Pearson Edexcel International A Level Biology: Proteins, Enzymes, DNA, Protein Synthesis and Inheritance (YBI11) – Revision Notes

Quick recall for specification statements 2.6 to 2.18 of the Pearson Edexcel International Advanced Subsidiary/Advanced Level Biology specification (YBI11), Issue 2. These statements complete Topic 2 (Membranes, Proteins, DNA and Gene Expression), which is part of the International AS (IAS) content and is examined in Unit 1. Statements 2.1 to 2.5 (gas exchange, membranes and transport) are in the separate gas exchange, membranes and osmosis revision notes.

Course pages: Edexcel A Level Biology hub, printable checklist, free 10-minute diagnostics and the IAL Biology exam preparation page.

Amino acids and polypeptides (2.6 i-ii)

Every amino acid has the same core: a central carbon atom bonded to an amine group (-NH₂), a carboxyl group (-COOH), a hydrogen atom and a variable R group. Only the R group differs between amino acids. You do not need the structures of named amino acids.

• Two amino acids join by a condensation reaction: the -OH of one carboxyl group and an -H of the other amine group leave as water, and a peptide bond forms between them.
• Two amino acids give a dipeptide; many give a polypeptide. A protein is one or more polypeptides folded into a specific shape.
• Hydrolysis (adding water) breaks the peptide bond again.

Levels of protein structure (2.6 iii)

Level	What it is	Held by
Primary	The sequence of amino acids in the chain	Peptide bonds
Secondary	Local coiling or folding: α-helix or β-pleated sheet	Hydrogen bonds between groups of the backbone
Tertiary	The overall 3-D shape of one polypeptide	Hydrogen bonds, ionic bonds, disulfide bonds and hydrophobic interactions between R groups
Quaternary	Two or more polypeptides together (sometimes with a non-protein group)	The same bonds as tertiary

The key idea. The primary structure decides where every R group sits, so it decides which bonds form, and therefore the secondary and tertiary structure, the shape and the properties of the protein. Change one amino acid and the shape can change.

Globular and fibrous proteins (2.6 iii-iv)

	Globular	Fibrous
Shape	Compact, roughly spherical	Long strands
Solubility	Soluble: hydrophilic R groups face outwards	Insoluble
Role	Metabolic: transport, enzymes, hormones	Structural
Example	Haemoglobin	Collagen

Haemoglobin. Four polypeptide chains (two α and two β), each with a haem group containing an iron ion that binds oxygen. Its solubility lets it be carried in the cytoplasm of red blood cells; its quaternary shape lets it load and unload oxygen.

Collagen. Three polypeptide chains wound round each other in a tight triple helix. Glycine, the smallest amino acid, is every third amino acid, so the chains pack closely. Many molecules are cross-linked side by side into fibrils and fibres, giving high tensile strength for tendons, skin and artery walls.

Recommended additional practical. Biuret reagent turns from blue to purple (lilac) with protein. Comparing the colour against a set of colour standards of known concentration gives a semi-quantitative estimate.

Enzymes (2.7)

• Enzymes are biological catalysts: they speed up reactions and are unchanged at the end.
• They work by lowering the activation energy of the reaction.
• The active site has a specific 3-D shape, set by the enzyme’s tertiary structure. Only a substrate with a complementary shape fits, so each enzyme is specific.
• The substrate binds to form an enzyme-substrate complex, the reaction happens, and the products leave the active site.
• Intracellular enzymes catalyse reactions inside cells (for example DNA polymerase in the nucleus). Extracellular enzymes are secreted and act outside the cell (for example digestive enzymes such as amylase).

Lock and key versus induced fit. In the lock-and-key model the active site is a rigid, exactly complementary shape. In the induced-fit model the active site changes shape slightly as the substrate binds, which puts strain on the substrate’s bonds and helps lower the activation energy.

Core Practical 4: factors affecting the initial rate (2.8)

Factor	Pattern	Reason
Temperature	Rate rises to an optimum, then falls steeply	More kinetic energy gives more successful collisions; above the optimum, bonds holding the tertiary structure break, the active site changes shape and the enzyme is denatured
pH	Rate highest at the optimum pH, lower on either side	H⁺ and OH⁻ ions disrupt ionic and hydrogen bonds, changing the active site
Enzyme concentration	Rate rises in proportion while substrate is in excess	More active sites available
Substrate concentration	Rate rises, then levels off	At high concentration all active sites are occupied; enzyme concentration becomes the limiting factor

Initial rate. Measure the rate at the very start of the reaction (the gradient of a tangent drawn at time zero on a product-time graph), before substrate is used up. Control every variable except the one being changed, and repeat each condition.

