AH Biology: Unit 1 Proteomics and Protein

Structure 3Binding to Ligands

Think

• How is protein production controlled?

• Why is it important that protein production is controlled?

• Why is protein structure important in relation to its function?

Binding to ligands

• A ligand is a substance that can bind to a protein.

• R groups not involved in protein folding can allow binding to these other molecules.

• Binding sites will have complementary shape and chemistry to the ligand.

• The ligand can either be a substrate or a molecule that affects the activity of the protein.

Nucleosomes

Nucleosomes

• Nucleosomes animation

• DNA replication animation

Transcription

• Other proteins have binding sites that are specific to particular sequences of double-stranded DNA and when bound to can either stimulate or inhibit initiation of transcription.

• lac Operon

• Transcription animation

Binding changes the conformation of a protein

• Enzymes and proteins are three-dimensional and have a specific shape or conformation.

• As a ligand binds to a protein binding site, or a substrate binds to an enzyme’s active site, the conformation of the protein changes.

• This change in conformation causes a functional change in the protein and may activate or deactivate it.

Induced fit

• In enzymes, specificity between the active site and substrate is related to induced fit.

• When the correct substrate starts to bind, a temporary change in shape of the active site occurs, increasing the binding and interaction with the substrate.

• Induced fit

Induced fit

Activation energy lowered

Allosteric enzymes

• An allosteric enzyme is an enzyme that can have its activity altered by a ligand called a modulator.

• In allosteric enzymes, modulators bind at secondary binding sites away from the active site.

• The conformation of the enzyme changes and this alters the affinity of the active site for the substrate.

Modulators

• Negative modulators reduce the enzyme’s affinity for the substrate.

• Positive modulators increase enzyme affinity for the substrate.

Negative modulators

Negative modulators

• End product inhibition occurs when the final product of a cascade of enzyme reactions interacts with an allosteric site of the first enzyme in the cascade to inhibit it and thus the production of the end product.

• This is an example of negative feedback.

• End product inhibition animation

Competitive inhibition

Competitive inhibition example 1

• Ethanol is metabolised in the body to acetaldehyde by oxidation with alcohol dehydrogenase, which is in turn further oxidised to acetic acid by aldehyde oxidase enzymes.

• Normally, the second reaction is rapid so acetaldehyde does not accumulate in the body.

• A drug called disulfiram (Antabuse) inhibits the aldehyde oxidase, which causes the accumulation of acetaldehyde with subsequent unpleasant side effects of nausea and vomiting.

• This drug is sometimes used to help people overcome alcoholism.

Competitive inhibition example 2

• Methanol poisoning occurs because methanol is oxidised to formaldehyde and formic acid, which attack the optic nerve and cause blindness.

• Ethanol is given as an antidote for methanol poisoning because ethanol competitively inhibits the oxidation of methanol.

• Ethanol is oxidised in preference to methanol and consequently the oxidation of methanol is slowed down and the toxic by-products do not have a chance to accumulate.

• The methanol is then excreted in the urine.

Competitive inhibition example 3

• Ethylene glycol, if ingested, can be poisonous.

• Ethylene glycol is oxidised by the same enzymes used in the previous two examples.

• Ethylene glycol → glycolaldehyde → glycolic acid.

• Glycolic acid is toxic to the nervous system and kidneys.

• Describe how ethanol can be used as an antidote.

Non-competitive inhibition

Enzyme kinetics and inhibition

Competitive inhibition

Competitive inhibition

• If the concentration of inhibitor is less than that of the substrate and the substrate has a higher affinity for the active site, is the enzyme inhibited a lot or a little?

• If the concentration of inhibitor is more than that of the substrate is the enzyme inhibited a lot or a little?

• If the enzyme is inhibited and we then increase the substrate concentration what happens to the initial rate of reaction?

Non-competitive inhibition

Competitive inhibition

Non-competitive inhibition

Enzyme kinetics and inhibition

Positive modulators

• Positive modulators increase the enzyme affinity for the substrate by altering the shape of the active site so that it has a better fit for the substrate.

• Positive modulation animation of a steroid on a GABAA receptor linked ion channel.

Enzyme kinetics questions

• Enzyme kinetics questions.

Cooperativity in haemoglobin

• Binding and release of oxygen in haemoglobin.

Cooperativity in hemoglobin• Deoxyhaemoglobin has a relatively low affinity for oxygen.

• As one molecule of oxygen binds to one of the four haem groups in a hemoglobin molecule it increases the affinity of the remaining three haem groups to bind oxygen.

• Conversely, oxyhaemoglobin increases its ability to loose oxygen as oxygen is released by each successive haem.

• This creates the classic sigmoid shape of the oxygen dissociation curve.

Cooperativity in haemoglobin

Effects of temperature and pH

• Low pH = low affinity.

• High temperature = low affinity.

• Exercise increases body temperature and produces CO2, acidifying the blood.

• This has a corresponding effect on the oxyhaemoglobin dissociation curve.

Bohreffect

Oxygen dissociation curve

• Oxygen dissociation review in relation to a patient admitted to hospital.

• What sort of conditions affect the ability of red blood cells to transport oxygen?

• Under what conditions would haemoglobin struggle to bind oxygen?

Red blood cell disorders

• Sickle cell anaemia

• Thalassaemia

High-altitude conditions

• High-altitude medicine

• High-altitude effects: BBC Horizon, ‘How to Kill a Human Being’

Think

• How is protein production controlled?

• Why is it important that protein production is controlled?

• Why is protein structure important in relation to its function?