Biology - Cell Biology and Biochemistry

Cell Structure

Cell Theory

All living organisms are composed of one or more cells
The cell is the basic unit of structure and function in all living organisms
All cells arise from pre-existing cells

Prokaryotic vs Eukaryotic Cells

Feature	Prokaryotic Cells	Eukaryotic Cells
Nucleus	No true nucleus (nucleoid region)	True nucleus with nuclear envelope
Membrane-bound organelles	Absent	Present
DNA	Circular, naked	Linear, associated with histones
Ribosomes	70S (smaller)	80S (larger)
Cell size	1-5 micrometres	10-100 micrometres
Cell wall	Present (peptidoglycan in bacteria)	Present in plants (cellulose), absent in animals
Examples	Bacteria, Archaea	Animals, Plants, Fungi, Protists

Plant vs Animal Cells

Feature	Plant Cells	Animal Cells
Cell wall	Present (cellulose)	Absent
Chloroplasts	Present	Absent
Large central vacuole	Present	Small, temporary vacuoles
Centrioles	Absent	Present
Plasmodesmata	Present	Absent
Shape	Fixed (rectangular)	Variable (irregular)
Stored carbohydrate	Starch	Glycogen

Cell Organelles

Nucleus

The nucleus is the control centre of the cell. It contains:

Nuclear envelope: Double membrane with nuclear pores that control the movement of substances in and out
Nucleolus: Dark-staining region where ribosomal RNA (rRNA) is synthesised
Chromatin: DNA wrapped around histone proteins; condenses into chromosomes during cell division

Functions:

Controls cell activities through gene expression
Stores genetic information (DNA)
Site of DNA replication and transcription

Mitochondria

Mitochondria are the sites of aerobic respiration, producing ATP through the Krebs cycle and oxidative phosphorylation.

Structure:

Outer membrane: Permeable to small molecules
Inner membrane: Folded into cristae to increase surface area; site of the electron transport chain
Matrix: Contains enzymes for the Krebs cycle, mitochondrial DNA, and ribosomes

$\mathrm{C}_6\mathrm{H}_{12}\mathrm{O}_6 + 6\mathrm{O}_2 \to 6\mathrm{CO}_2 + 6\mathrm{H}_2\mathrm{O} + \mathrm{ATP}$

Endoplasmic Reticulum (ER)

Rough ER (RER):

Studded with ribosomes
Involved in protein synthesis and transport
Proteins enter the ER lumen for folding and modification

Smooth ER (SER):

No ribosomes
Involved in lipid synthesis, detoxification, and calcium storage

Golgi Apparatus

A stack of flattened membrane-bound sacs (cisternae) that modifies, sorts, and packages proteins and lipids.

Functions:

Modifies proteins (e.g., adding carbohydrate groups to form glycoproteins)
Packages proteins into vesicles for transport
Forms lysosomes (in animal cells)

Ribosomes

Ribosomes are the sites of protein synthesis (translation).

Free ribosomes: Float in the cytoplasm; synthesise proteins for use within the cell
Bound ribosomes: Attached to the RER; synthesise proteins for secretion or for the cell membrane

Lysosomes

Membrane-bound vesicles containing digestive enzymes (hydrolytic enzymes). Functions include:

Breaking down worn-out organelles (autophagy)
Digesting material engulfed by phagocytosis
Releasing enzymes outside the cell (extracellular digestion)

Chloroplasts (Plant Cells Only)

The site of photosynthesis.

Structure:

Double membrane: Outer and inner membrane
Thylakoids: Flattened sacs containing chlorophyll; site of the light-dependent reactions
Grana: Stacks of thylakoids
Stroma: Fluid-filled space; site of the light-independent reactions (Calvin cycle)

$6\mathrm{CO}_2 + 6\mathrm{H}_2\mathrm{O} \xrightarrow{\mathrm{light}} \mathrm{C}_6\mathrm{H}_{12}\mathrm{O}_6 + 6\mathrm{O}_2$

Cell Membrane

The cell membrane (plasma membrane) is a phospholipid bilayer with embedded proteins.

Fluid Mosaic Model:

Fluid: Individual phospholipid molecules can move laterally within the layer
Mosaic: Various proteins are embedded in the bilayer, creating a pattern

Components:

Phospholipids: form the basic bilayer structure
Intrinsic (integral) proteins: span the entire membrane; involved in transport and signalling
Extrinsic (peripheral) proteins: attached to the surface; involved in cell recognition and enzymatic activity
Cholesterol: regulates membrane fluidity
Glycolipids and glycoproteins: involved in cell recognition

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The cell membrane is selectively permeable: it allows some substances to pass through freely but restricts others. Small, non-polar molecules (e.g., $\mathrm{O}_2$ , $\mathrm{CO}_2$ ) diffuse through easily, while large or charged molecules require transport proteins.

Membrane Transport

Passive Transport (No Energy Required)

Simple Diffusion

Movement of molecules from a region of higher concentration to a region of lower concentration, directly through the phospholipid bilayer.

Only for small, non-polar molecules (e.g., $\mathrm{O}_2$ , $\mathrm{CO}_2$ , lipid-soluble substances)
Net movement stops at equilibrium (dynamic equilibrium)
Rate depends on: concentration gradient, temperature, surface area, distance

Facilitated Diffusion

Movement of molecules down their concentration gradient through transport proteins.

Channel proteins: Form hydrophilic pores for specific ions (e.g., $\mathrm{Na}^+$ , $\mathrm{K}^+$ , $\mathrm{Ca}^{2+}$ )
Carrier proteins: Bind to specific molecules, undergo conformational change, and release on the other side
Used for larger or polar molecules (e.g., glucose, amino acids, ions)

Osmosis

The movement of water molecules from a region of higher water potential to a region of lower water potential, through a selectively permeable membrane.

Water potential ( $\Psi$ ) is measured in kilopascals (kPa). Pure water has $\Psi = 0 \mathrm{ kPa}$ . Adding solutes decreases water potential (makes it more negative).

Osmosis in animal cells:

Solution	Water Potential	Effect on Cell
Hypotonic	Higher than cell	Cell swells and may burst (lysis)
Isotonic	Equal to cell	No net movement
Hypertonic	Lower than cell	Cell shrinks (crenation)

Osmosis in plant cells:

Solution	Effect on Cell
Hypotonic	Cell becomes turgid (firm); useful for plant support
Isotonic	No net movement
Hypertonic	Cytoplasm and vacuole shrink; cell becomes plasmolysed

Active Transport (Energy Required)

Movement of molecules against their concentration gradient (from low to high concentration), requiring ATP and carrier proteins.

Specific to certain molecules (e.g., $\mathrm{Na}^+/\mathrm{K}^+$ pump, absorption of minerals by root hair cells)
Can become saturated at high concentrations (carrier proteins are limiting)
Inhibited by metabolic poisons (e.g., cyanide) that block ATP production

Bulk Transport

Endocytosis

The cell membrane engulfs material to bring it into the cell.

Phagocytosis: "Cell eating" — engulfing solid particles (e.g., white blood cells engulfing bacteria)
Pinocytosis: "Cell drinking" — engulfing liquid droplets

Exocytosis

Vesicles fuse with the cell membrane to release contents outside the cell (e.g., secretion of hormones, neurotransmitters).

Biological Molecules

Carbohydrates

General formula: $\mathrm{C}_x(\mathrm{H}_2\mathrm{O})_y$

Monosaccharides:

Glucose ( $\mathrm{C}_6\mathrm{H}_{12}\mathrm{O}_6$ ): primary energy source
Fructose: found in fruits
Galactose: component of milk sugar
Ribose and deoxyribose: in RNA and DNA respectively

Disaccharides (formed by condensation, broken by hydrolysis):

Disaccharide	Component Monosaccharides
Maltose	Glucose + Glucose
Sucrose	Glucose + Fructose
Lactose	Glucose + Galactose

Polysaccharides:

Starch: Energy storage in plants (amylose: helical; amylopectin: branched)
Glycogen: Energy storage in animals (highly branched)
Cellulose: Structural in plants (beta-glucose, straight chains, hydrogen bonds)
Chitin: Structural in arthropod exoskeletons and fungal cell walls

Tests for carbohydrates:

Benedict's test: Reducing sugars (e.g., glucose) produce a brick-red precipitate when heated with Benedict's reagent
Iodine test: Starch turns blue-black

Proteins

Proteins are polymers of amino acids.

Amino acid structure:

Each amino acid has an amino group ( $\mathrm{NH}_2$ ), a carboxyl group ( $\mathrm{COOH}$ ), a hydrogen atom, and an R group (side chain), all bonded to a central carbon atom.

Peptide bond formation:

Amino acids join by condensation reactions, forming peptide bonds ( $\mathrm{-CO-NH-}$ ) and releasing water.

Dipeptide: 2 amino acids
Polypeptide: many amino acids

Protein structure levels:

Level	Description	Bonds
Primary	Sequence of amino acids	Peptide bonds
Secondary	Alpha-helix or beta-pleated sheet	Hydrogen bonds
Tertiary	3D folding of the polypeptide	H-bonds, ionic bonds, disulphide bridges, hydrophobic interactions
Quaternary	Multiple polypeptide chains	Same as tertiary + more

Tests for proteins:

Biuret test: Add Biuret reagent (NaOH + CuSO $_4$ ); violet/purple colour indicates protein

Lipids

Lipids are organic molecules that are insoluble in water but soluble in organic solvents.

Triglycerides:

Formed from one glycerol + three fatty acids
Joined by ester bonds (condensation reaction)
Energy storage molecules
Contain more energy per gram than carbohydrates

Phospholipids:

Similar to triglycerides but one fatty acid is replaced by a phosphate group
Amphipathic: hydrophilic head (phosphate) and hydrophobic tail (fatty acids)
Form the cell membrane bilayer

Saturated vs unsaturated fatty acids:

Saturated: no double bonds (C-C), solid at room temperature (animal fats)
Unsaturated: one or more double bonds (C=C), liquid at room temperature (plant oils)

Test for lipids:

Ethanol emulsion test: Dissolve in ethanol, pour into water; cloudy white emulsion indicates lipids

Nucleic Acids

DNA (Deoxyribonucleic Acid):

Double-stranded helix
Sugar: deoxyribose
Bases: adenine (A), thymine (T), guanine (G), cytosine (C)
Base pairing: A-T (2 H-bonds), G-C (3 H-bonds)
Stores genetic information

RNA (Ribonucleic Acid):

Usually single-stranded
Sugar: ribose
Bases: A, U (uracil replaces thymine), G, C
Types: mRNA (messenger), tRNA (transfer), rRNA (ribosomal)

Enzymes

Definition

Enzymes are biological catalysts produced by living cells. They are globular proteins that speed up biochemical reactions without being consumed.

