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AQA

AS Biology

Unit 1:

‘Biology & Disease’

Summary Notes

Biochemistry

Organisation of matter

• Matter: anything that occupies space and has mass.

• All forms of matter are made up of elements.

• The elements hydrogen, carbon and oxygen make up most of the human body.

• Atoms: the smallest unit of matter that are unique to a particular element.

• Molecules: units of two or more atoms bonded together.

• Protons: positive particles.

• Neutrons: neutral particles.

• Electrons: negative particles.

Bonding

Ionic bonding:

• An association between 2 oppositely charged ions.

• Charged particles (ions) have a change in the number of their electrons.

• Negative ions gain electrons.

• Positive ions lose electrons.

Covalent bonding:

• Atoms share electrons.

• Single bond – 1 pair shared, eg H2.

• Double bond – 2 pairs shared, eg O2.

• Triple bond – 3 pairs shared, eg N2.

• Polarity: Some covalent molecules are polar.

o Atoms of different elements do not exert the same pull.

o The net charge is balanced.

o Eg. water.

Hydrogen bonding:

• ‘Van Der Waal’s forces’.

• An atom of a molecule interacts with another hydrogen atom that is already taking part in a covalent bond.

• Due to polarity – the overall charge of each molecule is neutral, but the distribution of electrons is uneven.

• Individually weak.

• Collectively stabilising.

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• Examples:

o Between water molecules.

o Between water and ammonia.

o Between water and glucose.

o Within DNA – base pairing.

Polymers and Monomers

Biological molecules such as carbohydrates and proteins are often polymers and are based on a small number of chemical elements.

|Group Name |Polymers |Polymer example |Monomers |Monomer example |

|Carbohydrates |Polysaccharides |Starch |Monosaccharides |α-glucose |

|Proteins |Polypeptides |Amylase |Amino acids |Leucine |

|Nucleic acids |Polynucleotides |DNA |Nucleotides |Adenosine phosphate |

Carbohydrates

General details:

• Hydrates of carbon.

• Contain carbon, hydrogen and oxygen.

• General formula Cx(H2O)y.

• 3 groups:

o Monosaccharides – single sugars.

o Disaccharides – double sugars.

o Polysaccharides – many sugars (more than 2).

• Uses:

o Structural – cellulose, chitin.

o Energy – glucose.

o Storage – glycogen, starch.

o In nucleic acids – ribose, deoxyribose.

Monosaccharides

• The basic molecular units (monomers) of which carbohydrates are composed.

• General formula CH2On

• Glucose - C6H12O6.

• Hexose sugar.

• Main substrate for respiration.

• Transported in mammalian blood.

• Monomer for starch, glycogen and cellulose.

• The structure of α-glucose:

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• α-glucose link together by glycosidic bonds

• This is a condensation reaction - Involves the loss of a water molecule.

• It joins 2 sugars by an oxygen.

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• Hydrolysis reaction – required to split the glycosidic bond.

• This requires the use of a water molecule to reform the hydroxyl groups on each of the two new sugars where the bond is split.

Disaccharides

• Maltose is formed by condensation of two α-glucose molecules

• Maltose has an α 1,4 glycosidic bond – between carbons 1 and 4.

• Maltose is a reducing sugar.

• Sucrose is formed by condensation of glucose and fructose.

• Sucrose is a non-reducing sugar.

• Lactose is formed by condensation of glucose and galactose.

• Lactose is a reducing sugar.

Polysaccharides

• Polysaccharide = ‘many sugars’.

• Polymers of monosaccharides.

• Formed by condensation reactions.

• Variable numbers of monosaccharides.

• Branched or unbranched chains.

• May be folded.

• Insoluble due to size.

• Exert no osmotic influence.

• Do not diffuse easily.

• Split into disaccharides and monosaccharides by hydrolysis.

Starch

• Found in most parts of a plant in starch grains.

• Food reserve from excess glucose.

• Food supply in seeds for germination.

• Important food supply in animals.

• Made of α glucose.

• Compact for storage.

• 2 constituent structures:

o Amylose:

▪ Approx 20% of starch.

▪ α 1,4 glycosidic bonds.

▪ Spiral structure held together by hydrogen bonds.

o Amylopectin:

▪ Approx 80& of starch.

▪ α 1,4 and α 1,6 bonds.

▪ Branched chains.

