B1.2Theme B — Form and function

Proteins — IB Biology SL Revision Notes & Topical Questions

5 min read 11 parts Lesson 3 of 13 2 quizzes

0%read

Lesson summary

B1.2 Proteins — IB BIOLOGY SL notes: Describe amino acid and peptide bond structure, protein diversity and roles, and the effect of heat and pH on protein structure.Protein = a polymer made of amino acid monomers, whose sequence, type and number decide its shape and functionAll g…

Polypeptide
Hydrolysis
Recognising the bond
Non-essential amino acids
Vegetarian and vegan diets
Choice at each position

Part 1 of 9Proteins and amino acids

General three-dimensional structure of an alpha amino acid.

Protein

Protein a polymer made of amino acid monomers, whose sequence, type and number decide its shape and function

All genes code for proteins, so all the reactions of life depend on protein function.

Amino acid

20 types are common to all living organisms
A central alpha carbon is bonded to an amine group (NH₂), a carboxyl group (COOH), a hydrogen atom and an R group.
The R group is the only part that differs.
R groups range from a single hydrogen in glycine to an aromatic ring in phenylalanine.
R groups can be polar or non-polar and acidic or basic, which decides how the chain folds.

Part 2 of 9Peptide bond formation

Peptide bond

Peptide bond formed by a condensation reaction between two amino acids
An OH is lost from the carboxyl group of one amino acid and an H from the amine group of the other.
The remaining carbon with its double-bonded oxygen bonds to the nitrogen of the second amino acid.
Water is released.

Dipeptide

Dipeptide two amino acids joined by one peptide bond, as in amino acid + amino acid → dipeptide + water

Polypeptide

Polypeptide three or more amino acids, and a protein may have one or several chains

Hydrolysis

Hydrolysis adding water breaks peptide bonds and releases amino acids, as in digestion

Recognising the bond

Recognising the bond look for nitrogen bonded to a carbon that has a double bond to oxygen, and the R group is not involved

Modelling

Modelling molecular modelling kits show how the peptide bond forms

Part 3 of 9Dietary amino acids

Dietary amino acids

Non-essential amino acids

11 of the 20 can be made by body cells from other amino acids

Essential amino acids

Essential amino acids the other nine must come from the diet

Vegetarian and vegan diets

Vegetarian and vegan diets meat contains all nine, so a plant diet must be varied and balanced, for example legumes with grains

Part 4 of 9Diversity of polypeptides

1Choice at each position

20 amino acids can be added at every step on a ribosome
The mRNA codon decides which amino acid is added.

2Variation

Variation chains range from a few to thousands of amino acids
The DNA base sequence codes for the number and order of the amino acids.

3Number of sequences

20ⁿ for a chain of n amino acids

A short 50-amino-acid chain has 20⁵⁰ = about 1.13 × 10⁶⁵ possible sequences.
The average protein has 300 amino acids, so the variety is effectively infinite.

Part 5 of 9Roles of proteins

Role	Example
Catalysis	Enzymes such as rubisco, pepsin and lipase
Transport	Haemoglobin carries oxygen in blood
Contraction	Myosin and actin shorten muscle fibres
Structure	Keratin in hair and nails, collagen in skin and tendons
Defence	Immunoglobulins recognise pathogens
Signalling	Hormones such as insulin and receptors such as rhodopsin

Other roles
- Blood clotting, where blood proteins form a gel-like scab over a wound.
- The cytoskeleton, which moves chromosomes in the cell cycle.
- Cell adhesion between cells of the same tissue.
- Histone proteins that compact DNA in chromosomes.
- Membrane channel and carrier proteins that decide which substances cross.
- Cell receptors for hormones, tastes, light and sound.

Part 6 of 9Named proteins

Rubisco

Rubisco an enzyme made of 16 polypeptide chains that fixes CO₂ in photosynthesis
It is the source of all organic carbon and the most abundant enzyme on Earth.
It is a slow catalyst but the most effective to have evolved.

