AQA A-Level Biology 7402

Complete Specification — A/A* Revision Notes

Course Map

• 3.1 Biological molecules
• 3.2 Cells
• 3.3 Organisms exchange substances with their environment
• 3.4 Genetic information, variation and relationships between organisms
• 3.5 Energy transfers in and between organisms
• 3.6 Organisms respond to changes in their internal and external environments
• 3.7 Genetics, populations, evolution and ecosystems
• 3.8 The control of gene expression

Exam Map

• Paper 1: Topics 3.1–3.4 + relevant practical skills.
• Paper 2: Topics 3.5–3.8 + relevant practical skills.
• Paper 3: Topics 3.1–3.8, practical/data analysis and synoptic essay.

3.1 Biological Molecules

Mark-scheme precision rule: Biology marking is terminology-sensitive. Where a biological mechanism is described, preserve the causal sequence and the exact named structures/processes. Do not replace terms such as hydrogen bond, glycosidic bond, peptide bond, phosphodiester bond, complementary base pairing, enzyme–substrate complex, tertiary structure, hydrolysis, condensation, competitive inhibitor, or non-competitive inhibitor with generic wording.

1. Specification Coverage

SPEC: 3.1 — Biological molecules

All life shares a common biochemical basis. AQA uses this similarity as indirect evidence for evolution.

The complete section contains:

• 3.1.1 Monomers and polymers
• 3.1.2 Carbohydrates
• 3.1.3 Lipids
• 3.1.4 Proteins
  • 3.1.4.1 General properties of proteins
  • 3.1.4.2 Many proteins are enzymes
• 3.1.5 Nucleic acids are important information-carrying molecules
  • 3.1.5.1 Structure of DNA and RNA
  • 3.1.5.2 DNA replication
• 3.1.6 ATP
• 3.1.7 Water
• 3.1.8 Inorganic ions

This section also contains:

• Required Practical 1: Investigation into the effect of a named variable on the rate of an enzyme-controlled reaction.

2. Core Content — Extreme Detail

2.1 SPEC: 3.1.1 — Monomers and Polymers

2.1.1 Common biochemical basis of life

Despite the enormous diversity of living organisms, all living cells contain a relatively small number of major groups of carbon-based compounds.

These include:

• carbohydrates;
• lipids;
• proteins;
• nucleic acids.

This common chemistry supports the idea that living organisms share evolutionary ancestry.

Examiner-safe phrasing

“The presence of the same major biological molecules and similar biochemical processes in different organisms provides indirect evidence for common ancestry.”

2.1.2 Monomers

DEFINITION — Monomer
A small molecular unit from which larger molecules can be made.

AQA examples include:

• monosaccharides;
• amino acids;
• nucleotides.

A monomer is not simply “a small molecule”; it is a unit capable of being joined to form a larger molecule.

2.1.3 Polymers

DEFINITION — Polymer
A large molecule made from many repeating monomer units joined together.

Examples include:

• polysaccharides from monosaccharides;
• polypeptides from amino acids;
• polynucleotides from nucleotides.

Important qualification

Not every biological macromolecule is a true polymer.

For example:

• triglycerides are large biological molecules;
• but they are not polymers, because they are not formed from long chains of repeating monomer units.

2.1.4 Condensation reactions

DEFINITION — Condensation reaction
A reaction in which two molecules join by formation of a chemical bond with the elimination of a molecule of water.

General pattern:

[ \text{molecule A}+\text{molecule B} \rightarrow \text{larger molecule}+\mathrm{H_2O} ]

Condensation forms covalent bonds such as:

• glycosidic bonds;
• peptide bonds;
• ester bonds;
• phosphodiester bonds.

Mark-scheme wording

“A chemical bond forms and a molecule of water is released.”

Do not write only:

“Water is made.”

The key event is bond formation.

2.1.5 Hydrolysis reactions

DEFINITION — Hydrolysis reaction
A reaction in which a chemical bond is broken using a molecule of water.

General pattern:

[ \text{large molecule}+\mathrm{H_2O} \rightarrow \text{smaller molecules} ]

Hydrolysis is important in:

• digestion;
• ATP hydrolysis;
• breakdown of polysaccharides;
• breakdown of proteins;
• breakdown of nucleic acids.

Mark-scheme wording

“Water is used to break the chemical bond.”

Do not confuse hydrolysis with “breaking down by water” without naming the bond.

2.2 SPEC: 3.1.2 — Carbohydrates

2.2.1 Monosaccharides

DEFINITION — Monosaccharide
A single sugar unit that acts as a monomer for larger carbohydrates.

AQA requires recognition of:

• glucose;
• galactose;
• fructose.

Glucose is especially important because it is:

• a respiratory substrate;
• a monomer of starch;
• a monomer of glycogen;
• a monomer of cellulose.

2.2.2 Alpha- and beta-glucose

Glucose exists as two important isomers:

• α-glucose
• β-glucose

They have the same molecular formula but differ in the arrangement around carbon 1.

For the Haworth representation used at A-level:

• in α-glucose, the hydroxyl group on carbon 1 is below the plane of the ring;
• in β-glucose, the hydroxyl group on carbon 1 is above the plane of the ring.

DEFINITION — Isomer
Molecules with the same molecular formula but a different arrangement of atoms.

This small difference has major biological consequences because it produces different polysaccharide structures.

2.2.3 Glycosidic bonds

DEFINITION — Glycosidic bond
A covalent bond formed between two monosaccharides by a condensation reaction.

During the reaction:

• an (-OH) group from one monosaccharide;
• and an (-H) from another;

combine to form:

[ \mathrm{H_2O} ]

The remaining atoms form the glycosidic bond.

Hydrolysis reverses the process.

2.3 Disaccharides

DEFINITION — Disaccharide
A carbohydrate formed by the condensation of two monosaccharides.

AQA requires the following:

Maltose

[ \text{glucose}+\text{glucose} \rightarrow \text{maltose}+\mathrm{H_2O} ]

Sucrose

[ \text{glucose}+\text{fructose} \rightarrow \text{sucrose}+\mathrm{H_2O} ]

Lactose

[ \text{glucose}+\text{galactose} \rightarrow \text{lactose}+\mathrm{H_2O} ]

These reactions form glycosidic bonds.

2.4 Polysaccharides

DEFINITION — Polysaccharide
A carbohydrate polymer formed from many monosaccharides joined by glycosidic bonds.

AQA requires:

• starch;
• glycogen;
• cellulose.

2.5 Starch

Starch is a storage polysaccharide in plants.

It is formed from:

[ \boxed{\alpha\text{-glucose}} ]

Starch contains:

• amylose;
• amylopectin.

2.5.1 Amylose

Amylose is:

• a long;
• unbranched;
• chain of α-glucose;
• joined mainly by (\alpha)-1,4 glycosidic bonds.

The chain coils into a compact helix.

Structure–function relationship

The coiled structure makes amylose:

• compact;
• able to store many glucose units in a small volume.

Starch is insoluble, so it:

• does not lower the water potential of the cell substantially;
• does not diffuse out of cells.

It can be hydrolysed to release glucose when needed.

2.5.2 Amylopectin

Amylopectin is formed from α-glucose and is:

• branched;
• contains (\alpha)-1,4 bonds in chains;
• and (\alpha)-1,6 bonds at branch points.

Structure–function relationship

Branching provides:

• many terminal ends;
• many sites at which enzymes can act simultaneously;
• rapid hydrolysis;
• rapid glucose release.

2.6 Glycogen

Glycogen is a storage polysaccharide in animals and fungi.

It is made from:

[ \boxed{\alpha\text{-glucose}} ]

Glycogen is:

• highly branched;
• more highly branched than amylopectin;
• compact;
• insoluble.

Structure–function relationship

Highly branched

• many ends;
• enzymes can hydrolyse many glycosidic bonds simultaneously;
• glucose can be released rapidly.

Compact

• large amount can be stored in a small volume.

Insoluble

• does not diffuse out;
• does not significantly reduce cell water potential.

This suits animal cells because animals may require glucose rapidly for respiration.

2.7 Cellulose

Cellulose is a structural polysaccharide in plant cell walls.

It is formed from:

[ \boxed{\beta\text{-glucose}} ]

A condensation reaction forms:

[ \beta\text{-1,4 glycosidic bonds} ]

Because of the orientation of β-glucose, alternate glucose molecules are inverted by:

[ 180^\circ ]

This produces:

• long;
• straight;
• unbranched;

cellulose chains.

2.7.1 Hydrogen bonds and microfibrils

Many hydroxyl groups are exposed on cellulose chains.

Hydrogen bonds form between adjacent chains.

Although each hydrogen bond is individually weak, many hydrogen bonds together give substantial strength.

Chains group into:

[ \boxed{\text{microfibrils}} ]

which provide high tensile strength.

2.7.2 Cellulose structure–function relationship

Cellulose cell walls:

• resist tensile forces;
• prevent cells bursting when water enters by osmosis;
• allow plants to maintain turgor;
• provide structural support.

High-mark phrasing

“Many hydrogen bonds form between adjacent cellulose chains, producing strong microfibrils with high tensile strength.”

Avoid:

“Cellulose has strong hydrogen bonds.”

The key is many bonds between chains.

2.8 Biochemical Tests for Carbohydrates

2.8.1 Benedict's test for reducing sugars

Reducing sugars include:

• glucose;
• fructose;
• maltose;
• lactose.

Method

1. Add Benedict's reagent to the sample.
2. Heat in a water bath.
3. Observe colour change.

Positive result:

[ \text{blue}\rightarrow\text{green/yellow/orange/brick-red precipitate} ]

The exact final colour depends on concentration.

Negative result

Solution remains:

[ \boxed{\text{blue}} ]

2.8.2 Semi-quantitative Benedict's test

A more concentrated reducing-sugar solution generally produces:

• a more intense orange/red colour;
• more precipitate.

However, visual colour comparison is subjective.

A more quantitative method can use:

• standard solutions;
• controlled heating time;
• controlled temperature;
• equal reagent volumes;
• colorimetry where suitable;
• calibration curve.

2.9 Test for Non-Reducing Sugars

A non-reducing sugar such as sucrose does not initially give a positive Benedict's test.

Method

1. Test the original sample with Benedict's reagent.
2. If negative, take a fresh sample.
3. Add dilute hydrochloric acid.
4. Heat to hydrolyse glycosidic bonds.
5. Cool.
6. Neutralise the acid using an alkali, e.g. sodium hydrogencarbonate.
7. Add Benedict's reagent.
8. Heat in a water bath.

Positive result after hydrolysis:

[ \boxed{\text{reducing sugars were produced}} ]

therefore a non-reducing sugar was present in the original sample.

Why acid is used

It hydrolyses the glycosidic bond.

Why neutralise

Benedict's reagent requires alkaline conditions.

2.10 Iodine Test for Starch

Add:

• iodine solution in potassium iodide;

to the sample.

Positive result:

[ \boxed{\text{orange-brown}\rightarrow\text{blue-black}} ]

Negative result:

[ \boxed{\text{remains orange-brown}} ]

2.11 Chromatography of Monosaccharides

AQA may assess chromatography as a practical skill.

Key ideas:

• mixture is spotted onto stationary phase;
• solvent moves through the stationary phase;
• components move different distances due to different solubilities/attractions;
• compare with known standards.

Retention factor:

[ \boxed{ R_f= \frac{\text{distance travelled by solute}} {\text{distance travelled by solvent front}} } ]

The (R_f) value has no unit.

For valid comparison, chromatograms should be run under the same conditions.

2.12 Calibration Curve for Glucose

AQA identifies the opportunity to make:

• a dilution series;
• a calibration curve;
• use colorimetry to determine unknown glucose concentration.

General procedure:

1. prepare known glucose concentrations;
2. carry out the same colour-producing reaction on each;
3. measure absorbance/transmission;
4. plot known concentration against instrument reading;
5. measure unknown;
6. use calibration curve to interpolate concentration.

Critical variables

Keep constant:

• reagent volume;
• sample volume;
• temperature;
• reaction time;
• wavelength/filter;
• cuvette path length.

2.13 SPEC: 3.1.3 — Lipids

AQA requires two lipid groups:

• triglycerides;
• phospholipids.

Lipids are not polymers because they are not chains of repeating monomers.

2.14 Triglycerides

A triglyceride is formed from:

• one glycerol;
• three fatty acids.

A condensation reaction occurs between:

• hydroxyl groups of glycerol;
• carboxyl groups of fatty acids.

This forms:

[ \boxed{\text{ester bonds}} ]

and releases water.

Overall:

[ \text{glycerol}+3\text{ fatty acids} \rightarrow \text{triglyceride}+3\mathrm{H_2O} ]

2.14.1 Ester bond

DEFINITION — Ester bond
The covalent bond formed between glycerol and a fatty acid during a condensation reaction.

In biological lipids, ester bonds link glycerol to fatty-acid chains.

2.15 Saturated and Unsaturated Fatty Acids

Saturated fatty acid

DEFINITION — Saturated fatty acid
A fatty acid whose hydrocarbon chain contains no carbon–carbon double bonds.

It is saturated with hydrogen.

Unsaturated fatty acid

DEFINITION — Unsaturated fatty acid
A fatty acid whose hydrocarbon chain contains one or more carbon–carbon double bonds.

A double bond, particularly a cis double bond, introduces a bend/kink.

This can affect packing and melting temperature.

2.16 Triglyceride Structure and Function

Triglycerides are useful energy stores because:

• they contain many carbon–hydrogen bonds;
• oxidation releases substantial energy;
• they have a high energy content per unit mass;
• they are insoluble in water;
• storage therefore has little effect on water potential;
• they can be stored compactly;
• they can provide metabolic water when oxidised.

Lipids are particularly useful for long-term energy storage.

2.17 Phospholipids

A phospholipid resembles a triglyceride except:

• one fatty acid is replaced by a phosphate-containing group.

Thus it has:

• two hydrophobic fatty-acid tails;
• a hydrophilic phosphate-containing head.

DEFINITION — Hydrophilic
Attracted to and able to interact with water.

DEFINITION — Hydrophobic
Repelled by water / does not readily interact with water.

This makes phospholipids:

[ \boxed{\text{amphipathic}} ]

meaning they contain both hydrophilic and hydrophobic regions.

2.17.1 Phospholipid bilayers

In aqueous conditions:

• hydrophilic heads face water;
• hydrophobic tails orient away from water.

Therefore phospholipids form bilayers.

This is fundamental to:

• cell-surface membranes;
• membranes around organelles.

2.18 Triglycerides vs Phospholipids

Examiner wording

“Phospholipids have a hydrophilic phosphate-containing head and hydrophobic fatty-acid tails, so they form bilayers in water.”

2.19 Emulsion Test for Lipids

Method

1. Add ethanol to the sample.
2. Shake.
3. Add water.

Positive result:

[ \boxed{\text{white/milky emulsion}} ]

Why?

• lipids dissolve in ethanol;
• when water is added, lipid comes out of solution as tiny droplets;
• droplets scatter light.

Negative result:

• solution remains clear.