Nucleotides, DNA and RNA (2.9)

A mononucleotide = a pentose sugar + a phosphate group + a nitrogenous base.

	DNA	RNA
Sugar	Deoxyribose	Ribose
Bases	A, T, C, G	A, U, C, G
Strands	Two, antiparallel, in a double helix	One, usually shorter

• Nucleotides join by condensation reactions between the phosphate of one nucleotide and the sugar of the next, forming phosphodiester bonds. This gives a sugar-phosphate backbone.
• In the double helix the bases pair by complementary base pairing: A with T, and C with G. The pairs are held together by hydrogen bonds (two between A and T, three between C and G).
• Many hydrogen bonds together hold the two strands firmly, yet each one is weak, so the strands can be separated for replication and transcription.

DNA replication (2.10 i)

1. The double helix unwinds and the hydrogen bonds between the bases break, separating the two strands (an enzyme, DNA helicase, does this).
2. Each strand acts as a template.
3. Free DNA nucleotides line up against the exposed bases by complementary base pairing.
4. DNA polymerase joins the adjacent nucleotides, forming phosphodiester bonds.
5. Each new molecule contains one original strand and one new strand: replication is semi-conservative.

Meselson and Stahl (2.10 ii)

Method. Bacteria were grown for many generations on a medium containing heavy nitrogen (¹⁵N), so all their DNA was heavy. They were moved to a medium containing light nitrogen (¹⁴N) and allowed to divide. DNA was extracted after each generation and centrifuged, so that DNA of different densities formed bands at different positions.

Generation in ¹⁴N	Result	What it showed
0	One heavy band	Starting point
1	One intermediate band only	Rules out conservative replication, which would give one heavy and one light band
2	One intermediate and one light band (equal amounts)	Rules out dispersive replication, which would give a single band that gets lighter each generation

Only semi-conservative replication fits both results. This is the data that supported the accepted theory and refuted the competing ones.

The genetic code and genes (2.11-2.12)

• Gene: a sequence of bases on a DNA molecule that codes for a sequence of amino acids in a polypeptide chain.
• Triplet code: three bases (a codon on mRNA) code for one amino acid.
• Non-overlapping: each base is read as part of only one triplet.
• Degenerate: there are 64 possible triplets but only 20 amino acids, so most amino acids are coded for by more than one triplet.
• Start codon (AUG on mRNA) begins translation; stop codons code for no amino acid and end it.

Protein synthesis (2.13)

Transcription (in the nucleus)

1. The DNA of the gene unwinds and the hydrogen bonds break.
2. One strand, the template (antisense) strand, is used.
3. Free RNA nucleotides pair with its bases (U pairs with A).
4. RNA polymerase joins them into a strand of messenger RNA (mRNA).
5. The mRNA leaves the nucleus through a nuclear pore. Its sequence matches the non-template (sense) strand, with U in place of T.

Translation (at a ribosome in the cytoplasm)

1. The mRNA attaches to a ribosome, and translation begins at the start codon.
2. Each transfer RNA (tRNA) molecule carries one specific amino acid and has an anticodon of three bases.
3. A tRNA whose anticodon is complementary to the codon on the mRNA pairs with it.
4. A second tRNA pairs with the next codon; a peptide bond forms between the two amino acids.
5. The ribosome moves along one codon at a time, and the first tRNA leaves to collect another amino acid.
6. At a stop codon the polypeptide is released.

Term	Where	Pairs with
Template strand	DNA	Read to make mRNA
Codon	mRNA	Anticodon
Anticodon	tRNA	Codon

Worked reminder. Template DNA TAC GGA TTC gives mRNA AUG CCU AAG, and the anticodons on the tRNAs that read it are UAC, GGA and UUC.

Mutation (2.14)

• A gene mutation is a change in the base sequence of DNA, which can arise from errors during replication.
• Substitution: one base replaced by another. Only one codon changes, and because the code is degenerate the amino acid may stay the same.
• Insertion or deletion: a base added or lost. Every triplet after the change is read differently (a frameshift), so many amino acids change.
• A changed amino acid sequence (primary structure) can change the bonds in the tertiary structure, so the protein’s shape and function change.
• Some mutations lead to cancer or genetic disorders, but many have no observable effect, for example when the new codon codes for the same amino acid, or the change is in a non-coding sequence.

