pass on these traits to their offspring. Found to NOT be true because organisms pass on their GENES to their offspring—only traits that are controlled by GENES can be passed on (we call these inherited traits).
Malthus: looked at how human populations were growing and realized that, if they kept growing, they could eventually run out of resources. The lack of resources would mean that people would have to start competing for resources and this idea was later transferred to the animal world to argue that all animals must compete for limited resources in their environments.
Charles Darwin: Sailed around the world on the Beagle from 1832-1836. Traveled to the Galapagos Islands in addition to many other places where to noted the variations of organisms and how these variations were tailored to the organisms environments. Darwin spent many years doing research until a young scientist names Wallace sent him a paper going over the same theory Darwin had been working on for years. They presented the idea together, but Darwin gets most of the credit because he really explored the theory in his book The Origin of Species . He is called the father of evolution.
Evolution by Natural Selection:
1. All species have genetic variation
2. There are limited resources in all environments and so organisms compete for resources to survive and produce more offspring than can survive (Malthus)
3. Some organisms (often because of their genes) do better at surviving than others
4. Those that do better at surviving will have more offspring and pass on their genes
5. The genes that help organisms survive and compete will become more common in the population and gradually the population will change
Evolution is the gradual change in the inherited characteristics (genes) of a population
As populations evolve, they tend to become more adapted to their environment and increase their fitness (ability to survive). We call this decent with modification. Because of this, those species that are the more fit will out-compete other species and survive (“Survival of the Fittest”)
Common Misconceptions:
INDIVIDUALS CANNOT EVOLVE: only the population can change. An individual cannot change its genes!
THE POPULATIONS DON’T CHOOSE HOW THEY CHANGE-the environment selects what traits will become more or less common and can only select from the traits that exist in the genes of the population (created by mutations).
Evidence for Evolution
Artificial Selection-Humans have taken natural diversity and selectively bred animals and plants for the traits we want. We pick the traits we like and cause the change in gene frequencies (corn, dogs).
Virus and Bacteria Evolution-We can observe the rapid evolution of bacteria and viruses to the drugs we use against them. Because they reproduce so quickly, they can also evolve very quickly and can evolve so that antibiotics or anti-virals no longer work on them. Those that have that mutation will have more offspring and eventually all of them will be resistant to our drugs.
Fossil Record- We can use the fossil record to reconstruct the evolutionary history of organisms that lived in the past and how organisms have changed over time. Fossils are made when an organism is buried and mud, the mud gets compressed (squeezed) into rock, and the bones, shells or other parts of the organisms are replaced by minerals. Fossils shows that 99% of all organisms that ever lived are now dead. We can also use radioactive isotopes to DATE many fossils
Embryology- We can look at embryos of different organisms early in development-if they appear similar, then we have evidence that there share a common ancestor because their similar development means they share genes for that method of development.
Homologous Structures- If organisms share the same number and arrangements of bones or body structures, that provides evidence that they share a common ancestor and are related
Vestigial Organs- Vestigial organs are organs or structures in the body that used to serve a purpose in the ancestor of that species but no longer have one-they provide evidence that organisms have changed over time ex) leg bones in a whale.
Physiological and DNA Similarities- Closely related organisms share the same enzymes, metabolic pathways, and proteins (amino acid sequences). Scientists use DNA most commonly today to figure out relationships-the higher the amount that they share in common, the shorter a period they have been different species
Changes in populations and species
Species-a group of organisms that can interbreed and produce fertile (can reproduce) offspring
Population-a group of a species that live together, compete for resources, and interbreed
Speciation-the creation of two or more species from a common ancestor. For speciation to happen, a population must become isolated in some way that prevents it from breeding with other populations.
1. Geographic isolation-a physical barrier separates a population into different groups (river, mountain)
2. Temporal isolation-two populations breed at different times (day and night, seasons)
3. Behavioral isolation- the different behaviors of the two populations prevent them from breeding
4. Reproductive isolation-two species mate but their offspring is not fertile (gametes don’t match)
Once to populations are separated, their allele frequencies must change if they are to become two separate species. When we look at populations, we can look at the differences between them by examining the gene pool-combined genetic information (allele frequencies) of all members of a population
How can the allele frequencies change over time?