Properties of Enzymes

Specific: each enzyme catalyses one particular reaction (or a small group of reactions)
Not used up: can be reused many times
Work in small amounts
Affected by temperature and pH
Protein in nature: denatured by extreme conditions

Lock and Key Hypothesis

The substrate (reactant) fits into the active site of the enzyme like a key fits into a lock. The active site has a specific complementary shape to the substrate.

Induced Fit Hypothesis

A more refined model: the active site changes shape slightly when the substrate binds, improving the fit. This lowers the activation energy of the reaction.

Factors Affecting Enzyme Activity

Temperature:

Rate increases with temperature (up to the optimum)
Beyond the optimum, the enzyme denatures (active site changes shape irreversibly)
Human enzymes: optimum around $37^\circ\mathrm{C}$

pH:

Each enzyme has an optimum pH
Extreme pH causes denaturation by disrupting ionic and hydrogen bonds
Pepsin: optimum pH 2 (stomach)
Trypsin: optimum pH 8 (small intestine)

Substrate concentration:

Increasing substrate concentration increases the rate (up to a point)
At saturation, all active sites are occupied; rate plateaus (Vmax)

Enzyme concentration:

Increasing enzyme concentration increases the rate (provided substrate is not limiting)

warning

Denaturation is irreversible. Once an enzyme is denatured by heat or extreme pH, it cannot regain its function. This is different from a temporary decrease in activity at sub-optimal conditions.

Worked Example 1

An enzyme has an optimum temperature of $40^\circ\mathrm{C}$ . At $20^\circ\mathrm{C}$ , the reaction rate is $0.3$ units/s. At $40^\circ\mathrm{C}$ , the rate is $1.2$ units/s. Calculate the Q10 (temperature coefficient).

$Q_{10} = \frac{\mathrm{Rate at }(T + 10)}{\mathrm{Rate at } T}$

Between $20^\circ\mathrm{C}$ and $30^\circ\mathrm{C}$ : $Q_{10}$ might be approximately 2 (typical for biological reactions). Without the $30^\circ\mathrm{C}$ data, we can estimate the overall effect:

From $20^\circ\mathrm{C}$ to $40^\circ\mathrm{C}$ (a $20^\circ\mathrm{C}$ increase):

$\mathrm{Rate increase factor} = \frac{1.2}{0.3} = 4$

This is consistent with $Q_{10} \approx 2$ (since $2^2 = 4$ ).

Enzyme Inhibition

Competitive inhibition:

Inhibitor has a similar shape to the substrate
Competes with the substrate for the active site
Can be overcome by increasing substrate concentration
Example: malonate inhibiting succinate dehydrogenase

Non-competitive inhibition:

Inhibitor binds to a site other than the active site (allosteric site)
Changes the shape of the active site
Cannot be overcome by increasing substrate concentration
Example: heavy metal ions (lead, mercury)

Cellular Respiration

Glycolysis (Cytoplasm)

Glucose (6C) is phosphorylated (uses 2 ATP)
Glucose is split into two molecules of triose phosphate (3C)
Triose phosphate is oxidised and dehydrogenated (produces 2 NADH)
Net production: 2 ATP, 2 NADH, 2 pyruvate (3C)

Link Reaction (Mitochondrial Matrix)

Pyruvate (3C) is decarboxylated and dehydrogenated
Forms acetyl CoA (2C) + $\mathrm{CO}_2$ + NADH

Krebs Cycle (Mitochondrial Matrix)

For each glucose molecule (two turns of the cycle):

2 $\mathrm{CO}_2$ released
3 NADH produced per turn (6 total)
1 FADH $_2$ produced per turn (2 total)
1 ATP produced per turn (2 total)
Regenerates oxaloacetate (4C)

Oxidative Phosphorylation (Inner Mitochondrial Membrane)

NADH and FADH $_2$ donate electrons to the electron transport chain
Energy released pumps protons across the inner membrane
Protons flow back through ATP synthase, producing ATP
Oxygen is the final electron acceptor, forming water

ATP Yield per Glucose

Stage	ATP (net)
Glycolysis	2
Krebs cycle	2
Oxidative phosphorylation (from NADH)	28
Oxidative phosphorylation (from FADH $_2$ )	4
Total	approximately 36-38

info

The actual ATP yield may be less than 38 due to the cost of transporting NADH from glycolysis into the mitochondria. Many textbooks now quote approximately 30-32 ATP per glucose.

Photosynthesis

Light-Dependent Reactions (Thylakoid Membrane)

Light energy is absorbed by chlorophyll in Photosystem II
Water is split (photolysis): $\mathrm{H}_2\mathrm{O} \to 2\mathrm{H}^+ + 2e^- + \frac{1}{2}\mathrm{O}_2$
Electrons pass through the electron transport chain, generating ATP
Light is absorbed by Photosystem I; electrons are re-energised
Electrons reduce NADP $^+$ to NADPH

Products: ATP, NADPH, $\mathrm{O}_2$

Light-Independent Reactions / Calvin Cycle (Stroma)

$\mathrm{CO}_2$ is fixed by ribulose bisphosphate (RuBP, 5C) using the enzyme RuBisCO
Forms an unstable 6C compound that splits into two molecules of glycerate-3-phosphate (GP, 3C)
GP is reduced to triose phosphate (TP, 3C) using ATP and NADPH
Some TP is used to make glucose and other organic compounds
Most TP is used to regenerate RuBP (uses ATP)

For every 3 $\mathrm{CO}_2$ molecules fixed: 1 molecule of triose phosphate (3C) is produced. It takes 6 $\mathrm{CO}_2$ molecules to produce 1 molecule of glucose (6C).

Limiting Factors in Photosynthesis

Factor	Effect
Light intensity	Increases rate up to a plateau (light saturation point)
$\mathrm{CO}_2$ concentration	Increases rate up to a plateau
Temperature	Increases rate up to optimum, then decreases (enzyme denaturation)

Summary Table

Topic	Key Concept	Location
Prokaryote vs Eukaryote	Nucleus, organelles, ribosome size	All cells
Membrane transport	Diffusion, osmosis, active transport	Cell membrane
Carbohydrates	Monosaccharides, disaccharides, polysaccharides	All organisms
Proteins	Amino acids, peptide bonds, 4 levels of structure	All organisms
Enzymes	Lock and key, induced fit, denaturation	All organisms
Respiration	Glycolysis, Krebs, oxidative phosphorylation	Mitochondria
Photosynthesis	Light-dependent, Calvin cycle	Chloroplasts

Exam Tips

Always distinguish between prokaryotic and eukaryotic cells in comparison questions.
For membrane transport, clearly state whether energy is required and the direction of movement relative to the concentration gradient.
In enzyme questions, always mention the effect on the active site when discussing denaturation.
For photosynthesis limiting factor graphs, identify which factor is limiting at each point on the curve.
When describing biochemical pathways (respiration, photosynthesis), name the specific location of each stage.

Worked Example: Cell Membrane Structure

Explain how the fluid mosaic model of the cell membrane accounts for the following properties: (a) selective permeability, (b) ability of cells to communicate, (c) flexibility for phagocytosis.

If you get this wrong, revise: Cell Organelles -- Cell Membrane

Solution

(a) Selective permeability: The phospholipid bilayer allows small, non-polar molecules (O $_2$ , CO $_2$ ) to diffuse through freely, while blocking large or charged molecules. Channel and carrier proteins provide selective pathways for specific ions and polar molecules (e.g., glucose via carrier proteins, Na $^+$ via channel proteins). Cholesterol modulates fluidity, maintaining permeability at different temperatures.

(b) Cell communication: Glycoproteins and glycolipids on the cell surface act as recognition markers (e.g., MHC proteins for immune recognition, hormone receptors). Extrinsic proteins on the outer surface can bind signalling molecules, triggering intracellular responses via signal transduction.

(c) Flexibility: The phospholipid molecules can move laterally within the bilayer (fluid nature), allowing the membrane to bend and change shape. This enables vesicle formation during endocytosis (phagocytosis) and exocytosis, and allows cells to change shape (e.g., red blood cells squeezing through capillaries).

Exam-Style Practice Questions

Question 1: Describe the structure of the cell membrane and explain how its structure relates to its function.

The cell membrane is a phospholipid bilayer with embedded proteins (fluid mosaic model). The hydrophobic tails face inward and hydrophilic heads face outward, making the membrane a barrier to water-soluble substances. Channel and carrier proteins allow selective transport. Cholesterol maintains fluidity. Glycoproteins on the surface enable cell recognition. The fluid nature allows vesicle formation (endocytosis/exocytosis).

Question 2: Explain the effect of increasing temperature on enzyme activity from $0^\circ\mathrm{C}$ to $60^\circ\mathrm{C}$ .

From $0^\circ\mathrm{C}$ to the optimum (approximately $37-40^\circ\mathrm{C}$ ): increasing temperature increases kinetic energy, leading to more frequent collisions between enzyme and substrate molecules, increasing the rate of reaction. Beyond the optimum temperature, the increased kinetic energy breaks the bonds maintaining the tertiary structure of the enzyme, causing the active site to change shape (denaturation). The substrate can no longer fit, and the reaction rate decreases sharply.

Question 3: Compare and contrast aerobic and anaerobic respiration.

Similarities: Both begin with glycolysis; both produce ATP.

Differences: Aerobic respiration requires oxygen and occurs in the mitochondria, producing approximately 36-38 ATP per glucose with $\mathrm{CO}_2$ and $\mathrm{H}_2\mathrm{O}$ as by-products. Anaerobic respiration occurs without oxygen, only in the cytoplasm, producing 2 ATP per glucose. In animals, it produces lactate; in yeast, it produces ethanol and $\mathrm{CO}_2$ .

Cell Division

Mitosis

Mitosis is the process of cell division that produces two genetically identical daughter cells, each with the same number of chromosomes as the parent cell.