2.20 SPEC: 3.1.4 — Proteins

2.20.1 Amino acids

DEFINITION — Amino acid
A biological monomer containing an amino group, a carboxyl group, a hydrogen atom and a variable R group attached to a central carbon.

General structure:

Where:

• (\mathrm{NH_2}) = amino group;
• (\mathrm{COOH}) = carboxyl group;
• (R) = variable side chain.

The 20 amino acids commonly found in proteins differ in their R groups.

2.21 Peptide Bonds

A condensation reaction occurs between:

• carboxyl group of one amino acid;
• amino group of another.

Water is released.

A:

[ \boxed{\text{peptide bond}} ]

forms.

DEFINITION — Peptide bond
A covalent bond formed between the carboxyl group of one amino acid and the amino group of another in a condensation reaction.

Dipeptide

Two amino acids joined:

[ \boxed{\text{dipeptide}} ]

Polypeptide

Many amino acids joined by peptide bonds:

[ \boxed{\text{polypeptide}} ]

A functional protein may contain:

• one polypeptide;
• more than one polypeptide.

2.22 Levels of Protein Structure

2.22.1 Primary structure

DEFINITION — Primary structure
The specific sequence of amino acids in a polypeptide chain.

The primary structure determines where different R groups occur.

Therefore it determines:

• subsequent bonding;
• folding;
• final three-dimensional shape;
• function.

A change in one amino acid can alter protein function.

2.23 Secondary structure

DEFINITION — Secondary structure
Localised folding of a polypeptide chain produced mainly by hydrogen bonding between parts of the peptide backbone.

Examples include:

• α-helices;
• β-pleated sheets.

Do not confuse secondary structure with the entire 3D structure of a protein.

2.24 Tertiary structure

DEFINITION — Tertiary structure
The overall three-dimensional shape of a single polypeptide chain produced by interactions between amino-acid R groups and other parts of the chain.

AQA specifically requires roles of:

• hydrogen bonds;
• ionic bonds;
• disulfide bridges.

Other interactions can contribute, but these three must be known.

2.24.1 Hydrogen bonds

Hydrogen bonds can form between polar groups.

They are individually weak but collectively contribute to stability.

2.24.2 Ionic bonds

Ionic attractions form between oppositely charged R groups.

Changes in pH can alter charges on R groups and disrupt ionic interactions.

2.24.3 Disulfide bridges

Disulfide bridges are strong covalent bonds between sulfur-containing R groups.

They stabilise tertiary structure.

2.25 Quaternary structure

DEFINITION — Quaternary structure
The arrangement of multiple polypeptide chains, and sometimes non-protein components, into a functional protein.

Examples:

• haemoglobin has multiple polypeptide subunits;
• some proteins include prosthetic groups.

The specification requires understanding of how primary, secondary, tertiary and quaternary structure relate to function.

2.26 Protein Structure Determines Function

Examples throughout AQA Biology include:

• enzymes;
• antibodies;
• haemoglobin;
• membrane proteins;
• receptors;
• collagen;
• protein hormones.

The key principle is:

[ \boxed{ \text{amino-acid sequence}\rightarrow\text{folding}\rightarrow\text{3D shape}\rightarrow\text{function} } ]

A change in:

• primary structure;
• temperature;
• pH;

may alter bonding and therefore tertiary structure.

If a protein's shape changes, its function may change.

2.27 Biuret Test for Protein

Method

Add Biuret reagent / appropriate alkaline copper(II) reagent.

Positive result:

[ \boxed{\text{blue}\rightarrow\text{lilac/purple}} ]

The test detects peptide bonds.

Negative result:

[ \boxed{\text{remains blue}} ]

2.28 Amino-Acid Chromatography

Chromatography can separate amino acids based on differences in:

• solubility;
• interaction with stationary phase.

Use:

[ R_f= \frac{\text{distance travelled by amino acid}} {\text{distance travelled by solvent front}} ]

Compare with standards under the same conditions.

2.29 SPEC: 3.1.4.2 — Enzymes

DEFINITION — Enzyme
A biological catalyst, usually a globular protein, that increases reaction rate without being permanently changed by the reaction.

The specification specifically requires:

• activation energy;
• induced-fit model;
• tertiary structure of active site;
• enzyme–substrate complex;
• specificity;
• effects of:
  • enzyme concentration;
  • substrate concentration;
  • competitive inhibitor concentration;
  • non-competitive inhibitor concentration;
  • pH;
  • temperature.

2.30 Activation Energy

DEFINITION — Activation energy
The minimum energy required for a reaction to begin.

Enzymes:

[ \boxed{\text{lower activation energy}} ]

They do not:

• supply energy to the reaction;
• change the overall energy change;
• alter the final equilibrium position merely by catalysis.

They provide an alternative reaction pathway with lower activation energy.

2.31 Active Site

DEFINITION — Active site
The specific region of an enzyme with a tertiary structure that allows complementary substrate molecule(s) to bind and form an enzyme–substrate complex.

The active site's properties depend on:

• amino-acid sequence;
• R-group interactions;
• tertiary structure.

2.32 Enzyme–Substrate Complex

DEFINITION — Enzyme–substrate complex
The temporary complex formed when substrate molecule(s) bind to an enzyme's active site.

Binding brings reacting groups into appropriate positions and enables the reaction to proceed with lower activation energy.

2.33 Induced-Fit Model

AQA requires the induced-fit model.

The active site is not simply a perfectly rigid shape.

Instead:

1. substrate approaches;
2. substrate binds to active site;
3. interaction induces a slight change in enzyme shape;
4. active site becomes more complementary to substrate/transition state;
5. bonds in substrate may be strained;
6. activation energy is lowered;
7. products form;
8. products leave.

High-mark wording

“Binding of the substrate causes a conformational change in the enzyme so that the active site becomes more complementary, placing strain on substrate bonds and lowering activation energy.”

Do not rely only on the outdated rigid lock-and-key description.

2.34 Enzyme Specificity

Enzymes are specific because:

• active sites have specific tertiary structures;
• only substrate(s) with complementary shape/chemical properties bind effectively;
• enzyme–substrate complex forms.

A change to tertiary structure can alter the active site and reduce activity.

2.35 Temperature and Enzyme Rate

At low to moderate temperature:

• increased temperature gives molecules more kinetic energy;
• molecules move faster;
• collisions occur more frequently;
• more collisions have sufficient energy;
• more enzyme–substrate complexes form;
• rate increases.

At high temperature:

• vibrations disrupt bonds maintaining tertiary structure;
• enzyme changes shape;
• active site changes;
• substrate becomes less complementary;
• fewer enzyme–substrate complexes form;
• enzyme becomes denatured;
• rate falls.

DEFINITION — Denaturation
A change in a protein's tertiary structure that alters its functional shape, usually causing loss of function.

Critical wording

Do not say:

“The enzyme dies.”

Enzymes are molecules, not living organisms.

2.36 pH and Enzyme Rate

Changes in pH alter:

• (\mathrm{H^+}) concentration;
• charges on amino-acid R groups;
• ionic bonds;
• hydrogen bonding.

This can alter tertiary structure and active-site shape.

Away from optimum pH:

• fewer enzyme–substrate complexes form;
• rate decreases.

Extreme pH may denature the enzyme.

2.37 Substrate Concentration

At low substrate concentration:

• many active sites are free;
• increasing substrate concentration increases collision frequency;
• more enzyme–substrate complexes form;
• rate increases.

At high substrate concentration:

• all/most active sites are occupied;
• enzyme concentration becomes limiting;
• rate reaches a maximum.

Graph:

• rises steeply;
• gradually levels off at maximum rate.

2.38 Enzyme Concentration

If substrate is in excess:

• increasing enzyme concentration increases number of active sites;
• more enzyme–substrate complexes form per unit time;
• rate increases approximately proportionally.

Eventually substrate may become limiting.

2.39 Competitive Inhibition

DEFINITION — Competitive inhibitor
A molecule that binds to the active site of an enzyme and competes with the substrate.

It often has a shape/chemical structure similar enough to substrate to bind.

Effects:

• fewer active sites available to substrate;
• fewer enzyme–substrate complexes;
• lower rate.

Increasing substrate concentration can reduce the effect because substrate has a greater probability of occupying active sites.

Mark-scheme wording

“The inhibitor competes with substrate for the active site.”

Do not say:

“The inhibitor destroys the active site.”

2.40 Non-Competitive Inhibition

DEFINITION — Non-competitive inhibitor
A molecule that binds to a site other than the active site and alters the enzyme's tertiary structure so the active site is less complementary to the substrate.

Effects:

• active-site shape changes;
• substrate binds less effectively;
• fewer enzyme–substrate complexes;
• lower rate.

Increasing substrate concentration does not overcome this effect in the same way as competitive inhibition.

2.41 Models of Enzyme Action Change with Evidence

AQA requires appreciation that models change over time.

The older lock-and-key model treated the active site as rigid.

The induced-fit model reflects evidence that:

• proteins are flexible;
• substrate binding can alter enzyme conformation.

Exam wording

“The model changed because new evidence showed that the active site changes shape when the substrate binds.”

2.42 Intracellular and Extracellular Enzymes

Intracellular

Act within cells.

Examples include enzymes involved in:

• respiration;
• DNA replication;
• metabolic pathways.

Extracellular

Secreted from cells and act outside them.

Examples include digestive enzymes.

Enzyme-controlled reactions determine structures and functions from:

• cellular;
• tissue;
• organ;
• whole-organism;

levels.

2.43 Required Practical 1 — Enzyme-Controlled Reaction

AQA Required Practical 1: Investigation into the effect of a named variable on the rate of an enzyme-controlled reaction.

Possible variables:

• temperature;
• pH;
• substrate concentration;
• enzyme concentration;
• inhibitor concentration.

The exact method depends on the chosen enzyme.

Common model systems:

• amylase + starch;
• catalase + hydrogen peroxide;
• lipase + lipid.

2.43.1 General experimental design

Independent variable

The variable deliberately changed.

Dependent variable

Rate of enzyme-controlled reaction.

Control variables

Depending on method:

• enzyme concentration;
• substrate concentration;
• pH;
• temperature;
• total volume;
• mixing;
• sampling interval.

2.43.2 Rate calculation

Rate may be:

[ \boxed{ \text{rate}= \frac{\text{change in quantity}} {\text{time}} } ]

If measuring time to a fixed endpoint:

[ \boxed{ \text{rate}\propto\frac{1}{t} } ]

where (t) is endpoint time.

2.43.3 Initial rate from a graph

If product/substrate is plotted against time:

1. draw tangent at (t=0);
2. choose two widely separated points on tangent;
3. calculate:

[ \boxed{ \text{initial rate}= \frac{\Delta y}{\Delta x} } ]

Use correct units.

2.43.4 Uncertainty

Percentage uncertainty:

[ \boxed{ \frac{\text{absolute uncertainty}} {\text{measured value}}\times100 } ]

To reduce percentage timing uncertainty:

• measure a longer interval where possible;
• repeat;
• calculate mean;
• use objective sensor/data logger if appropriate.

2.44 SPEC: 3.1.5 — Nucleic Acids

DNA and RNA are information-carrying molecules.

AQA requires understanding that:

• DNA stores genetic information;
• RNA transfers genetic information from DNA to ribosomes;
• ribosomes contain RNA and protein.

2.45 Nucleotides

DEFINITION — Nucleotide
A monomer made from a pentose sugar, a nitrogen-containing organic base and a phosphate group.

DNA and RNA are polymers of nucleotides.

2.46 DNA Nucleotide

A DNA nucleotide contains:

• deoxyribose;
• phosphate;
• one base:
  • adenine, A;
  • cytosine, C;
  • guanine, G;
  • thymine, T.

2.47 RNA Nucleotide

An RNA nucleotide contains:

• ribose;
• phosphate;
• one base:
  • adenine, A;
  • cytosine, C;
  • guanine, G;
  • uracil, U.

DNA vs RNA

2.48 Phosphodiester Bonds

A condensation reaction between nucleotides forms:

[ \boxed{\text{phosphodiester bond}} ]

DEFINITION — Phosphodiester bond
A covalent bond joining adjacent nucleotides in a polynucleotide chain through the sugar-phosphate backbone.

Repeated condensation forms a polynucleotide.

2.49 DNA Structure

DNA consists of:

• two polynucleotide chains;
• arranged as a double helix;
• with sugar-phosphate backbones on the outside;
• bases projecting inward;
• strands held together by hydrogen bonds between complementary bases.

2.50 Complementary Base Pairing

In DNA:

[ \boxed{ A-T } ]

[ \boxed{ C-G } ]

Hydrogen bonds form between complementary bases.

A–T forms:

[ 2 ]

hydrogen bonds.

C–G forms:

[ 3 ]

hydrogen bonds.

AQA's core requirement is the specific complementary pairing and role of hydrogen bonds.

2.51 Base-Ratio Calculations

In double-stranded DNA:

[ %A=%T ]

and:

[ %C=%G ]

If:

[ A=28% ]

then:

[ T=28% ]

So:

[ C+G=44% ]

and:

[ C=G=22% ]

2.52 RNA Structure

RNA is:

• a relatively short polynucleotide;
• usually single-stranded;
• contains ribose;
• contains uracil instead of thymine.

RNA transfers genetic information from DNA to ribosomes.

Ribosomes themselves contain:

• RNA;
• proteins.

2.53 Why DNA Was Initially Doubtful as Genetic Material

AQA asks students to appreciate that the relative chemical simplicity of DNA led scientists to doubt it carried the genetic code.

Proteins appeared more structurally varied because:

• there are 20 common amino acids;
• proteins have complex structures.

DNA appeared comparatively simple with only four bases.

Scientific ideas changed when experimental evidence supported DNA as the genetic material.

2.54 SPEC: 3.1.5.2 — Semi-Conservative DNA Replication

DEFINITION — Semi-conservative replication
DNA replication in which each new DNA molecule contains one original parental strand and one newly synthesised strand.

This preserves genetic continuity.

2.55 DNA Replication — Exact Sequence

AQA requires:

1. DNA double helix unwinds;
2. DNA helicase breaks hydrogen bonds between complementary bases;
3. the two polynucleotide strands separate;
4. each original strand acts as a template;
5. free DNA nucleotides are attracted to exposed bases;
6. complementary base pairing occurs;
7. DNA polymerase catalyses condensation reactions;
8. phosphodiester bonds form between adjacent nucleotides;
9. two DNA molecules form;
10. each contains one original and one newly synthesised strand.

2.55.1 DNA helicase

DEFINITION — DNA helicase
An enzyme that unwinds DNA and breaks the hydrogen bonds between complementary base pairs.

Do not say helicase breaks:

• phosphodiester bonds.

It breaks:

[ \boxed{\text{hydrogen bonds}} ]

2.55.2 DNA polymerase

DEFINITION — DNA polymerase
An enzyme that catalyses condensation reactions joining adjacent DNA nucleotides by phosphodiester bonds during DNA replication.

AQA wording focuses on:

• condensation;
• adjacent nucleotides.

Do not say DNA polymerase:

“joins the bases together.”

The bases pair by hydrogen bonding; the polymerase joins nucleotides in the backbone.

