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

This study guide teaches IB Diploma Programme Biology topic B1.2 (Proteins) in depth. It follows the IB Biology guide, first assessment 2025. Statements B1.2.1 to B1.2.5 are SL and HL. Statements B1.2.6 to B1.2.12 are additional higher level and are marked “HL only”.

Use it with the revision notes and the practice set. Wider theme: Theme B: Form and Function. Course pages: IB DP Biology hub, printable checklist and free 10-minute diagnostics.

What this unit covers

Statement	What you must be able to do	Level
B1.2.1	Draw a generalized amino acid	SL and HL
B1.2.2	Write the word equation for condensation; draw a dipeptide	SL and HL
B1.2.3	Explain essential and non-essential amino acids and vegan diets	SL and HL
B1.2.4	Explain why the number of possible peptide chains is effectively unlimited	SL and HL
B1.2.5	Describe the effects of pH and temperature; use “denaturation”	SL and HL
B1.2.6	Link R-group chemistry to protein properties	HL only
B1.2.7	Link primary structure to conformation	HL only
B1.2.8	Describe alpha helices and beta-pleated sheets	HL only
B1.2.9	Explain the bonds that hold tertiary structure	HL only
B1.2.10	Explain the role of polar and non-polar amino acids	HL only
B1.2.11	Describe quaternary structure; conjugated and non-conjugated proteins	HL only
B1.2.12	Relate form to function in globular and fibrous proteins	HL only

B1.2.1 Generalized amino acid

Every amino acid has a central carbon, the alpha carbon, with four groups attached:

• an amine group, NH2
• a carboxyl group, COOH
• a hydrogen atom
• a variable R-group

        R
        |
H2N --- C --- COOH
        |
        H

Only the R-group differs between the amino acids. The drawing must show all four groups joined to the same carbon. A common mistake is to attach the R-group to the nitrogen or to the carboxyl carbon.

B1.2.2 Condensation and peptide bonds

A condensation reaction joins two amino acids and releases one molecule of water. One amino acid loses the OH of its carboxyl group, and its partner loses an H from its amine group. A covalent peptide bond forms between the carboxyl carbon and the amine nitrogen.

Word equation: amino acid + amino acid → dipeptide + water

 H2N-CH(R1)-CO-OH + H-NH-CH(R2)-COOH
      →  H2N-CH(R1)-CO-NH-CH(R2)-COOH + H2O

Building a model of the reaction with molecular models shows the water leaving. A chain of amino acids is a polypeptide. The end with a free amine group is the amine end and the end with a free carboxyl group is the carboxyl end. Further amino acids are always added at the carboxyl end, by ribosomes during translation.

Worked example 1: counting bonds

A polypeptide has 150 amino acids joined in one unbranched chain. How many peptide bonds were formed and how much water was released?

1. Each condensation links two units, so n units need n - 1 links.
2. Peptide bonds = 150 - 1 = 149.
3. One water per bond, so 149 water molecules.
4. If the average mass of an amino acid unit in the chain is 110 daltons (this already allows for water lost), the chain is 150 × 110 = 16 500 daltons.

Hydrolysis, using water, is the reverse reaction. Digestion by proteases splits peptide bonds.

B1.2.3 Dietary requirements

Essential amino acids cannot be made by the body, so they must be eaten in protein. Non-essential ones are manufactured by the body from other amino acids. You do not have to name examples of either group.

Vegan diets need attention because some plant proteins are low in one or more essential amino acids. Eating a range of plant foods during the day, so that the shortfall in one is covered by another, supplies all of them.

Worked example 2: complementary foods

Food X is low in essential amino acid J. Food Y is low in essential amino acid K. Explain why a meal of both is better than either alone.

• Food Y supplies the J that food X lacks.
• Food X supplies the K that food Y lacks.
• Together the meal provides all essential amino acids in enough quantity for protein synthesis.

B1.2.4 Infinite variety of peptide chains

The genetic code specifies twenty different amino acids. A chain can contain any number of them, from a few to thousands, in any order. Each position can be filled in 20 ways, so a chain n units long has 20 to the power n possible sequences.

Worked example 3: counting sequences

1. Dipeptides: 20 × 20 = 400.
2. Tripeptides: 20 × 20 × 20 = 8000.
3. A chain of 12: 20^12 = 4.096 × 10^15 (about 4.1 × 10^15).
4. A chain of 100: about 1.3 × 10^130, a number far too large for every sequence ever to exist.

Cells make only a small fraction of the possible sequences, but the potential variety explains why the proteome of an organism is so diverse. Be familiar with examples of polypeptides, such as insulin, collagen and the haemoglobin chains.

B1.2.5 pH, temperature and denaturation

A protein’s shape depends on weak interactions between parts of the chain. Changes in pH or heat disturb them.

• Temperature: heating raises the vibrational energy of the atoms. Hydrogen bonds and other weak interactions break and the chain unfolds.
• pH: hydrogen ions bind to or leave groups in the amino acids, which changes their charge. Attractions and repulsions in the chain change and the shape alters.