1. Genetic Drift- the random change in gene frequencies over time (volcano explodes and randomly kills some of the population, a gene randomly gets passed on more frequently)
Founders Effect-the gene frequency of the group that starts a new population can be different from the population they came from by random chance
2. Gene Flow- organisms leave the population and new organisms come into the population
3. Natural selection-the environment determines which traits make an individual most fit
4. Sexual selection-the opposite sex determines which traits make an organism the best mate.
When we have small populations, it is much easier for changes in the gene pool to take place because there are fewer individuals and thus it takes less time for a new gene to become a large part of the gene pool. However, these small populations are also more likely to have problems adapting to changes in the environment because they do not have a large amount of genetic variation for natural selection to work on. Natural selection can only choose from the variation available in the population. This is one reason it is so hard to save species when their population number get small-they will not have the genetic variation needed to adapt to changes in the future.
Results of Evolution (adaptations)
Adaptation-a physical or behavioral trait that helps an organism survive
Stabilizing selection: favors the average individuals
Directional selection: favors individuals with an extreme of a trait (biggest, smallest)
Disruptive selection: favors individual with either extreme of a trait (biggest and smallest)
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Hibernation-the ability to slow down the metabolic pathways of the body and sleep through periods of low food (low heart rate, low breathing rate).
Living in groups: easier to spot predators, protection in numbers, easier to find food
More competition for resources and mates, easy for a disease to spread
Plant seeds: adapted for dispersal by wind, by attaching to animals, or by being in fruit so animals will transport the seeds and drop them off in fertilizer
Night adaptations: many animals are nocturnal (come out at night). This allows them to avoid being seen by animals that want to eat them. They often have big eyes so they can see better in the dark.
History of Life
Scientists believe that the Earth is 4.6 billion years old. For the first 400 million years, the Earth was really hot and mostly magma, but eventually it cooled down which allowed all the water vapor in the air to condense and come down as rain. This HUGE rain storm formed the oceans around 4.2 billion years ago.
The first evidence for life places it beginning around 3.8 billion years ago. There is still a lot of debate on how life began: some scientists think that simple molecules collected in mud and formed very basic molecules that could make copies of themselves. Other believe that lightening stuck the ocean which had many chemicals in it and that formed the first organic compounds. Still others think that life was brought to earth from another planet by meteors. Early life was really simple and lived in a world that did not have oxygen in the atmosphere (there were chemosynthetic).
Around 3.0 billion years ago, we saw the first photosynthetic organisms and the first creation of oxygen. However, there was a lot of iron in the ocean and all that oxygen bonded to the iron and fell to the ocean floor (creating all the iron reserves that we now mine today!). It wasn’t until 2.4 billion years ago that we finally got rid of the iron and started to have oxygen in the atmosphere! Only after we had this oxygen in the atmosphere did aerobic organisms evolve (because the needed the oxygen around in order to be aerobic!).
Endosymbiosis- When we looked at the DNA in mitochondria and chloroplasts, we found that they actually were really closely related to BACTERIA. Endosymbiosis is the idea that an early Eukaryotic cell engulfed a prokaryotic purple bacteria that stayed in the cell, produced energy, and became the mitochondria. Later, one of these cells engulfed a cyanobacteria and stayed in the cell, continued to go through photosynthesis, and become the chloroplast. This is what led to the evolution of Eukaryotes!
Multicellular life like jellyfish began around 580 million years ago and life continued to get more complex from there. Plants were the first organisms to move onto the land and were followed by insects and reptiles. Dinosaurs evolved around 230 million years ago and dominated the land until 65 million years ago when an asteroid hit the earth and killed them all. After this, mammals really took over and culminated in humans which split from our common ancestor with chimps around 2 million years ago and evolved into modern humans around 200,000 years ago.
Phylogenetic Trees (Cladograms)
Scientists use morphological (physical) traits and genetic traits to reconstruct family trees of related organisms into diagrams we call Phylogenetic trees or Cladograms. These trees not only help us to examine how closely related different organisms are to each other, but also the order in which they split into different species.
Any point where two lines meet represents the common ancestor of those two species and the closer to the top you get, the more recent that common ancestor existed. When looking to see which organisms are the most closely related, you look for which set has two lines meeting the closest to the top!
Very often, we can use traits to help us figure out the order in which species separated. We usually assume that traits are gained or lost only once in the history of a group of closely related organisms, so we try to keep all the organisms that have or don’t have a trait as close to each other as possible when making our tree.