2.56 Complementary Base Pairing During Replication

Each exposed base attracts a complementary free nucleotide:

[ A\leftrightarrow T ]

[ C\leftrightarrow G ]

This allows the base sequence of the original strand to determine the sequence of the new strand.

Thus genetic information is copied accurately.

2.57 Evidence for Semi-Conservative Replication

AQA may assess evaluation of evidence validating the Watson–Crick model.

The classic evidence is the Meselson–Stahl experiment.

Conceptually:

1. bacteria grown with heavy nitrogen incorporate it into DNA;
2. moved to light nitrogen;
3. DNA separated by density;
4. after one replication, intermediate-density DNA appears;
5. after two replications, intermediate and light DNA appear;
6. pattern supports semi-conservative replication.

Evaluation point

The experimental pattern differs from predictions of alternative models.

The strength of evidence comes from:

• making predictions;
• observing data;
• comparing data with model predictions.

2.58 SPEC: 3.1.6 — ATP

DEFINITION — ATP
Adenosine triphosphate, a nucleotide derivative consisting of adenine, ribose and three phosphate groups.

ATP is not described simply as:

“energy.”

It is a molecule that transfers energy in cells.

2.59 ATP Structure

ATP contains:

• adenine;
• ribose;
• three phosphate groups.

Adenine + ribose:

[ \boxed{\text{adenosine}} ]

Therefore:

[ \boxed{\text{adenosine triphosphate}} ]

2.60 ATP Hydrolysis

ATP hydrolase catalyses:

[ \boxed{ \mathrm{ATP}+\mathrm{H_2O} \rightarrow \mathrm{ADP}+P_i } ]

where:

• ADP = adenosine diphosphate;
• (P_i) = inorganic phosphate.

This releases energy in a small, manageable quantity.

2.61 Coupling ATP Hydrolysis to Cellular Processes

Energy released from ATP hydrolysis can be coupled to energy-requiring processes such as:

• active transport;
• muscle contraction;
• biosynthesis;
• phosphorylation;
• movement of motor proteins.

High-mark wording

“ATP hydrolysis releases energy that can be coupled directly to an energy-requiring cellular process.”

2.62 Phosphorylation

The inorganic phosphate released by ATP hydrolysis may be added to another molecule.

DEFINITION — Phosphorylation
Addition of a phosphate group to a molecule.

This can make the molecule:

• more reactive;
• change its shape;
• change its charge;
• alter its function.

AQA specifically requires that phosphorylation often makes compounds more reactive.

2.63 ATP Resynthesis

ATP is resynthesised by condensation:

[ \boxed{ \mathrm{ADP}+P_i \rightarrow \mathrm{ATP}+\mathrm{H_2O} } ]

The enzyme:

[ \boxed{\text{ATP synthase}} ]

catalyses ATP synthesis during:

• respiration;
• photosynthesis.

2.64 Why ATP Is Useful

ATP is useful because:

• releases energy in small quantities;
• hydrolysis is rapid;
• can be rapidly resynthesised;
• soluble;
• can transfer energy within cells;
• phosphate can phosphorylate compounds.

Do not write:

“ATP stores lots of energy long term.”

Long-term energy storage is not its main role.

2.65 SPEC: 3.1.7 — Water

Water is the major component of cells.

Its biological importance arises from its:

• polarity;
• hydrogen bonding.

The specification requires five key roles/properties.

2.66 Water as a Metabolite

Water participates directly in metabolic reactions.

Examples:

• hydrolysis uses water;
• condensation releases water.

Therefore water is not merely a medium; it is a reactant/product in metabolism.

2.67 Water as a Solvent

Water is polar.

Ions and polar molecules can dissolve because they interact with water molecules.

This makes water a medium for:

• metabolic reactions;
• transport in blood;
• transport in tissue fluid;
• transport in xylem/phloem solutions;
• intracellular chemical reactions.

Examiner-safe phrasing

“Water is a solvent for ions and polar molecules, allowing reactants to remain in solution and collide during metabolic reactions.”

2.68 High Specific Heat Capacity

DEFINITION — Specific heat capacity
The energy required to raise the temperature of a unit mass of a substance by one degree.

Water has a relatively high specific heat capacity because substantial energy is required to disrupt hydrogen bonds.

Biological significance:

• temperature changes slowly;
• aquatic habitats have stable temperatures;
• body fluids buffer temperature change;
• enzymes are protected from rapid temperature fluctuations.

AQA wording

“Water buffers changes in temperature.”

2.69 High Latent Heat of Vaporisation

DEFINITION — Latent heat of vaporisation
The energy required to change a liquid to a gas without a change in temperature.

Water has a relatively high latent heat of vaporisation because many hydrogen bonds must be broken.

Therefore evaporation removes substantial heat energy.

Examples:

• sweating;
• panting;
• transpiration.

A relatively small amount of water loss can produce effective cooling.

2.70 Cohesion

DEFINITION — Cohesion
Attraction between molecules of the same substance.

Hydrogen bonding causes strong cohesion between water molecules.

This:

• supports continuous columns of water in xylem;
• helps maintain the transpiration stream.

2.71 Surface Tension

At an air–water boundary, cohesive forces produce:

[ \boxed{\text{surface tension}} ]

This can support small organisms at the surface and is evidence of strong intermolecular cohesion.

2.72 SPEC: 3.1.8 — Inorganic Ions

Inorganic ions occur dissolved in:

• cytoplasm;
• tissue fluid;
• blood plasma;
• other body fluids.

Some occur at high concentrations and others at very low concentrations.

Their roles depend on:

• charge;
• chemical reactivity;
• ability to interact with biological molecules.

AQA requires recognition of four specified examples.

2.73 Hydrogen Ions and pH

[ \boxed{ \mathrm{H^+} } ]

concentration determines pH.

[ \boxed{ \mathrm{pH}=-\log_{10}[\mathrm{H^+}] } ]

Higher (\mathrm{H^+}) concentration:

[ \boxed{\text{lower pH}} ]

Changes in pH can alter:

• charges on proteins;
• ionic bonds;
• enzyme tertiary structure;
• enzyme activity.

2.74 Iron Ions in Haemoglobin

Iron ions are components of haem groups in haemoglobin.

Haemoglobin binds oxygen reversibly.

The iron-containing haem group is therefore essential to:

• oxygen transport in blood.

AQA expects recognition of iron ions as a component of haemoglobin, not detailed coordination chemistry at this stage.

2.75 Sodium Ions in Co-Transport

[ \boxed{ \mathrm{Na^+} } ]

is involved in co-transport of:

• glucose;
• amino acids;

across epithelial cell membranes, especially in the ileum.

A sodium-ion concentration gradient provides the driving force for coupled uptake.

Detailed transport mechanisms are developed in section 3.3.

2.76 Phosphate Ions

Phosphate groups/ions are components of:

• DNA nucleotides;
• RNA nucleotides;
• ATP.

They contribute to:

• sugar-phosphate backbones of nucleic acids;
• ATP structure;
• phosphorylation.

3. Exact AQA Exam Language

3.1 Define

For definitions, include every required biological qualifier.

Condensation

“A reaction in which two molecules join by formation of a chemical bond with the elimination of a molecule of water.”

Hydrolysis

“A reaction in which a chemical bond is broken using a molecule of water.”

Isotope-style precision does not apply here; define the biological term asked, not a loose synonym.

3.2 Describe

State the sequence/observation without causal explanation unless requested.

Example:

“As substrate concentration increases, rate increases and then levels off.”

3.3 Explain

Use:

[ \boxed{ \text{cause}\rightarrow\text{molecular mechanism}\rightarrow\text{effect} } ]

Example:

“Increasing temperature increases kinetic energy, so enzyme and substrate molecules collide more frequently and more enzyme–substrate complexes form per unit time, increasing the rate.”

3.4 Compare

Always address both.

Example:

“Both starch and glycogen are polymers of α-glucose, but glycogen is more highly branched, allowing faster glucose release.”

3.5 Suggest

Use biological context.

Do not give generic:

“Do more repeats.”

Better:

“Repeat each enzyme-rate measurement and calculate a mean to reduce the effect of random variation.”

3.6 Evaluate

Use:

• supporting evidence;
• contradictory evidence;
• limitations;
• sample size;
• controls;
• statistical significance where given;
• biological mechanism.

End with a justified conclusion.

3.7 Calculate

Show:

1. formula;
2. substitution;
3. processing;
4. units;
5. appropriate significant figures.

For pH:

[ \mathrm{pH}=-\log_{10}[\mathrm{H^+}] ]

4. Common Misconceptions & Lost Marks

4.1 Calling triglycerides polymers

❌ Triglycerides are not polymers.

They are formed from one glycerol and three fatty acids.

4.2 Condensation “adds water”

❌ Condensation releases/removes water.

Hydrolysis uses water.

4.3 Glycosidic bond formed by hydrolysis

❌ It is formed by condensation.

4.4 Starch made from β-glucose

❌ Starch and glycogen are made from α-glucose.

Cellulose is made from β-glucose.

4.5 Cellulose described as branched

❌ Cellulose chains are straight and unbranched.

4.6 “Hydrogen bonds in cellulose are strong”

Better:

“Many hydrogen bonds form between adjacent chains, collectively giving high tensile strength.”

4.7 Benedict's test without heating

Heating in a water bath is required.

4.8 Testing non-reducing sugar without neutralising acid

After acid hydrolysis, neutralise before Benedict's reagent.

4.9 Iodine positive result written “black”

Use:

[ \boxed{\text{blue-black}} ]

4.10 Lipid emulsion test missing water

Ethanol dissolves lipid; addition of water produces the white emulsion.

4.11 Peptide bond confused with hydrogen bond

Peptide bond is covalent and joins amino acids.

Hydrogen bonds help stabilise protein structure.

4.12 Primary structure = number of amino acids

Incomplete.

Primary structure is the sequence of amino acids.

4.13 Tertiary structure described only as “folding”

Name bonds/interactions:

• hydrogen;
• ionic;
• disulfide.

4.14 Enzyme “dies”

Enzymes denature.

4.15 Temperature explanation missing collisions

For the increasing phase, mention:

• kinetic energy;
• collision frequency;
• enzyme–substrate complexes.

4.16 Denaturation means peptide bonds break

Normally, denaturation disrupts interactions maintaining higher-order structure, not the primary peptide-bond sequence.

4.17 Competitive inhibitor binds “near” active site

It competes for/binds to the active site.

4.18 Non-competitive inhibitor binds active site

It binds elsewhere and alters tertiary structure/active-site shape.

4.19 DNA helicase breaks phosphodiester bonds

❌ DNA helicase breaks hydrogen bonds between complementary bases.

4.20 DNA polymerase forms hydrogen bonds

❌ DNA polymerase catalyses condensation forming phosphodiester bonds between adjacent nucleotides.

4.21 DNA nucleotide contains ribose

DNA contains deoxyribose.

RNA contains ribose.

4.22 RNA contains thymine

RNA uses uracil.

4.23 ATP is “stored energy”

Better:

“ATP transfers energy and releases it by hydrolysis for coupled reactions.”

4.24 ATP hydrolysis releases phosphate by “breaking a high-energy bond”

Avoid oversimplified bond-energy language.

State:

“ATP hydrolysis to ADP and (P_i) releases energy that can be coupled to cellular reactions.”

4.25 Water has high heat capacity “because it is polar”

More precise:

“Hydrogen bonding means substantial energy is required to increase molecular kinetic energy.”

4.26 Cohesion confused with adhesion

AQA's required point is strong cohesion between water molecules.

5. Worked Exam-Style Questions

Question 1 — Carbohydrates [6 marks]

Explain how the structure of glycogen makes it suitable as an energy store in animal cells.

Model answer

“Glycogen is a polymer of α-glucose and is highly branched. The branching gives many terminal ends, so enzymes can hydrolyse glycosidic bonds at many positions simultaneously and glucose can be released rapidly for respiration. Glycogen is compact, allowing a large amount to be stored in a small volume. It is insoluble, so it does not diffuse out of cells and has little effect on cell water potential.”

Indicative marking points:

• α-glucose polymer;
• highly branched;
• many ends;
• rapid hydrolysis/glucose release;
• compact;
• insoluble / little osmotic effect.

Question 2 — Lipids [5 marks]

Explain why phospholipids form bilayers in water whereas triglycerides do not.

Model answer

“A phospholipid has a hydrophilic phosphate-containing head and hydrophobic fatty-acid tails. In water, the heads interact with water while the tails orient away from it, so two layers form with the tails facing inward. Triglycerides have three fatty-acid chains and no hydrophilic phosphate-containing head, so they do not form the same bilayer arrangement.”

Question 3 — Enzyme Rate [8 marks]

An enzyme-controlled reaction is measured at increasing temperatures. Rate rises from (10^\circ\mathrm C) to (40^\circ\mathrm C) and then falls sharply.

Explain the pattern.

Model answer

“Between (10^\circ\mathrm C) and (40^\circ\mathrm C), increasing temperature increases the kinetic energy of enzyme and substrate molecules. They move faster and collide more frequently, so more successful collisions occur and more enzyme–substrate complexes form per unit time. Above the optimum temperature, increased molecular vibration disrupts bonds maintaining the enzyme's tertiary structure. The active site changes shape and becomes less complementary to the substrate, so fewer enzyme–substrate complexes form. The enzyme becomes denatured and the reaction rate falls.”

Question 4 — DNA Replication [8 marks]

Describe semi-conservative replication of DNA.

Full-mark model answer

“DNA helicase unwinds the double helix and breaks hydrogen bonds between complementary bases, separating the two polynucleotide strands. Each original strand acts as a template. Free DNA nucleotides are attracted to exposed bases and complementary base pairing occurs: A with T and C with G. DNA polymerase catalyses condensation reactions between adjacent nucleotides, forming phosphodiester bonds in the new polynucleotide strand. Two DNA molecules are produced, each containing one original strand and one newly synthesised strand, so replication is semi-conservative.”

Question 5 — ATP [6 marks]

Explain why ATP is well suited to transferring energy within cells.

Model answer

“ATP can be hydrolysed rapidly to ADP and inorganic phosphate. The hydrolysis releases a small, manageable quantity of energy that can be coupled directly to energy-requiring reactions. The phosphate released can phosphorylate other compounds, often making them more reactive. ATP can be rapidly resynthesised from ADP and inorganic phosphate by condensation, so it can be reused continuously.”

Question 6 — Water [6 marks]

Explain two properties of water that are important in living organisms.

Model answer

High heat capacity:

“Hydrogen bonds between water molecules require substantial energy to disrupt, so water undergoes relatively small temperature changes when energy is transferred. This buffers temperature changes and helps maintain conditions suitable for enzyme activity.”

High latent heat of vaporisation:

“A large amount of energy is required to separate water molecules during evaporation because hydrogen bonds must be disrupted. Evaporation therefore removes substantial thermal energy and provides cooling, for example in sweating or transpiration.”

Question 7 — Required Practical 1 [8 marks]

A student investigates the effect of substrate concentration on an enzyme-controlled reaction.

Explain how the student should produce valid quantitative data.