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Proteins

• Polymers of amino acids.

• Large molecular mass.

• Wide variety of functions.

• Carbon, hydrogen, oxygen and nitrogen.

• Usually sulphur as well.

• Each species has a particular range of proteins.

• Determined by the genetic code.

• Make up two-thirds of total dry mass of cell

• Make up 18% of human body (second only to water)

• Most complex and diverse group of biological compounds

Range of Functions:

|Function |Examples |

|Structure |Collagen (bone, cartilage, tendon), Keratin (hair) Actin (muscle) |

|Enzymes |Amylase, pepsin, catalase |

|Transport |Haemoglobin (oxygen) |

|Active transport |Sodium – Potassium pumps in cell membranes |

|Muscles |Myosin and actin |

|Hormones |Insulin, glucagon |

|Antibodies |Immunoglobulins |

Amino Acids

• Proteins are made up of amino acid chains.

• The general structure of an amino acid is:

R

I

H2N – C – COOH

I

H

• The central carbon has 4 groups attached to it:

o a hydrogen atom

o a basic amino group

o an acidic carboxyl group

o a variable ‘R’ group (or side chain)

• There are 20 naturally occurring amino acids in living organisms.

• Half of these can be created in the body – non-essential amino acids.

• The other half must be consume in the diet – essential amino acids.

Peptide Bond

• When 2 amino acids join together they form a dipeptide using a peptide bond or link.

• This is a condensation reaction.

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• To break this bond requires a hydrolysis reaction.

• This requires the use of a water molecule to reform the amino and caboxyl groups on each of the two new amino acids where the bond is split.

Polypeptides

• Many amino acids make up a polypeptide chain.

• Amino acid polymerisation for polypeptides is part of protein synthesis.

• The sequence of amino acids in a chain is determined by the sequence of the genetic code in DNA.

Protein structure

Protein structure can be broken down into 4 levels:

Primary structure

• The primary structure refers to the sequence of amino acids

• Determines rest of protein structure

Secondary structure

• Amino acid chains fold and move to take up a particular shape

• Amino acids find the most stable hydrogen bonds

• Most common secondary structures are α-helix and the β-sheet

Alpha –helix:

• A regular spiral

• Held together by hydrogen bonds

• Very stable

• Forms part of most proteins

Beta-pleated sheet:

• A zig-zag formation

• Consisting of two or more chains

• Running parallel to each other

• Linked by hydrogen bonds.

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Tertiary structure

• Overall three-dimensional shape formed by the folding up of a whole polypeptide chain.

• Every protein has a unique tertiary structure, which is responsible for its properties and function.

• Tertiary structure held together by bonds between the R groups of the amino acids. There are 3 different types:

o hydrogen bonds – weak

o ionic bonds – between oppositely charged R groups, quite strong

o disulphide bridges – strong covalent bonds between sulphur on cysteine R groups.

Quarternary structure

• Final three-dimensional structure

• This is how different polypeptide chains are joined together.

• Also includes non-protein prosthetic groups which are present in some proteins.

• Eg, haemoglobin is a globular protein with 4 polypeptide chains, each with a haem group (containing an atom of iron).

Fibrous proteins:

• Long supercoiled chains.

• Secondary structure is important.

• Many polypeptide chains run parallel, cross-linked with bonds, eg disulphide bridges.

• Stable, and structurally strong.

• Examples:

o Keratin – skin, hair, bones.

o Collagen – skin, bones and tendons.

o Fibrin – blood clots

Globular Proteins:

• More spherical.

• Smaller ones are soluble.

• Specific shape.

• Tertiary and quaternary structure forms specific shape.

• Often part of the protein has a complementary shape to another specific molecule.

• Examples:

o Hormones – eg insulin and glucagon attach to receptors on cell membranes

o Enzymes – active site specific to substrate

o Antibodies – complementary to specific antigens

o Haemoglobin

Lipids

General details:

• Large, varied group of organic compounds.

• Contain carbon, hydrogen and oxygen.

• Insoluble in water.

• Dissolve in organic solvents, eg alcohol.

• 3 main types:

o Triglycerides.

o Phospholipids.

o Steroids.

The molecule

• 2 main sections:

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o Glycerol:

• An alcohol containing 3 carbon atoms.

• Each carbon has a hydroxyl group.

o Fatty acids:

• These determine the characterisitics of the lipid.