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Living Organisms and Their Environment
Living Things (biotic vs. abiotic)
Abiotic: Things that are not alive (rock, dirt, air, cloud, sun, oxygen, nitrogen, carbon)
Biotic: Things that are alive (plants, animals, bacteria, protists, fungi) Made of cells, can reproduce on their own, grow and develop, have DNA or RNA, obtain and use energy, maintain a fairly stable internal environment (homeostasis), respond to changes in their environment
Energy Flow and Food Webs
Autotrophs (producers): produce their own food by photosynthesis or chemosynthesis
Heterotrophs (consumers): must consume (eat) other organisms for energy
Primary consumers: consume autotrophs (producers).
Are herbivores (eat plants)
Secondary consumer: consume heterotrophs (consumers).
Are carnivores (eat meat) or omnivores (eat both).
Decomposers: break down dead organisms into detritus
Food chain/food web: shows the flow of energy from:
autotrophs(herbivores( carnivores
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Ecosystem Interdependence- even a small change in the natural relationships can have a big impact on an ecosystem. When you look at a food web, the change in one group will affect all of the groups connected to it the most, but there will be an impact on every level in some way.
Energy and Biomass Pyramids
Energy pyramid: shows energy in each trophic level. Only 10% of the energy is transferred to the next trophic level (so you start with 100% in producers, then 10% in herbivores, then 1% in carnivores. This helps explain why there are less carnivores than herbivores).
Biomass: the amount of dry organic material an organism has
Biomass pyramid: shows the amount of organic (living) material in a given trophic level.
Every step in the food web, energy pyramid or biomass pyramid represents a trophic level.
Trophic levels show many times energy has been transferred (like a trophy!)
Producers usually have the greatest biomass and the most energy. The higher you go in both pyramids, the less energy and less biomass is present. Ultimately, all organisms rely on the sun for their energy!
Ecological relationships
Symbiotic relationships- “symbiosis=living together”. Both need the other to survive (lichen)
Mutualism: both species benefit from the relationship’
Commensalism: only one species benefits and the other isn’t effected
Parasitism: one organism benefits at the expense of the other (parasite/host)
Predator-Prey: when one organism (predator) hunts and feed on another organism (prey)
Levels of Ecological Organization
Organism-individual living thing
Population-group of organisms of the same species that live at the same place at the same time Community-all the populations of different species living in the same place at the same time
Ecosystem-Community of living things and their environment around them (soil, rocks, water)
Biosphere-all of the ecosystems on Earth (all the places on Earth organisms can live).
Types of Growth
Natural Population Growth: s shaped curve. The rate starts off fast and then growth slows when the environment reaches the carrying capacity (the largest number of organisms of a species that can be supported by the environment). Limiting factors: limit how large a population can grow
Unrestricted population growth-non native species is introduced; few natural predators, large food supply. Just keeps going up and up because there is nothing to limit the growth.
[pic] [pic]
Water, Carbon, Nitrogen and Oxygen Cycle
Biosphere- land, air, & water (biogeochemical cycles)
Nitrogen Cycle:
Nitrogen is used to make amino acids
78% of the Earth’s atmosphere is Nitrogen (not many organisms can use it)
Nitrogen Fixation: bacteria trap N2 and form NH3 (ammonia)
Nitrification: other bacteria change the ammonia into Nitrates (NO3) and Nitrites (NO2)
-Plants can use Nitrates and Nitrites to make proteins, animals eat these proteins and release them back into the Earth as waste (fertilizers).
-When animals die they are broken down by decomposers which put nitrogen back into the soil.
Denitrification: bacteria change the nitrates back into nitrogen gas (N2) and release it into the atmosphere.
N2
NO2 and NO3 NH3 (ammonia)
Water Cycle:
Precipitation-water moves from the atmosphere to the ground (rain, snow, sleet)
Evaporation- water becomes water vapor back in the atmosphere
Transpiration- plants put water back in the atmosphere
Carbon Cycle:
Plants use Carbon Dioxide (CO2) from the atmosphere to form organic molecules (glucose)
Animals eat these organic molecules (glucose) and release C02 back into the atmosphere through respiration. When the animals die, the decomposers release CO2 back in the air and some of the carbon is trapped in the ground where it will become fossil fuels (coal, oil). Burning fossil fuels or organic matter releases more CO2 in the atmosphere.
[pic]
Oxygen Cycle:
Photosynthesis-water molecules are split into hydrogen and oxygen. The oxygen is released into the air.
Cellular Respiration-animals use oxygen in respiration and release CO2.
Most of the Earth’s oxygen is found in the Earth’s crust and is not usable.
