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1.3.3Biological Molecules

Protein Structure and Function — AQA A Level Biology 7402 Revision Notes & Topical Questions

5 min read 9 parts Lesson 14 of 49 1 quiz

📚 AQA A Level Biology 7402 Hub / Topical Revision
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Lesson summary

1.3.3 Protein Structure and Function — AQA A Level Biology 7402 notes: Describe the four levels of protein structure, name the bonds that stabilise each, and relate structure to the function of globular and fibrous proteins.An amino acid has a central carbon bonded to an amino gr…

  • primary structure
  • secondary structure
  • alpha-helix
  • beta-pleated sheet
  • tertiary structure
  • Hydrogen bonds

Part 1 of 7Amino acids and the primary structure

An amino acid has a central carbon bonded to an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom and a variable R group.

Amino acids and the primary structure
Twenty different R groups occur in proteins.
Amino acids join by condensation to form peptide bonds.
Primary structure
The primary structure is the sequence of amino acids in the polypeptide chain.
It is specified by the DNA base sequence of a gene, and it decides all higher levels of structure; one change can alter the whole protein.

Part 2 of 7Secondary and tertiary structure

The secondary structure is the regular folding of the chain caused by hydrogen bonds between the C=O and N-H groups of the peptide backbone: the alpha-helix (a coil) and the beta-pleated sheet. The tertiary structure is the overall three-dimensional folding of a whole polypeptide, held by interactions between R groups:

Secondary and tertiary structure
Hydrogen bonds
Hydrogen bonds between polar R groups (weak, but numerous).
Ionic bonds
Ionic bonds between oppositely charged R groups (broken by pH change).
Disulfide bridges
Disulfide bridges between cysteine residues (strong covalent bonds).
Hydrophobic interactions
Hydrophobic interactions as non-polar R groups cluster in the core, away from water.

The tertiary structure gives enzymes their specific active site shape and decides which proteins are globular.

Part 3 of 7Quaternary structure

The quaternary structure is the arrangement of two or more polypeptide chains (and sometimes a non-protein prosthetic group) in one functional protein.

Quaternary structure
Haemoglobin has four polypeptide chains (two alpha, two beta), each with a haem group containing iron that binds oxygen.
Insulin has two chains linked by disulfide bridges.
Not all proteins have a quaternary structure; an enzyme such as lysozyme is a single polypeptide.

Part 4 of 7Globular and fibrous proteins

FeatureGlobularFibrous
ShapeCompact, roundedLong strands or sheets
SolubilitySoluble: hydrophilic R groups outsideInsoluble
RoleMetabolic: enzymes, hormones, haemoglobin, antibodiesStructural: collagen, keratin
SequenceIrregular amino acid sequenceRepetitive sequence

Collagen has three polypeptide chains wound into a triple helix, with every third amino acid glycine (small, allowing close packing). Strength comes from hydrogen bonds and covalent cross-links between molecules, giving high tensile strength in tendons, skin and artery walls. Haemoglobin is soluble and has a precise shape for binding oxygen.

Part 5 of 7Denaturation and function

High temperature breaks the hydrogen and ionic bonds, and extreme pH disrupts ionic bonds.

Denaturation and function
Denaturation
The tertiary structure unfolds and the protein loses its shape: this is denaturation.
Enzymes lose their active-site shape; membrane proteins fail to transport.
Because function depends on shape,
  • and shape depends on the primary structure, a mutation altering one amino acid (as in sickle cell haemoglobin,
  • where glutamic acid is replaced by valine) may change the function.
This links to the enzyme and genetics topics.

Part 6 of 7Putting structure to work: worked reasoning

When an exam question asks you to explain a protein's function, build the argument in a chain: the sequence of amino acids, the folding into the tertiary structure, the resulting shape or surface property, and the function that follows.

Putting structure to work: worked reasoning
For haemoglobin, the haem group in each chain binds oxygen, and the quaternary structure of four chains allows cooperative binding.
For an enzyme, the shape of the active site follows from tertiary structure.
For collagen, the primary structure with glycine at every third position allows the tight triple helix.

Keratin, another fibrous protein, is rich in cysteine, and so many disulfide bridges make it strong and, in hair or nails, inflexible. By contrast, insulin is a small globular protein whose shape allows it to bind to a receptor on target cells. A table of structure and function for each protein is an effective way to revise.

Protein structure is lost during cookingheat denatures the proteins in an egg white, which turn from clear and runny to opaque and solid because the unfolded chains tangle and aggregate.

Putting structure to work: worked reasoning
This is irreversible.
In cells, chaperone proteins help new polypeptides to fold correctly, an idea that links to disease,
  • such as prion disorders, in which an abnormally folded protein causes other copies to misfold.

Part 7 of 7Exam-style questions

  1. Describe the four levels of protein structure. [4]4 marks

  2. Explain why collagen is suited to its role in tendons. [3]3 marks

  3. A mutation changes a hydrophilic amino acid in a protein's interior to a hydrophobic one on its surface. Predict and explain the effect on the tertiary structure. [3]3 marks

Key terms

TermMeaning
Primary structureThe sequence of amino acids in a polypeptide.
Secondary structureRegular folding of a chain into helices or sheets by hydrogen bonds.
Tertiary structureThe overall three-dimensional shape of a polypeptide.
Quaternary structureThe arrangement of multiple polypeptides in a protein.
Disulfide bridgeCovalent bond between sulfur atoms of two cysteine residues.
Prosthetic groupA non-protein component permanently bound to a protein.
Globular proteinCompact, soluble protein with a metabolic role.
Fibrous proteinLong, insoluble structural protein.
DenaturationLoss of the three-dimensional structure of a protein.

Avoid these mistakes

1
Saying that peptide bonds hold the tertiary structure. They hold the primary structure; R-group bonds hold the tertiary.
2
Stating that hydrogen bonds in the secondary structure are between R groups. They are between backbone C=O and N-H groups.
3
Using 'denatured' to describe the breaking of peptide bonds. Denaturation affects the higher-order structure only.
4
Describing globular proteins as having a repeating sequence; fibrous proteins have the repetition.

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