Water and its properties

Water is polar (V-shaped, uneven charge distribution), letting it hydrogen bond. This gives it a high specific heat capacity (buffers temperature), high latent heat of vaporisation (cooling by sweating/transpiration), cohesion (surface tension, water column in the xylem) and it acts as a solvent for polar/charged substances and a metabolite in reactions like hydrolysis and condensation.

Monomers, polymers and reactions

Monomers join by condensation reactions, releasing a water molecule and forming a new bond (glycosidic, peptide or ester). Hydrolysis reactions add a water molecule to break these bonds back down. Polymers are chains of monomers - polysaccharides, polypeptides and polynucleotides.

Carbohydrates

Monosaccharides include glucose, fructose and galactose (all C6H12O6). Alpha-glucose and beta-glucose are isomers differing only in the position of the OH group on carbon 1. Two monosaccharides join via a glycosidic bond by condensation to form a disaccharide: glucose+glucose=maltose, glucose+fructose=sucrose, glucose+galactose=lactose. Starch (amylose+amylopectin) and glycogen are made of alpha-glucose and are storage polysaccharides - compact, insoluble, branched (glycogen more so) for rapid hydrolysis. Cellulose is made of beta-glucose chains linked by 1,4-glycosidic bonds, forming straight chains cross-linked by hydrogen bonds into strong microfibrils for cell walls.

Lipids

Triglycerides = one glycerol + three fatty acids joined by ester bonds via condensation. Saturated fatty acids have no C=C double bonds (solid at room temp); unsaturated have at least one double bond, causing a kink that lowers melting point (liquid oils). Phospholipids have a phosphate head (hydrophilic) and two fatty acid tails (hydrophobic), forming the bilayer.

Proteins

Amino acids share a central carbon with an amine group, carboxyl group, H, and a variable R group - it is the R group that differs between the 20 amino acids. Peptide bonds form between amino acids by condensation. Primary structure = amino acid sequence; secondary = alpha helices/beta pleated sheets held by hydrogen bonds; tertiary = 3D folding held by ionic, hydrogen and disulfide bonds plus hydrophobic interactions; quaternary = multiple polypeptide chains together (e.g. haemoglobin, four chains plus haem groups).

Common mistakes

Do not say water molecules are simply 'attracted' - name hydrogen bonding specifically. Do not confuse condensation (releases water) with hydrolysis (uses water). Remember starch is a mixture of two polymers, not one. Always describe bonding types by name (glycosidic/peptide/ester) rather than just 'bond'.

Cell structure basics

Eukaryotic cells (animal, plant, fungal) have a nucleus and membrane-bound organelles. Prokaryotic cells (bacteria) do not: no nucleus, DNA is a single circular loop free in the cytoplasm, plus small extra circles called plasmids. Bacteria are much smaller, typically 1-5 micrometres, versus 10-100 micrometres for eukaryotic cells.

Key organelles and their jobs

• Nucleus: holds DNA, controls the cell, has a nuclear envelope with pores.
• Mitochondria: site of aerobic respiration, make ATP, have their own DNA and a folded inner membrane called cristae.
• Ribosomes: make proteins; 80S in eukaryotes, 70S in prokaryotes (and in mitochondria and chloroplasts) - this size difference is a classic exam point.
• Rough ER: has ribosomes attached, folds and transports proteins.
• Smooth ER: makes lipids and steroids, no ribosomes.
• Golgi apparatus: modifies, sorts and packages proteins into vesicles, e.g. adding carbohydrate to make glycoproteins.
• Lysosomes: contain digestive enzymes, break down worn-out organelles and pathogens.

Cell membranes and transport

The fluid mosaic model describes the membrane as a bilayer of phospholipids with proteins floating within it. Transport methods:

• Diffusion: passive, high to low concentration, no ATP.
• Facilitated diffusion: passive, via channel or carrier proteins, no ATP.
• Osmosis: passive movement of water from high to low water potential across a partially permeable membrane.
• Active transport: uses ATP, moves substances against their concentration gradient via carrier proteins.