Genetic terms and monohybrid inheritance (2.15 i-ii)

Term	Meaning
Gene	A base sequence on DNA coding for a polypeptide
Allele	One of the different forms of a gene
Genotype	The alleles an organism has
Phenotype	Its observable characteristics, from the genotype and the environment
Dominant	Allele expressed in the phenotype when one copy is present
Recessive	Allele expressed only when no dominant allele is present (two copies)
Codominance	Both alleles are expressed in the phenotype of a heterozygote
Homozygote	Two identical alleles of the gene
Heterozygote	Two different alleles of the gene

Monohybrid crosses. Two heterozygotes (Aa × Aa) give offspring genotypes AA : Aa : aa in the ratio 1 : 2 : 1, so 3 : 1 dominant to recessive phenotype. Aa × aa gives 1 : 1.

Reading a pedigree. Two unaffected parents with an affected child means the allele is recessive and both parents are heterozygous carriers.

Sex linkage (2.15 iii)

• Genes carried on the X chromosome have no matching allele on the much smaller Y chromosome, so a male (XY) has only one copy.
• Red-green colour blindness is caused by a recessive allele on the X chromosome. Write genotypes as Xᴮ (normal) and Xᵇ.
• A male with Xᵇ Y is colour blind. A female needs Xᵇ Xᵇ; Xᴮ Xᵇ is a carrier with normal vision. This is why more males than females are affected.
• A son receives his X chromosome from his mother, so a father cannot pass the allele to his sons.

Worked reminder. Carrier mother (Xᴮ Xᵇ) × unaffected father (Xᴮ Y): half the sons are colour blind; half the daughters are carriers; no daughters are colour blind.

Cystic fibrosis (2.16)

Cystic fibrosis is caused by a recessive allele of the gene for the CFTR protein, a channel in the membranes of epithelial cells that moves chloride ions out of the cell. A mutation (most often a deletion of three bases, removing one amino acid) gives a protein that does not work. Too few chloride ions leave the cells, so less water follows by osmosis and the mucus is thick and sticky.

System	Effect of the thick mucus
Gaseous exchange	Mucus blocks bronchioles and is hard for cilia to clear; more lung infections; fewer working alveoli and a longer diffusion path, so less gas exchange
Digestive	The pancreatic duct is blocked, so fewer digestive enzymes reach the small intestine and food is poorly digested and absorbed; mucus in the intestine also reduces absorption
Reproductive	In males the sperm ducts (vas deferens) may be blocked or absent; in females thick cervical mucus makes it harder for sperm to reach the egg; fertility is reduced

Genetic screening and its issues (2.17-2.18)

Method	What it involves	When
Carrier testing	Testing adults for one copy of a recessive allele, for example a relative of someone with cystic fibrosis	Before or during family planning
Pre-implantation genetic diagnosis (PGD)	Embryos are made by IVF; one cell is removed from each and tested; only unaffected embryos are implanted	Before pregnancy begins
Amniocentesis	A sample of amniotic fluid, containing fetal cells, is taken through the abdomen with a needle	Later in pregnancy (from about 15 weeks)
Chorionic villus sampling (CVS)	A small sample of placental tissue (chorionic villi) is taken	Earlier in pregnancy (from about 10 weeks)

Both prenatal tests carry a small risk of miscarriage, and no test is completely reliable.

Implications of prenatal screening. Parents may face a decision about terminating the pregnancy; a result can prepare them for caring for a child with the condition; false positive or false negative results are possible; the waiting and the decision can cause anxiety.

Discussing the issues (2.18). Build an answer from more than one viewpoint:

• Religious: some believe life begins at conception, so discarding embryos (PGD) or termination is wrong.
• Moral: screening can prevent suffering, but who decides which conditions are serious enough? Could it lead to selecting embryos for non-medical traits?
• Social: cost to health services, the right of the individual to know or not know, and the view of people living with the condition.

Must-know distinctions

• Primary versus tertiary structure: the sequence versus the 3-D shape it produces.
• Globular versus fibrous: soluble and metabolic versus insoluble and structural.
• Intracellular versus extracellular enzymes: acting inside versus outside the cell.
• DNA polymerase versus RNA polymerase: joins DNA nucleotides in replication versus RNA nucleotides in transcription.
• Codon versus anticodon: on mRNA versus on tRNA.
• Substitution versus insertion or deletion: one codon changed versus a frameshift.
• Dominance versus codominance: one allele masks the other versus both are expressed.
• Amniocentesis versus CVS: amniotic fluid later versus placental tissue earlier.