Functions of mitosis:

Growth: increasing the number of cells in an organism
Repair: replacing damaged or dead cells
Asexual reproduction: in some organisms

Stages of Mitosis

Stage	Key Events
Prophase	Chromatin condenses into chromosomes; nucleolus disappears; centrioles move to poles; spindle fibres form; nuclear membrane begins to break down
Metaphase	Chromosomes line up at the equator (metaphase plate); spindle fibres attach to centromeres
Anaphase	Sister chromatids separate at the centromere; spindle fibres pull chromatids to opposite poles; chromosomes have a V-shape
Telophase	Chromosomes arrive at poles and decondense; nuclear membrane reforms; nucleolus reappears; spindle fibres break down
Cytokinesis	Cytoplasm divides; in animal cells, a cleavage furrow forms; in plant cells, a cell plate forms

Worked Example 2 (Cell Division)

A cell in the G2 phase of the cell cycle has 46 chromosomes. How many chromosomes and chromatids will be present in each daughter cell after mitosis?

After mitosis: each daughter cell has 46 chromosomes (each consisting of one chromatid).

During S phase (before mitosis), each chromosome replicates to form two sister chromatids. So at the start of mitosis, there are 46 chromosomes (92 chromatids). After anaphase, the chromatids separate, and each daughter cell receives 46 single-chromatid chromosomes.

Meiosis

Meiosis is a type of cell division that produces four genetically different daughter cells, each with half the number of chromosomes of the parent cell. It is essential for sexual reproduction.

Key differences from mitosis:

Feature	Mitosis	Meiosis
Number of divisions	One	Two
Number of daughter cells	Two	Four
Chromosome number	Same as parent (diploid)	Half of parent (haploid)
Genetic variation	Identical daughter cells	Different daughter cells
Function	Growth, repair, asexual reproduction	Production of gametes (sex cells)

Sources of genetic variation in meiosis:

Crossing over: During prophase I, homologous chromosomes exchange segments of DNA. This creates new combinations of alleles on the same chromosome.
Independent assortment: During metaphase I, homologous pairs line up randomly at the equator. Different combinations of maternal and paternal chromosomes are distributed to daughter cells.
Random fertilisation: Any sperm can fertilise any egg, further increasing genetic diversity.

Meiosis Stages

Meiosis I (reductional division):

Prophase I: Homologous chromosomes pair up (synapsis); crossing over occurs
Metaphase I: Homologous pairs line up at the equator
Anaphase I: Homologous chromosomes separate (sister chromatids remain together)
Telophase I: Two cells form, each with half the chromosome number (but each chromosome still has two chromatids)

Meiosis II (equational division):

Prophase II: Chromosomes condense again
Metaphase II: Chromosomes line up singly at the equator
Anaphase II: Sister chromatids separate
Telophase II: Four haploid daughter cells form

The Cell Cycle

The cell cycle describes the sequence of events from one cell division to the next.

Phase	Description	Duration (typical)
G1 (Gap 1)	Cell growth, normal metabolism, organelle duplication	Variable
S (Synthesis)	DNA replication	6-8 hours
G2 (Gap 2)	Preparation for mitosis, protein synthesis	2-4 hours
M (Mitosis)	Cell division	1-2 hours
Cytokinesis	Cytoplasmic division	Overlaps with M phase

G1, S, and G2 together are called interphase, which accounts for approximately 90% of the cell cycle.

Control of the Cell Cycle

The cell cycle is controlled by checkpoints:

G1 checkpoint: Checks if the cell is large enough and DNA is undamaged before entering S phase
G2 checkpoint: Checks if DNA has been replicated correctly before entering M phase
Spindle checkpoint (M checkpoint): Checks if all chromosomes are properly attached to spindle fibres before anaphase

Cancer and Uncontrolled Cell Division

Cancer is a disease caused by uncontrolled cell division, resulting in the formation of tumours.

Benign tumours: Grow slowly, remain localised, do not spread
Malignant tumours: Grow rapidly, invade surrounding tissues, can spread to other parts of the body (metastasis)

Causes of cancer:

Mutations in proto-oncogenes (become oncogenes, promoting cell division)
Mutations in tumour suppressor genes (losing their inhibitory function)
Exposure to carcinogens: UV radiation, tobacco smoke, certain chemicals, ionising radiation
Some viruses (e.g., HPV, hepatitis B and C)

DNA Replication

Semi-Conservative Replication

DNA replication is semi-conservative: each new DNA molecule consists of one original strand and one newly synthesised strand.

Process

Helicase unwinds and separates the double helix by breaking hydrogen bonds between complementary bases
DNA polymerase adds complementary nucleotides to each template strand, following the base pairing rules (A-T, C-G)
Leading strand: Synthesised continuously in the 5-prime to 3-prime direction
Lagging strand: Synthesised in short fragments (Okazaki fragments) that are later joined by DNA ligase
Each new DNA molecule contains one original strand and one new strand

Accuracy

DNA polymerase has a proofreading function. If an incorrect nucleotide is added, it is removed and replaced. This gives an error rate of approximately 1 in $10^9$ base pairs.

Protein Synthesis

Transcription

Transcription is the process of copying the genetic information from DNA to messenger RNA (mRNA).

RNA polymerase binds to the promoter region on the DNA template strand
The DNA double helix unwinds locally
RNA polymerase synthesises a complementary mRNA strand using the DNA template (A pairs with U, T pairs with A, C pairs with G, G pairs with C)
The mRNA molecule is released when RNA polymerase reaches the terminator region
In eukaryotes, the pre-mRNA is processed:
- A cap is added to the 5-prime end
- A poly-A tail is added to the 3-prime end
- Introns (non-coding regions) are removed by splicing
- Exons (coding regions) are joined together

Translation

Translation is the process of synthesising a polypeptide chain from the mRNA template.

The mRNA binds to a ribosome
The ribosome reads the mRNA in codons (groups of three bases)
Transfer RNA (tRNA) molecules bring specific amino acids to the ribosome
Each tRNA has an anticodon that is complementary to the codon on the mRNA
Peptide bonds form between adjacent amino acids (catalysed by peptidyl transferase in the ribosome)
Translation stops when a stop codon (UAA, UAG, UGA) is reached
The polypeptide chain is released and folds into its functional 3D shape

The Genetic Code

The genetic code is degenerate: most amino acids are coded for by more than one codon
The genetic code is universal: the same codons code for the same amino acids in nearly all organisms
The genetic code is non-overlapping: each base is part of only one codon

Additional Practice Questions

Homeostasis and Cell Communication

Cell Signalling

Cells communicate through chemical messengers called ligands that bind to specific receptors.

Types of cell signalling:

Type	Description	Distance	Example
Autocrine	Cell signals to itself	Same cell	Growth factors
Paracrine	Cell signals to nearby cells	Short distance	Neurotransmitters
Endocrine	Hormone travels in blood	Long distance	Insulin, adrenaline
Synaptic	Signal across a synapse	Very short	Acetylcholine
Contact-dependent	Direct cell-to-cell contact	Adjacent cells	Immune recognition

Receptors

Cell-surface receptors: For large or hydrophilic signalling molecules that cannot cross the cell membrane (e.g., insulin, adrenaline).

Intracellular receptors: For small or hydrophobic signalling molecules that can diffuse through the membrane (e.g., steroid hormones like testosterone, oestrogen).

Signal Transduction

When a ligand binds to a cell-surface receptor, it triggers a cascade of intracellular events:

Signal reception: The ligand binds to the receptor
Signal transduction: The signal is relayed inside the cell, often involving:
- G-proteins: Activate or inhibit enzymes
- Second messengers: Small molecules that amplify the signal (e.g., cAMP, $\mathrm{Ca}^{2+}$ )
- Enzyme cascades: Kinase cascades that phosphorylate target proteins
Cellular response: The cell changes its activity (e.g., gene expression, metabolism, secretion)

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Second messengers greatly amplify the signal. One receptor activation can produce many second messenger molecules, each of which can activate many enzyme molecules, creating a large response from a small stimulus.

Immune System

Non-Specific (Innate) Immunity

First line of defence:

Skin: physical barrier
Mucous membranes: trap pathogens
Stomach acid: destroys pathogens
Tears, saliva: contain lysozyme (an enzyme that breaks down bacterial cell walls)

Second line of defence:

Phagocytes (neutrophils, macrophages): engulf and digest pathogens by phagocytosis
Inflammation: increased blood flow, swelling, heat, pain; brings phagocytes to the infection site
Fever: raises body temperature, inhibiting pathogen growth and enhancing immune function
Interferons: proteins produced by virus-infected cells that inhibit viral replication in neighbouring cells

Specific (Adaptive) Immunity

Cell-mediated response (T cells):

T helper cells: release cytokines that stimulate B cells and cytotoxic T cells
Cytotoxic T cells (killer T cells): destroy virus-infected cells and cancer cells by inducing apoptosis
Memory T cells: provide long-term immunity

Humoral response (B cells):

B cells produce antibodies (immunoglobulins) specific to the antigen
Plasma cells: short-lived cells that secrete large quantities of antibodies
Memory B cells: provide long-term immunity; respond faster and more strongly upon re-exposure

Antibody Structure

An antibody (immunoglobulin) is a Y-shaped protein with:

Two identical heavy chains
Two identical light chains
Variable regions: specific to the antigen (at the tips of the Y)
Constant regions: the same for all antibodies of the same class

Types of Antibodies

Type	Location	Function
IgG	Blood, tissue fluid	Most abundant; crosses placenta
IgA	Saliva, tears, breast milk, mucus	Protects mucous membranes
IgM	Blood	First antibody produced in primary response
IgE	Bound to mast cells	Allergic reactions; parasitic infections
IgD	B cell surface	B cell activation

Primary vs Secondary Immune Response

Feature	Primary Response	Secondary Response
Speed	Slow (5-10 days)	Fast (1-3 days)
Antibody level	Lower	Higher
Antibody class	Mainly IgM	Mainly IgG
Duration	Short	Long
Memory cells	Produced	Already present

Worked Example 3 (Immune)

Explain how vaccination provides immunity against a disease.

A vaccine contains a weakened or dead form of the pathogen (or parts of it like antigens). When introduced into the body, it triggers a primary immune response without causing the disease. B cells produce antibodies and memory B cells are formed. If the person is later exposed to the actual pathogen, the memory B cells quickly produce large quantities of antibodies in a secondary response, destroying the pathogen before symptoms develop. This provides active artificial immunity.

Additional Topics

Stem Cells

Definition: Undifferentiated cells that can divide and differentiate into specialised cell types.