The immune system

Pathogens are recognised by antigens on their surface. The immune response has two main arms:

• Cell-mediated response: T lymphocytes mature in the thymus. T-helper cells release cytokines to activate other cells; T-killer cells destroy infected cells directly.
• Humoral response: B lymphocytes mature in the bone marrow and produce antibodies once activated by T-helper cells (clonal selection). Some become memory cells and some become plasma cells that secrete antibodies.

Antibodies are Y-shaped proteins with a variable region that binds a specific antigen, causing agglutination (clumping) of pathogens so phagocytes can engulf them more easily.

Common mistakes to avoid

• Do not say bacteria have a nucleus - they never do.
• Do not confuse antigen (the marker) with antibody (the immune protein that binds it).
• Remember active transport needs ATP from respiration, not just any energy source.
• Primary immune response is slow with low antibody levels; secondary response (memory cells) is faster and produces more antibodies - this is the basis of vaccination.
• Phagocytosis is non-specific and part of the innate immune response, unlike the specific responses of T and B cells.

Why organisms need exchange surfaces

As organisms get bigger, their surface area to volume (SA:V) ratio falls. A cube of side 1mm has SA:V of 6:1, but a cube of side 10mm has SA:V of only 0.6:1. Diffusion alone (Fick's Law) is too slow over large distances, so large/active organisms need specialised exchange surfaces plus mass transport systems (blood, xylem, phloem) to keep supply matching demand.

Features of a good exchange surface

• Large surface area (folding, projections like villi or alveoli)
• Thin (often one cell thick) to shorten diffusion distance
• Good blood supply or ventilation to maintain a steep concentration gradient
• Partially permeable membrane

Gas exchange in humans

The lungs contain about 300-500 million alveoli, giving a huge surface area (~70m^2). Alveolar walls and capillary walls are each one cell thick (squamous epithelium), so the diffusion distance is under 1 micrometre. Ventilation (breathing) and blood flow both maintain steep O2 and CO2 gradients. Common mistake: students say 'oxygen diffuses into the blood' without naming the gradient or structures - always mention SA, thinness, and gradient together.

Gas exchange in insects and fish

Insects use a tracheal system: air enters through spiracles (which can close to reduce water loss) and travels down tracheae and tracheoles directly to tissues, so gas exchange bypasses the blood system. Fish use gills with a counter-current flow system - blood and water flow in opposite directions, maintaining a diffusion gradient along the entire gill lamellae so up to 80% of available oxygen can be extracted, versus far less with parallel flow.

The circulatory system

Humans have a double closed circulatory system: the pulmonary circuit (heart to lungs) and systemic circuit (heart to body), meaning blood passes through the heart twice per full circuit. This gives faster, higher-pressure delivery than a single circulation. Know the heart's four chambers, valves (atrioventricular and semi-lunar) preventing backflow, and the cardiac cycle (systole/diastole).

Xylem and transpiration

Water moves up xylem vessels via the transpiration pull (cohesion-tension theory): water evaporates from leaf mesophyll cells, pulling a continuous water column up due to cohesion (hydrogen bonding) and adhesion to vessel walls. Factors increasing transpiration rate: higher temperature, lower humidity, more wind, more light (stomata open).

Phloem and translocation

Phloem transports sugars (mainly sucrose) from source (e.g. leaves) to sink (e.g. roots, fruits) via mass flow, requiring active loading using companion cells and ATP.

Common mistakes

• Confusing xylem (one-way, dead cells, water) with phloem (two-way, living cells, sugars)
• Forgetting counter-current exchange is more efficient than parallel flow
• Not linking SA:V ratio explicitly to the need for exchange surfaces

DNA, genes and alleles

• A gene is a length of DNA coding for a specific polypeptide, found at a fixed locus on a chromosome.
• An allele is a different version of a gene, arising from mutation, differing in base sequence.
• Humans are diploid (2n = 46, 23 pairs), so carry two alleles per gene (one from each parent).
• Homozygous = two identical alleles; heterozygous = two different alleles.
• Genotype is the genetic makeup (allele combination); phenotype is the observable characteristic, resulting from genotype AND environment.