Quick self-test

1. Name the bond formed between two amino acids and the type of reaction that forms it.
2. Name four types of bond or interaction that hold a tertiary structure.
3. Give two ways the structure of collagen suits its function.
4. Explain why an enzyme is specific to one substrate.
5. Why does the rate level off at high substrate concentration?
6. State three differences between DNA and RNA nucleotides or molecules.
7. After two generations in ¹⁴N, what bands did Meselson and Stahl see, and which theory did this rule out?
8. Explain what “degenerate” means for the genetic code.
9. Template DNA reads TAC CAG. Give the mRNA and the tRNA anticodons.
10. Why does a deletion usually have a bigger effect than a substitution?
11. A carrier woman for colour blindness has children with a colour-blind man. What fraction of their daughters would be colour blind?
12. Explain why a person with cystic fibrosis has thick mucus.
13. Give one advantage of CVS over amniocentesis.

Answers

1. A peptide bond, formed by a condensation reaction (water is released).
2. Hydrogen bonds, ionic bonds, disulfide bonds and hydrophobic interactions.
3. Any two: three chains in a triple helix; glycine every third amino acid lets the chains pack closely; cross-links between molecules form fibres with high tensile strength; insoluble.
4. The active site has a specific 3-D shape from the tertiary structure; only a substrate with a complementary shape fits and forms an enzyme-substrate complex.
5. All the active sites are occupied, so enzyme concentration limits the rate.
6. Any three: deoxyribose versus ribose; thymine versus uracil; DNA double-stranded versus RNA single-stranded; DNA much longer.
7. One intermediate and one light band; this ruled out dispersive replication (the first generation had already ruled out conservative).
8. Most amino acids are coded for by more than one triplet (64 triplets, 20 amino acids).
9. mRNA AUG GUC; anticodons UAC CAG.
10. A deletion shifts the reading frame, so every later triplet changes; a substitution changes one codon at most, and may change nothing.
11. Mother Xᴮ Xᵇ, father Xᵇ Y: daughters are Xᴮ Xᵇ or Xᵇ Xᵇ, so 1/2 are colour blind.
12. The faulty CFTR channel moves too few chloride ions out of epithelial cells, so less water leaves by osmosis and the mucus stays thick and sticky.
13. It can be done earlier in pregnancy, so a result and any decision come sooner.

Where marks are usually lost

• Saying a peptide bond forms by hydrolysis, or forgetting that water is released.
• Writing “the active site is the same shape as the substrate” instead of complementary.
• Saying high temperature “kills” an enzyme instead of describing denaturation of the active site.
• Forgetting that the first Meselson-Stahl generation rules out conservative and the second rules out dispersive.
• Mixing up codons (mRNA) with anticodons (tRNA), or using T in an RNA sequence.
• Saying a mutation always changes the protein.
• Drawing a sex-linked cross without X and Y chromosomes in the genotypes.
• Describing cystic fibrosis as “too much mucus” without linking it to chloride ions and water movement.
• Giving only one viewpoint in a screening ethics question.

Frequently asked questions

What is the difference between lock and key and induced fit? In the lock-and-key model the active site is a rigid shape that fits the substrate exactly. In the induced-fit model the active site changes shape slightly as the substrate binds.

What did the Meselson and Stahl experiment show? Bacteria grown on heavy nitrogen and then moved to light nitrogen gave results that only semi-conservative replication fits: each new DNA molecule has one original strand and one new strand.

What does it mean that the genetic code is degenerate? There are 64 possible triplets but only 20 amino acids, so most amino acids are coded for by more than one triplet.

How is red-green colour blindness inherited? It is caused by a recessive allele on the X chromosome. A male with one recessive allele is colour blind, while a female needs two copies, so sons inherit it from their mothers.

What is the difference between amniocentesis and CVS? Amniocentesis samples amniotic fluid later in pregnancy; chorionic villus sampling takes cells from the placenta earlier. Both carry a small risk of miscarriage.

Official syllabus

Pearson Edexcel International Advanced Subsidiary/Advanced Level in Biology, Specification, Issue 2 (February 2021), Pearson Education Limited: Topic 2, statements 2.6 to 2.18, including Core Practical 4 and the recommended additional practical on protein concentration.