Some of the oxygen is found in the ozone which shields the Earth from harmful Ultraviolet rays
Land Biomes
Tundra- cold temperatures, high winds, less than 25 mm of rain yearly (Northern Alaska/Canada, Russia)
Permafrost: thick subsoil that always remains frozen
Small plants that grow quickly/ have a short growing season
Small rodents, musk ox, caribou (have thick fur and large stores of fat to keep warm). No cold blooded reptiles!
Coniferous forest (taiga)-Cool summers, cold winters, plenty of rain (Northern North America)
Plants: Conifers, mosses, flowering shrubs
Animals: bears, deer, elk, beaver, bobcat (thick fur and layers of fat; hibernation)
Deciduous Forest/Temperate Forest- 4 distinct seasons, warm summers, cool winters, year round rainfall, fertile soil (you decided to live in Mississippi, people in Mississippi have a bad temper)
Plants: some conifers, mostly deciduous forests (decide to shed their leaves), wildflowers
Animals: birds, deer, bear, raccoons, turkeys, squirrels, skunks, insects
Grassland- make up the largest part of the United States; moderate rainfall but not enough for trees, hot summers, cold winters, fertile soil (middle United States)
Plants: grasses, no trees
Animals: insects, reptiles, antelope, buffalo, prairie dogs, coyotes, wolves
Chaparral- Southern California, hot dry summers; mild, cool, rainy winters
Plants: Woody shrubs with leathery leaves or needles
Animals: insects, reptiles, coyotes, mountain lion, owls, birds
Desert: Southwest United States, Mexico, North Africa
Hot days, cold nights, less than 25 mm of rain per year
Plants: cacti and succulents (store water). Deep and spread out roots that help them collect water.
Animals: Bobcats, mountain lions, rats, lizards, snakes, owls
Savanna: Special type of Grassland located in Africa. Warm with seasonal rainfall
Plants: grasses, small clusters of trees and shrubs
Animals: elephants, rhinos, zebra, giraffe, lions, leopards
Tropical Rain Forest: has more species of living organisms than all of the other terrestrial biomes combined. All of them are near the equator (Africa, South America, Asia, and Australia)
Year round high temperatures, high rainfall
Broad leaf evergreen trees, ferns, large variety of other plants
All types of animals in a large variety, most biodiverse
Water Biomes
Freshwater biomes:
Rivers/streams (moving water)- may be fast or slow.
Plants: little plant life in fast moving areas, more in slower regions
Animals: have hooks or suckers to keep them anchored, fish (like trout) are streamlined
Lakes and ponds (standing water)- Heat, oxygen, and nutrients circulate
Plants: phytoplankton (algae)
Animals: zooplankton feed on phytoplankton, fish and other organisms that feed on zooplankton
Saltwater biomes:
Intertidal Zone: area between the low tide and high tide; subject to tidal changes
Organisms that can survive temperature changes and that can live in or out of water. Because the tides come in and out, usually they are adapted to holding on to the rocks with sucker or are attached permanently. Starfish, sea urchins, some sea weeds, muscles.
Estuaries: where freshwater rivers/streams merge with the ocean (varying salt concentrations)
Organisms: algae, seaweed, marsh grass, oysters, shrimp, worms, crabs, waterfowl, saltwater fish eggs, immature fish (saltwater fish lay their eggs here-it is very important an a nursery)
Coastal Zone- area from the low-tide mark to the outer continental shelf. There is land here for plants to attach to and organisms to live in allowing for varied places to hide and live.
Plants: kelp, algae
Animals: fish, seals, otters, sea urchins, sting rays
Coral Reefs: made of calcium carbonate formed by cnidarians (coral), warm salt water
Organism: very biodiverse, corals, colorful fishes, sea anemones, starfish (the rainforest of the ocean).
Open Ocean: The great majority of the ocean where only water is present. There is no place to hide, so many organisms are silvery to reflect the sunlight. This is where you will find the largest fish and other organisms (whales, sharks). The only producers present are phytoplankton.
Aphotic zone- “no light” Deep in the ocean where no sunlight reaches
Organisms: chemosynthetic autotrophs (Archea), crabs, tubeworms, angler fish
Succession
Ecological Succession: a series of predictable changes in an ecosystem
Primary Succession-starts on earth’s surface where there is no soil after a major disturbance (volcano eruption, glacier). Pioneer Species: first organisms to live on the surface (usually lichens). Climax Community: final community of organisms (stable stage)
Lichens (pioneer)(mosses(grasses(shrubs & seedlings(trees (climax)
Secondary Succession-occurs when something changes an existing community but does so without removing the soil (large wildfire, plowing). Occurs more quickly because you start with soil.
