Topic 2 - Membranes, Proteins, DNA and Gene Expression

A gas-exchange surface is effective when it has a large area, a short diffusion distance and a steep concentration gradient. Fick’s law summarises this as rate ∝ surface area × concentration difference ÷ barrier thickness.

Alveoli provide a huge folded surface, a thin moist epithelium and a dense capillary network. Ventilation refreshes alveolar air and blood flow removes oxygen, maintaining the gradient.

If surface area doubles while thickness and gradient stay constant, the predicted diffusion rate doubles. If mucus thickens the barrier, diffusion slows even if oxygen concentration outside remains unchanged.

Small organisms can rely on their body surface because their surface-area-to-volume ratio is high. Larger organisms need specialised surfaces and transport systems to keep internal cells within diffusion distance.

Fick’s law is a proportional model, not a promise that every biological change is linear. Permeability, binding and active regulation can also limit transfer.

A cell-surface membrane is a phospholipid bilayer with hydrophilic phosphate heads facing water and hydrophobic fatty-acid tails facing inward. Proteins, cholesterol and carbohydrate chains give the membrane a fluid but selective structure.

Small non-polar molecules can diffuse through the hydrophobic core; ions and larger polar molecules require channel or carrier proteins. Cholesterol helps limit excessive fluidity and permeability.

Oxygen can cross the bilayer down its concentration gradient, whereas a charged sodium ion needs a membrane protein. A receptor protein can also convert an external signal into a cell response.

When explaining movement, identify the substance, its gradient, the membrane barrier and the protein or energy requirement. “Partially permeable” describes selectivity, not an absolute gate for every molecule.

The membrane is not a rigid wall and not an open sieve. Protein number, temperature and lipid composition can change the observed rate.

A permeability experiment uses a measurable proxy for material crossing a membrane, such as pigment leaking from beetroot cells. The proxy is not the membrane itself; it is evidence that membrane integrity or permeability changed.

Cut equal tissue pieces, rinse away surface pigment, place them in controlled volumes at different temperatures or treatments, and measure colour intensity with a colorimeter after the same time.

A colorimeter converts absorbance into comparable data, while repeats and a blank reduce random and background effects. Control tissue size, surface area, solvent volume and time so the tested variable is isolated.

If hotter water causes greater pigment absorbance, infer that membrane permeability increased under that condition. Do not infer a precise molecular pore size from colour alone.

The conclusion concerns the chosen tissue, treatment and proxy. It does not automatically generalise to every membrane or prove that all cell contents escaped.

Osmosis is the net movement of water across a partially permeable membrane from higher water potential to lower water potential. Water potential combines pressure effects and solute effects, so it is not simply “water concentration”.

A concentrated solution has a more negative solute potential. Water leaves a cell placed in a lower-water-potential solution, reducing turgor; water enters when the external solution has higher water potential.

If potato cylinders lose mass in a sucrose solution, the solution had a lower water potential than the potato cells. The concentration at which there is no net mass change estimates the tissue’s initial water potential.

Use equal cylinders, blot them consistently, control time and temperature, repeat at several concentrations and plot percentage mass change rather than relying on one sample.

Water still moves in both directions at the microscopic level; “no net movement” means equal opposing fluxes. Do not equate a mass change directly with solute entering the cells.

Simple diffusion moves small suitable molecules through the bilayer down a concentration gradient. Facilitated diffusion uses a channel or carrier but still moves down the gradient; active transport uses energy to move a substance against its electrochemical gradient.

Channels provide a hydrophilic route and can be gated. Carrier proteins bind a solute and change shape. Pumps use ATP directly or couple movement to another gradient.

Glucose may enter a cell through a carrier down its gradient, while a sodium–potassium pump uses ATP to maintain ion gradients that support nerve and epithelial transport.

The mechanism predicts sensitivity: diffusion depends on gradient and permeability; active transport depends on ATP supply, pump density and the gradient being maintained.

A membrane protein does not automatically imply active transport. State the direction, energy source and coupling before assigning the mechanism.

Amino acids share an amino group, carboxyl group and variable R group. Peptide bonds join amino acids by condensation to form a polypeptide; its sequence is the primary structure.

Hydrogen bonds, ionic interactions, disulfide bonds and hydrophobic interactions fold the chain into secondary, tertiary and sometimes quaternary structure. Shape determines binding and function.

Replacing one amino acid can alter charge or hydrophobicity, changing folding and a protein’s activity. A denatured enzyme may keep its peptide bonds but lose the shape of its active site.

Fibrous proteins form long structural arrangements; globular proteins fold into compact shapes with functional sites. Both depend on the same chemical principle that sequence constrains folding.

Primary structure is the amino-acid sequence, not the gene itself. A change in DNA can affect a protein, but environment and folding conditions also influence the final phenotype.

