IB DP Biology: Proteins: amino acids, peptides and protein structure (DP Biology) – Revision Notes

These notes condense IB Diploma Programme Biology topic B1.2 (Proteins) from the IB Biology guide, first assessment 2025. For fuller explanations, read the study guide. Test yourself with the practice set. Statements B1.2.6 to B1.2.12 are additional higher level and marked “HL only”; B1.2.1 to B1.2.5 are SL and HL.

Course pages: IB DP Biology hub, printable checklist, free 10-minute diagnostics and Theme B revision notes.

Amino acids and peptides (B1.2.1 to B1.2.2)

Item	Key fact
Generalized amino acid	Central (alpha) carbon carrying NH2, COOH, H and a variable R-group
What varies	Only the R-group
Condensation	Amino acid + amino acid → dipeptide + water
Peptide bond	Covalent bond between the carboxyl carbon of one unit and the amine nitrogen of the next
Hydrolysis	Adds water and splits a peptide bond (digestion)

Method: counting a chain

1. Bonds in an unbranched chain of n units = n - 1.
2. Water released = number of peptide bonds.
3. Separate chains joined by disulfide bonds do not add peptide bonds.

Small reminder: a chain of 30 units has 29 peptide bonds and loses 29 water molecules. New units are added at the carboxyl end of the growing chain, and a dipeptide has one amine end and one carboxyl end.

Diet and variety (B1.2.3 to B1.2.4)

• Essential amino acids cannot be made and must be eaten. Non-essential ones can be made from other amino acids. You need no named examples.
• Vegan diets need planning: some plant proteins are short of one or more essential amino acids, so a mix of plant sources is needed.
• The genetic code specifies twenty different amino acids. Chains can be a few to thousands long and the order is free.
• Number of sequences of length n = 20^n. Dipeptides 400, tripeptides 8000, tetrapeptides 160 000.
• Examples of polypeptides: insulin chains, the polypeptides of collagen and haemoglobin.

pH, temperature and denaturation (B1.2.5)

Factor	What it does	Result
High temperature	More kinetic energy breaks weak interactions	Chain unfolds
pH change	Alters charges on R-groups, so ionic and hydrogen bonds change	Shape changes

• Denaturation is a change in three-dimensional shape that stops the protein working, usually irreversible.
• Peptide bonds are not broken, so the primary structure survives.
• For enzymes the active site no longer fits the substrate.

Method: describing a rate curve

1. State the optimum from the data, and note it is the highest tested value.
2. Describe the rise, peak and fall with figures.
3. Explain the fall with denaturation and the bonds that are disturbed.

Levels of structure (HL only: B1.2.6 to B1.2.10)

Level	What it is	Held by
Primary	Order of the amino acids in the chain	Peptide bonds
Secondary	Coils (alpha helix) or pleats (beta sheet)	Hydrogen bonds in regular positions along the backbone
Tertiary	Overall folded form of a single chain	Interactions between R-groups: hydrogen, ionic, disulfide, hydrophobic
Quaternary	Two or more polypeptides together	Same kinds of interactions between chains

R-groups (HL only)

• Hydrophobic: non-polar.
• Hydrophilic: polar, or charged. Charged groups are acidic (lose H+, negative) or basic (gain H+, positive).
• The R-groups determine the properties of the assembled polypeptide.
• The sequence and exact position of each amino acid fix the 3D shape. The shape is precise, predictable and repeatable.

Tertiary interactions (HL only)

Interaction	Between	Note
Hydrogen bond	Polar R-groups	Weak
Ionic bond	Positive and negative R-groups	Altered by pH
Disulfide bond	Two cysteines	Covalent, strong
Hydrophobic interaction	Non-polar R-groups	Gather in the centre

• Soluble globular proteins: hydrophobic amino acids in the core, polar ones outside.
• Integral membrane proteins: hydrophobic regions embed in the bilayer.

Quaternary structure and form to function (HL only: B1.2.11 to B1.2.12)

Protein	Type	Structure	Function link
Insulin	Non-conjugated, globular	Two chains	Soluble hormone carried in blood
Collagen	Non-conjugated, fibrous	Three chains in a triple helix	Strong, insoluble support
Haemoglobin	Conjugated, globular	Four chains each with a haem group	Carries oxygen

• A conjugated protein has a non-protein prosthetic group; a non-conjugated protein has none.
• Globular: compact and soluble. Fibrous: long, rope-like and usually insoluble.
• Nature of science: cryogenic electron microscopy images single protein molecules.