• They contain a carboxyl group (-COOH).

• This is attached to a variable R group - a hydrocarbon chain.

• 2 groups of fatty acids:

• Saturated:

o No double bonds between carbon atoms.

o Eg butyric acid found in butter.

o Eg palmitic acid found in animal and vegetable fats.

o A high proportion in the diet may increase risk of heart disease.

• Unsaturated:

o On or more double bonds,

o Eg linoleic acid – linseed oil.

o Eg oleic acid – found in olive oil.

o Polyunusaturated have 2 or more.

o Monounsaturated have one.

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Bonding:

• Fatty acids bond to glycerol by an ester linkage.

• Formation is a condensation reaction.

• Hydrolysis reactions break the bond.

• An oxygen atom joins a carbon on the glycerol with carbon on the carboxyl end of the fatty acid.

Triglycerides

• 3 fatty acid chains.

• Differ according to type and length of chains.

o Oils:

▪ Relatively short fatty acids or unsaturated fatty acids.

▪ Tend to be liquid at room temperature.

o Fats:

▪ Longer fatty acid chains or saturated fatty acids.

▪ More likely to be solid at room temperature.

▪ Main use is as an energy source.

▪ Can be broken down into glucose (gluconeogenesis) and used in respiration.

Uses:

• Animal energy stores.

• Twice as much energy per gram as carbohydrates.

• Ideal for the low mass required for locomotion.

• Insulation:

• Conduct heat slowly.

• Protection of vital organs.

• Waterproofing fur and feathers with oil secretions.

Phospholipids

• One fatty acid group is replaced by a phosphate group.

• The fatty acid chains are hydrophobic.

• The phosphate group and glycerol part are hydrophilic.

• Main role is in cell membranes.

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Microscopes

Units of measure

1 meter = 1,000 mm = 1,000,000 µm = 1,000,000,000 nm

1 millimeter (mm) = 1/1000 m

1 micrometer (µm) = 1/1,000,000 m = 1/1000 mm

1 nanometer (nm) = 1/1,000,000,000 m = 1/1000,000 mm = 1/1000 µm

Examples:

Frog egg = 1mm

Human egg = 100 µm

Most animal cell = 10 to 30 µm

Most plant cells = 10 to 100 µm

Prokaryotic cells = 1 µm

Mitochondria = 0.5 to 1 µm

Chloroplast = 5 µm

Nucleus = 7 µm

Virus = 10 to 300 nm

Ribosome = 30 nm

Magnification:

• The ratio of how much bigger a sample appears when viewed under the microscope than its actual size.

• The resolution limits how much detail can be seen.

Calculating magnification from photographs:

Magnification = length in photograph

Real length

Calculating real length from photographs:

Real length = Length in photograph

Magnification

NB for both, convert the length in the photograph into the same units that are used for the specimen. This is usually in micrometers.

Resolution

• The smallest separation at which two separate objects can be distinguished (or resolved).

• The greater the resolving power, the more detail can be seen.

• The resolution of an image is limited by the wavelength of radiation used to view the sample.

• When objects in the specimen are smaller than the wavelength of the radiation being used, they do not interrupt the waves, and so are not detected.

• The resolving power of a light microscope is limited by the wavelength of light (400-600nm for visible light).

• Objects closer than 200nm will still only be seen as one point, no matter how great the magnification. 

• Electrons have a much lower wavelength than light.

• A beam of electrons has an effective wavelength of less than 1 nm.

• Electron microscopes have higher resolution.

Light Microscopy

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• Most widely used form of microscopy.

• Specimens are illuminated with light

• Focussed using glass lenses.

• Modern microscopes - Compound microscopes use several lenses to obtain high magnification.

• Light microscopy has a resolution of about 200 nm:

• View cells, and large organelles but not the details of organelles

• Specimens can be living or dead.

• Specimens often need to be stained with a coloured dye to make them visible.

• Many different stains are available that stain specific parts of the cell such as DNA, lipids, cytoskeleton, etc.

Electron Microscopy.

• Developed in 1930s.

• Uses a beam of electrons to "illuminate" the specimen.

• Electrons behave like waves.

• Produced using a hot wire

• Focussed using electromagnets

• Detected using a phosphor screen or photographic film

• A beam of electrons has an effective wavelength of less than 1 nm.

• Resolving power is enough to view small sub-cellular ultrastructure.

