IB DP Biology: Proteins: amino acids, peptides and protein structure (DP Biology) – Practice Questions

These are original questions written for Marlbridge, for revision and practice on this content. They are not reproduced past-paper questions, and they do not replicate the exam’s exact structure, question count or mark tariffs – the IB holds copyright in its own papers. Use these alongside the official past papers available through your school or the IB store.

These questions cover IB Diploma Programme Biology topic B1.2 (Proteins) from the IB Biology guide, first assessment 2025. Questions 1 to 7 cover B1.2.1 to B1.2.5 (SL and HL). Questions 8 to 12 cover B1.2.6 to B1.2.12 and are labelled “HL only”.

Study first with the study guide or the revision notes. Course pages: IB DP Biology hub, printable checklist and free 10-minute diagnostics.

Questions

1. Sketch a generalized amino acid. Label the alpha carbon and the three groups and one atom attached to it. [3]

2. A dipeptide is made from two amino acids.

(a) Write the word equation for this reaction. [1] (b) Name the bond formed and state which two parts are removed to make the small molecule. [2] (c) State how many water molecules are produced when a tetrapeptide forms. [1]

3. A polypeptide contains 240 amino acids in one unbranched chain. The average mass of an amino acid unit in the chain, after water loss, is 110 daltons.

(a) State the number of peptide bonds. [1] (b) State the number of water molecules released during its formation. [1] (c) Calculate the mass of the polypeptide. [2]

4. Rice protein is short of essential amino acid L. Lentil protein is short of essential amino acid M.

(a) Define “essential amino acid”. [1] (b) Explain why a vegan diet needs attention to protein sources. [1] (c) Suggest, with reasoning, how a cook could use both foods. [2]

5. Peptide chains can be built from the 20 amino acids coded for in the genetic code.

(a) State how many different tripeptides are possible. [1] (b) Calculate how many different chains of eight amino acids are possible. [2] (c) Explain why the number of different proteins is far greater than 20. [2]

6. The table shows the activity of a bacterial enzyme after incubation at different temperatures. Activity is in arbitrary units.

Temperature (degrees Celsius)	25	40	50	60	70
Activity	40	92	68	15	3

(a) Identify the optimum temperature from these data. [1] (b) Calculate the percentage decrease in activity between 40 and 60 degrees Celsius. [2] (c) Explain the fall in activity above the optimum. [3]

7. Outline how you would test whether pH changes the rate at which a protease digests a protein. Include the variable you change, one way to measure the response, and two variables to keep constant. [4]

8. (HL only) Four R-groups are described: a hydrocarbon chain; a hydroxyl group; a carboxyl group; an amine group. For each, state whether the R-group is hydrophobic or hydrophilic and, if charged, whether it is acidic or basic. [4]

9. (HL only) In an enzyme, cysteine at position 12 and cysteine at position 87 form a disulfide bond. A mutation replaces the cysteine at 87 with alanine, an amino acid with a non-polar R-group.

(a) Explain the effect on the tertiary structure. [3] (b) Explain why a change in primary structure can change function. [2]

10. (HL only) A region of a protein contains 63 amino acids in an alpha helix. There are 3.6 amino acids per turn and each adds 0.15 nm to the length (data supplied).

(a) Calculate the number of turns. [2] (b) Calculate the length of the helix in nm. [2] (c) Describe how the helix is stabilized. [2]

11. (HL only) Soluble globular proteins and integral membrane proteins both contain hydrophobic amino acids.

(a) Describe where the hydrophobic amino acids are in a soluble globular protein and why. [2] (b) Describe their role in an integral protein. [2] (c) A basic R-group and an acidic R-group form an ionic bond. Explain how a large drop in pH could break it. [3]

12. (HL only) Insulin consists of two polypeptides of 21 and 30 amino acids. Collagen consists of three polypeptides wound together. Haemoglobin has four polypeptides each with a haem group.

(a) Distinguish between conjugated and non-conjugated proteins, classifying all three. [3] (b) Calculate the number of peptide bonds in insulin. [1] (c) Explain how the shape of insulin and collagen suits the function of each. [3] (d) Suggest how cryogenic electron microscopy has advanced knowledge of protein structure. [2]

Answers

1. Central carbon drawn and labelled alpha carbon [1]; amine group NH2 and carboxyl group COOH both bonded to it [1]; hydrogen atom and R-group both bonded to it [1]. [3] Examiner insight: Diagram questions usually reward correct attachment, so check that all four labels join the same carbon and that the R-group is not on the nitrogen.

2. (a) Amino acid + amino acid → dipeptide + water [1] (b) Peptide bond [1]; OH from the carboxyl group of one and H from the amine group of the other [1]. (c) Three [1], because four units have three bonds. [4] Examiner insight: Naming the bond and also the atoms removed shows you understand condensation. A bare “water” does not say where it came from.

3. (a) 239 [1] (b) 239 [1] (c) 240 × 110 [1] = 26 400 daltons [1]. [4] Examiner insight: Show the multiplication. A common slip is 240 bonds, from forgetting that n units have n - 1 links.