Model answer

“Prepare a range of known substrate concentrations while keeping enzyme concentration constant. Keep temperature and pH constant using a water bath and buffer respectively, and use equal total reaction volumes. Start the reaction in the same way for each concentration and measure the initial rate using an objective measure of product formation or substrate disappearance. Repeat each concentration and calculate a mean to reduce random variation. Plot mean initial rate against substrate concentration. If rate is obtained from a progress curve, use a tangent at time zero and calculate its gradient. Use the same apparatus and measurement method throughout and identify anomalous results only with evidence.”

6. Links to Other Topics

6.1 3.2 Cells

Biological molecules form:

• plasma membranes;
• organelle membranes;
• ribosomes;
• chromosomes;
• enzymes.

Phospholipids are central to membrane structure.

6.2 3.3 Exchange

Links include:

• carbohydrate digestion;
• protein digestion;
• lipid digestion;
• sodium-glucose co-transport;
• water movement.

6.3 3.4 Genetic Information

DNA structure leads directly to:

• genes;
• genetic code;
• protein synthesis;
• mutations;
• meiosis and variation.

6.4 3.5 Energy Transfers

ATP is central to:

• photosynthesis;
• respiration;
• phosphorylation;
• active transport.

Water and enzymes are also fundamental to metabolic pathways.

6.5 3.6 Responses

Protein receptors, ion channels, enzymes and ATP are central to:

• nervous coordination;
• muscle contraction;
• homeostasis.

6.6 3.8 Gene Expression

DNA/RNA structure is required for:

• transcription;
• translation;
• mutations;
• epigenetics;
• gene technology.

7. Summary Notes

7.1 Monomers and polymers

Monomer: small unit used to make larger molecules.

Polymer: molecule made from many monomers.

Examples:

• monosaccharides;
• amino acids;
• nucleotides.

Condensation:

[ \boxed{\text{bond forms + water released}} ]

Hydrolysis:

[ \boxed{\text{bond broken + water used}} ]

7.2 Carbohydrates

Monosaccharides:

• glucose;
• galactose;
• fructose.

Disaccharides:

[ \text{glucose+glucose}\rightarrow\text{maltose} ]

[ \text{glucose+fructose}\rightarrow\text{sucrose} ]

[ \text{glucose+galactose}\rightarrow\text{lactose} ]

Bond:

[ \boxed{\text{glycosidic}} ]

Starch:

• α-glucose;
• plant storage;
• amylose + amylopectin.

Glycogen:

• α-glucose;
• animal storage;
• highly branched.

Cellulose:

• β-glucose;
• alternate molecules inverted;
• straight chains;
• many hydrogen bonds;
• microfibrils;
• high tensile strength.

7.3 Food tests

Reducing sugar:

• Benedict's;
• heat;
• blue → coloured precipitate.

Non-reducing sugar:

• acid hydrolysis;
• heat;
• neutralise;
• Benedict's;
• heat.

Starch:

• iodine/potassium iodide;
• blue-black positive.

Lipids:

• ethanol;
• add water;
• white/milky emulsion.

Protein:

• Biuret;
• lilac/purple positive.

7.4 Lipids

Triglyceride:

[ \boxed{ 1\text{ glycerol}+3\text{ fatty acids} } ]

Bond:

[ \boxed{\text{ester}} ]

Saturated:

• no C=C.

Unsaturated:

• one or more C=C.

Phospholipid:

• glycerol;
• two fatty acids;
• phosphate-containing group;
• hydrophilic head;
• hydrophobic tails;
• forms bilayers.

7.5 Proteins

Amino acid contains:

• amino group;
• carboxyl group;
• H;
• R group.

Bond:

[ \boxed{\text{peptide}} ]

Primary:

[ \boxed{\text{amino-acid sequence}} ]

Secondary:

• local folding;
• hydrogen bonds.

Tertiary:

• overall 3D shape;
• hydrogen;
• ionic;
• disulfide interactions.

Quaternary:

• multiple polypeptide subunits.

7.6 Enzymes

Enzymes:

[ \boxed{\text{lower activation energy}} ]

Induced fit:

• substrate binds;
• active site changes shape;
• enzyme–substrate complex;
• substrate bonds strained;
• lower activation energy.

Temperature:

• low/moderate → kinetic energy ↑ → collisions ↑ → complexes ↑;
• high → tertiary structure changes → active site changes → denaturation.

pH:

• changes charges/bonds;
• tertiary structure changes;
• activity falls.

Substrate concentration:

• rate rises then plateaus when active sites saturated.

Enzyme concentration:

• rate increases if substrate is available.

Competitive inhibitor:

[ \boxed{\text{binds active site}} ]

Non-competitive inhibitor:

[ \boxed{\text{binds elsewhere and alters active site}} ]

7.7 DNA and RNA

Nucleotide:

• pentose;
• phosphate;
• organic base.

DNA:

• deoxyribose;
• A, T, C, G;
• double helix;
• two polynucleotide strands.

RNA:

• ribose;
• A, U, C, G;
• relatively short;
• usually single-stranded.

Bond between nucleotides:

[ \boxed{\text{phosphodiester}} ]

Complementary DNA bases:

[ A-T ]

[ C-G ]

Strands held together by:

[ \boxed{\text{hydrogen bonds}} ]

7.8 DNA replication

1. helicase unwinds;
2. helicase breaks hydrogen bonds;
3. strands separate;
4. each original strand is template;
5. free nucleotides complementary pair;
6. DNA polymerase catalyses condensation;
7. phosphodiester bonds form;
8. each new DNA molecule contains one old and one new strand.

[ \boxed{\text{semi-conservative}} ]

7.9 ATP

ATP:

• adenine;
• ribose;
• three phosphate groups.

Hydrolysis:

[ \boxed{ ATP+H_2O\rightarrow ADP+P_i } ]

enzyme:

[ \boxed{\text{ATP hydrolase}} ]

Functions:

• releases usable energy;
• phosphorylation;
• couples energy-requiring reactions.

Resynthesis:

[ \boxed{ ADP+P_i\rightarrow ATP+H_2O } ]

enzyme:

[ \boxed{\text{ATP synthase}} ]

during:

• respiration;
• photosynthesis.

7.10 Water

Required roles:

• metabolite in condensation/hydrolysis;
• solvent;
• high heat capacity;
• high latent heat of vaporisation;
• cohesion;
• supports water columns;
• surface tension.

Hydrogen bonding underlies many properties.

7.11 Inorganic ions

[ \mathrm{H^+} ]

• pH;
• enzyme/protein effects.

Iron ions:

• haemoglobin.

[ \mathrm{Na^+} ]

• co-transport of glucose/amino acids.

Phosphate:

• DNA;
• ATP;
• phosphorylation.

3.2 Cells

3.2 Specification Coverage

SPEC: 3.2.1 Cell structure

• 3.2.1.1 Structure of eukaryotic cells
• 3.2.1.2 Structure of prokaryotic cells and viruses
• 3.2.1.3 Methods of studying cells

SPEC: 3.2.2 All cells arise from other cells

• cell cycle
• mitosis
• cancer
• binary fission
• viral replication
• Required Practical 2

SPEC: 3.2.3 Transport across cell membranes

• fluid-mosaic model
• diffusion
• facilitated diffusion
• osmosis and water potential
• active transport
• co-transport
• Required Practicals 3 and 4

SPEC: 3.2.4 Cell recognition and the immune system

• cell-surface antigens
• phagocytosis
• T lymphocytes
• B lymphocytes
• antibodies
• monoclonal antibodies
• vaccination
• HIV
• ethical issues associated with vaccines and monoclonal antibodies
• Required Practical 6

3.2.1 Structure of Eukaryotic Cells

DEFINITION — Eukaryotic cell
A cell containing a nucleus and membrane-bound organelles.

Cell-surface membrane

A cell-surface membrane is a selectively permeable phospholipid bilayer containing proteins and other molecules. It controls exchange, cell signalling and cell recognition.

Nucleus

The nucleus:

• is surrounded by a nuclear envelope;
• contains linear DNA associated with histone proteins;
• contains one or more nucleoli;
• controls cell activities through gene expression.

The nucleolus synthesises ribosomal RNA and assembles ribosomal subunits.

Mitochondrion

Adapted for aerobic respiration:

• double membrane;
• inner membrane folded into cristae, increasing area for electron-transfer chains and ATP synthase;
• matrix contains enzymes for the link reaction and Krebs cycle;
• contains circular DNA and 70S ribosomes.

Chloroplast

Found in plants and algae:

• double envelope;
• flattened membrane sacs called thylakoids;
• stacks of thylakoids = grana;
• grana connected by lamellae;
• stroma contains enzymes for the Calvin cycle;
• contains circular DNA and 70S ribosomes.

Golgi apparatus

A stack of flattened membrane sacs that:

• modifies proteins and lipids;
• sorts them;
• packages them into vesicles;
• produces secretory vesicles and lysosomes.

Lysosome

A membrane-bound organelle containing hydrolytic enzymes. It can digest:

• worn-out organelles;
• material engulfed by phagocytosis;
• pathogens.

Ribosome

Site of translation/protein synthesis.

• eukaryotic cytoplasm: mainly 80S;
• prokaryotes, mitochondria and chloroplasts: 70S.

Rough endoplasmic reticulum

Membranous network bearing ribosomes. It:

• synthesises proteins destined for secretion/membranes/lysosomes;
• transports proteins to the Golgi.

Smooth endoplasmic reticulum

Lacks ribosomes and is associated with:

• lipid synthesis;
• steroid synthesis;
• other metabolic functions.

Cell wall

Plant and algal walls contain cellulose; fungal walls contain chitin. Functions:

• mechanical support;
• maintains shape;
• prevents osmotic bursting.

Plant vacuole

Contains cell sap and is surrounded by the tonoplast. Functions:

• maintains turgor;
• stores solutes/pigments/waste;
• supports plant tissues.

A* application: specialised cells

Always link an adaptation to its effect:

“Many mitochondria provide ATP for active transport.” “Microvilli increase membrane surface area, increasing the number of transport proteins and therefore rate of absorption.”

3.2.1.2 Prokaryotic Cells and Viruses

DEFINITION — Prokaryotic cell
A cell lacking a nucleus and membrane-bound organelles.

Prokaryotes have:

• cytoplasm with no membrane-bound organelles;
• smaller 70S ribosomes;
• one circular DNA molecule free in cytoplasm and not associated with histones in the AQA model;
• cell wall containing murein.

Many also possess:

• plasmids;
• capsule;
• flagella.

Viruses

Viruses are acellular and non-living. Virus particles contain:

• genetic material, DNA or RNA;
• a protein capsid;
• attachment proteins.

Some viruses possess a lipid envelope, but the AQA core structure required is genetic material + capsid + attachment protein.

Viruses do not divide. They replicate only inside host cells by using host-cell machinery.

3.2.1.3 Studying Cells

Magnification

[ \boxed{\text{magnification}=\frac{\text{image size}}{\text{actual size}}} ]

Rearrange carefully: [ \text{actual size}=\frac{\text{image size}}{\text{magnification}} ]

Resolution

DEFINITION — Resolution
The minimum distance apart at which two objects can still be distinguished as separate.

Higher resolution reveals more detail.

Optical microscope

Advantages:

• living specimens can be viewed;
• colour images possible;
• simple preparation.

Limitations:

• lower resolution than electron microscopes;
• limited by wavelength of visible light.

Transmission electron microscope (TEM)

• electrons pass through thin specimen;
• very high resolution;
• shows internal ultrastructure;
• 2D image.

Limitations:

• vacuum required;
• specimens dead;
• complex preparation may introduce artefacts.

Scanning electron microscope (SEM)

• scans surface;
• produces 3D-appearing surface image;
• lower resolution than TEM but greater depth information.

Artefacts

DEFINITION — Artefact
A structure or appearance produced by specimen preparation rather than naturally present in the living specimen.

Cell fractionation

1. Homogenisation breaks cells open in a cold, isotonic, buffered solution.
2. Filter removes large debris.
3. Ultracentrifugation separates organelles by size/mass/density using increasing speeds.

Why conditions matter:

• cold slows enzymes that could digest organelles;
• isotonic prevents osmotic damage;
• buffered maintains pH and protein structure.

3.2.2 Cell Cycle and Mitosis

DEFINITION — Cell cycle
The sequence of growth, DNA replication and division in a cell that retains the ability to divide.

Interphase

Includes:

• cell growth;
• organelle replication;
• DNA replication;
• ATP/protein synthesis.

Mitosis

Mitosis produces nuclei genetically identical to one another and to the parent nucleus, assuming no mutation.

Stages:

Prophase

• chromosomes condense and become visible;
• each chromosome consists of two sister chromatids;
• nuclear envelope breaks down;
• spindle forms.

Metaphase

• chromosomes align at equator;
• spindle fibres attach to centromeres.

Anaphase

• centromeres divide;
• sister chromatids move to opposite poles.

Telophase

• chromosomes reach poles and decondense;
• nuclear envelopes reform.

Cytokinesis

• cytoplasm divides to form two daughter cells.

Mitotic index

[ \boxed{\text{mitotic index}= \frac{\text{number of cells in mitosis}}{\text{total number of cells}}} ]

Cancer

Cancer can result from uncontrolled cell division. Tumours arise when control of the cell cycle is disrupted. Treatments may target rapidly dividing cells, which explains side effects in healthy tissues with rapidly dividing cells.

Binary fission

In prokaryotes:

1. circular DNA replicates;
2. plasmids replicate;
3. cell enlarges;
4. DNA molecules move apart;
5. cytoplasm divides.

Daughter cells receive one circular chromosome and a variable number of plasmids.

Viral replication

Virus attaches to host, introduces genetic material, hijacks host machinery to synthesise viral nucleic acid/proteins, assembles new particles and releases them.

Required Practical 2 — Root Tip Squash and Mitosis

Core method:

1. obtain actively growing root tip;
2. soften/hydrolyse tissue where required;
3. stain DNA/chromosomes;
4. squash under coverslip into a thin layer;
5. use optical microscope;
6. identify mitotic stages;
7. calculate mitotic index.

Good drawing:

• clear continuous lines;
• no shading;
• correct proportions;
• label observable structures only.

Safety:

• stains/acids may be irritants or corrosive;
• use appropriate PPE and handling.

3.2.3 Membrane Structure

The fluid-mosaic model describes phospholipids forming a bilayer with proteins embedded within or associated with it.

Components:

• phospholipids;
• intrinsic/integral proteins;
• extrinsic/peripheral proteins;
• channel proteins;
• carrier proteins;
• glycoproteins;
• glycolipids;
• cholesterol.

Cholesterol

Fits between phospholipids and restricts their movement, helping regulate membrane fluidity and stability.

Glycoproteins/glycolipids

Functions include:

• receptors;
• antigens;
• cell adhesion;
• cell recognition.

Transport Across Membranes

Simple diffusion

DEFINITION — Diffusion
Net movement of particles from a region of higher concentration to a region of lower concentration due to random molecular motion.

Rate increases with:

• greater concentration gradient;
• greater surface area;
• shorter diffusion distance;
• higher temperature.