Inheritance patterns

• Dominant alleles are expressed even when heterozygous; recessive alleles are only expressed when homozygous.
• Codominance: both alleles are fully expressed in the phenotype, eg the AB blood group.
• Multiple alleles: more than two alleles exist for a gene in the population, eg the three alleles (I-A, I-B, i) controlling ABO blood groups.
• Sex linkage: genes carried on the X chromosome (the Y is much shorter and carries far fewer genes), so recessive X-linked conditions like haemophilia and red-green colour blindness appear far more often in males (XY) than females (XX).
• Use a genetic cross diagram every time: parental phenotypes, genotypes, gametes (in circles), then a Punnett square to get offspring ratios. Common mistake: forgetting to show gametes as haploid, or mislabelling which parent contributes which allele.

Variation and its sources

• Genetic variation arises from: mutation (a change in the base sequence of DNA), independent assortment during meiosis I, crossing over (recombination) during meiosis I, and random fertilisation.
• Independent assortment: with 23 pairs of chromosomes, there are 2^23 possible combinations in a human gamete purely from this process.
• Continuous variation (eg height, produces a normal distribution, controlled by many genes plus environment) vs discontinuous variation (eg ABO blood group, controlled by one or few genes, discrete categories).
• Mutations can be gene mutations (substitution, insertion, deletion of bases) or chromosome mutations (changes in chromosome number or structure, eg non-disjunction causing trisomy 21/Down's syndrome).

Chi-squared test

• Used to test whether observed genetic ratios differ significantly from expected ratios.
• Formula: chi-squared = sum of (O minus E) squared divided by E.
• Compare to critical value at p = 0.05 (95% confidence) with the correct degrees of freedom (number of categories minus 1).
• If calculated chi-squared exceeds the critical value, reject the null hypothesis: the difference IS significant, not due to chance.
• Common mistake: using percentages instead of raw counts, or getting degrees of freedom wrong.

Exam tips

• Always define terms precisely using exact specification wording (eg 'allele' not just 'gene version').
• Show full working in genetic diagrams for full marks, even if the answer seems obvious.
• Link genotype to phenotype using clear causal language: 'because the recessive allele is only expressed when homozygous'.

Photosynthesis: the basics

Photosynthesis converts light energy into chemical energy stored in glucose. It happens in the chloroplast and has two stages.

• Light-dependent reactions happen on the thylakoid membrane
• Light-independent reactions (Calvin cycle) happen in the stroma

Light-dependent reactions

Chlorophyll absorbs light, exciting electrons. This drives:

• Photolysis of water: splits into H+, electrons, and oxygen (2H2O -> 4H+ + 4e- + O2)
• Electron transport chain builds a proton gradient across the thylakoid membrane
• Chemiosmosis through ATP synthase makes ATP
• NADP+ is reduced to NADPH using H+ and electrons
• Cyclic photophosphorylation uses only photosystem I and makes ATP only, no NADPH or oxygen
• Non-cyclic photophosphorylation uses both photosystems I and II, makes ATP, NADPH and oxygen

Light-independent reactions (Calvin cycle)

CO2 is fixed onto ribulose bisphosphate (RuBP), a 5-carbon compound, by the enzyme rubisco. This forms an unstable 6-carbon compound that splits into two molecules of glycerate 3-phosphate (GP), a 3-carbon compound. GP is reduced to triose phosphate (TP) using ATP and NADPH from the light reactions. Most TP regenerates RuBP; one in six TP molecules is used to make glucose and other organic molecules.

Common mistake: students confuse GP and TP, or forget that RuBP regeneration needs ATP too, not just GP reduction.

Limiting factors

Light intensity, CO2 concentration and temperature can each limit the rate of photosynthesis. Whichever factor is in shortest supply limits the rate, shown as a plateau on a graph even if the other factors increase.