Must-know distinctions

Compare	First	Second
Essential vs non-essential	Must come from food	Made from other amino acids
Condensation vs hydrolysis	Releases water, forms bond	Uses water, breaks bond
Primary vs secondary	Order of units	Regular folding by backbone hydrogen bonds
Alpha helix vs beta-pleated sheet	One chain coiled	Strands side by side, pleated
Hydrogen vs ionic vs disulfide	Weak, polar groups	Charged groups, then covalent between cysteines
Globular vs fibrous	Compact, soluble	Long, insoluble, strong
Conjugated vs non-conjugated	Has prosthetic group	Amino acids only
Denaturation vs digestion	Shape lost, bonds kept	Peptide bonds hydrolysed

Worked reminders

Percentage change from data

A protein sample shows relative activity of 96 at 40 degrees Celsius and 18 at 60 degrees Celsius.

1. Change = 18 - 96 = -78.
2. Percentage change = -78 / 96 × 100 = -81.25, so a decrease of about 81 %.
3. Explain: the extra thermal energy broke weak hydrogen and ionic interactions, so most active sites lost their shape.

Helix length

Length = number of amino acids × rise per amino acid. With 0.15 nm per unit, 45 units give 6.75 nm. Turns = 45 / 3.6 = 12.5.

Writing a full explanation of denaturation

Use this order and you will cover the usual points:

1. Cause: heat or a pH change.
2. Bonds: hydrogen bonds, ionic bonds and hydrophobic interactions are disturbed. Disulfide bonds are stronger and usually survive moderate conditions.
3. Shape: the tertiary structure unfolds.
4. Consequence: the active site, binding site or receptor site no longer fits its partner.
5. Primary structure unchanged.

Linking structure to consequence (HL only)

• A single changed amino acid alters which R-groups are near each other, so interactions change and the folded shape can change. Sickle cell disease, in which one amino acid in a haemoglobin chain is replaced, is the standard example.
• Replacing a polar amino acid on the outside of a soluble protein with a hydrophobic one can make molecules stick together instead of dissolving.
• Replacing a hydrophobic amino acid in the core with a charged one can destabilize the fold.
• Losing a cysteine removes a disulfide bond that held two parts of the chain together.
• A membrane protein with hydrophobic amino acids on the outside of its transmembrane region sits securely in the bilayer; polar groups lining the inside can form a channel.

Method: answering a structure question

1. Name the level of structure.
2. Name the interaction and the groups involved.
3. State the effect on the whole shape.
4. Link the shape to the function.

Quick self-test

1. Name the four groups attached to the alpha carbon.
2. How many peptide bonds are in a polypeptide of 51 amino acids?
3. How many different tetrapeptides are possible?
4. Why can the same 20 amino acids make so many proteins?
5. What is the difference between essential and non-essential amino acids?
6. Does denaturation break peptide bonds? Explain.
7. A chain of 45 amino acids forms an alpha helix of 3.6 units per turn. How many turns?
8. Which bond forms between two cysteines?
9. Why do hydrophobic amino acids sit in the core of a soluble globular protein?
10. State one difference between conjugated and non-conjugated proteins, with an example of each.

Answers

1. NH2, COOH, H and the R-group.
2. 50 peptide bonds.
3. 20^4 = 160 000.
4. The order and length of the chain are unlimited, so sequences vary without limit.
5. Essential ones must be eaten; non-essential ones can be made from other amino acids.
6. No. Weak interactions break and the shape changes; the sequence stays the same.
7. 45 / 3.6 = 12.5 turns.
8. A covalent disulfide bond.
9. They avoid water and cluster together, leaving polar groups outside to dissolve.
10. A conjugated protein has a non-protein part, for example haemoglobin with haem; collagen has none.

Where marks are usually lost

• Drawing the R-group on the wrong atom of the amino acid.
• Leaving out the water in a condensation equation.
• Using n bonds instead of n - 1 for n amino acids.
• Saying denaturation “kills” the protein or breaks peptide bonds.
• Saying heat “destroys” enzymes without naming a change in shape.
• Writing “hydrophobic bonds” and not explaining clustering away from water.
• Confusing secondary and tertiary structure, or hydrogen bonds in the backbone with those between R-groups.
• Describing a graph without quoting values from it.
• Stating a function of collagen or insulin without linking it to shape.

Official syllabus

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