Small non-polar/lipid-soluble molecules cross phospholipid bilayer more readily.

Facilitated diffusion

Passive movement down concentration gradient via:

• channel proteins;
• carrier proteins.

No ATP required.

Osmosis

DEFINITION — Osmosis
Net movement of water molecules from a region of higher water potential to a region of lower water potential through a partially permeable membrane.

Pure water has water potential: [ 0\text{ kPa} ] under standard conditions; adding solute makes water potential more negative.

Active transport

Moves substances against concentration gradient using:

• carrier proteins;
• ATP hydrolysis.

Sequence:

1. molecule/ion binds;
2. ATP hydrolysis causes phosphorylation/conformational change;
3. molecule moves across;
4. carrier returns to original shape.

Co-transport: sodium and glucose in ileum

1. Na(^+) actively transported from epithelial cell into blood, lowering intracellular Na(^+).
2. Na(^+) enters epithelial cell from lumen down gradient via co-transporter.
3. Glucose/amino acid enters with Na(^+), possibly against its own concentration gradient.
4. Glucose leaves epithelial cell into blood by facilitated diffusion.

Adaptations for rapid transport

• microvilli increase area;
• many channels/carriers;
• many mitochondria for ATP;
• steep gradients maintained by blood flow/active transport.

Required Practical 3 — Water Potential of Plant Tissue

Core design:

1. prepare dilution series of known solute concentrations;
2. cut equal-size plant tissue pieces;
3. measure initial mass/length;
4. incubate equal times in equal volumes;
5. blot consistently;
6. measure final mass/length;
7. calculate percentage change: [ \boxed{%\text{ change}=\frac{\text{final}-\text{initial}}{\text{initial}}\times100} ]
8. plot percentage change against concentration/water potential;
9. find point where change = 0;
10. infer tissue water potential.

Controls:

• temperature;
• tissue source;
• dimensions/surface area;
• time;
• volume;
• blotting method.

Required Practical 4 — Membrane Permeability

Typical beetroot model:

• pigment stored in vacuoles;
• membrane damage releases pigment.

Possible independent variables:

• temperature;
• ethanol concentration;
• pH.

Method quality:

• equal-size cylinders;
• wash cut tissue to remove leaked pigment;
• equal volumes;
• controlled exposure time;
• colorimeter for objective absorbance;
• blank/calibrate colorimeter;
• repeats and mean.

Interpretation: greater absorbance = more pigment released = greater membrane permeability.

3.2.4 Cell Recognition and Immunity

Antigens

DEFINITION — Antigen
A molecule, usually a protein, that is recognised as foreign by the immune system and can stimulate an immune response.

Cell-surface molecules allow recognition of:

• pathogens;
• foreign cells from the same species;
• abnormal body cells;
• toxins.

Antigenic variation

Pathogens may change antigens. Memory cells formed against one antigen may not recognise a new variant, reducing immunity and complicating vaccination.

Phagocytosis

1. phagocyte recognises/binds pathogen;
2. membrane engulfs pathogen into a phagosome;
3. lysosomes fuse with phagosome;
4. lysozymes hydrolyse pathogen;
5. phagocyte may present pathogen antigens on its surface.

T Lymphocytes — Cellular Response

1. antigen-presenting cell displays foreign antigen.
2. Complementary T helper cell binds.
3. T cell becomes activated and divides by mitosis — clonal expansion.
4. T helper cells release cytokines and activate B cells/phagocytes.
5. T killer cells can destroy infected/abnormal cells.
6. T memory cells remain for faster secondary response.

B Lymphocytes — Humoral Response

1. specific B cell binds complementary antigen.
2. Activated by T helper signals.
3. Clonal expansion occurs.
4. Cells differentiate into:
   • plasma cells producing antibodies;
   • memory B cells.

Antibody

DEFINITION — Antibody
A protein produced by plasma cells with a specific binding site complementary to a particular antigen.

Antibodies may:

• agglutinate pathogens;
• neutralise toxins;
• mark pathogens for phagocytosis.

Primary vs secondary response

Primary:

• slower;
• lower antibody concentration;
• memory cells formed.

Secondary:

• faster;
• larger antibody concentration;
• longer lasting due to memory cells.

Vaccination

Vaccines introduce antigenic material safely enough to stimulate:

• primary immune response;
• memory cells.

Future infection triggers rapid secondary response before severe symptoms develop.

Herd immunity reduces transmission when a high proportion of population is immune.

Potential limitations:

• antigenic variation;
• pathogen reservoirs;
• incomplete coverage;
• immunocompromised individuals;
• waning immunity.

Monoclonal Antibodies

DEFINITION — Monoclonal antibody
Identical antibodies produced from a single clone of cells and therefore specific to one antigen/epitope.

Production principle:

1. immunise mouse;
2. isolate B lymphocytes;
3. fuse B cells with tumour cells to form hybridoma;
4. select clone producing desired antibody;
5. culture clone;
6. harvest/purify antibody.

Uses:

• diagnosis;
• locating specific molecules;
• targeted drug delivery;
• pregnancy testing;
• cancer treatment.

Evaluation must consider:

• specificity;
• side effects;
• ethical use of animals;
• false positives/negatives.

HIV and AIDS

HIV:

• enters T helper cells;
• reverse transcriptase produces DNA from viral RNA;
• viral DNA integrates into host DNA;
• virus replicates;
• T helper cell numbers decline.

AIDS results when immune function is severely impaired, increasing susceptibility to opportunistic infections/cancers.

Antibiotics do not treat viruses because viruses lack bacterial targets.

Required Practical 6 — Antimicrobial Substances and Microbial Growth

Aseptic principles:

• sterilise media/equipment;
• minimise lid opening;
• use sterile instruments;
• tape lid appropriately rather than fully sealing if protocol requires;
• incubate at safe school temperature;
• dispose safely.

Disc-diffusion interpretation: larger clear zone of inhibition suggests stronger inhibition, but comparisons require:

• same microbial lawn;
• same disc size;
• same antimicrobial volume/concentration;
• same agar depth;
• same incubation conditions.

Area can be calculated: [ A=\pi r^2 ]

3.2 Common Misconceptions & Lost Marks

• Magnification is not resolution.
• Prokaryotes do not have a nucleus or membrane-bound organelles.
• Viruses are not cells and do not divide by binary fission.
• Mitosis separates sister chromatids; DNA replication occurs before mitosis in interphase.
• Osmosis concerns water potential, not “water concentration”.
• Facilitated diffusion does not require ATP.
• Active transport requires carrier proteins and energy from ATP hydrolysis.
• Antibodies are produced by plasma cells, not by antigens.
• Antibiotics do not kill viruses.
• Monoclonal antibodies are identical and specific because they originate from one clone.

3.2 Worked Exam-Style Questions

Q1 [6 marks] Explain why a secretory cell contains abundant RER, Golgi apparatus and mitochondria.

Model answer: RER ribosomes synthesise polypeptides for secretion; RER transports proteins to Golgi; Golgi modifies and packages proteins into vesicles; exocytosis requires membrane trafficking; mitochondria produce ATP supporting protein synthesis/vesicle movement and other active processes.

Q2 [6 marks] Explain co-transport of glucose from the ileum lumen into blood.

Model answer: Na(^+) is actively transported from epithelial cells into blood using ATP, maintaining a low intracellular Na(^+) concentration. Na(^+) then moves from lumen into epithelial cells down its electrochemical gradient via a co-transporter, carrying glucose into the cell. Glucose then moves into blood through a carrier by facilitated diffusion.

Q3 [6 marks] Explain why vaccination can prevent symptoms on later infection.

Model answer: Vaccine antigen activates specific lymphocytes; clonal expansion occurs; plasma cells produce antibodies; memory cells remain; later exposure causes rapid clonal expansion and a faster/larger secondary response; pathogen is destroyed before it reaches a population sufficient to cause severe symptoms.

3.3 Organisms Exchange Substances with Their Environment

3.3.1 Surface Area to Volume Ratio

As an organism increases in size:

• surface area increases approximately with length²;
• volume increases approximately with length³;
• SA:V falls.

Small organisms may exchange sufficiently by diffusion across body surface. Large active organisms require:

• specialised exchange surfaces;
• ventilation;
• mass transport systems.

Adaptations of effective exchange surfaces:

• large surface area;
• thin barrier;
• steep concentration gradient;
• movement of medium/blood maintains gradient.

3.3.2 Gas Exchange

Insects

Tracheal system:

• spiracles connect exterior to tracheae;
• tracheae branch into tracheoles;
• tracheoles reach respiring cells.

Gas exchange by diffusion; abdominal movements can ventilate. Water loss reduced by:

• closable spiracles;
• waterproof cuticle;
• small surface-area adaptations.

Fish gills

Features:

• gill filaments;
• many lamellae = large surface area;
• thin exchange barrier;
• blood flow opposite water flow = counter-current.

Counter-current maintains oxygen concentration gradient along entire lamella; blood continues to encounter water with higher O₂ concentration, maximising uptake.

Dicot leaf

Gas exchange through stomata:

• CO₂ diffuses to mesophyll;
• O₂ diffuses out;
• mesophyll air spaces provide internal surface area;
• thin moist mesophyll surfaces facilitate diffusion.

Guard cells regulate stomatal aperture.

Mammalian lungs

Although detailed alveolar structure is familiar, exam answers should link:

• many alveoli → large area;
• squamous epithelium → short diffusion path;
• capillary network/blood flow → maintains gradient;
• ventilation → maintains alveolar O₂/CO₂ gradients;
• surfactant helps reduce surface tension (context dependent).

Pulmonary ventilation: [ \boxed{\text{PVR}=\text{tidal volume}\times\text{breathing rate}} ]

3.3.3 Digestion and Absorption

Digestion hydrolyses large molecules into small soluble molecules.

Carbohydrates

• amylase hydrolyses starch to maltose/short sugars;
• membrane-bound disaccharidases produce monosaccharides.

Proteins

• endopeptidases hydrolyse peptide bonds within polypeptide chains;
• exopeptidases remove terminal amino acids/dipeptides;
• membrane-bound dipeptidases hydrolyse dipeptides.

Lipids

Lipase hydrolyses ester bonds: [ \text{triglyceride}\rightarrow\text{monoglycerides + fatty acids} ]

Bile salts:

• emulsify lipids, increasing surface area;
• form micelles with lipid digestion products.

Micelles

Micelles carry monoglycerides/fatty acids to epithelial membrane. Products leave micelle, diffuse into cells, are re-esterified and packaged into chylomicrons.

Ileum adaptations

• villi;
• microvilli;
• thin epithelium;
• capillary network;
• lacteals;
• many mitochondria/transport proteins.

3.3.4.1 Mass Transport in Animals

Haemoglobin

Haemoglobin:

• globular protein;
• quaternary structure;
• four haem groups;
• each can bind O₂.

Cooperative binding

First O₂ changes haemoglobin shape, increasing affinity of remaining sites. This generates an S-shaped oxyhaemoglobin dissociation curve.

Loading/unloading

High pO₂ in lungs → haemoglobin loads O₂. Lower pO₂ in respiring tissues → unloads O₂.

Bohr effect

Higher CO₂ concentration:

• lowers haemoglobin affinity for O₂;
• curve shifts right;
• promotes unloading in respiring tissues.

Different haemoglobins can have different affinities, adaptive to environment.

Mammalian Circulation

Double circulation:

• pulmonary circuit;
• systemic circuit.

Required named vessels particularly include those entering/leaving:

• heart;
• lungs;
• kidneys; plus coronary arteries.

Heart

Know:

• atria;
• ventricles;
• septum;
• AV valves;
• semilunar valves;
• vena cava;
• pulmonary artery;
• pulmonary vein;
• aorta;
• coronary arteries.

Cardiac cycle

Atrial systole: atria contract, forcing blood into ventricles. Ventricular systole: ventricular pressure rises; AV valves close; semilunar valves open once ventricular pressure exceeds arteries. Diastole: ventricles relax; semilunar valves close; AV valves open when atrial pressure exceeds ventricular.

Valves ensure unidirectional flow due to pressure differences.

Cardiac output

[ \boxed{\text{cardiac output}=\text{stroke volume}\times\text{heart rate}} ]

Blood Vessels

Arteries

• thick smooth muscle/elastic tissue;
• narrow lumen relative to wall;
• withstand high pressure;
• elastic recoil maintains pressure.

Arterioles

• smooth muscle controls lumen diameter;
• controls blood distribution and resistance.

Veins

• thinner walls;
• larger lumen;
• valves prevent backflow;
• low pressure.

Capillaries

• one-cell-thick endothelium;
• narrow diameter;
• extensive networks;
• short diffusion distance;
• large total cross-sectional area slows flow and aids exchange.

Tissue Fluid

Formation at arteriole end:

• hydrostatic pressure of blood exceeds opposing forces;
• water and small solutes forced out;
• cells and most plasma proteins remain in capillary.

At venule end:

• blood hydrostatic pressure has fallen;
• plasma proteins lower blood water potential;
• water returns by osmosis.

Excess tissue fluid enters lymphatic vessels and later rejoins blood.

Cardiovascular Risk

Evaluate associations with:

• smoking;
• diet;
• high blood pressure;
• cholesterol;
• inactivity;
• obesity;
• genetic factors.

A correlation alone does not prove causation. Consider confounding variables and study design.

Required Practical 5 — Dissection

May involve gas exchange or mass-transport system/organ.

Exam skills:

• safe use of instruments;
• identify structures;
• relate observed anatomy to function;
• produce biological drawings with scale/proportion;
• distinguish observation from interpretation.

3.3.4.2 Mass Transport in Plants

Xylem

Transports:

• water;
• mineral ions; mainly upward.

Adaptations:

• dead hollow vessels;
• no end walls;
• lignified walls prevent collapse;
• pits allow lateral movement.

Cohesion-tension theory

1. water evaporates from mesophyll;
2. leaf water potential decreases;
3. water drawn from xylem;
4. tension created in xylem;
5. cohesion due to hydrogen bonding maintains continuous water column;
6. column pulled upward.

Transpiration increases with:

• temperature;
• wind;
• light (through stomatal opening); and decreases with high humidity.

Potometer measures water uptake, used as an estimate of transpiration rate.

Phloem and Translocation

Phloem transports assimilates such as sucrose from sources to sinks.

Mass-flow hypothesis

At source:

1. sucrose actively loaded into companion cells/sieve tubes;
2. lowers water potential;
3. water enters from xylem by osmosis;
4. raises hydrostatic pressure.

At sink:

1. sucrose removed for use/storage;
2. water potential rises;
3. water leaves phloem;
4. hydrostatic pressure lower.

Pressure gradient drives bulk flow.

Evidence:

• ringing experiments;
• radiolabelled tracers;
• pressure/exudation data.

Limitations/evaluation may include energetic loading and bidirectional transport in different sieve tubes.

3.3 Common Misconceptions

• Counter-current is not simply “blood and water flow differently”; they flow in opposite directions to maintain gradient along entire exchange surface.
• Bile salts do not chemically digest lipids; they emulsify and form micelles.
• Tissue fluid does not normally contain red blood cells or large plasma proteins.
• Xylem transport does not require ATP in vessel elements.
• Potometers measure water uptake, not direct transpiration.
• Phloem transports organic solutes and can move in different directions in different sieve tubes.