An enzyme is a globular protein whose tertiary structure creates a specific active site. A substrate binds by complementary shape and chemical interactions, forming an enzyme–substrate complex that lowers activation energy.

The induced-fit idea explains why binding can alter the active site slightly and position reactants for reaction. Temperature, pH and inhibitors can change the active site or block it, changing rate without changing the substrate itself.

If an enzyme’s active site loses its shape at extreme pH, the substrate concentration may remain high but fewer productive complexes form. A competitive inhibitor lowers the chance that substrate occupies the site.

Explain a rate change through collision frequency, active-site occupancy and protein structure. Distinguish denaturation from reversible inhibition when the conditions allow recovery.

The “lock and key” picture is a useful starting model, not a claim that the enzyme is rigid. Specificity does not mean an enzyme works at only one temperature or pH.

To investigate temperature, pH, enzyme concentration or substrate concentration, measure the initial rate of an enzyme reaction while changing one independent variable and controlling the others.

Use equal volumes, a defined mixing time and a signal that changes predictably, such as colour, gas volume or product concentration. Take several early readings, calculate a gradient and repeat at each condition.

Initial rate avoids later distortion when substrate is depleted or product accumulates. A water bath, buffer and matched enzyme volumes make the comparison fair.

A rate–temperature curve rises while collisions become more frequent, reaches an optimum and falls when the protein begins to lose structure. A plateau with increasing substrate may indicate that active sites are saturated.

A final colour or total gas volume is not automatically a rate. State the proxy, time interval, controls and uncertainty before interpreting the pattern.

A nucleotide contains a pentose sugar, phosphate group and nitrogenous base. DNA nucleotides contain deoxyribose and A, T, C or G; RNA nucleotides contain ribose and A, U, C or G.

Nucleotides join by phosphodiester bonds between the phosphate and sugars, forming a sugar–phosphate backbone. Complementary bases pair through hydrogen bonds: A with T in DNA or U in RNA, and C with G.

The base sequence stores information while the backbone gives the polymer continuity. The 2′ hydroxyl in ribose makes RNA chemically less stable than DNA and suits its shorter-lived information-carrying roles.

A DNA template with the base A pairs with a T in the complementary strand; an RNA transcript uses U instead. Replacing T with U is a molecule-level difference, not a change in the genetic message by itself.

A nucleotide is not just a base, and DNA/RNA strands are not held together by phosphodiester bonds between strands. Keep covalent backbone links separate from hydrogen-bonded base pairing.

Before cell division, DNA strands separate and each acts as a template. Free nucleotides pair by complementarity, DNA polymerase joins them into new strands, and each daughter DNA molecule contains one original and one new strand.

Helicase separates the strands; complementary nucleotides align; DNA polymerase forms phosphodiester bonds in the new strand. The two molecules then carry the same base sequence, apart from copying errors.

Meselson and Stahl grew bacteria with heavy nitrogen, moved them to light nitrogen and separated DNA by density. An intermediate-density band after one generation supported semi-conservative replication; later generations produced light and intermediate DNA.

The density pattern distinguishes semi-conservative replication from conservative and dispersive alternatives because it tracks old and newly synthesised DNA together.

DNA polymerase adds nucleotides to a template; it does not “copy a whole chromosome” in one step. Experimental evidence supports a model under stated conditions, not a claim that mutations never occur.

The genetic code is a triplet code: each three-base codon specifies one amino acid or a start/stop signal. Codons are read sequentially and non-overlapping on mRNA.

There are more codons than amino acids, so the code is degenerate: several codons can specify the same amino acid. This can make some substitutions silent but does not make every mutation harmless.

Changing a base in a codon may leave the amino acid unchanged, replace it with another, or create a stop codon. The outcome depends on the codon and on where it occurs in the coding sequence.

Translate from the correct start codon in the correct reading frame, then stop at a stop codon. A one-base insertion can shift every downstream triplet.

“Universal” means broadly shared across organisms, not that every codon has multiple meanings. Triplets are read on mRNA during translation, not as overlapping DNA words.

A gene is a sequence of DNA bases that contains information used to produce a functional polypeptide or RNA. The base sequence is transcribed and, for a protein-coding gene, translated into an amino-acid sequence.

The sequence determines codons, codons determine amino acids and the polypeptide folds into a functional shape. Regulatory sequences and expression level also affect when and where the product is made.

A mutation in a gene can alter one codon, introduce a stop signal or shift the reading frame. The phenotype changes only if the resulting product or its expression changes the relevant pathway.

A gene is not the same as a chromosome, allele or protein: a chromosome contains many genes, an allele is one version of a gene and a protein is a possible product.

Do not infer that every DNA difference changes phenotype. Degeneracy, non-coding changes, regulation and environmental conditions can all weaken a direct gene-to-trait claim.