Insulin

Insulin a short globular hormone of 2 polypeptide chains made by beta cells of the pancreas
It binds reversibly to receptors on liver, fat and muscle cells, causing glucose uptake from the blood.

Immunoglobulin

Immunoglobulin a Y-shaped antibody with variable binding tips that bind specific antigens
It is the most diverse protein group and can be made against millions of antigens.

Rhodopsin

Rhodopsin a retinal pigment containing retinal, derived from vitamin A
A photon changes its shape, which sends a nerve impulse along the optic nerve to the brain.

Collagen

Collagen a fibrous protein of three chains wound together, about 25% of human protein
It forms networks in skin and blood vessel walls that resist tearing and reduces the brittleness of bones and teeth.

Spider silk

Spider silk as strong as steel but lighter, with rope-like fibrous regions and coiled regions that stretch
It does not denature easily at extreme temperatures.
It can be made in goats' milk by genetic engineering.

Part 7 of 9Globular and fibrous proteins

Haemoglobin is a compact globular protein with four interacting subunits.

Globular haemoglobin and fibrous collagen illustrate contrasting protein forms.

Feature	Globular	Fibrous
Shape	Compact and rounded	Long strands
Solubility	Usually soluble	Insoluble
Role	Metabolic, for example enzymes and hormones	Structural support
Sequence	Irregular	Often repetitive
Example	Insulin	Collagen

Conformation
- the specific 3D shape of a protein, held by weak bonds between R groups

Part 8 of 9Denaturation by heat and pH

Denaturation

Denaturation a change in the 3D shape of a protein that is almost always irreversible

The weak bonds between R groups break easily, whereas peptide bonds stay intact.
Active sites and binding sites then no longer fit their substrates or ligands.

Heat

Heat vibrations break hydrogen and ionic bonds, so the shape is lost

Extreme pH

Extreme pH changes the charges on R groups, so ionic bonds fail

Small reversible changes

Small reversible changes some proteins, such as haemoglobin, tolerate slight pH fluctuations

Optimum

Optimum at the optimum pH or temperature the 3D structure is not denatured
Pepsin has an optimum of pH 2 in the stomach.

Part 9 of 9Denaturation in practice

Albumin in egg white is soluble with its hydrophobic groups inside.

Heat increases molecular vibration.

Hydrogen and ionic bonds between R groups break.

The chain unfolds and exposes the hydrophobic groups.

Unfolded molecules clump and become insoluble.

A solid white layer forms that cannot revert.

Extremophiles

Thermus aquaticus lives in hot springs at 80 °C because its proteins stay stable

Stomach

Stomach acid at pH 2 denatures dietary proteins before they are hydrolysed

Protein drugs

Protein drugs they are injected because stomach acid would denature them

Enzyme experiments

Enzyme experiments find the optimum pH or temperature of an enzyme such as pepsin or lipase

Key terms

Term	Meaning
Amino acid	The monomer of proteins with an amine group, a carboxyl group and a variable R group on a central carbon.
Peptide bond	The covalent link formed by condensation between the carboxyl group of one amino acid and the amine group of the next.
Polypeptide	A chain of three or more amino acids.
Essential amino acid	An amino acid the body cannot make, so it must come from the diet.
Denaturation	The loss of 3D shape, and so function, of a protein caused by heat or pH change.
Conformation	The specific 3D shape of a protein held by weak bonds between R groups.
Globular protein	A rounded, usually soluble protein, such as an enzyme or insulin.
Fibrous protein	A long, insoluble structural protein, such as collagen.

Avoid these mistakes

Confusing peptide bonds with the bonds holding the 3D shape — peptide bonds make the chain and weaker bonds fold it

Saying denaturation breaks peptide bonds — it breaks the weaker bonds between R groups

Saying amino acids differ in their amine or carboxyl group — only the R group differs

Thinking denaturation is easily reversed — it is almost always irreversible

Last updated: 26 October 2026