3.3 Exam Questions

Q1 [6] Explain counter-current exchange in fish gills.

Water and blood flow in opposite directions; at every point water has a higher O₂ concentration than blood; diffusion gradient is maintained along lamella; equilibrium is not reached early; O₂ continues diffusing into blood; high extraction efficiency results.

Q2 [6] Explain tissue-fluid formation and return.

High capillary hydrostatic pressure forces water/small solutes out at arteriole end; proteins remain lowering blood water potential; hydrostatic pressure decreases along capillary; at venule end lower blood water potential draws water back by osmosis; excess enters lymph.

Q3 [6] Explain mass flow in phloem.

Sucrose actively loaded at source, lowers water potential, water enters from xylem, raises hydrostatic pressure; sucrose unloaded at sink, water potential rises, water leaves; pressure gradient causes bulk flow.

3.4 Genetic Information, Variation and Relationships

3.4.1 DNA, Genes and Chromosomes

Prokaryotic DNA

• short;
• circular;
• not associated with histones in AQA model.

Eukaryotic nuclear DNA

• very long;
• linear;
• associated with histones;
• DNA + proteins = chromosome.

Mitochondria/chloroplasts:

• short circular DNA;
• not associated with histones in AQA model.

Gene

DEFINITION — Gene
A base sequence of DNA that codes for the amino-acid sequence of a polypeptide or a functional RNA.

Locus

DEFINITION — Locus
Fixed position of a gene on a DNA molecule/chromosome.

Genetic code

A sequence of three DNA bases = triplet.

Properties:

• universal — same triplets usually code for same amino acids across organisms;
• non-overlapping — each base belongs to one triplet in a reading frame;
• degenerate — more than one triplet may code for the same amino acid.

Introns and exons

Eukaryotic genes contain:

• exons — coding sequences retained in mature mRNA;
• introns — non-coding sequences removed during splicing.

3.4.2 DNA and Protein Synthesis

Genome

Complete set of genetic information/genes in a cell/organism.

Proteome

Full range of proteins a cell is able to produce.

mRNA

• single-stranded;
• sequence complementary to template DNA;
• carries codons to ribosome.

tRNA

• folded single strand;
• anticodon;
• amino-acid attachment site.

Transcription

1. DNA at gene unwinds and hydrogen bonds break.
2. RNA nucleotides align by complementary base pairing to template strand.
3. RNA polymerase joins nucleotides by phosphodiester bonds.
4. In prokaryotes, mRNA can be used directly.
5. In eukaryotes, pre-mRNA is spliced: introns removed, exons joined.

Translation

1. mRNA attaches to ribosome.
2. Ribosome reads codon.
3. tRNA with complementary anticodon brings specific amino acid.
4. ATP supplies energy associated with tRNA/amino-acid processes.
5. peptide bonds form between amino acids.
6. ribosome moves along mRNA.
7. polypeptide released at stop codon.

No need to memorise specific codon table.

3.4.3 Mutation and Meiosis

Mutation

Gene mutation changes DNA base sequence. Chromosome mutation can alter chromosome number or structure.

Meiosis

Produces haploid cells and generates variation through:

• crossing over between homologous chromosomes;
• independent segregation of homologous chromosome pairs.

Random fertilisation adds further genetic variation.

Crossing over

During prophase I:

• homologous chromosomes pair;
• non-sister chromatids exchange corresponding DNA segments;
• new allele combinations form.

Independent segregation

At metaphase I, homologous pairs orient randomly. Maternal/paternal homologues segregate independently, producing many chromosome combinations in gametes.

3.4.4 Genetic Diversity and Adaptation

DEFINITION — Genetic diversity
Number/range of different alleles present in a population.

Natural selection:

1. mutation creates new alleles;
2. individuals vary genetically;
3. selection pressure causes differential survival/reproduction;
4. advantageous allele holders leave more offspring;
5. allele frequency increases over generations.

Types of adaptation:

• anatomical;
• physiological;
• behavioural.

3.4.5 Species and Taxonomy

DEFINITION — Species
A group of organisms able to interbreed to produce fertile offspring.

Courtship:

• species recognition;
• synchronises mating;
• ensures sexual readiness;
• reduces unsuccessful interspecific mating.

Taxonomy hierarchy

[ \boxed{\text{domain → kingdom → phylum → class → order → family → genus → species}} ]

Binomial naming

Genus + species, e.g. Homo sapiens.

Phylogenetic classification aims to reflect evolutionary relationships/common ancestry.

Evidence can include:

• DNA sequence;
• protein sequence;
• immunological comparisons.

3.4.6 Biodiversity

Species richness

DEFINITION — Species richness
Number of different species present in a community.

Index of diversity

AQA formula: [ \boxed{d=\frac{N(N-1)}{\sum n(n-1)}} ] where:

• (N) = total organisms of all species;
• (n) = organisms of each species.

Higher (d) generally indicates greater diversity.

Farming can reduce biodiversity through:

• monoculture;
• herbicides/pesticides;
• habitat removal;
• hedgerow removal;
• drainage;
• intensive grazing.

Conservation strategies can balance food production and biodiversity.

3.4.7 Investigating Diversity

Compare genetic diversity using:

• observable/measurable characteristics;
• DNA base sequences;
• mRNA sequences;
• amino-acid sequences.

Greater sequence similarity generally indicates closer evolutionary relationship, but interpretation must consider mutation rates and data quality.

Sampling should be:

• random where appropriate;
• sufficiently large;
• representative.

3.4 Common Misconceptions

• A gene is not “a chromosome”; it is a DNA base sequence at a locus.
• Degenerate does not mean ambiguous: one codon specifies one amino acid, but several codons may specify the same amino acid.
• RNA polymerase makes RNA; DNA polymerase replicates DNA.
• Crossing over occurs between non-sister chromatids of homologous chromosomes.
• Natural selection acts on phenotypes; allele frequencies change across generations.
• “Fittest” means greatest reproductive success in the environment, not strongest.

3.4 Exam Questions

Q1 [6] Explain how meiosis generates genetic variation.

Crossing over exchanges DNA between non-sister chromatids of homologous chromosomes, producing new allele combinations. Homologous pairs orient randomly and segregate independently, creating different chromosome combinations in gametes. Random fertilisation then combines gametes unpredictably.

Q2 [6] Explain transcription and RNA splicing.

DNA unwinds; complementary RNA nucleotides pair with template; RNA polymerase forms phosphodiester bonds; pre-mRNA produced in eukaryotes; introns removed; exons joined; mature mRNA leaves nucleus.

Q3 [4] Calculate diversity using supplied (N) and (n) values.

Use (d=N(N-1)/\sum n(n-1)); calculate each species term before summing; use adequate precision.

3.5 Energy Transfers in and Between Organisms

3.5.1 Photosynthesis

Chloroplast adaptations

• thylakoid membranes contain chlorophyll, electron carriers and ATP synthase;
• grana increase area;
• stroma contains Calvin-cycle enzymes;
• compartmentalisation maintains proton gradients.

Light-Dependent Reaction

1. chlorophyll absorbs photons;
2. electrons become excited and leave chlorophyll — photoionisation;
3. electrons pass along electron-transfer chain;
4. energy is used to pump H(^+) across thylakoid membrane;
5. proton electrochemical gradient forms;
6. H(^+) flows through ATP synthase;
7. ATP formed from ADP + (P_i) — photophosphorylation;
8. electrons/protons reduce NADP to reduced NADP;
9. photolysis replaces electrons: [ \boxed{2H_2O\rightarrow4H^+ +4e^-+O_2} ]

Oxygen is a by-product.

Calvin Cycle / Light-Independent Reaction

1. CO₂ combines with RuBP (5C).
2. Reaction catalysed by rubisco.
3. Unstable 6C compound forms and splits into two GP (3C).
4. ATP + reduced NADP reduce GP to triose phosphate (TP).
5. Some TP makes organic compounds.
6. Most TP regenerates RuBP using ATP.

Products derived from TP can include:

• glucose/hexose;
• starch;
• cellulose;
• lipids;
• amino acids (with mineral ions).

Limiting Factors

Photosynthesis can be limited by:

• light intensity;
• CO₂ concentration;
• temperature.

At any moment, the factor in shortest effective supply limits rate.

Commercial growers may control:

• lighting;
• CO₂ enrichment;
• temperature; but must evaluate cost vs yield/profit.

Required Practical 7 — Photosynthetic Pigments by Chromatography

Method principles:

• grind leaf in suitable solvent;
• spot pigment extract on chromatography medium;
• keep origin above solvent;
• allow solvent to rise;
• mark solvent front;
• identify bands;
• calculate: [ R_f=\frac{\text{distance pigment}}{\text{distance solvent front}} ]

Control:

• solvent;
• medium;
• run time;
• plant tissue mass;
• extraction procedure.

Required Practical 8 — Chloroplast Dehydrogenase Activity

Common indicator: DCPIP.

• oxidised DCPIP: blue;
• reduced DCPIP: colourless.

Light-dependent reactions transfer electrons, reducing indicator.

Possible variables:

• light intensity;
• wavelength;
• temperature;
• chloroplast concentration.

Rate:

• time to decolourise;
• change in absorbance per unit time using colorimeter.

Controls:

• equal chloroplast volume/concentration;
• temperature;
• DCPIP concentration;
• light exposure.

3.5.2 Respiration

Glycolysis

Occurs in cytoplasm and is anaerobic.

1. glucose phosphorylated using ATP;
2. glucose phosphate converted to triose phosphate;
3. triose phosphate oxidised;
4. reduced NAD formed;
5. ATP formed by substrate-level phosphorylation;
6. pyruvate produced.

Net products per glucose commonly considered:

• 2 pyruvate;
• reduced NAD;
• net ATP.

Anaerobic Pathways

Mammals

[ \boxed{\text{pyruvate + reduced NAD → lactate + NAD}} ]

Yeast/plants in suitable contexts

[ \boxed{\text{pyruvate → ethanol + CO₂}} ] with reduced NAD oxidised.

Purpose:

• regenerate oxidised NAD so glycolysis can continue.

Link Reaction

Pyruvate enters mitochondrial matrix by active transport.

Pyruvate:

• decarboxylated;
• dehydrogenated;
• forms acetate;
• NAD reduced.

Acetate + coenzyme A: [ \boxed{\text{acetylcoenzyme A}} ]

Krebs Cycle

Acetyl-CoA (2C) combines with 4C compound → 6C compound.

Series of reactions:

• decarboxylation releases CO₂;
• dehydrogenation reduces NAD/FAD;
• substrate-level phosphorylation forms ATP;
• 4C acceptor regenerated.

The purpose is not simply ATP direct production; it generates many reduced coenzymes for oxidative phosphorylation.

Oxidative Phosphorylation / Chemiosmosis

1. reduced NAD/FAD donate electrons to electron-transfer chain on inner mitochondrial membrane.
2. electrons move through carriers in redox reactions.
3. energy pumps protons from matrix into intermembrane space.
4. electrochemical proton gradient forms.
5. H(^+) diffuses through ATP synthase.
6. ATP synthase catalyses ATP formation.
7. oxygen is final electron acceptor and combines with electrons/H(^+) to form water.

No oxygen → electron chain stops → reduced coenzymes cannot be reoxidised efficiently → aerobic respiration stops.

Other Respiratory Substrates

Lipids:

• glycerol can enter glycolysis pathways;
• fatty acids converted to acetyl-CoA.

Proteins:

• amino acids deaminated;
• carbon skeletons enter glycolysis/Krebs intermediates.

Required Practical 9 — Respiration Rate in Single-Celled Organisms

Possible organisms:

• yeast.

Variables:

• temperature;
• substrate concentration;
• substrate type.

Measurements:

• CO₂ production;
• O₂ consumption;
• redox indicator change.

Controls:

• organism density;
• pH;
• total volume;
• equilibration time.

3.5.3 Energy and Ecosystems

Biomass and productivity

Gross primary production (GPP) = chemical energy stored by photosynthesis.

Net primary production (NPP): [ \boxed{\text{NPP}=\text{GPP}-R} ] where (R) = respiratory losses by producers.

NPP is energy/biomass available for plant growth and consumers.

For consumers: [ \boxed{\text{net production}=\text{ingested energy}-(\text{faecal loss}+\text{respiratory loss})} ]

Efficiency

[ \boxed{\text{efficiency}=\frac{\text{energy transferred}}{\text{energy available}}\times100} ]

Losses:

• respiration/heat;
• movement;
• excretion;
• uneaten material;
• indigestible material.

Increasing agricultural efficiency:

• reduce movement;
• maintain optimal temperature;
• selective breeding;
• high-quality feed;
• control disease.

Evaluate ethics, welfare and environmental costs.

3.5.4 Nutrient Cycles

Nitrogen cycle

Key processes:

Nitrogen fixation

Atmospheric (N_2) → ammonium compounds by nitrogen-fixing bacteria:

• free-living;
• symbiotic in root nodules.

Ammonification

Decomposers convert organic nitrogen in dead matter/waste to ammonium ions.

Nitrification

Aerobic nitrifying bacteria: [ NH_4^+\rightarrow NO_2^-\rightarrow NO_3^- ]

Assimilation

Plants absorb nitrate/ammonium and make amino acids/proteins; nitrogen passes through food chains.

Denitrification

Anaerobic denitrifying bacteria convert nitrate to (N_2), returning nitrogen to atmosphere.

Phosphorus cycle

Phosphate released from:

• weathering of rocks;
• decomposition;
• excretion.

Plants absorb phosphate; moves through food chains; returns by decomposition. Some enters sediments and geological stores.

Fertilisers and eutrophication

Nitrate/phosphate enrichment can cause:

1. algal bloom;
2. light blocked;
3. submerged plants die;
4. decomposers increase;
5. aerobic respiration increases;
6. dissolved O₂ falls;
7. aquatic animals die.

3.5 Common Misconceptions

• Oxygen from photosynthesis comes from water, not CO₂.
• Light-independent reaction does not mean it only happens at night; it depends indirectly on products of light-dependent reaction.
• Glycolysis occurs in cytoplasm.
• Oxygen is the final electron acceptor in oxidative phosphorylation.
• ATP synthase uses proton flow down electrochemical gradient.
• NPP is not GPP + respiration; it is GPP − respiration.
• Nitrification is aerobic; denitrification is associated with anaerobic conditions.

3.5 Exam Questions

Q1 [8] Explain chemiosmosis in mitochondria.

Reduced coenzymes donate electrons; electrons pass through ETC; energy pumps H(^+) from matrix; proton electrochemical gradient across inner membrane; H(^+) returns through ATP synthase; ATP formed from ADP + Pi; oxygen accepts electrons and H(^+), forming water.

Q2 [6] Explain Calvin cycle.

CO₂ + RuBP catalysed by rubisco; unstable 6C → 2 GP; ATP and reduced NADP reduce GP to TP; some TP makes organic compounds; most regenerates RuBP using ATP.

Q3 [5] Explain eutrophication.