4. (a) An amino acid the body cannot make and must obtain from food [1]. (b) Some plant proteins are short of one or more essential amino acids [1]. (c) Combine rice and lentils in the same day [1], because each supplies the amino acid the other lacks, giving all essential amino acids [1]. [4] Examiner insight: “Suggest” wants a reason linked to the data in the stem, so name both missing amino acids rather than only saying “balanced diet”.

5. (a) 20^3 = 8000 [1] (b) 20^8 [1] = 2.56 × 10^10 (25 600 000 000) [1] (c) Chains can be any length from a few to thousands of units [1]; the 20 amino acids can be arranged in any order [1]. [5] Examiner insight: Mention both length and order. Saying only “many combinations” without these gains little.

6. (a) 40 degrees Celsius (the highest activity tested) [1] (b) (92 - 15) / 92 × 100 [1] = 83.7 % decrease [1] (c) Higher temperature gives more kinetic energy [1]; hydrogen and ionic bonds maintaining the folded shape break, so the enzyme unfolds (denaturation) [1]; the active site changes shape so substrate no longer binds, and activity falls [1]. [6] Examiner insight: State the denominator in a percentage change. Answers that say peptide bonds break lose credit because denaturation leaves them intact.

7. Independent variable: different buffer pH values, for example pH 3 to 11 [1]; measure the response such as time for the protein substrate to clear or the mass of product formed [1]; keep two of temperature, enzyme concentration, substrate concentration and volume constant [1]; repeat each pH and take a mean [1]. [4] Examiner insight: “Outline” needs each element named. Listing “keep everything the same” earns nothing without two specific variables.

8. Hydrocarbon chain: hydrophobic (non-polar) [1]; hydroxyl group: hydrophilic, polar and uncharged [1]; carboxyl group: hydrophilic and acidic, negatively charged after losing H+ [1]; amine group: hydrophilic and basic, positively charged after gaining H+ [1]. [4] Examiner insight: Give the charge change as well as the label. “Acidic” alone does not show why a carboxyl group can join an ionic bond.

9. (a) The disulfide bond between positions 12 and 87 can no longer form [1]; this covalent link held two parts of the chain together, so the folding changes [1]; alanine is hydrophobic, so new hydrophobic interactions may form that alter the shape [1]. (b) The sequence decides which R-groups interact [1], so a change alters the 3D shape and the active site or binding site no longer fits [1]. [5] Examiner insight: Link the lost bond to the whole shape and then to function. Stopping after “the bond is lost” is incomplete.

10. (a) 63 / 3.6 [1] = 17.5 turns [1] (b) 63 × 0.15 [1] = 9.45 nm [1] (c) Hydrogen bonds [1] between groups of the backbone in regular positions along the chain [1]. [6] Examiner insight: Show the division or multiplication and give units. Say the bonds are in the backbone, not between R-groups.

11. (a) Hydrophobic amino acids gather in the centre of the molecule [1], away from the surrounding water, with polar ones outside [1]. (b) The hydrophobic regions are in the part within the bilayer’s hydrophobic core [1], which helps the protein embed in the membrane [1]. (c) At low pH the acidic group gains H+ and loses its negative charge [1]; the attraction with the positive basic group is lost, so the ionic bond breaks [1]; the tertiary structure then changes [1]. [7] Examiner insight: A good pH answer follows the hydrogen ions: which group gains or loses them and what charge results.

12. (a) A conjugated protein contains a non-protein part [1]; insulin and collagen are non-conjugated [1]; haemoglobin is conjugated, with haem [1]. (b) (21 - 1) + (30 - 1) = 49 [1] (c) Insulin is compact and globular, soluble in blood, and its shape fits the receptor [1]; collagen is long and fibrous, with three chains wound together [1], giving strength and insolubility for support [1]. (d) Cryo-electron microscopy can image single protein molecules [1] and their interactions with other molecules, which cannot be seen unaided [1]. [9] Examiner insight: For form and function, name the shape feature and the property it gives. Naming the function alone does not link the two.

Where marks are usually lost

• Attaching the R-group to the wrong atom in a diagram.
• Writing n bonds for n amino acids instead of n - 1.
• Saying denaturation breaks peptide bonds.
• Giving the optimum as a value between measured points without saying it is only the best tested.
• Not stating the denominator in a percentage change.
• Describing a hydrophobic effect as “bonds” without saying the groups cluster away from water.
• Confusing hydrogen bonds in secondary structure with those between R-groups in tertiary structure.
• Naming a function without linking it to shape.
• Leaving out units on lengths and masses.

Next steps

• Re-read the revision notes and the study guide.
• Course pages: IB DP Biology hub and printable checklist.
• Try all free 10-minute diagnostics.
• Book a free trial class.

Official syllabus

IB Diploma Programme Biology guide, first assessment 2025, published by the International Baccalaureate Organization. Topic B1.2 Proteins.