• Mitochondria, ER and membranes can be seen in detail.

Problems

• Specimens must be fixed in plastic or covered in heavy metals.

• Viewed in a vacuum.

• Therefore, specimens must be dead.

• The electron beam can damage specimens.

• Must be stained with an electron-dense chemical, usually heavy metals like osmium, lead or gold.

• People argue that many observed structures could be artefacts - due to the preparation process and not real.

Transmission electron microscope (TEM)

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• Works much like a light microscope.

• A beam of electrons is passed through a thin specimen.

• Electrons are focussed to form an image on a fluorescent screen or on film.

• Most common form of electron microscope.

• Best resolution – 0.2 nm

• Creates a 2-dimensional flat image.

The scanning electron microscope (SEM)

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• A fine beam of electron is scanned onto a specimen.

• Electrons are scattered by the surface, due to the heavy metal covering.

• A fluorescent screen or film is used to detect the reflected electrons.

• This has poorer resolution – 10 nm

• Gives 3-dimentional images of surfaces.

• The electrons do not have to pass through the sample in order to form the image.

• Larger, thicker structures can be seen under the SEM.

Separating Cell Components

Cell Fractionation

• The separation of different parts and organelles of a cell.

• Relative proportions of each organelle can be discovered.

• Biochemical contents of each organelle can be investigated.

Process:

1. Place tissue (e.g. liver, heart, leaf, etc) in ice-cold isotonic buffer.

• Cold to stop enzyme reactions.

• Isotonic to stop osmosis.

• Buffer to stop pH changes.

2. Grind tissue in a blender to break open cells –homogenation.

3. Filter to remove insoluble tissue e.g. fat, connective tissue, plant cell walls, etc. This filtrate is now called a cell-free extract.

Differential Centrifugation

• A centrifuge is a piece of equipment, driven by a motor, that puts an object in rotation around a fixed axis, applying a force that is perpendicular to the axis.

• The centrifuge works using the sedimentation principle, where the centripetal acceleration is used to separate substances of greater and lesser density.

• Svedberg unit – used to compare sizes of ribosomes – a measure of their density.

Process:

1. Centrifuge filtrate at low speed and remove pellet.

2. Repeat at increasingly higher speeds.

3. Each pellet removed contains structures of lower density.

Density gradient centrifugation.

• The cell-free extract is centrifuged in a dense solution

• Eg sucrose or caesium chloride

• The fractions separate out into layers with the densest fractions near the bottom of the tube.

Heaviest Nuclei

Mitochondria

Lysosomes

Lightest Ribosomes

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Cells

• Cell = the smallest unit of life.

• All living organisms are made of cells.

• There are unicellular organisms that consist of one cell:

o Bacteria

o Blue-green bacteria

o Protozoa

o Yeast

• These individual cells must carry out all of the essential life proceses

• Other organisms are made of many cells.

• These are multicellular organisms:

o Animals

o Plants

o Mushrooms

o Seaweed

• In these the life processes can be delegated to different organs and tissues.

Two main divisions of cells

• Prokaryotic cells:

o Bacteria

o Blue-green bacteria

• Eukaryotic cells

o Animals

o Plants

o Fungi

o Protoctista

• Pro = before

• Eu = true

• Karyo = nucleus

Prokaryotic Cells

• Example:

o Cholera – Vibrio cholerae

• Prokaryote = ‘before the nucleus’

• Simple cells containing no membrane bound organelles

• Considered to be the earliest form of life on Earth.

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|Structure |Function |

|Cell wall |Provide shape |

| |Protect against rupture by osmosis |

| |Some protection against other organisms |

| |Rigid |

| |Made of peptidoglycans – polymers of sugars and amino acids |

|Plasma membrane |Phospholipids and proteins |

| |Proteins include enzymes for metabolic processes |

| |Eg respiration, nucleic acid synthesis (in all) and photosynthesis (in some) |