This can also take place in a small scale when something disturbs the climax community like a tree falling. Then the area that the tree was shading will get more sunlight allowing plants that need more light to start growing and starting the succession cycle at shrubs.
Human Impacts
Technology(rapid human growth means that we compete for food, water and space with other organisms. We use huge chunks of land for farming which take away the homes of animals. We put on tons of fertilizers which mess up the nitrogen cycle and some of the fertilizer runs off into the ocean and creates algae blooms (large growths of algae). When these algae die, they use all the oxygen in the water and create a dead zone where living things cannot survive because there is no oxygen. We also use tons of insecticides and pesticides like DDT to kill pests of our crops. These chemicals gets magnified (increases) as you go up the food pyramid (biomagnifications) and can kill or hurt the upper trophic levels (it almost killed bald eagles!).
Use of natural resources: Renewable (can be used over and over like wind, sunlight, trees, and water) Nonrenewable (can only be used once like gas, oil, coal). We dig up big chunks of land to find these resources, burn them (which increase greenhouse gases) and sometimes spill them (like the gulf oil spill)
Urban development-As cities grow, we use more and more land. This use of land leads to competition with other organisms and humans usually win which means the other species dies off. This has lead to a huge loss in diversity in the world-we are actually in the middle of the 6th major extinction event all caused by humans. We also hunt animals for food, put chemicals on the roads and our lawns that affect them, bring in non-native plants for decoration or animals that we like which can escape and harm the ecosystems around us as invasive species. We also destroy or use plants which help hold the soil in place. When we remove these plants, the soil is easily moves away as well in a process called erosion. This is especially important for plants on the shores of river and streams.
Thinning Ozone from CFC’s- hairspray cans, freezers and air conditioners used to use a chemical called CFC (chloro-floro-carbons). This chemical would get into the atmosphere and destroy the ozone layer that protects us from the suns UV rays. This hole in the ozone got really big and people started getting skin cancer more often. Luckily, the world got together and banned their use and the whole in the ozone is now closing back up!
Global Climate Change (Global Warming)- As we burn more and more fossil fuels, we release more and more greenhouse gasses (CO2 mostly) into the atmosphere. The more CO2 in the atmosphere, the more heat the Earth keeps from the sun and the warmer the earth becomes. As the Earth heats up, a lot of bad things could happen like the ice caps melting, coastal cities flooding, and more severe weather, but predicting what will happen is really hard and getting everyone to stop using fossil fuels is even harder!
EXTRAS!!!
Photosynthesis and Respiration Song
(To the tune of Baby by Justin Bieber)
You take the glucose, swallow it down
C 6 H 12 O 6 is in town
You need some O 2, that’s oxygen
So the respiration party can begin
Now do the flip side--girl just switch it
Take some water, and then you mix it
With some CO2 and see to your surprise
That this photosynthesis thing ain’t no lie
And I was like H-2-H-2-H-2 O
Just C O 2 and H 2 O
Will make some oxygen-that’s O
And all the sugar is mine, mine
H-2-H-2-H-2 O
Just C O 2 and H 2 O
Will make some oxygen-that’s O
And all the sugar is mine, mine
Vascular Tissue Rap
(to the beat of Teach me how to Dougie)
Vascular is transport
Vascular is transport
Xylem & the phloem
Xylem, xylem, & the phloem
Xylem takes up water
From the roots to the leaves
It is stuck in the middle
of the plants including trees
Phloem flows with food
From the leaves to all around
It carries all that that glucose
From the top down to the ground
Marcomolecule Rap
Carbs are made of glucose, energy is so sweet,
Lipids or triglycerides, fatty acid chains in your seat
Proteins are a mean old acid, peptides make you buff
Nucleic acids, nucleotides, keep all your genetic stuff
Macromolecules, macromolecules, macromolecules, macromolecules
Break it down
PMAT
Prophase-Tighten up!
Metaphase-Line up!
Anaphase-Separate!
Telophase-Relax
Do the PMAT, Do the PMAT, Do the PMAT, Do the PMAT
-----------------------
NAME:
Stomata
Cuticle
Denitrification
Nitrogen Fixation
Nitrification Fixation
Photosynthesis
Respiration
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