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1.3.4Biological Molecules

Protein Interactions — AQA A Level Biology 7402 Revision Notes & Topical Questions

5 min read 8 parts Lesson 15 of 49 1 quiz

📚 AQA A Level Biology 7402 Hub / Topical Revision
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1.3.4 Protein Interactions — AQA A Level Biology 7402 notes: Explain how proteins bind specifically to other molecules, giving examples of antibodies, enzymes, membrane and transport proteins, and haemoglobin.Most protein functions depend on binding to another molecule, called a …

  • induced-fit model
  • variable regions
  • carrier protein
  • channel protein
  • structure determines specificity
  • Exam-style question 1

Part 1 of 7Shape and specific binding

Most protein functions depend on binding to another molecule, called a ligand.

The protein's three-dimensional surface forms a binding site with a precise shape and pattern of charged, polar and hydrophobic R groups.
Specific
Only molecules with a complementary shape and chemical properties fit, so binding is specific.
Binding is by weak, reversible interactions (hydrogen bonds, ionic attractions, hydrophobic effects), allowing the ligand to be released again.

Part 2 of 7Enzymes

An enzyme's active site binds its substrate to form an enzyme-substrate complex, lowering the activation energy of the reaction.

Induced-fit model
In the induced-fit model the active site changes shape slightly as the substrate binds, which strains bonds in the substrate.
The R groups at the active site are in specific positions because of the tertiary structure; if that structure is denatured, the substrate no longer fits.

Part 3 of 7Antibodies and antigens

An antibody is a quaternary-structure protein with four polypeptide chains (two heavy and two light) held by disulfide bridges.

Variable regions
It has a Y shape with two identical variable regions at the tips.
Antigen
The variable region has a shape complementary to one specific antigen, so each antibody binds one antigen type.
The constant region is the same for each class and binds to receptors on phagocytes.
Binding causes agglutination (clumping) of pathogens, neutralises toxins, and marks pathogens for phagocytosis.
Vaccines and monoclonal antibodies, used in pregnancy tests and treatments, depend on this specificity.

Part 4 of 7Transport and membrane proteins

Channel and carrier proteins in membranes bind specific ions or molecules.

Carrier protein
A carrier protein binds a solute, changes shape and releases it on the other side; a channel protein has a pore lined with charged or polar groups of the right size and charge,
  • so only particular ions pass.
Haemoglobin
Receptor proteins on a cell surface bind signalling molecules such as hormones: insulin binds a receptor on liver and muscle cells and triggers glucose uptake. Haemoglobin binds oxygen reversibly at its four haem groups; binding the first oxygen changes shape and makes it easier for the next to bind (cooperative binding),
  • which gives an S-shaped dissociation curve.
This links to gas exchange and the circulatory system.

Part 5 of 7Summary and evaluation

ProteinBindsResult
EnzymeSubstrateCatalysis
AntibodyAntigenImmune response
Carrier or channelSpecific ion or moleculeTransport across membrane
ReceptorHormone or neurotransmitterCell response
HaemoglobinOxygenOxygen transport

In all cases the key idea is the same: structure determines specificity. Changes in temperature, pH or the amino acid sequence change the binding site and reduce or stop function. This is why antigenic variation in a virus such as influenza means that antibodies from earlier infection no longer fit.

Part 6 of 7Extending the idea of binding

The principle of specific binding extends to many other cell processes.

Extending the idea of binding
Cell recognition depends on glycoproteins on the cell-surface membrane that act as antigens or receptors.
Hormones such as insulin or adrenaline bind receptor proteins on target cells,
  • and cells without the receptor do not respond, explaining why hormones can circulate in blood but only affect specific tissues.
Neurotransmitters such as acetylcholine bind to receptor proteins on the postsynaptic membrane,
  • which are ligand-gated channels that open when the transmitter binds, and the transmitter is then removed by an enzyme so that the response is brief.

Binding strength matters.

Extending the idea of binding
If the interaction is too weak, the ligand binds poorly; if it is too strong, it cannot be released.
Haemoglobin shows this balance: it binds oxygen in the lungs,
  • where the partial pressure is high,
  • and releases it in respiring tissues,
  • where the partial pressure is low.
Fetal haemoglobin has a higher affinity for oxygen than adult haemoglobin, so oxygen passes across the placenta to the fetus.

In exam answers, name the molecules involved, describe the complementary shape, state what happens after binding (a response, transport or breakdown), and link a change in the protein structure to loss of function. Precise terms such as ligand, receptor and binding site gain credit over general terms like 'fits'.

Part 7 of 7Exam-style questions

  1. Explain how the structure of an antibody allows it to bind to a specific antigen. [3]3 marks

  2. Describe how a carrier protein transports a molecule across a membrane. [3]3 marks

  3. Influenza viruses change their surface proteins. Explain why a person who has recovered from last year's strain may be infected again. [3]3 marks

Key terms

TermMeaning
LigandA molecule that binds to a protein.
Binding siteThe region of a protein with a shape complementary to a ligand.
AntibodyA protein made by B cells that binds a specific antigen.
AntigenA molecule that triggers an immune response.
Variable regionThe part of an antibody that binds the antigen.
Carrier proteinA membrane protein that changes shape to move a solute across.
Channel proteinA membrane protein with a pore for specific ions.
ReceptorA protein that binds a signalling molecule and triggers a response.

Avoid these mistakes

1
Saying the whole antibody is specific. Only the variable regions are.
2
Describing carrier proteins as pores. Carriers change shape; channels form pores.
3
Saying binding is permanent. Most protein-ligand binding is reversible.
4
Confusing enzyme specificity with antibody specificity, rather than saying both rely on complementary shape.

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