Nitrate/phosphate enters water; algal growth; light penetration falls; plants/algae die; decomposers respire; oxygen depleted; aerobic aquatic organisms die.

3.6 Organisms Respond to Changes

Core pathway

[ \boxed{\text{stimulus → receptor → coordinator → effector → response}} ]

Receptors are specific to stimuli.

Nervous responses are usually:

• rapid;
• localised;
• short-lived.

Hormonal responses are often:

• slower;
• widespread;
• longer-lasting.

3.6.1.1 Survival and Response

Plant tropisms and IAA

IAA is produced in growing regions and affects cell elongation.

Shoots:

• IAA generally stimulates elongation;
• asymmetric IAA distribution causes bending.

Roots:

• higher IAA concentrations inhibit elongation;
• differential growth generates gravitropic response.

Explain phototropism/gravitropism by:

1. directional stimulus;
2. unequal IAA distribution;
3. different elongation rates;
4. curvature.

Taxes

Directional movement toward/away from stimulus.

Kineses

Non-directional change in speed/turning rate related to stimulus intensity, increasing time spent in favourable conditions.

Reflex arc

Three-neurone reflex:

• sensory neurone;
• relay neurone;
• motor neurone;
• synapses;
• rapid protective response without conscious processing first.

Required Practical 10 — Animal Movement

Choice chamber/maze:

• change one environmental variable;
• provide control/neutral conditions;
• randomise sides to avoid positional bias;
• equal starting positions;
• enough organisms;
• repeat;
• ethical treatment.

Can use chi-squared when testing association between categorical choices.

3.6.1.2 Receptors

Pacinian corpuscle

Pressure deforms lamellae:

1. stretch-mediated Na(^+) channels open;
2. Na(^+) enters sensory neurone;
3. generator potential forms;
4. if threshold reached, action potentials generated.

Stronger stimulus → larger generator potential → higher impulse frequency, not larger action potentials.

Retina

Rod cells

• very sensitive to low light;
• rhodopsin;
• many rods converge on one bipolar neurone;
• spatial summation increases sensitivity;
• low visual acuity;
• monochromatic.

Cone cells

• less sensitive;
• three types with different pigments;
• colour vision;
• often one cone to one bipolar neurone in fovea;
• high visual acuity.

Fovea:

• many cones;
• little convergence;
• high acuity.

Peripheral retina:

• more rods;
• high sensitivity.

3.6.1.3 Control of Heart Rate

Heart is myogenic.

Sequence:

1. SAN initiates wave of excitation across atria;
2. atria contract;
3. AVN delays impulse;
4. bundle of His conducts through septum;
5. Purkyne tissue carries excitation to ventricular walls;
6. ventricles contract from apex upwards.

Control:

• chemoreceptors detect CO₂/pH;
• pressure receptors detect blood pressure;
• cardiovascular centre alters autonomic output;
• sympathetic activity increases heart rate;
• parasympathetic decreases.

3.6.2.1 Nerve Impulses

Resting potential

Created by:

• Na(^+)/K(^+) pump moves 3 Na(^+) out, 2 K(^+) in;
• membrane more permeable to K(^+);
• K(^+) diffuses out;
• inside becomes negative relative to outside.

Action potential

1. stimulus depolarises membrane to threshold;
2. voltage-gated Na(^+) channels open;
3. Na(^+) enters → rapid depolarisation;
4. Na(^+) channels close/inactivate;
5. K(^+) channels open;
6. K(^+) leaves → repolarisation;
7. temporary hyperpolarisation;
8. resting conditions restored.

All-or-nothing

Below threshold: no action potential. At/above threshold: full action potential of fixed size. Stimulus intensity encoded by frequency of action potentials.

Refractory period

During recovery, membrane cannot immediately generate another action potential. Importance:

• impulses discrete;
• limits maximum frequency;
• helps one-way propagation.

Myelination

Myelin electrically insulates axon. Depolarisation occurs at nodes of Ranvier; impulse effectively jumps node to node — saltatory conduction.

Speed increases with:

• myelination;
• larger axon diameter;
• higher temperature within viable range.

3.6.2.2 Synaptic Transmission

Cholinergic synapse

1. action potential reaches presynaptic knob;
2. voltage-gated Ca(^{2+}) channels open;
3. Ca(^{2+}) enters;
4. vesicles fuse with presynaptic membrane;
5. acetylcholine released by exocytosis;
6. diffuses across cleft;
7. binds receptors on postsynaptic membrane;
8. Na(^+) channels open;
9. depolarisation may reach threshold;
10. acetylcholinesterase hydrolyses acetylcholine;
11. components recycled.

Unidirectionality

• transmitter vesicles presynaptic;
• receptors postsynaptic.

Summation

Temporal: repeated impulses from one presynaptic neurone combine. Spatial: impulses from multiple presynaptic neurones combine.

Inhibition

Inhibitory neurotransmitters can open channels causing hyperpolarisation, making threshold less likely.

Neuromuscular junction

Similar chemical transmission, but postsynaptic target is muscle fibre; action potential triggers contraction.

3.6.3 Skeletal Muscle

Structure

Muscle:

• bundles of fibres;
• fibres contain myofibrils;
• myofibrils composed of repeating sarcomeres;
• thin actin filaments;
• thick myosin filaments.

Sliding-filament mechanism

1. action potential causes Ca(^{2+}) release from sarcoplasmic reticulum;
2. Ca(^{2+}) binds to regulatory proteins and moves tropomyosin away from actin binding sites;
3. myosin heads bind actin → actinomyosin bridges;
4. myosin head changes angle, pulling actin — power stroke;
5. ATP binds myosin causing detachment;
6. ATP hydrolysis re-cocks myosin head;
7. cycle repeats while Ca(^{2+}) and ATP available.

AQA does not require detailed role of troponin.

Phosphocreatine

Rapidly regenerates ATP: [ \text{phosphocreatine + ADP → creatine + ATP} ]

Slow fibres

• many mitochondria;
• high myoglobin;
• dense capillary supply;
• suited to sustained aerobic activity;
• fatigue resistant.

Fast fibres

• fewer mitochondria;
• less myoglobin;
• larger glycogen stores;
• rapid powerful contraction;
• fatigue faster.

3.6.4 Homeostasis

DEFINITION — Homeostasis
Maintenance of a stable internal environment within restricted limits.

Important for:

• enzyme activity;
• blood pH;
• core temperature;
• blood glucose;
• water potential.

Negative feedback

A deviation is detected and responses oppose the change, restoring the variable toward normal.

Separate mechanisms may correct increases and decreases.

3.6.4.2 Blood Glucose

Liver roles:

• glycogenesis: glucose → glycogen;
• glycogenolysis: glycogen → glucose;
• gluconeogenesis: glucose from non-carbohydrate sources.

Insulin

Released when blood glucose high. Binds receptors on target cells and:

• increases glucose uptake in some cells;
• increases glycogenesis;
• increases glucose use.

Glucagon

Released when blood glucose low. Binds cell-surface receptors, leading to:

• glycogenolysis;
• gluconeogenesis.

Adrenaline

Also promotes glycogenolysis.

Second messenger model

1. hormone binds cell-surface receptor;
2. activates adenylate cyclase;
3. ATP converted to cAMP;
4. cAMP activates protein kinase;
5. enzyme cascade changes metabolism.

Diabetes

Type I:

• immune destruction of pancreatic beta cells;
• little/no insulin;
• controlled with insulin, monitoring, diet.

Type II:

• reduced responsiveness to insulin and/or inadequate insulin secretion;
• associated with genetic and lifestyle factors;
• managed with diet, activity, medication, sometimes insulin.

Required Practical 11 — Glucose Calibration Curve

1. prepare dilution series of known glucose concentrations;
2. react under identical conditions;
3. use colorimeter;
4. blank instrument;
5. plot absorbance against concentration;
6. measure unknown urine analogue;
7. interpolate from calibration curve.

Controls:

• temperature;
• reaction time;
• reagent volumes;
• cuvette;
• wavelength/filter.

3.6.4.3 Osmoregulation

Ultrafiltration

At glomerulus:

• afferent arteriole wider than efferent;
• high hydrostatic pressure;
• small molecules forced through capillary endothelium, basement membrane and podocyte gaps;
• proteins/cells retained.

Filtrate contains:

• water;
• glucose;
• ions;
• urea.

Proximal convoluted tubule

Selective reabsorption:

• Na(^+) actively transported;
• glucose/amino acids co-transported;
• water follows by osmosis.

Loop of Henle

Creates low water potential/high Na(^+) concentration in medulla using counter-current multiplier principles.

• ascending limb impermeable to water, actively transports Na(^+)/Cl(^-);
• descending limb permeable to water;
• medullary gradient allows water reabsorption from collecting duct.

ADH

If blood water potential falls:

1. osmoreceptors in hypothalamus detect;
2. posterior pituitary releases ADH;
3. ADH binds collecting duct/distal tubule receptors;
4. aquaporins inserted into membranes;
5. permeability to water increases;
6. more water reabsorbed;
7. small volume concentrated urine.

When water potential rises, ADH secretion decreases.

3.6 Common Misconceptions

• Stronger stimulus increases impulse frequency, not action-potential amplitude.
• Na(^+)/K(^+) pump is important for maintaining gradients, not the rapid depolarisation step itself.
• Synaptic transmission is unidirectional because transmitter release and receptors are asymmetrically located.
• ATP causes myosin detachment; ATP hydrolysis re-cocks the head.
• ADH does not “add water to blood”; it increases collecting-duct water permeability.
• Insulin lowers blood glucose; glucagon generally raises it.

3.7 Genetics, Populations, Evolution and Ecosystems

3.7.1 Inheritance

Key terms

Genotype: genetic constitution. Phenotype: observable expression of genotype interacting with environment. Allele: alternative form of a gene. Homozygous: two same alleles at locus. Heterozygous: two different alleles. Dominant: expressed in heterozygote. Recessive: expressed only without dominant allele. Codominant: both alleles expressed in heterozygote.

Students must interpret/predict:

• monohybrid crosses;
• dihybrid crosses;
• codominance;
• multiple alleles;
• sex linkage;
• autosomal linkage;
• epistasis.

Use fully labelled genetic diagrams with:

• parental genotypes;
• gametes;
• offspring;
• phenotypes;
• ratios/probabilities.

Sex linkage

Genes on sex chromosomes. X-linked recessive alleles are more likely expressed in XY males because only one X allele is present.

Autosomal linkage

Genes on same autosome tend to be inherited together unless crossing over separates them.

Epistasis

One gene affects expression of another gene at a different locus.

Chi-Squared Test

[ \boxed{\chi^2=\sum\frac{(O-E)^2}{E}} ]

Steps:

1. null hypothesis: no significant difference between observed and expected; differences due to chance.
2. calculate expected values.
3. calculate (\chi^2).
4. degrees of freedom: [ \boxed{df=\text{number of categories}-1} ]
5. compare with critical value.
6. if calculated value > critical: reject null hypothesis.
7. if ≤ critical: fail to reject null hypothesis.

Use “significant” only in statistical sense.

3.7.2 Populations and Hardy–Weinberg

DEFINITION — Population
Organisms of the same species occupying a particular place at a particular time and potentially able to interbreed.

Gene pool: all alleles of all genes in a population. Allele frequency: proportion of a particular allele.

Hardy–Weinberg: [ \boxed{p+q=1} ] [ \boxed{p^2+2pq+q^2=1} ]

where:

• (p^2): one homozygous genotype;
• (2pq): heterozygotes;
• (q^2): other homozygous genotype.

Conditions:

• large population;
• random mating;
• no mutation;
• no migration/gene flow;
• no selection.

3.7.3 Evolution and Speciation

DEFINITION — Evolution
Change in allele frequencies in a population over generations.

Natural selection

Alleles increasing reproductive success rise in frequency.

Genetic drift

Random changes in allele frequency, especially significant in small populations.

Speciation

1. population isolated;
2. gene flow stops;
3. different mutations, drift and selection act;
4. allele frequencies diverge;
5. reproductive isolation develops;
6. populations can no longer interbreed to produce fertile offspring.

Isolation can be geographic or reproductive/ecological in mechanism.

3.7.4 Populations in Ecosystems

Abiotic factors

Examples:

• temperature;
• light;
• pH;
• water availability;
• oxygen;
• mineral ions.

Biotic factors

• competition;
• predation;
• disease;
• food availability.

Niche

DEFINITION — Ecological niche
The role of a species in an ecosystem, including how it uses resources and interacts with biotic/abiotic factors.

No two species can occupy exactly the same niche indefinitely under identical limiting conditions without competitive exclusion.

Population Growth

Typical sigmoid curve:

1. lag phase;
2. exponential/log phase;
3. stationary phase at carrying capacity.

Limiting factors become more important as population increases.

Competition

Intraspecific: within species. Interspecific: between species.

Competition reduces growth/reproduction/survival where resources are limiting.

Predator–Prey Cycles

Predator and prey population changes can be linked with a time lag, but real ecosystems are affected by many additional factors. Avoid claiming predator abundance is the only cause.

Succession

DEFINITION — Succession
Directional change in community composition over time.

Primary succession:

1. pioneer species colonise bare habitat;
2. weathering/organic matter forms soil;
3. conditions change;
4. larger plants establish;
5. biodiversity and biomass often increase;
6. relatively stable climax community may develop.

Conservation may deliberately prevent succession to maintain a desired plagioclimax.

Sampling

Random sampling

Quadrats placed using random coordinates to reduce bias.

Systematic sampling

Along transect to study change across gradient.

Abundance

Can estimate:

• frequency;
• percentage cover;
• density.

Mark–release–recapture

[ \boxed{N=\frac{n_1\times n_2}{m}} ] where:

• (n_1) = first captured/marked;
• (n_2) = second sample;
• (m) = marked recaptured.

Assumptions:

• population closed;
• marking does not affect survival/capture;
• marks not lost;
• marked individuals mix fully;
• sufficient time but not too much reproduction/migration.

Required Practical 12 — Environmental Factor and Species Distribution

Possible factors:

• light intensity;
• soil moisture;
• pH;
• distance from shore;
• trampling.

Method:

• transect through gradient;
• quadrats at fixed/random distances;
• measure abiotic factor;
• record abundance;
• repeat;
• analyse association/correlation.

Use Spearman's rank for correlation where appropriate.

Spearman's Rank

[ \boxed{r_s=1-\frac{6\sum d^2}{n(n^2-1)}} ]

Null hypothesis:

no significant correlation between the two variables.

Compare calculated value with critical value considering (n) and significance level.

Correlation does not itself prove causation.

3.8 The Control of Gene Expression

3.8.1 Gene Mutations

Mutations include:

• addition;
• deletion;
• substitution;
• inversion;
• duplication;
• translocation of bases.

Substitution

May:

• change one codon;
• be silent due to degeneracy;
• alter one amino acid;
• create stop codon depending on data.

Addition/deletion

If not multiple of three, causes frameshift:

• changes all downstream triplets;
• often major effect on polypeptide.

Mutation rate can be increased by mutagenic agents such as ionising radiation and some chemicals.