Type	Source	Potential
Totipotent	Early embryo (up to 8-cell stage)	Can become any cell type + placenta
Pluripotent	Blastocyst (inner cell mass)	Can become any cell type
Multipotent	Adult tissues (e.g., bone marrow)	Can become limited range of cell types
Unipotent	Specific tissues	Can become only one cell type

Therapeutic uses:

Treatment of leukaemia (bone marrow transplants)
Potential for regenerative medicine (repairing damaged tissues)
Research into disease mechanisms

Ethical considerations:

Embryonic stem cells involve destruction of embryos
Adult stem cells have more limited potential
Induced pluripotent stem cells (iPSCs) offer an alternative

Water Potential and Osmosis Calculations

The water potential of a solution is:

$\Psi = \Psi_s + \Psi_p$

Where:

$\Psi_s$ = solute potential (always negative or zero)
$\Psi_p$ = pressure potential (positive in turgid plant cells, zero in animal cells)

For a solution with no pressure applied:

$\Psi = \Psi_s = -iCRT$

Where:

$i$ = ionisation constant (number of particles per molecule)
$C$ = molar concentration
$R$ = gas constant ( $8.314 \mathrm{ J mol}^{-1} \mathrm{ K}^{-1}$ )
$T$ = temperature in Kelvin

Worked Example 4 (Water Potential)

Calculate the water potential of a $0.3 \mathrm{ mol/dm}^3$ sucrose solution at $25^\circ\mathrm{C}$ . ( $i = 1$ for sucrose)

$\Psi_s = -iCRT = -(1)(0.3)(8.314)(298) = -743.3 \mathrm{ kPa}$

Since there is no pressure: $\Psi = -743.3 \mathrm{ kPa}$

Worked Example 5 (Water Potential)

Calculate the water potential of a $0.2 \mathrm{ mol/dm}^3$ $\mathrm{NaCl}$ solution at $20^\circ\mathrm{C}$ . ( $i = 2$ for $\mathrm{NaCl}$ )

$\Psi_s = -(2)(0.2)(8.314)(293) = -974.4 \mathrm{ kPa}$

$\Psi = -974.0 \mathrm{ kPa}$

Problem Set

Problem 1: Describe three structural differences between prokaryotic and eukaryotic cells, and explain how each difference relates to the cell's function.

If you get this wrong, revise: Cell Structure -- Prokaryotic vs Eukaryotic Cells

Solution

Nucleus: Eukaryotic cells have a true nucleus with a nuclear envelope, while prokaryotic cells have a nucleoid region (no membrane). The nuclear envelope in eukaryotes separates transcription from translation, allowing mRNA processing (splicing, capping, poly-A tail), enabling more complex gene regulation.
Mitochondria: Eukaryotic cells have mitochondria for aerobic respiration (high ATP yield via oxidative phosphorylation), while prokaryotic cells carry out respiration on their cell membrane (less efficient, limited surface area). Mitochondria provide a large internal surface area (cristae) for the electron transport chain.
Ribosomes: Eukaryotic cells have 80S ribosomes (larger), while prokaryotic cells have 70S ribosomes (smaller). This difference is the basis of antibiotic specificity -- drugs like tetracycline target 70S ribosomes in bacteria without affecting eukaryotic 80S ribosomes.

Problem 2: A red blood cell is placed in a 0.5 mol/dm $^3$ sucrose solution. Predict what will happen to the cell and explain your reasoning. (The water potential of the red blood cell cytoplasm is approximately -700 kPa.)

If you get this wrong, revise: Membrane Transport -- Osmosis; Water Potential and Osmosis Calculations

Solution

The water potential of the 0.5 mol/dm $^3$ sucrose solution is:

$\Psi_s = -iCRT = -(1)(0.5)(8.314)(298) = -1238.8 \mathrm{ kPa}$

Since the solution has a more negative water potential (-1238.8 kPa) than the cell cytoplasm (-700 kPa), water will move out of the cell by osmosis (from higher to lower water potential). The red blood cell will lose water, shrink, and become crenated (wrinkled appearance).

Problem 3: Explain the effect of increasing temperature on enzyme activity from 0 degrees C to 60 degrees C. Refer to kinetic energy, collision frequency, and enzyme structure in your answer.

If you get this wrong, revise: Enzymes -- Factors Affecting Enzyme Activity

Solution

From 0 degrees C to the optimum (~37-40 degrees C): increasing temperature increases the kinetic energy of both enzyme and substrate molecules, leading to more frequent effective collisions between them. The rate of reaction increases as more enzyme-substrate complexes form per unit time.

Beyond the optimum temperature, the increased kinetic energy breaks the hydrogen bonds, ionic bonds, and other weak interactions maintaining the tertiary structure of the enzyme. The active site changes shape (denaturation), and the substrate can no longer bind. Since denaturation is irreversible, the reaction rate decreases sharply and the enzyme is permanently inactivated.

Problem 4: A cell in the G1 phase of the cell cycle has 46 chromosomes. How many chromosomes and DNA molecules are present at the end of S phase, during metaphase of mitosis, and after cytokinesis?

If you get this wrong, revise: Cell Division -- Mitosis; The Cell Cycle

Solution

End of S phase: 46 chromosomes, 92 DNA molecules (each chromosome has been replicated into two sister chromatids, but chromosome count remains 46 because sister chromatids are still joined at the centromere).

Metaphase of mitosis: 46 chromosomes (each with 2 chromatids), 92 DNA molecules. The chromosomes are aligned at the metaphase plate with spindle fibres attached to centromeres.

After cytokinesis: 46 chromosomes, 46 DNA molecules. Each daughter cell receives 46 single-chromatid chromosomes (the chromatids separated during anaphase). The chromosome number is the same as the original cell, maintaining genetic continuity.

Problem 5: Compare the structure and function of DNA and mRNA.

If you get this wrong, revise: DNA Replication; Protein Synthesis

Solution

Structure: DNA is double-stranded (double helix) with a deoxyribose sugar and thymine as a base. mRNA is single-stranded with a ribose sugar and uracil replacing thymine. DNA is very long (entire genome), while mRNA is a shorter copy of a single gene.

Function: DNA stores genetic information long-term in the nucleus. mRNA carries a transient copy of the genetic information from the nucleus to the ribosomes in the cytoplasm for protein synthesis (translation). DNA is self-replicating; mRNA is not.

Stability: DNA is chemically stable (deoxyribose is less reactive than ribose; double-stranded structure provides protection). mRNA is short-lived (ribose is more reactive; single-stranded structure is vulnerable to nucleases), allowing rapid changes in gene expression.

Problem 6: Describe the stages of mitosis and explain their significance in ensuring genetic continuity.

If you get this wrong, revise: Cell Division -- Stages of Mitosis

Solution

Prophase: Chromatin condenses into visible chromosomes (each consisting of two sister chromatids joined at the centromere). The nuclear envelope breaks down, spindle fibres form, and centrioles move to opposite poles. Significance: organises and packages the genetic material for even distribution.

Metaphase: Chromosomes align at the metaphase plate (cell equator) with spindle fibres attached to centromeres. Significance: ensures each daughter cell receives one copy of each chromosome.

Anaphase: Sister chromatids separate at the centromeres and are pulled to opposite poles by shortening spindle fibres. Significance: the critical step that distributes identical genetic material to each daughter cell.

Telophase: Chromosomes decondense, nuclear envelopes reform, nucleoli reappear, and spindle fibres break down. Significance: re-establishes the interphase state in each daughter cell.

Cytokinesis: The cytoplasm divides, producing two separate daughter cells, each genetically identical to the parent cell.

Problem 7: Explain how vaccination provides immunity against a disease, referring to both the primary and secondary immune responses.

If you get this wrong, revise: Immune System -- Specific (Adaptive) Immunity; Primary vs Secondary Immune Response

Solution

A vaccine contains a weakened or dead form of the pathogen (or specific antigens). When introduced into the body, it triggers a primary immune response: B cells are activated by the antigen, divide by mitosis, and differentiate into plasma cells (which secrete antibodies) and memory B cells. T helper cells are also activated and support the B cell response.

If the person is later exposed to the actual pathogen, memory B cells recognise the antigen and rapidly divide, producing large quantities of antibodies in a secondary response. The secondary response is faster (1-3 days vs 5-10 days), produces more antibodies (mainly IgG), and lasts longer. The pathogen is destroyed before it can cause symptoms, providing active artificial immunity.

Problem 8: Describe the role of the Golgi apparatus in protein processing and transport.

If you get this wrong, revise: Cell Organelles -- Golgi Apparatus

Solution

The Golgi apparatus receives proteins from the rough ER in transport vesicles. It modifies these proteins by adding carbohydrate groups (glycosylation) to form glycoproteins. It sorts proteins based on their destination and packages them into secretory vesicles. Different vesicles are targeted to different locations: some fuse with the cell membrane for export (exocytosis), some become lysosomes (in animal cells), and others are transported to other organelles. The Golgi acts as a processing and distribution centre, ensuring proteins reach their correct destinations.

Problem 9: Calculate the water potential of a 0.15 mol/dm $^3$ NaCl solution at 25 degrees C. ( $i = 2$ for NaCl.) Determine whether a plant cell with $\Psi = -800 \mathrm{ kPa}$ and $\Psi_p = 200 \mathrm{ kPa}$ would gain or lose water in this solution.

If you get this wrong, revise: Water Potential and Osmosis Calculations

Solution

$\Psi_s = -iCRT = -(2)(0.15)(8.314)(298) = -742.5 \mathrm{ kPa}$

Since there is no pressure applied to the external solution: $\Psi_{\mathrm{solution}} = -742.5 \mathrm{ kPa}$

For the plant cell:

$\Psi_{\mathrm{cell}} = \Psi_s + \Psi_p = -800 + 200 = -600 \mathrm{ kPa}$

Since $\Psi_{\mathrm{solution}}$ (-742.5 kPa) is more negative than $\Psi_{\mathrm{cell}}$ (-600 kPa), water moves from the cell (higher water potential) into the solution (lower water potential). The plant cell would lose water.

Problem 10: Explain how the structure of the mitochondrion is adapted to its function in aerobic respiration.

If you get this wrong, revise: Cell Organelles -- Mitochondria; Cellular Respiration

Solution

The mitochondrion has a double membrane. The inner membrane is folded into cristae, providing a large surface area for the electron transport chain and ATP synthase. The intermembrane space between the two membranes allows protons to accumulate, creating the electrochemical gradient needed for chemiosmosis. The matrix contains enzymes for the Krebs cycle, mitochondrial DNA (allowing the mitochondrion to produce some of its own proteins), and ribosomes. The small volume of the matrix ensures high concentrations of substrates and enzymes, maximising the rate of the Krebs cycle. These features collectively maximise the rate of ATP production through oxidative phosphorylation.

Cellular Respiration in Detail

Glycolysis (Detailed)

Glycolysis occurs in the cytoplasm and does not require oxygen. It is the first stage of both aerobic and anaerobic respiration.