Protein synthesis has two linked stages: transcription copies a gene into mRNA, then translation reads the mRNA to assemble a polypeptide. The DNA template (antisense) strand is used for transcription; codons are read on mRNA and anticodons pair on tRNA.

During transcription, RNA polymerase opens the DNA locally and joins complementary RNA nucleotides. The mRNA leaves the nucleus and binds to a ribosome. In translation, tRNA brings amino acids whose anticodons match successive mRNA codons; peptide bonds join the chain from the start codon until a stop codon.

A template triplet TAC produces an mRNA codon AUG. The ribosome recognises AUG as the start signal and the matching tRNA brings methionine; later codons determine the rest of the sequence.

RNA polymerase makes RNA during transcription; DNA polymerase is used in DNA replication. The mRNA sequence matches the coding strand except that RNA uses U instead of T.

A mutation is a change in a DNA base sequence. Its effect depends on the kind of change and on how that altered sequence is translated into a polypeptide; many mutations have little or no observable effect.

Insertion or deletion usually shifts the reading frame, changing every downstream triplet. A substitution changes one base triplet and may be silent, missense or nonsense. Duplication can provide an extra gene copy, while inversion reverses a DNA segment.

A one-base insertion before the second codon changes all later triplets and can produce a non-functional protein. A substitution may instead leave the amino acid unchanged because the genetic code is degenerate, or create a premature stop codon.

A mutation is not automatically harmful, and a changed amino acid is not automatically fatal. The consequence depends on the codon, the protein region, expression and the resulting phenotype.

A gene occupies a locus and its alternative forms are alleles. An individual's genotype is the allele combination; the phenotype is the observable result. Homozygous means two matching alleles, heterozygous means two different alleles, and dominance describes expression in a heterozygote—not importance.

For a monohybrid cross, write parental genotypes, list the alleles in their gametes, combine them in a Punnett square and convert genotypes to phenotypes. Pedigrees use symbols and family links to infer possible genotypes and whether an allele is likely dominant or recessive.

For Bb × Bb, the predicted genotypes are 1 BB : 2 Bb : 1 bb and, with complete dominance, phenotypes are 3 dominant : 1 recessive. Those are probabilities across many offspring, not a guarantee for four births.

Codominance or incomplete dominance changes the phenotype rule; sex-linked alleles require the X/Y chromosome context. Do not infer a person's exact genotype when the pedigree only supports several possibilities.

Cystic fibrosis is caused by recessive CFTR alleles that produce faulty chloride ion channels. Reduced chloride transport changes water movement by osmosis, making mucus unusually thick in several body systems.

In the airways, sticky mucus is harder for cilia to clear, so infection risk rises and blocked airways reduce gas exchange. In the digestive system, mucus can block pancreatic ducts and hinder enzyme delivery and nutrient absorption. In the reproductive system, thick mucus can obstruct sperm movement or passage.

Two unaffected carrier parents can each pass the recessive allele: the child-risk calculation is 1/4 affected, 1/2 carrier and 1/4 non-carrier. The inheritance probability and the physiological symptoms are linked but are not the same claim.

Not every CFTR mutation has an identical effect, and a recessive allele can be carried without symptoms. Explain the chain from gene to channel to water movement to system function rather than treating the disorder as only a lung disease.

Genetic screening tests DNA to identify a carrier, assess an embryo before implantation, or test a foetus during pregnancy. It informs a decision; it does not by itself predict every aspect of a person's future health.

Carrier testing checks an asymptomatic person's allele status. Pre-implantation genetic diagnosis analyses embryo cells during IVF before implantation. Prenatal testing uses chorionic villus sampling or amniocentesis to obtain foetal DNA during pregnancy.

Chorionic villus sampling is earlier than amniocentesis, while both can provide information about a familial disorder. A result may help parents prepare or consider options, but sampling carries procedure risks and tests can give false results.

Keep the test, the probability and the decision separate: a positive screen is not a guarantee of disease severity, and a negative result is not proof that no health problem exists. Genetic counselling helps interpret uncertainty.

The social and ethical question is not simply whether screening is possible, but how its information should be used. Judgements can concern autonomy, disability, privacy, fairness, pregnancy decisions and the interests of a future child.

Different viewpoints may weigh the same result differently: a family may value preparation or avoiding a severe disorder, while another may stress the risk of pressure, discrimination, unequal access or a narrow idea of which lives are worthwhile.

A carrier result can help a couple plan, yet sharing genetic data with insurers or employers could create harm. Prenatal or embryo results may support informed choice, but false positives, false negatives and procedure risks limit certainty.

An ethical discussion must identify whose values and evidence are involved rather than presenting one answer as scientifically forced. Screening information does not determine a person's worth or make a decision ethically automatic.