Denaturation is a permanent change in the three-dimensional shape of a protein, so that it can no longer carry out its function. It does not break peptide bonds, so the primary structure stays the same. Enzymes lose their active site shape; boiled egg white is the everyday example. Some small proteins can refold, so say “usually irreversible”.

Worked example 4: reading pH data

An enzyme gives these relative activities after incubation at constant temperature.

pH	3	5	7	9	11
Relative activity (%)	12	58	100	55	9

1. Optimum: about pH 7 (the highest activity of those tested; the true optimum may lie between 5 and 9).
2. Fall from pH 7 to pH 5: 100 - 58 = 42 percentage points, a 42 % decrease.
3. Explanation: at pH 5 more groups are protonated, charges change, ionic and hydrogen bonds near the active site alter, and fewer molecules keep an active site that fits the substrate.
4. At pH 11 and pH 3 most molecules are denatured.

Say “percentage points” for differences between percentages, and “percentage change” when a value is divided by the starting value.

B1.2.6 R-group diversity (HL only)

R-groups determine the properties of a polypeptide. You do not need specific examples. They fall into types:

Type	Behaviour in water	Notes
Non-polar	Hydrophobic	Avoids water
Polar, uncharged	Hydrophilic	Hydrogen bonds
Acidic (charged)	Hydrophilic	Carboxyl, loses H+, becomes negative
Basic (charged)	Hydrophilic	Amine, gains H+, becomes positive

Because 20 R-groups can be arranged in any order, the surface and interior of a protein can have endless combinations of chemistry. This is the basis of the diversity of form and function.

B1.2.7 Primary structure and conformation (HL only)

The primary structure is the sequence of amino acids. It decides which R-groups are near which, and so which interactions form. The position of each amino acid matters. The result is a precise, predictable and repeatable three-dimensional shape, even though proteins are complex. Replacing one amino acid with a different one can change shape and function; this is why some single-base mutations have large effects.

B1.2.8 Secondary structure (HL only)

Secondary structure is local folding of the backbone, stabilized by hydrogen bonds between the C=O of one peptide group and the N-H of another, in regular positions.

• Alpha helix: a coil, with a bond between each group and the one four residues further along.
• Beta-pleated sheet: strands run side by side and are joined by hydrogen bonds between them, giving a pleated surface.

Worked example 5: helix dimensions

A helix has 3.6 amino acids per turn and each amino acid adds 0.15 nm to its length (data supplied). Find the number of turns and length of a helix of 72 amino acids.

1. Turns = 72 / 3.6 = 20.
2. Length = 72 × 0.15 = 10.8 nm.

B1.2.9 Tertiary structure (HL only)

Tertiary structure is the overall three-dimensional shape of one polypeptide. Four interactions between R-groups hold it:

Interaction	Between	Strength
Hydrogen bonds	Polar R-groups	Weak
Ionic bonds	Oppositely charged R-groups	Moderate
Disulfide bonds	Two cysteine R-groups (covalent S-S)	Strong
Hydrophobic interactions	Non-polar R-groups clustering together	Weak but numerous

Amine and carboxyl groups in R-groups gain or lose hydrogen ions and become charged, so can then form ionic bonds. Cysteine is the only amino acid you must name here.

B1.2.10 Polar and non-polar amino acids (HL only)

• In a water-soluble globular protein, hydrophobic amino acids cluster in the core, away from water, and polar amino acids face outward to interact with water. This makes the protein soluble.
• Integral membrane proteins have a region of hydrophobic amino acids where they cross the hydrophobic centre of the bilayer, which keeps them embedded.

B1.2.11 Quaternary structure (HL only)

Quaternary structure is the association of two or more polypeptides in one protein.

• Non-conjugated proteins contain only amino acids. Insulin has two chains and collagen has three.
• Conjugated proteins also contain a non-protein part, a prosthetic group. Haemoglobin has four polypeptides, each with a haem group holding iron, which binds oxygen.

Worked example 6: haemoglobin

Haemoglobin has two chains of 141 and two of 146 amino acids. Find the total number of amino acids and peptide bonds (data supplied).

1. Amino acids = 2 × 141 + 2 × 146 = 574.
2. Peptide bonds = 2 × 140 + 2 × 145 = 570. Bonds between separate chains are not peptide bonds.
3. Four haem groups, so it can bind four oxygen molecules.

Nature of science: cryogenic electron microscopy lets researchers image single protein molecules and their interactions, which cannot be seen with unaided senses.

B1.2.12 Globular and fibrous proteins (HL only)

Feature	Globular (insulin)	Fibrous (collagen)
Shape	Compact, roughly spherical	Long strands
Solubility	Soluble	Insoluble
Function	Hormone signalling in blood	Strength in skin, tendon, bone
Reason	Shape fits receptor	Three chains wound together form strong ropes

Collagen has glycine, the smallest amino acid, at every third position, which lets three chains pack tightly into a triple helix.

Common errors

• Writing that denaturation breaks peptide bonds.
• Saying hydrogen bonds hold the primary structure.
• Forgetting that one water forms per peptide bond.
• Saying “20 amino acids” means only 20 proteins.
• Calling disulfide bonds weak.

Official syllabus

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