Stages of glycolysis:

Stage	Key Steps	Energy Change
Phosphorylation	Glucose (6C) is phosphorylated twice using 2 ATP, forming hexose biphosphate (6C). This "traps" glucose inside the cell and raises its energy level	Consumes 2 ATP (investment phase)
Splitting	Hexose biphosphate is split into two molecules of triose phosphate (3C each)	No ATP change
Oxidation	Each triose phosphate is oxidised (dehydrogenated) by NAD $^+$ , producing 2 NADH (one per triose phosphate)	Produces 2 NADH
ATP production	Each triose phosphate is converted to pyruvate (3C), producing 2 ATP per triose phosphate (substrate-level phosphorylation)	Produces 4 ATP (2 per triose phosphate)
Net yield		2 ATP + 2 NADH per glucose

$\text{Glucose (6C)} + 2\mathrm{NAD}^+ + 2\mathrm{ADP} + 2\mathrm{P}_i \to 2\text{ Pyruvate (3C)} + 2\mathrm{NADH} + 2\mathrm{H}^+ + 2\mathrm{ATP} + 2\mathrm{H}_2\mathrm{O}$

The Link Reaction and Krebs Cycle

Link reaction (pyruvate oxidation):

Occurs in the mitochondrial matrix
Each pyruvate (3C) is decarboxylated (loses $\mathrm{CO}_2$ ) and dehydrogenated (NAD $^+$ reduced to NADH)
The remaining 2-carbon acetyl group combines with coenzyme A to form acetyl CoA
Per glucose: 2 pyruvate $\to$ 2 acetyl CoA + 2 $\mathrm{CO}_2$ + 2 NADH

Krebs cycle (citric acid cycle):

Occurs in the mitochondrial matrix
Each acetyl CoA (2C) combines with oxaloacetate (4C) to form citrate (6C)
Through a series of reactions, citrate is converted back to oxaloacetate, releasing:
- 2 $\mathrm{CO}_2$ (decarboxylation)
- 3 NADH (dehydrogenation)
- 1 FADH $_2$ (dehydrogenation)
- 1 ATP (substrate-level phosphorylation via GTP)
Per glucose: 2 turns of the cycle produce 4 $\mathrm{CO}_2$ , 6 NADH, 2 FADH $_2$ , 2 ATP

Oxidative Phosphorylation

Occurs on the inner mitochondrial membrane (cristae)
NADH and FADH $_2$ donate electrons to the electron transport chain
Electrons pass through a series of carriers (complexes I-IV), releasing energy used to pump $\mathrm{H}^+$ into the intermembrane space
$\mathrm{H}^+$ flows back through ATP synthase (chemiosmosis), producing ATP
Oxygen is the final electron acceptor, combining with $\mathrm{H}^+$ and electrons to form water

Total ATP Yield (Per Glucose)

Stage	ATP (or equivalent)
Glycolysis (net)	2 ATP + 2 NADH
Link reaction	2 NADH
Krebs cycle	2 ATP + 6 NADH + 2 FADH $_2$
Oxidative phosphorylation	Each NADH produces approximately 2.5 ATP; each FADH $_2$ produces approximately 1.5 ATP
Total (approximate)	30-32 ATP

info

The exact ATP yield varies because the shuttle mechanism that transfers electrons from cytoplasmic NADH into the mitochondria can cost 1 ATP per NADH. The theoretical maximum is 38 ATP, but in practice, the yield is closer to 30-32 ATP due to proton leakage across the inner mitochondrial membrane and the cost of transporting molecules.

Anaerobic Respiration

When oxygen is unavailable, pyruvate cannot enter the mitochondria for oxidative phosphorylation. Cells must regenerate NAD $^+$ by alternative pathways to keep glycolysis running.

In animal cells (lactic acid fermentation):

$\text{Pyruvate} + \mathrm{NADH} \xrightarrow{\text{LDH}} \text{Lactate} + \mathrm{NAD}^+$

Net yield: 2 ATP per glucose (only from glycolysis)
Lactate accumulates in muscles, causing fatigue and cramping
Lactate is transported to the liver and converted back to pyruvate (Cori cycle), which can be oxidised in the Krebs cycle or converted back to glucose

In yeast and plant cells (alcoholic fermentation):

$\text{Pyruvate} \xrightarrow{\text{decarboxylase}} \text{Ethanal} + \mathrm{CO}_2$

$\text{Ethanal} + \mathrm{NADH} \xrightarrow{\text{alcohol dehydrogenase}} \text{Ethanol} + \mathrm{NAD}^+$

Net yield: 2 ATP per glucose
$\mathrm{CO}_2$ and ethanol are produced as waste products
This process is used in brewing (beer) and baking (bread rises due to $\mathrm{CO}_2$ production)

Cancer Biology

What is Cancer?

Cancer is a group of diseases characterised by uncontrolled cell division, leading to the formation of malignant tumours that can invade surrounding tissues and spread to other parts of the body (metastasis).

Causes of Cancer

Cancer is caused by mutations in genes that regulate the cell cycle. These mutations can be caused by:

Factor	Description
Chemical carcinogens	Chemicals that damage DNA (e.g., tar in cigarette smoke, benzene, asbestos, aflatoxin in mouldy peanuts)
Radiation	Ionising radiation (X-rays, gamma rays, UV light) causes DNA damage
Viral infection	Some viruses integrate their DNA into the host genome, disrupting tumour suppressor genes or activating oncogenes
Hereditary factors	Inherited mutations in tumour suppressor genes (e.g., BRCA1/BRCA2 mutations increase breast cancer risk)
Chronic inflammation	Inflammatory cells produce reactive oxygen species that can damage DNA

Gene Type	Normal Function	Effect When Mutated
Proto-oncogenes	Promote controlled cell division (accelerate cell cycle)	Become oncogenes when mutated; cause excessive cell division
Tumour suppressor genes	Inhibit cell division; promote DNA repair; trigger apoptosis	Lose function when mutated; cell division is no longer restrained
Examples	Proto-oncogene: ras (signals for cell division)	p53 (tumour suppressor; halts cell cycle for DNA repair or triggers apoptosis)

Tumour Suppressor p53

The p53 protein is often called the "guardian of the genome." It plays a critical role in preventing cancer:

If DNA damage is detected, p53 halts the cell cycle (at G1 checkpoint) to allow time for DNA repair
If the damage is repairable, p53 activates DNA repair enzymes
If the damage is too severe to repair, p53 triggers apoptosis (programmed cell death), preventing the damaged cell from dividing and potentially becoming cancerous
Approximately 50% of all human cancers involve mutations in the p53 gene

Benign vs Malignant Tumours

Feature	Benign Tumour	Malignant Tumour
Growth rate	Slow	Rapid
Encapsulation	Encapsulated (contained within a fibrous capsule)	Not encapsulated; invades surrounding tissue
Metastasis	Does NOT spread to other parts of the body	CAN spread (metastasise) via blood or lymph
Cell differentiation	Well-differentiated (cells look normal)	Poorly differentiated (cells look abnormal)
Health impact	Usually harmless unless pressing on organs	Life-threatening if untreated
Recurrence	Rarely recurs after removal	May recur after removal

Worked Example: Carcinogens and DNA Damage

A person smokes 20 cigarettes per day for 30 years. Explain how the chemicals in cigarette smoke can lead to lung cancer, referring to the role of proto-oncogenes and tumour suppressor genes.

Solution

Cigarette smoke contains over 60 known carcinogens, including benzopyrene (a polycyclic aromatic hydrocarbon) and nitrosamines. These chemicals enter the lungs during inhalation and are absorbed into lung epithelial cells.

DNA damage: Carcinogens are metabolised into reactive intermediates that bind to DNA, forming DNA adducts. These adducts cause mutations during DNA replication. Benzopyrene, for example, causes a specific G to T transversion mutation in the p53 gene.
Proto-oncogene activation: Mutations can convert proto-oncogenes (e.g., ras) into oncogenes, causing them to be permanently activated. The ras oncogene produces a protein that continuously signals cells to divide, even in the absence of growth factor signals.
Tumour suppressor gene inactivation: Mutations can inactivate tumour suppressor genes (e.g., p53). Without functional p53, cells with damaged DNA are not arrested for repair and do not undergo apoptosis. Mutations accumulate, and damaged cells continue to divide uncontrollably.
Multiple mutations required: A single mutation is usually insufficient to cause cancer. Cancer typically requires mutations in multiple genes (approximately 5-10 driver mutations). The long duration of exposure (30 years) allows multiple mutations to accumulate in the same cell lineage.
Tumour formation: Once enough mutations accumulate, a cell begins dividing uncontrollably, forming a malignant tumour that can invade surrounding lung tissue and metastasise to other organs via the bloodstream or lymphatic system.

Additional Problem Set

Problem 11: Compare aerobic and anaerobic respiration in terms of location, substrates, products, and ATP yield. Explain why anaerobic respiration produces much less ATP per glucose molecule.

If you get this wrong, revise: Cellular Respiration in Detail

Solution

Feature	Aerobic Respiration	Anaerobic Respiration (animals)
Location	Cytoplasm (glycolysis) + mitochondria (link reaction, Krebs cycle, oxidative phosphorylation)	Cytoplasm only (glycolysis only)
Oxygen	Required (final electron acceptor)	Not required
Substrates	Glucose	Glucose
Products	$\mathrm{CO}_2$ , $\mathrm{H}_2\mathrm{O}$ , ATP (30-32)	Lactate, ATP (2)
ATP yield	Approximately 30-32 ATP per glucose	2 ATP per glucose
NAD $^+$ regeneration	Via oxidative phosphorylation (electron transport chain)	Via conversion of pyruvate to lactate (NADH oxidised to NAD $^+$ )

Anaerobic respiration produces much less ATP because only glycolysis occurs, yielding a net 2 ATP. The much larger ATP yield of aerobic respiration comes from oxidative phosphorylation, which requires the electron transport chain in the inner mitochondrial membrane. NADH and FADH $_2$ from glycolysis, the link reaction, and the Krebs cycle donate electrons to the electron transport chain, and the energy released pumps protons across the membrane. The resulting proton gradient drives ATP synthase, producing approximately 28-30 ATP. Without oxygen as the final electron acceptor, the electron transport chain cannot operate, and this massive ATP yield is lost.

Problem 12: Explain the roles of proto-oncogenes and tumour suppressor genes in regulating the cell cycle. Explain how mutations in both types of gene can contribute to cancer development.