| |Fluid mosaic |

| |Barrier for selective exchange of nutrients and waste products |

| |Movement by diffusion (including osmosis) and active transport |

|DNA |Singular, circular chromosome |

| |DNA helix |

| |In cytoplasm, not nucleus |

| |Attached to plasma membrane |

| |Eg E.coli 4 x 106 base pairs (A, C, T and G), about 4000 genes |

|Ribosomes |Smaller than in eukaryotic cells |

| |Site of protein synthesis |

|Flagella |Hollow cylinder |

| |Made of rigid protein strands (flagellin) |

| |Arise from basal bodies in plasma membrane in some bacteria |

| |Rotate from base like a rotor blade |

| |Bring about movement |

|Plasmids |Additional hereditary material |

| |Small rings of DNA, 10 – 30 genes |

| |In cytoplasm of some, not all, bacteria |

| |Eg antibiotic resistance |

| |Can be transferred through conjugation tubes |

| |Exploited as vectors in genetic engineering |

|Capsule |Tangled mat of polysaccharide fibres |

| |Slimy physical barrier |

| |Outer protective layer in some bacteria |

| |Protects against chemicals and dessication |

| |Protects against attack by phagocytic cells |

| |Helps bacteria to form colonies |

Eukaryotic Cells

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• Eukaryote = ‘true nucleus’

• These cells contain organelles

Cell membrane

• Thin layer found round the outside of all cells.

• Made of phospholipids and proteins.

• Controls the movement of materials in and out of cell.

Microvilli

• Small finger-like extensions of the cell membrane found in certain cells

• eg, epithelial cells of the intestine and kidney.

• Increase surface area.

Cytoplasm

• Watery solution within cell membrane.

• Contains:

o Enzymes for metabolic reactions

o Sugars, salts, amino acids in solution.

Organelles

• Membranous sacs.

• Compartmentalise portions of the cytoplasm.

• Increase the surface area for reactions.

• Allow metabolic reactions to be sequenced.

• Isolate potentially harmful chemicals.

Nucleus

• The largest organelle (10μm diameter).

• Controls cell’s activities.

• Store genetic material – chromosomes which are made of DNA.

• Spherical

• Surrounded by nuclear envelope:

o 2 membranes filled with fluid

• Nuclear pores enable mRNA to enter the cytoplasm.

• Interior is nucleoplasm which is full of chromatin (DNA/protein).

• Nucleolus is a dark region of chromatin, site of RNA transcription.

Mitochondrion

o Site of aerobic respiration in all eukaryotic cells.

o 2.5 to 5 micrometers long.

o Spherical or rod shaped

o Double membrane

o Inner membrane folded into cristae - large surface area.

o Internal space is the matrix, a solution of metabolites and enzymes.

o Also contain loops of DNA.

o ATP synthase (stalked particles) are on the inner membrane.

o Site of latter stages of respiration.

o Metabolically active cells contain numerous mitochondria.

o Number of cristae also increases with increased activity.

Ribosomes

o Smallest and most abundant ‘organelles’

o Not membranous

o Site of protein synthesis

o Made in nucleolus

o Made of protein and RNA

o Found either in cytoplasm or attached to the rough endoplasmic reticulum (RER)

o Larger type (80S)

o Often found in groups called polysomes

Endoplasmic reticulum (ER)

o An elaborate system of membranes.

o Forms part of the cytoplasmic skeleton.

o Extends from the nuclear membrane.

o Series of flattened stacks called cisternae.

o Enables substances to be synthesised and transported.

o Rough ER (RER)

o Studded with ribosomes, gives it rough appearance

o Polypeptides synthesised by ribosomes are passed into it.

o Pass proteins to Golgi body for further processing.

o Smooth ER (SER)

o No ribosomes.

o Involved in synthesising and transporting steroids.

Vesicles

o Small membrane bound organelles.

o Deliver substance around cell.

o Take substances:

o From ER to Golgi

o From Golgi to cytoplasm - lysosomes

o From Golgi to cell membrane for exocytosis – secretory vesicles

o Eg release of digestive enzymes.

Golgi body (Golgi apparatus)

o Series of flattened membrane sacs.

o Similar structure to ER.

o More compact and curved.

o Transports proteins from the RER to the cell membrane

o Vesicles of RER fuse with the Golgi on one side

o Contents of the vesicles enter the Golgi

o Steroids may be modified.

o Proteins may acquire tertiary/quaternary structure.

o Other groups may be added.

o Vesicles bud off the other side and move into the cytoplasm.

Lysosomes

o A type of vesicle.

o Contain enzymes.

o Used to breakdown unwanted toxins or organelles to recycle materials.

o Eg used in phagocytosis.

Summary of differences between prokaryotic and eukaryotic cells

|Prokaryotic cells |Eukaryotic cells |

|Extremely small ( ................
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