Respiration

Aerobic respiration has four stages: glycolysis (cytoplasm, produces 2 ATP net and 2 pyruvate), link reaction (matrix, pyruvate to acetyl CoA, releases CO2), Krebs cycle (matrix, releases CO2 and reduced coenzymes), and oxidative phosphorylation (inner mitochondrial membrane, chemiosmosis via the electron transport chain, produces most ATP, oxygen is the final electron acceptor forming water).

• Total ATP yield from aerobic respiration of one glucose is approximately 30-32 ATP (older specifications quote 38, current Edexcel favours around 30)
• Anaerobic respiration in animals produces lactate from pyruvate, regenerating NAD+ but no further ATP
• Anaerobic respiration in yeast/plants produces ethanol and CO2 (alcoholic fermentation)

Common mistake: writing that anaerobic respiration produces no ATP at all - it still yields the 2 ATP from glycolysis.

Homeostasis basics

Homeostasis keeps the internal environment within narrow limits despite external change, using negative feedback.

• A stimulus is detected by a receptor, a coordinator (usually the CNS) processes it, and an effector (muscle or gland) brings the response.
• Negative feedback returns a variable to its set point; positive feedback amplifies change (eg childbirth contractions, blood clotting) and is rare and self-limiting.

Nervous vs hormonal control

• Nervous signals are electrical, fast (milliseconds), short-lived, and travel along neurones to precise targets.
• Hormonal signals are chemical, slower, longer-lasting, and travel in the blood to widespread targets.
• A reflex arc: receptor to sensory neurone to relay neurone in the CNS to motor neurone to effector. This is involuntary and protects the body quickly.

The nerve impulse

• Resting potential is about -70mV, maintained by the sodium-potassium pump (3 Na+ out, 2 K+ in, using ATP) and K+ leak channels.
• Depolarisation happens when voltage-gated Na+ channels open and Na+ floods in, reaching about +40mV at the peak.
• Repolarisation follows as Na+ channels close and voltage-gated K+ channels open, K+ leaves.
• The refractory period stops the impulse travelling backwards and sets a maximum frequency of firing.
• Myelinated neurones show saltatory conduction, the impulse jumps between nodes of Ranvier, which is much faster than continuous conduction in unmyelinated fibres.
• Common mistake: an action potential is all-or-nothing, it does not vary in size, only frequency codes for stimulus strength.

Synapses

• Depolarisation opens voltage-gated Ca2+ channels at the presynaptic knob, Ca2+ influx causes vesicles to fuse with the membrane and release neurotransmitter by exocitosis.
• Neurotransmitter diffuses across the synaptic cleft and binds receptors on the postsynaptic membrane, opening ion channels.
• Synapses ensure one-way transmission and allow summation (spatial and temporal) to reach threshold.

Control of blood glucose

• Beta cells in the islets of Langerhans secrete insulin when glucose is high, insulin increases glucose uptake into cells and glycogenesis in the liver and muscle.
• Alpha cells secrete glucagon when glucose is low, triggering glycogenolysis and gluconeogenesis in the liver.
• Type 1 diabetes is autoimmune destruction of beta cells (little or no insulin), Type 2 is reduced receptor sensitivity (insulin resistance), often linked to obesity.

Gene expression and control

• Not all genes are expressed in every cell, differentiation happens because different genes are switched on or off.
• Transcription factors control transcription by binding to specific DNA sites (promoters/enhancers) and either stimulating or inhibiting RNA polymerase binding.
• Epigenetic control alters gene expression without changing the DNA base sequence: DNA methylation (adding methyl groups to cytosine) generally silences genes, histone acetylation loosens chromatin and increases transcription, histone deacetylation condenses chromatin and reduces it.
• Oestrogen is a lipid-soluble hormone that diffuses through the cell membrane and binds directly to a transcription factor, altering gene expression, this is a key exam example.
• Common mistake: students confuse methylation (silences) with acetylation (activates) - remember 'acetylation = on'.