If you get this wrong, revise: Cancer Biology

Solution

Proto-oncogenes promote cell division when activated by growth factor signals. They encode proteins involved in cell cycle progression (e.g., ras encodes a GTPase that transmits growth signals; myc encodes a transcription factor that activates genes for cell division). When mutated, proto-oncogenes become oncogenes that are permanently activated, causing cells to divide continuously even without external growth signals. This is analogous to a car with a stuck accelerator.

Tumour suppressor genes inhibit cell division, promote DNA repair, or trigger apoptosis when DNA is damaged. For example, p53 halts the cell cycle at the G1 checkpoint if DNA damage is detected, allowing time for repair; if damage is irreparable, p53 triggers apoptosis. When mutated, tumour suppressor genes lose their function, so damaged cells continue dividing without repair or death. This is analogous to a car with no brakes.

Cancer typically requires mutations in BOTH types of gene: an oncogene drives excessive cell division (accelerator stuck), while loss of tumour suppressor function removes the brakes that would normally halt or eliminate damaged cells. This combination allows cells to divide uncontrollably and accumulate further mutations, leading to malignant tumour formation.

Membrane Transport in Detail

Facilitated Diffusion

Facilitated diffusion is the passive movement of molecules across a membrane via transmembrane proteins. Like simple diffusion, it moves molecules down their concentration gradient and does not require energy. Unlike simple diffusion, it requires specific carrier proteins or channel proteins.

Feature	Simple Diffusion	Facilitated Diffusion
Requires proteins	No	Yes (channel proteins or carrier proteins)
Selective	No (any small, non-polar molecule)	Yes (specific to particular molecules)
Saturation	No (rate increases with concentration indefinitely)	Yes (rate plateaus when all proteins are occupied)
Energy required	No	No
Direction	Down concentration gradient	Down concentration gradient
Molecules transported	$\mathrm{O}_2$ , $\mathrm{CO}_2$ , small lipids, water	Glucose (via GLUT transporters), amino acids, ions ( $\mathrm{Na}^+$ , $\mathrm{K}^+$ )

Channel proteins:

Form water-filled pores through the membrane
Allow specific ions or molecules to pass through by diffusion
Types:
- Ion channels: Allow specific ions to pass (e.g., $\mathrm{Na}^+$ channels, $\mathrm{K}^+$ channels, $\mathrm{Ca}^{2+}$ channels)
- Aquaporins: Channel proteins specific to water molecules; allow rapid osmosis (approximately 10 times faster than diffusion through the lipid bilayer)
Gated channels: Open or close in response to specific stimuli:
- Voltage-gated channels: Open in response to changes in membrane potential (essential for nerve impulse transmission)
- Ligand-gated channels: Open when a specific chemical (ligand) binds (e.g., neurotransmitter-gated channels at synapses)
- Mechanically-gated channels: Open in response to physical deformation (e.g., in hair cells of the cochlea)

Carrier proteins:

Bind to specific molecules and undergo a conformational change to transport them across the membrane
Can transport larger molecules (e.g., glucose, amino acids) that cannot pass through channels
Exhibit saturation kinetics: when all carrier proteins are occupied, the transport rate plateaus regardless of further increases in concentration
Example: GLUT1 transporter for glucose in red blood cells

Active Transport

Active transport moves molecules against their concentration gradient (from low to high concentration), requiring energy in the form of ATP.

Feature	Primary Active Transport	Secondary Active Transport (Co-transport)
Energy source	ATP hydrolysis directly	Uses an ion gradient established by primary active transport
Direct ATP use	Yes	No (indirect)
Example	$\mathrm{Na}^+/\mathrm{K}^+$ pump; $\mathrm{H}^+$ ATPase in stomach	$\mathrm{Na}^+$ -glucose co-transport in small intestine; $\mathrm{Na}^+$ -amino acid co-transport
Direction	Can move substances in either direction	Moves both the driving ion and the transported substance in the same (symport) or opposite (antiport) direction

The sodium-potassium pump (detailed mechanism):

Three $\mathrm{Na}^+$ ions bind to the intracellular side of the pump protein
ATP binds and is hydrolysed to ADP and $\mathrm{P}_i$
The phosphate group is transferred to the pump protein (phosphorylation), changing its conformation
The conformational change exposes the $\mathrm{Na}^+$ binding sites to the extracellular side; $\mathrm{Na}^+$ is released
Two $\mathrm{K}^+$ ions from the extracellular side bind to the pump
The phosphate group is released (dephosphorylation), returning the pump to its original conformation
The conformational change exposes the $\mathrm{K}^+$ binding sites to the intracellular side; $\mathrm{K}^+$ is released

Significance of the sodium-potassium pump:

Maintains the resting potential of neurons (by creating concentration gradients for $\mathrm{Na}^+$ and $\mathrm{K}^+$ )
Maintains cell volume (by controlling osmotic balance)
Provides the $\mathrm{Na}^+$ gradient that drives secondary active transport (e.g., $\mathrm{Na}^+$ -glucose co-transport in the small intestine and kidney)
Essential for nerve impulse transmission and muscle contraction

Bulk Transport: Endocytosis and Exocytosis

Large molecules (proteins, polysaccharides) and particles are transported across the membrane in membrane-bound vesicles.

Process	Description	Energy Required	Example
Endocytosis	Cell membrane engulfs material, forming a vesicle inside the cell	Yes (ATP)	White blood cells engulfing bacteria (phagocytosis)
Exocytosis	Vesicles inside the cell fuse with the cell membrane, releasing their contents outside	Yes (ATP)	Release of neurotransmitters at synapses; secretion of mucus and enzymes
Phagocytosis	"Cell eating": large solid particles are engulfed by extensions of the membrane (pseudopodia)	Yes (ATP)	Phagocytes engulfing bacteria
Pinocytosis	"Cell drinking": small droplets of extracellular fluid are taken into the cell in small vesicles	Yes (ATP)	Uptake of dissolved nutrients by microorganisms

Protein Synthesis in Detail

Transcription

Transcription is the process of copying the genetic code from DNA into mRNA.

Steps:

Initiation: RNA polymerase binds to the promoter region of the gene (upstream of the coding sequence). Transcription factors help position the polymerase correctly.
Elongation: RNA polymerase unwinds the DNA double helix and synthesises a complementary mRNA strand in the 5' to 3' direction, using the template (antisense) strand of DNA. RNA polymerase adds RNA nucleotides complementary to the DNA template: A pairs with U (not T in RNA), G pairs with C.
Termination: RNA polymerase reaches a terminator sequence and detaches from the DNA. The pre-mRNA is released.

Post-transcriptional modifications (in eukaryotes only):

5' capping: A modified guanine nucleotide (7-methylguanosine) is added to the 5' end. This protects the mRNA from degradation and helps ribosomes recognise it for translation.
3' polyadenylation: A poly-A tail (150-200 adenine nucleotides) is added to the 3' end. This aids in mRNA stability and export from the nucleus.
Splicing: Introns (non-coding regions) are removed, and exons (coding regions) are joined together by the spliceosome. Alternative splicing allows a single gene to produce multiple different mRNA variants (and therefore multiple different proteins).

Translation

Translation is the process of synthesising a polypeptide chain from the mRNA code.

Steps:

Initiation: The small ribosomal subunit binds to the 5' end of the mRNA and moves along until it reaches the start codon (AUG). The initiator tRNA carrying methionine binds to the start codon. The large ribosomal subunit joins, forming the complete ribosome with three sites: A (aminoacyl), P (peptidyl), and E (exit).
Elongation: A tRNA carrying the appropriate amino acid enters the A site, its anticodon base-pairing with the codon on the mRNA. A peptide bond forms between the amino acid in the P site and the new amino acid in the A site (catalysed by peptidyl transferase). The ribosome translocates by one codon: the empty tRNA moves to the E site and exits; the tRNA with the growing polypeptide moves to the P site; the next codon is exposed in the A site.
Termination: When a stop codon (UAA, UAG, or UGA) is reached in the A site, no tRNA can bind. A release factor protein enters the A site, causing the polypeptide to be released and the ribosome to dissociate.

One gene, one polypeptide (generally): Each gene codes for a specific polypeptide chain. The sequence of codons on the mRNA determines the sequence of amino acids in the polypeptide.

tip

Diagnostic Test Ready to test your understanding of Cell Biology and Biochemistry? The diagnostic test contains the hardest questions within the DSE specification for this topic, each with a full worked solution.

Unit tests probe edge cases and common misconceptions. Integration tests combine Cell Biology and Biochemistry with other biology topics to test synthesis under exam conditions.

See Diagnostic Guide for instructions on self-marking and building a personal test matrix.

Cell Division in Detail

The Cell Cycle

Phase	Description	Duration (typical mammalian cell)
G1 (Gap 1)	Cell grows in size; synthesises proteins and organelles; carries out normal metabolic functions; G1 checkpoint checks cell size and DNA integrity	~10-12 hours
S (Synthesis)	DNA replication occurs; each chromosome is duplicated to form two sister chromatids joined at the centromere	~6-8 hours
G2 (Gap 2)	Cell continues to grow; synthesises proteins needed for mitosis (e.g., tubulin for spindle fibres); G2 checkpoint checks DNA replication is complete and error-free	~3-4 hours
M (Mitosis)	Nuclear division; sister chromatids separate and move to opposite poles of the cell	~1-2 hours
C (Cytokinesis)	Cytoplasm divides; two daughter cells are formed	Occurs with or after M phase

Total cell cycle duration: ~24 hours (varies widely: intestinal epithelial cells divide every ~12 hours; nerve cells rarely or never divide after maturity)

Control of the Cell Cycle

The cell cycle is controlled by cyclins and cyclin-dependent kinases (CDKs):

Checkpoint	Location	What is Checked	Outcome if Failed
G1 checkpoint (restriction point)	Late G1 phase	Cell size adequate? Nutrients available? Growth signals present? DNA undamaged?	Cell enters G0 (resting phase) or undergoes apoptosis
G2 checkpoint	End of G2 phase	DNA replication complete and error-free? All proteins needed for mitosis synthesised?	Cell cycle arrests; DNA repair attempted; apoptosis if damage is irreparable
M checkpoint (spindle assembly checkpoint)	Metaphase of mitosis	Are all chromosomes properly attached to spindle fibres at the metaphase plate?	Anaphase is delayed; prevents unequal distribution of chromosomes

Cyclin-CDK mechanism:

Cyclins are proteins whose concentration rises and falls at specific points in the cell cycle
CDKs are enzymes that are always present but inactive on their own
When a cyclin binds to a CDK, the cyclin-CDK complex becomes active and phosphorylates target proteins, triggering the next phase of the cell cycle
After the phase is complete, the cyclin is degraded and the CDK becomes inactive again
Different cyclins control different checkpoints (e.g., cyclin D-CDK4/6 for G1 checkpoint; cyclin B-CDK1 for G2/M transition)

Mitosis vs Meiosis: Detailed Comparison

Feature	Mitosis	Meiosis
Number of divisions	1	2 (meiosis I and meiosis II)
Number of daughter cells	2	4
Chromosome number	Same as parent (diploid $\rightarrow$ diploid, 2n $\rightarrow$ 2n)	Half of parent (diploid $\rightarrow$ haploid, 2n $\rightarrow$ n)
Genetic variation	No (daughter cells are genetically identical to the parent and to each other)	Yes (daughter cells are genetically different from the parent and from each other due to crossing over and independent assortment)
Crossing over	No	Yes (during prophase I)
Homologous pairs separate	No (sister chromatids separate in anaphase)	Yes (homologous chromosomes separate in anaphase I)
Sister chromatids separate	Yes (in anaphase)	Yes (in anaphase II, NOT anaphase I)
Occurs in	Somatic cells (body cells) for growth, repair, and asexual reproduction	Germ cells in the gonads (testes and ovaries) to produce gametes
Metaphase I alignment	Individual chromosomes line up at the metaphase plate	Homologous pairs line up at the metaphase plate (bivalents/tetrads)

Meiosis I vs Meiosis II

Feature	Meiosis I	Meiosis II
Prophase	Homologous chromosomes pair up (synapsis) to form bivalents; crossing over occurs between non-sister chromatids	No pairing of homologous chromosomes; no crossing over
Metaphase	Bivalents (homologous pairs) align at the metaphase plate; one chromosome from each pair faces each pole	Individual chromosomes (each consisting of two sister chromatids) align at the metaphase plate
Anaphase	Homologous chromosomes separate and move to opposite poles (sister chromatids remain attached at the centromere)	Sister chromatids separate and move to opposite poles
Telophase	Two daughter cells are formed, each with half the number of chromosomes (each chromosome still consists of two chromatids)	Four daughter cells are formed, each with half the number of chromosomes (each chromosome consists of a single chromatid)
Reduction division?	Yes (diploid $\rightarrow$ haploid)	No (haploid $\rightarrow$ haploid, but each chromosome is now a single chromatid)

The Significance of Meiosis

Produces haploid gametes: Ensures that fertilisation restores the diploid chromosome number (n + n = 2n)
Generates genetic variation through:
- Crossing over (recombination): During prophase I, non-sister chromatids of homologous chromosomes exchange segments of DNA at chiasmata. This creates new combinations of alleles on the same chromosome
- Independent assortment: During metaphase I, the orientation of each bivalent on the metaphase plate is random. With 23 pairs of chromosomes in humans, this gives $2^{23}$ ( $\approx$ 8.4 million) possible combinations of chromosomes in the gametes
Prevents chromosome doubling: Without meiosis, the chromosome number would double with each generation (2n $\rightarrow$ 4n $\rightarrow$ 8n...)

Stem Cells

Types of Stem Cells

Type	Source	Potency	Uses / Potential Uses
Totipotent	Zygote; early embryo (up to 4-cell stage in humans)	Can develop into ANY cell type AND extraembryonic tissues (placenta, umbilical cord)	Research; not used therapeutically
Pluripotent	Embryonic stem cells (from the inner cell mass of the blastocyst, ~5-7 days after fertilisation)	Can develop into ANY cell type of the body (over 200 types), but NOT extraembryonic tissues	Research; potential for regenerative medicine; treatment of degenerative diseases
Multipotent	Adult (somatic) stem cells found in specific tissues (bone marrow, skin, brain, liver)	Can develop into a limited range of cell types related to their tissue of origin	Bone marrow transplants; skin grafts; treatment of leukaemia
Unipotent	Committed to developing into only ONE cell type	Can only produce one cell type	Limited use; muscle satellite cells

Sources of Stem Cells

Source	Type	Advantages	Disadvantages / Ethical Issues
Embryos (IVF clinics)	Embryonic (pluripotent)	Can differentiate into any cell type; unlimited self-renewal in culture	Ethical concerns (destruction of embryo); risk of tumour formation if not properly controlled
Umbilical cord blood	Adult (multipotent)	Rich in haematopoietic stem cells; less rejection risk (fewer MHC molecules on cord blood cells); non-invasive collection	Limited number of stem cells per cord; only treats blood-related disorders
Bone marrow	Adult (multipotent)	Well-established technique (bone marrow transplants since 1960s); donor can regenerate marrow	Painful extraction; risk of infection; limited cell types
Induced pluripotent stem cells (iPSCs)	Pluripotent (reprogrammed)	No embryo destruction; patient-specific (no rejection risk); can differentiate into any cell type	Risk of mutations during reprogramming; less efficient than embryonic stem cells
Adipose tissue (fat)	Adult (multipotent)	Abundant source; easy extraction (liposuction); can differentiate into bone, cartilage, fat, muscle cells	Limited differentiation potential compared to embryonic stem cells

Induced Pluripotent Stem Cells (iPSCs)

Discovered by Shinya Yamanaka (Nobel Prize, 2012)
Adult somatic cells (e.g., skin fibroblasts) are reprogrammed to a pluripotent state by introducing four transcription factors: Oct4, Sox2, Klf4, and c-Myc (the "Yamanaka factors")
iPSCs behave similarly to embryonic stem cells but avoid the ethical issues associated with embryo destruction
Potential applications: patient-specific cell therapy (e.g., replacing damaged neurons in Parkinson's disease), drug testing on patient-specific cells, disease modelling

Common Pitfalls

Chromosomes and chromatids are different. Before DNA replication: each chromosome consists of ONE chromatid. After DNA replication (S phase): each chromosome consists of TWO sister chromatids joined at the centromere. After anaphase of mitosis (or anaphase II of meiosis): the chromatids separate and are now called chromosomes
In meiosis I, homologous chromosomes separate, NOT sister chromatids. Sister chromatids separate in meiosis II (and in mitosis). If you confuse these, you will get the wrong chromosome numbers in the daughter cells
The cell cycle has THREE checkpoints (G1, G2, M), not two. Each checkpoint checks for different things
Mitosis produces 2 genetically identical diploid daughter cells; meiosis produces 4 genetically different haploid daughter cells. This is the fundamental distinction

Biological Molecules in Detail

Carbohydrates

Type	Elements	Description	Examples	Function(s)
Monosaccharides	C, H, O	Single sugar units; general formula (CH $_2$ O) $_n$ ; sweet-tasting; soluble in water	Glucose ( $\alpha$ and $\beta$ ), fructose, galactose, ribose, deoxyribose	Energy source; building blocks for larger carbohydrates; ribose/deoxyribose in nucleic acids
Disaccharides	C, H, O	Two monosaccharides joined by a glycosidic bond (condensation reaction); general formula C $_{12}$ H $_{22}$ O $_{11}$	Maltose (glucose + glucose); sucrose (glucose + fructose); lactose (glucose + galactose)	Energy source; transport form of sugars
Polysaccharides	C, H, O	Many monosaccharides joined by glycosidic bonds; insoluble (except glycogen); large molecules	Starch (plants), glycogen (animals), cellulose (plants), chitin (insects, fungi)	Energy storage (starch, glycogen); structural support (cellulose, chitin)

Starch: A mixture of two polysaccharides:

Amylose: Unbranched chain of $\alpha$ -glucose molecules joined by 1,4-glycosidic bonds; forms a helix; 20-30% of starch
Amylopectin: Branched chain of $\alpha$ -glucose molecules with 1,4-glycosidic bonds in the main chain and 1,6-glycosidic bonds at branch points; 70-80% of starch; more readily digested than amylose because the branches provide more ends for enzymes to work on

Cellulose: Long, unbranched chains of $\beta$ -glucose joined by 1,4-glycosidic bonds. Every alternate $\beta$ -glucose molecule is rotated 180 degrees, allowing hydrogen bonds to form between adjacent chains. These hydrogen bonds create strong, rigid microfibrils that provide structural support to plant cell walls. Cellulose is NOT digestible by humans because we lack the enzyme cellulase.

Glycogen: Highly branched polymer of $\alpha$ -glucose (similar to amylopectin but more branched); stored in liver and muscle cells; the many branch points provide many ends for rapid glycogenolysis when glucose is needed.

Lipids

Type	Description	Examples	Function(s)
Triglycerides	Glycerol + 3 fatty acids joined by ester bonds (condensation reaction)	Fats (solid at room temp, mostly saturated); oils (liquid at room temp, mostly unsaturated)	Energy storage (long-term); insulation; buoyancy; protection
Phospholipids	Glycerol + 2 fatty acids + phosphate group (hydrophilic head, hydrophobic tails)	Lecithin	Main component of cell membranes; forms the phospholipid bilayer
Cholesterol	Steroid lipid (four fused carbon rings); small, flat molecule	Found in animal cell membranes	Modulates membrane fluidity; precursor for steroid hormones (testosterone, oestrogen, cortisol) and bile salts
Waxes	Long-chain fatty acids bonded to long-chain alcohols	Cuticle on plant leaves; beeswax; earwax	Waterproof coating; protection

Proteins

Level	Description	Type of Bond
Primary structure	The specific sequence of amino acids in the polypeptide chain, determined by the gene (DNA sequence)	Peptide bonds (between amino acids)
Secondary structure	Regular folding patterns of the polypeptide chain caused by hydrogen bonding between amino groups and carboxyl groups of the peptide backbone	Hydrogen bonds
Tertiary structure	The overall 3D shape of a single polypeptide chain, stabilised by various interactions	Hydrogen bonds; ionic bonds; disulfide bridges; hydrophobic interactions
Quaternary structure	The arrangement of two or more polypeptide chains (subunits) into a functional protein	Same as tertiary (plus interactions between subunits)

Protein Type	Description	Examples
Globular proteins	Roughly spherical; soluble in water; function mainly in metabolic roles (enzymes, antibodies, hormones, transport proteins)	Haemoglobin; enzymes (amylase, catalase); antibodies; insulin
Fibrous proteins	Long, rod-shaped; insoluble in water; function mainly in structural roles	Collagen (tendons, skin, bones); keratin (hair, nails); elastin (artery walls, skin)