Phenotypic effect depends on:

• position;
• codon change;
• amino acid properties;
• effect on protein structure/function;
• whether mutation occurs in coding/regulatory/non-coding region.

3.8.2.1 Cell Differentiation and Stem Cells

Totipotent

Can form all body cell types and extraembryonic tissues; early embryonic cells.

Pluripotent

Can form many/all body cell types but not complete organism with supporting tissues.

Multipotent

Can form a limited range of related cell types.

Unipotent

Can form one cell type.

iPS cells

Adult somatic cells reprogrammed by transcription factors to pluripotent state.

Potential benefits:

• replace damaged cells;
• patient-specific therapy;
• disease modelling.

Risks/ethics:

• tumour formation;
• immune rejection;
• control of differentiation;
• embryo-use ethics for embryonic stem cells.

3.8.2.2 Regulation of Transcription and Translation

Transcription factors

Specific transcription factors:

• move into nucleus;
• bind DNA/regulatory regions;
• stimulate or inhibit transcription.

Oestrogen model

1. oestrogen diffuses through cell membrane;
2. binds complementary intracellular receptor;
3. receptor changes shape;
4. complex enters nucleus/binds DNA;
5. acts as transcription factor;
6. target gene transcription increases.

Epigenetics

DEFINITION — Epigenetics
Heritable changes in gene function/expression without alteration of DNA base sequence.

DNA methylation

Increased methylation commonly:

• reduces transcription;
• may prevent transcription-factor binding or promote condensed chromatin.

Histone acetylation

Acetylation generally:

• reduces positive charge interactions between histones and DNA;
• chromatin becomes less condensed;
• transcription easier.

Therefore decreased histone acetylation tends to inhibit transcription.

Environmental factors can alter epigenetic marks.

RNA Interference (RNAi)

Small RNA molecules can bind complementary mRNA:

• prevent translation;
• promote mRNA degradation.

Thus gene expression can be regulated after transcription.

3.8.2.3 Gene Expression and Cancer

Benign tumour

• localised;
• often encapsulated;
• does not invade/metastasise.

Malignant tumour

• invades tissues;
• can spread via blood/lymph;
• forms secondary tumours — metastasis.

Oncogenes

Proto-oncogenes normally stimulate cell division appropriately. Mutation/overexpression can produce oncogenes causing excessive division.

Tumour suppressor genes

Normally inhibit cell division/repair DNA/promote apoptosis. Inactivation can remove growth control.

Methylation

Abnormal methylation may:

• silence tumour suppressor genes;
• alter oncogene regulation.

Some breast cancers are influenced by increased oestrogen signalling.

Evaluate cancer evidence:

• correlation vs causation;
• genetic/environmental interactions;
• sample size;
• confounding variables.

3.8.3 Genome Projects

Sequencing whole genomes allows:

• genes to be identified;
• simple-organism proteomes predicted more readily;
• potential pathogen antigens identified;
• evolutionary comparisons;
• disease-associated variants identified.

In complex eukaryotes:

• non-coding DNA;
• introns;
• alternative splicing;
• regulatory genes;
• epigenetics; mean genome sequence does not straightforwardly predict proteome.

3.8.4.1 Recombinant DNA Technology

DEFINITION — Recombinant DNA
DNA formed by joining DNA from different sources.

Because genetic code/transcription/translation machinery are broadly universal, genes can function in transgenic organisms.

Obtaining DNA fragment

Methods:

1. reverse transcriptase converts mRNA to cDNA;
2. restriction endonuclease cuts desired DNA;
3. gene machine synthesises DNA.

Restriction endonucleases

Cut DNA at specific recognition sequences, often producing sticky ends.

DNA ligase

Joins DNA fragments by forming phosphodiester bonds.

PCR — In Vitro Amplification

Requirements:

• template DNA;
• primers;
• free DNA nucleotides;
• thermostable DNA polymerase;
• buffer.

Cycle:

1. denaturation ~ high temperature separates strands;
2. annealing lower temperature allows primers to bind;
3. extension polymerase synthesises complementary strands.

Repeated cycles produce exponential amplification.

In Vivo Amplification / Transformation

Typical bacterial vector:

• plasmid isolated;
• plasmid and desired DNA cut with same restriction enzyme;
• complementary sticky ends anneal;
• DNA ligase forms phosphodiester bonds;
• recombinant plasmid inserted into bacteria;
• transformed cells cultured.

Marker genes

Used to identify transformed cells:

• antibiotic resistance;
• fluorescent markers;
• enzyme markers.

Ethical/safety issues must be evaluated.

3.8.4.2 DNA Differences for Identification and Diagnosis

DNA probes

Short single-stranded DNA sequences labelled radioactively/fluorescently, complementary to target sequence.

Use:

1. separate DNA strands;
2. probe hybridises to complementary sequence;
3. detect label.

Applications:

• detect mutant alleles;
• identify pathogens;
• identify individuals.

3.8.4.3 Genetic Fingerprinting

Uses variable non-coding repeated DNA sequences such as VNTRs/STR-style regions in principle.

General sequence:

1. obtain DNA;
2. amplify relevant regions by PCR if needed;
3. cut/amplify fragments;
4. separate by electrophoresis;
5. transfer/denature if method requires;
6. hybridise labelled probes;
7. visualise band pattern;
8. compare profiles.

Applications:

• forensic identification;
• paternity/relatedness;
• population/evolution studies.

A match supports common origin but probability/statistical context matters.

3.8 Common Misconceptions

• A mutation does not always change phenotype.
• Degeneracy can make substitutions silent.
• Addition/deletion causes frameshift only when reading frame is disrupted.
• Epigenetic change does not alter DNA base sequence.
• DNA methylation generally inhibits transcription in the AQA model.
• Histone acetylation generally facilitates transcription; decreased acetylation inhibits.
• DNA ligase forms phosphodiester bonds; restriction enzymes cut DNA.
• PCR occurs in vitro; bacterial cloning is in vivo.
• A genetic fingerprint match is evidence, not absolute proof of identity.

Whole-Course Required Practicals — 1 to 12

1. Enzyme-controlled reaction.
2. Root-tip squash, mitosis and mitotic index.
3. Dilution series/calibration to determine plant-tissue water potential.
4. Variable affecting cell-surface membrane permeability.
5. Dissection of gas exchange/mass transport system or organ.
6. Aseptic technique and antimicrobials.
7. Leaf-pigment chromatography.
8. Chloroplast dehydrogenase activity.
9. Variable affecting respiration of single-celled organisms.
10. Environmental variable affecting animal movement in choice chamber/maze.
11. Glucose dilution series/colorimetry and unknown urine analogue.
12. Environmental factor affecting distribution of a species.

Whole-Course Mathematical Toolkit

Percentage change

[ \boxed{%\text{ change}=\frac{\text{new}-\text{original}}{\text{original}}\times100} ]

Percentage uncertainty

[ \boxed{%\text{ uncertainty}=\frac{\text{absolute uncertainty}}{\text{measured value}}\times100} ]

Magnification

[ \boxed{M=\frac{I}{A}} ]

Surface area to volume ratio

[ \boxed{\frac{\text{surface area}}{\text{volume}}} ]

Cardiac output

[ \boxed{CO=SV\times HR} ]

Pulmonary ventilation

[ \boxed{PVR=TV\times BR} ]

Diversity index

[ \boxed{d=\frac{N(N-1)}{\sum n(n-1)}} ]

Hardy–Weinberg

[ \boxed{p+q=1} ] [ \boxed{p^2+2pq+q^2=1} ]

Chi-squared

[ \boxed{\chi^2=\sum\frac{(O-E)^2}{E}} ]

Spearman rank

[ \boxed{r_s=1-\frac{6\sum d^2}{n(n^2-1)}} ]

Mark-release-recapture

[ \boxed{N=\frac{n_1n_2}{m}} ]

Productivity

[ \boxed{NPP=GPP-R} ]

Efficiency

[ \boxed{%\text{ efficiency}=\frac{\text{useful transfer}}{\text{available input}}\times100} ]

Exact AQA Biology Exam Language — Whole Course

Explain

Use a causal chain:

“X increases/decreases because…, which causes…, therefore…”

Biology marks are often lost by jumping from cause to final effect without the intermediate mechanism.

Compare

Write about both items in linked statements:

“Both…, whereas…” “X has…, but Y…”

Evaluate

Use evidence:

• support;
• limitation;
• alternative explanation;
• statistics;
• sample size;
• confounding factors;
• biological mechanism;
• justified conclusion.

Suggest

Ground the answer in supplied context. Avoid generic statements.

Practical improvement

Use:

“Change [specific method] because this reduces [named source of error/uncertainty], therefore improving [precision/validity/reliability].”

Statistical conclusions

Prefer:

“There is / is not a statistically significant difference/correlation at the stated probability level.”

Do not say “proved”.

Whole-Course High-Frequency Lost Marks

• Writing “more energy” without naming ATP or a defined energy transfer.
• Writing “more respiration” without explaining substrate/oxygen/ATP demand where relevant.
• Confusing concentration gradient with water-potential gradient.
• Saying active transport “uses energy” without linking to ATP hydrolysis/carrier proteins.
• Saying enzymes “die”.
• Saying antibodies kill pathogens directly in every context.
• Saying antibiotics treat viruses.
• Treating correlation as causation.
• Failing to distinguish allele frequency from genotype frequency.
• Using “gene” and “allele” interchangeably.
• Saying organisms adapt during their lifetime because they “need to”.
• Forgetting that natural selection acts on existing variation.
• Describing ATP as a long-term energy store.
• Saying DNA polymerase forms hydrogen bonds.
• Saying oxygen produced in photosynthesis comes from CO₂.
• Confusing photophosphorylation and oxidative phosphorylation.
• Omitting proton gradients/ATP synthase in chemiosmosis.
• Confusing source/sink in phloem.
• Claiming xylem transport is active.
• Saying stronger stimuli produce larger action potentials.
• Failing to name Ca(^{2+}), vesicles, neurotransmitter and receptors in synaptic transmission.
• Confusing glucagon with glycogen.
• Saying ADH is made by the posterior pituitary; it is produced in hypothalamic neurones and released from posterior pituitary.
• Treating a p-value threshold as probability the hypothesis is true.
• Giving units to (R_f) or relative ratios.

Whole-Course Synoptic Links for A* Questions

ATP

Links:

• enzymes/phosphorylation;
• active transport;
• co-transport;
• DNA/protein synthesis;
• photosynthesis;
• respiration;
• muscle contraction;
• gene technologies.

Membranes

Links:

• phospholipids;
• transport;
• receptors;
• action potentials;
• synapses;
• mitochondria/chloroplast chemiosmosis;
• kidneys;
• cell signalling.

Proteins

Links:

• enzymes;
• antibodies;
• haemoglobin;
• membrane carriers;
• receptors;
• actin/myosin;
• histones;
• transcription factors.

Gradients

Links:

• diffusion;
• water potential;
• gas exchange;
• tissue fluid;
• xylem;
• proton gradients;
• nerve impulses;
• loop of Henle.

DNA and Gene Expression

Links:

• replication;
• meiosis;
• mutations;
• evolution;
• protein synthesis;
• epigenetics;
• cancer;
• recombinant DNA/PCR.

Variation and Selection

Links:

• meiosis;
• mutation;
• genetic diversity;
• natural selection;
• antibiotic resistance;
• speciation;
• biodiversity.

Whole-Course Summary Notes

3.1 Biological molecules

• condensation forms bonds and releases water; hydrolysis breaks bonds using water;
• carbohydrates: alpha/beta glucose, glycosidic bonds, starch/glycogen/cellulose;
• lipids: triglycerides, ester bonds, phospholipids;
• proteins: amino acids → peptide bonds → primary/secondary/tertiary/quaternary structure;
• enzymes lower activation energy via induced fit;
• DNA/RNA are nucleotide polymers; DNA replication is semi-conservative;
• ATP transfers energy and phosphorylates compounds;
• water properties arise largely from polarity/hydrogen bonding;
• inorganic ions include H(^+), Fe ions, Na(^+), phosphate.

3.2 Cells

• eukaryotes have membrane-bound organelles; prokaryotes do not;
• optical/TEM/SEM differ in resolution and specimen preparation;
• cell fractionation separates organelles;
• cell cycle includes interphase and mitosis;
• membranes follow fluid-mosaic model;
• transport: diffusion, facilitated diffusion, osmosis, active transport, co-transport;
• immunity: antigens, phagocytes, T cells, B cells, antibodies, memory, vaccines;
• HIV attacks T helper cells.

3.3 Exchange

• SA:V decreases with size;
• effective exchange surfaces are large, thin and maintain gradients;
• insects use tracheae/tracheoles; fish use counter-current gills; plants use stomata/mesophyll;
• digestion hydrolyses macromolecules;
• haemoglobin shows cooperative binding and Bohr effect;
• heart/circulation maintain mass transport;
• tissue fluid formed by hydrostatic pressure and returns by osmosis;
• xylem uses cohesion-tension; phloem translocation follows pressure/mass-flow model.

3.4 Genetic information and diversity

• genes are DNA sequences coding for polypeptides or functional RNA;
• genetic code universal, non-overlapping, degenerate;
• transcription produces RNA; translation produces polypeptide;
• meiosis creates variation through crossing over and independent segregation;
• natural selection changes allele frequencies;
• species produce fertile offspring;
• phylogeny uses evolutionary relationships;
• biodiversity measured with species richness/diversity index.

3.5 Energy transfers

• photosynthesis: light-dependent reaction produces ATP/reduced NADP; Calvin cycle fixes CO₂;
• respiration: glycolysis → link → Krebs → oxidative phosphorylation;
• chemiosmosis requires proton gradients and ATP synthase;
• NPP = GPP − respiration;
• trophic transfer inefficient;
• nitrogen and phosphorus recycled by ecosystems.

3.6 Responses

• stimulus → receptor → coordinator → effector;
• IAA controls tropisms;
• receptors generate generator potentials;
• action potentials are all-or-nothing and frequency-coded;
• synapses use neurotransmitters;
• muscle contraction uses Ca(^{2+}), actin, myosin and ATP;
• homeostasis uses negative feedback;
• insulin/glucagon control blood glucose;
• ADH and nephron regulate water potential.

3.7 Genetics and ecosystems

• inheritance includes dominance, codominance, linkage, sex linkage and epistasis;
• use chi-squared for observed vs expected categorical ratios;
• Hardy–Weinberg models allele/genotype frequencies;
• evolution = allele-frequency change;
• drift strongest in small populations;
• isolation can cause speciation;
• population ecology includes competition, predation, succession and sampling;
• use Spearman for correlation and mark-release-recapture for population estimates.

3.8 Gene expression

• mutations alter DNA and may alter polypeptides;
• stem-cell potency ranges from totipotent to unipotent;
• transcription factors, DNA methylation, histone acetylation and RNAi regulate gene expression;
• oncogenes/tumour suppressor genes contribute to cancer;
• genome projects enable identification and medical applications;
• recombinant DNA uses restriction enzymes and ligase;
• PCR amplifies DNA in vitro;
• probes and genetic fingerprints exploit sequence differences.