Nucleic Acids

Component	DNA	RNA
Full name	Deoxyribonucleic acid	Ribonucleic acid
Sugar	Deoxyribose (one fewer oxygen than ribose)	Ribose
Bases	Adenine (A), Thymine (T), Cytosine (C), Guanine (G)	Adenine (A), Uracil (U), Cytosine (C), Guanine (G)
Structure	Double-stranded helix (two antiparallel strands held together by hydrogen bonds between complementary base pairs)	Usually single-stranded (though it can fold back on itself to form secondary structures such as hairpin loops)
Base pairing	A-T (2 hydrogen bonds); G-C (3 hydrogen bonds)	A-U (2 hydrogen bonds); G-C (3 hydrogen bonds)
Strands	Antiparallel (one strand runs 5' $\rightarrow$ 3', the other runs 3' $\rightarrow$ 5')	Single strand (5' $\rightarrow$ 3')
Location	Nucleus (in eukaryotes); also in mitochondria and chloroplasts	Nucleus (mRNA is transcribed here); cytoplasm (mRNA is translated here); also in ribosomes (rRNA)
Types	One type (DNA)	mRNA (messenger); tRNA (transfer); rRNA (ribosomal)
Function	Stores genetic information; passes genetic information from one generation to the next; template for RNA synthesis	mRNA: carries genetic information from DNA to the ribosome for protein synthesis. tRNA: carries amino acids to the ribosome. rRNA: structural and catalytic component of ribosomes

Water

Property of Water	Importance to Living Organisms
Solvent	Water is an excellent solvent for polar and ionic substances (due to its polarity); many biochemical reactions take place in aqueous solution
High specific heat capacity	Water absorbs a lot of heat energy before its temperature changes significantly; this helps organisms maintain a stable internal temperature (homeostasis) and prevents large temperature fluctuations in aquatic environments
High latent heat of vaporisation	A lot of energy is required to evaporate water; this makes sweating an effective cooling mechanism for mammals; evaporation of water from tropical forests contributes to cloud formation and rainfall
Cohesion and surface tension	Hydrogen bonds between water molecules create strong cohesion; this allows water to be pulled through xylem vessels (transpiration stream); surface tension allows some insects to walk on water
High density (ice floats)	Water is less dense as a solid (ice) than as a liquid because hydrogen bonds hold water molecules in an open lattice structure; this insulates the water below, allowing aquatic organisms to survive in winter
Transparency	Water is transparent to visible light; this allows photosynthesis to occur in aquatic environments (light can penetrate to submerged plants and algae)
Reactant	Water is a reactant in hydrolysis reactions (e.g., digestion of polymers) and photosynthesis; a product of condensation reactions and aerobic respiration

Enzymes in Detail

Lock-and-Key vs Induced-Fit Model

Model	Description	Evidence
Lock and key	The active site of the enzyme has a rigid, fixed shape that is exactly complementary to the shape of the substrate (like a key fits a lock)	Explains enzyme specificity but is an oversimplification
Induced fit	The active site is flexible; when the substrate enters the active site, the enzyme changes shape slightly to fit more closely around the substrate; this puts strain on the substrate, weakening bonds and lowering the activation energy	Supported by X-ray crystallography studies showing enzyme-substrate complexes; explains why some enzymes can catalyse reactions of slightly different substrates

Factors Affecting Enzyme Activity

Factor	Effect	Graph Shape	Explanation
Temperature	Rate increases up to an optimum, then decreases sharply	Bell curve	Increasing temperature increases kinetic energy (more enzyme-substrate collisions); above the optimum, the enzyme denatures (active site changes shape and substrate can no longer bind)
pH	Rate increases up to an optimum, then decreases	Bell curve	Changes in pH alter the charges on amino acid residues in the active site, disrupting the ionic and hydrogen bonds that maintain the tertiary structure; extreme pH causes denaturation
Substrate concentration	Rate increases proportionally at low concentrations, then plateaus (Vmax)	Hyperbolic (rectangular) curve	At low [substrate], increasing [substrate] increases the number of enzyme-substrate collisions; at high [substrate], all active sites are occupied at all times (enzyme saturation); Vmax depends on enzyme concentration
Enzyme concentration	Rate increases proportionally	Straight line (through origin)	More enzyme molecules = more active sites available = more enzyme-substrate complexes formed per unit time
Inhibitor concentration	Depends on inhibitor type (competitive or non-competitive)	Varies	See below

Types of Inhibition

Type	Description	Effect on Vmax	Effect on K $_m$	Reversibility
Competitive	Inhibitor has a similar shape to the substrate and competes for the active site	Vmax unchanged (high [substrate] outcompetes inhibitor)	K $_m$ increased (higher [substrate] needed to reach half Vmax)	Reversible (can be overcome by increasing [substrate])
Non-competitive	Inhibitor binds to a site other than the active site (allosteric site), causing a conformational change that alters the active site	Vmax decreased (inhibitor cannot be overcome)	K $_m$ unchanged (substrate affinity is not affected, but maximum rate is reduced)	Usually reversible

Common Pitfalls

Starch is NOT digestible by all organisms. Humans can digest starch (amylase breaks the $\alpha$ -glycosidic bonds) but CANNOT digest cellulose ( $\beta$ -glycosidic bonds). Herbivores (cows, rabbits) can digest cellulose because they have symbiotic bacteria in their gut that produce cellulase
Lipids contain more energy per gram than carbohydrates (approximately 39 kJ/g vs 17 kJ/g). This is because lipids have a higher proportion of C-H bonds (which release more energy when oxidised) and very little oxygen (more energy released per gram of carbon oxidised)
DNA and RNA differ in three ways: sugar (deoxyribose vs ribose), bases (T vs U), and structure (double-stranded vs single-stranded). Students often forget one of these differences
The primary structure of a protein is determined by the DNA sequence (gene). Changes in the DNA sequence (mutations) can alter the primary structure, which can change the tertiary structure, which can change the function of the protein. This is the molecular basis of many genetic diseases (e.g., sickle cell anaemia: a single amino acid change in the beta-globin protein)
Non-competitive inhibition reduces Vmax but does NOT change K $_m$ . Competitive inhibition increases K $_m$ but does NOT change Vmax. Students frequently confuse these effects**

Cell Structure​

Cell Theory​

Prokaryotic vs Eukaryotic Cells​

Plant vs Animal Cells​

Cell Organelles​

Nucleus​

Mitochondria​

Endoplasmic Reticulum (ER)​

Golgi Apparatus​

Ribosomes​

Lysosomes​

Chloroplasts (Plant Cells Only)​

Cell Membrane​

Membrane Transport​

Passive Transport (No Energy Required)​

Simple Diffusion​

Facilitated Diffusion​

Osmosis​

Active Transport (Energy Required)​

Bulk Transport​

Endocytosis​

Exocytosis​

Biological Molecules​

Carbohydrates​

Proteins​

Lipids​

Nucleic Acids​

Enzymes​

Definition​

Properties of Enzymes​

Lock and Key Hypothesis​

Induced Fit Hypothesis​

Factors Affecting Enzyme Activity​

Worked Example 1​

Enzyme Inhibition​

Cellular Respiration​

Glycolysis (Cytoplasm)​

Link Reaction (Mitochondrial Matrix)​

Krebs Cycle (Mitochondrial Matrix)​

Oxidative Phosphorylation (Inner Mitochondrial Membrane)​

ATP Yield per Glucose​

Photosynthesis​

Light-Dependent Reactions (Thylakoid Membrane)​

Light-Independent Reactions / Calvin Cycle (Stroma)​

Limiting Factors in Photosynthesis​

Summary Table​

Exam Tips​

Worked Example: Cell Membrane Structure​

Cell Division​

Mitosis​

Stages of Mitosis​

Worked Example 2 (Cell Division)​

Meiosis​

Meiosis Stages​

The Cell Cycle​

Control of the Cell Cycle​

Cancer and Uncontrolled Cell Division​

DNA Replication​

Semi-Conservative Replication​

Process​

Accuracy​

Protein Synthesis​

Transcription​

Translation​

The Genetic Code​

Additional Practice Questions​

Homeostasis and Cell Communication​

Cell Signalling​

Receptors​

Signal Transduction​

Immune System​

Non-Specific (Innate) Immunity​

Specific (Adaptive) Immunity​

Antibody Structure​

Types of Antibodies​

Primary vs Secondary Immune Response​

Worked Example 3 (Immune)​

Additional Topics​

Stem Cells​

Water Potential and Osmosis Calculations​

Cell Structure

Cell Theory

Prokaryotic vs Eukaryotic Cells

Plant vs Animal Cells

Cell Organelles

Nucleus

Mitochondria

Endoplasmic Reticulum (ER)

Golgi Apparatus

Ribosomes

Lysosomes

Chloroplasts (Plant Cells Only)

Cell Membrane

Membrane Transport

Passive Transport (No Energy Required)

Simple Diffusion

Facilitated Diffusion

Osmosis

Active Transport (Energy Required)

Bulk Transport

Endocytosis

Exocytosis

Biological Molecules

Carbohydrates

Proteins

Lipids

Nucleic Acids

Enzymes

Definition

Properties of Enzymes

Lock and Key Hypothesis

Induced Fit Hypothesis

Factors Affecting Enzyme Activity

Worked Example 1

Enzyme Inhibition

Cellular Respiration

Glycolysis (Cytoplasm)

Link Reaction (Mitochondrial Matrix)

Krebs Cycle (Mitochondrial Matrix)

Oxidative Phosphorylation (Inner Mitochondrial Membrane)

ATP Yield per Glucose

Photosynthesis

Light-Dependent Reactions (Thylakoid Membrane)

Light-Independent Reactions / Calvin Cycle (Stroma)

Limiting Factors in Photosynthesis

Summary Table

Exam Tips

Worked Example: Cell Membrane Structure

Cell Division

Mitosis

Stages of Mitosis

Worked Example 2 (Cell Division)

Meiosis

Meiosis Stages

The Cell Cycle

Control of the Cell Cycle

Cancer and Uncontrolled Cell Division

DNA Replication

Semi-Conservative Replication

Process

Accuracy

Protein Synthesis

Transcription

Translation

The Genetic Code

Additional Practice Questions

Homeostasis and Cell Communication

Cell Signalling

Receptors

Signal Transduction

Immune System

Non-Specific (Innate) Immunity

Specific (Adaptive) Immunity

Antibody Structure

Types of Antibodies

Primary vs Secondary Immune Response

Worked Example 3 (Immune)

Additional Topics

Stem Cells

Water Potential and Osmosis Calculations