1. AH Biology: Unit 1 Protein Structure 2
Binding to Ligands

2. 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?
Think about these questions and answer them as you study this section on protein structure.

3. Binding to ligands LOs
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.
Positively charged histone proteins bind to the negatively charged sugar-phosphate backbone of DNA in eukaryotes.
The DNA is wrapped around histones to form nucleosomes packing the DNA in chromosomes.
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.

4. 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.

5. Binding to ligands
In enzymes this specific shaping gives the ‘active site’ for the substrate to bind. In cell signalling ligand binding is essential to activate receptors or channels.

6. DNA as a ligand
Positively charged histone proteins bind to the negatively charged sugar-phosphate backbone of DNA in eukaryotes.
The DNA is wrapped around histones to form nucleosomes packing the DNA in chromosomes.
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.

7. Nucleosomes
Nucleosomes animation
DNA replication animation

8. 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

9. Binding to ligands Key Concepts
A _______ is a substance that can bind to a protein.
__ _____not involved in protein folding can allow binding to these other molecules.
Binding sites will have complementary ____ and ______ to the ligand.
The ligand can either be a ______ or a molecule that affects the activity of the ________.
Positively charged _______ proteins bind to the negatively charged sugar-phosphate backbone of DNA in _________.
The DNA is wrapped around histones to form ________ packing the DNA in chromosomes.
Other proteins have binding sites that are specific to particular sequences of double stranded DNA and when bound to can either ________ or ______ initiation of transcription.

10. Binding to ligands Key Concepts
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.
Positively charged histone proteins bind to the negatively charged sugar-phosphate backbone of DNA in eukaryotes.
The DNA is wrapped around histones to form nucleosomes packing the DNA in chromosomes.
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.

11. Binding changes the conformation of a protein LOs
Ligand binding changes the conformation of a protein. This causes a functional change in a protein.
In enzymes, specificity between the active site and substrate is related to induced fit.
When the substrate binds, a temporary change in the shape of the active site occurs that increases the binding and interaction with the substrate.
The chemical environment produced lowers the activation energy required for the reaction.
Once catalysis takes place, the original enzyme conformation is resumed and products are released from the active site.

12. 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.

13. 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

14. Induced fit

15. Activation energy lowered
The chemical environment produced lowers the activation energy required for the reaction.
Once catalysis takes place, the original enzyme conformation is resumed and products are released from the active site.
The enzyme is then free to react with more substrate.

16. Binding changes the conformation of a protein Key Concepts
Ligand binding changes the _______ of a protein. This causes a _______ change in a protein.
In enzymes, specificity between the active site and substrate is related to ______ ____.
When the substrate binds, a temporary change in the shape of the active site occurs that increases the ______ and ________ with the substrate.
The chemical environment produced lowers the ______ ________required for the reaction.
Once catalysis takes place, the original enzyme conformation is resumed and _______ are released from the _____ ______.

17. Binding changes the conformation of a protein Key Concepts
Ligand binding changes the conformation of a protein. This causes a functional change in a protein.
In enzymes, specificity between the active site and substrate is related to induced fit.
When the substrate binds, a temporary change in the shape of the active site occurs that increases the binding and interaction with the substrate.
The chemical environment produced lowers the activation energy required for the reaction.
Once catalysis takes place, the original enzyme conformation is resumed and products are released from the active site.

18. What can you remember? What is a ligand?
Where do you find Hydrophilic R groups in a protein?
Where do you find the hydrophobic R groups in a protein?
Why do peripheral proteins sit on the outside of the phospholipid bilyaer?
What is a nucleosome?
Describe an example of ligand binding causing a conformational change to a protein.

19. What is a ligand. A substance that binds to a protein
What is a ligand? A substance that binds to a protein. Where do you find Hydrophilic R groups in a protein? On the surface of a soluble protein in the cytoplasm Where do you find the hydrophobic R groups in a protein? Clustering in the centre to form a globular structure Why do peripheral proteins sit on the outside of the phospholipid bilayer? They have fewer hydrophobic R groups interacting with the phospholipids What is a nucleosome? DNA wrapped around histones Describe an example of ligand binding causing a conformational change to a protein. Induced fit enzymes

20. Allosteric enzymes LOs
In allosteric enzymes, modulators bind at secondary binding sites. The conformation of the enzyme changes and this alters the affinity of the active site for the substrate.
Positive modulators increase the enzyme affinity whereas negative modulators reduce the enzyme’s affinity for the substrate.
Some proteins with quaternary structure show cooperativity in which changes in binding at one subunit alter the affinity of the remaining subunits.
Cooperativity is involved in the binding and release of oxygen in heamoglobin.
Temperature and pH influence

21. 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.

22. Modulators
Negative modulators reduce the enzyme’s affinity for the substrate.
Positive modulators increase enzyme affinity for the substrate.

23. Negative modulators

24. 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

25. Competitive inhibition

26. Examples of Competitive Inhibition
Your task… In three groups you will explain three different examples of competitive inhibition:
Ethanol metabolism
Methanol poisoning
Ethylene glycol poisoning
Using the information given to you,
and any other sources,
you will describe and explain your example to the class. Without just reading off the information sheet!

27. 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.

28. 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.

29. 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.

30. The prevention of ethylene glycol metabolism is accomplished by the use of ethanol that inhibit alcohol dehydrogenase.
At a sufficiently high concentration, ethanol saturates alcohol dehydrogenase, preventing it from acting on ethylene glycol
This allows the ethylene glycol to be excreted unchanged by the kidneys

31. Non-competitive inhibition
Ligand binding to an allosteric site separate from the active site.
Non-competitive inhibition

32. 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?

33. 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.

34. Enzyme kinetics questions

35. Cooperativity in haemoglobin
Cooperativity is when the binding of a ligand to one subunit of the protein increases the affinity of another subunit.
E.g. Haemoglobin

36. Cooperativity in haemoglobin
Binding and release of oxygen in haemoglobin.
Some proteins with quaternary structure show cooperativity in which changes in binding at one subunit alter the affinity of the remaining subunits.
This occurs when oxygen binds to haemoglobin.
First task...
Find out the definition of cooperativity
Write your ideas on a show me board

37. 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.

38. Cooperativity in haemoglobin
Rightward shifts in the dissociation curve indicate decreased affinity of haemoglobin for oxygen, making it harder to bind the oxygen in the lungs but easier to release oxygen to respiring tissues. A higher partial pressure of oxygen is therefore required in the lungs for uptake of oxygen by deoxyhaemoglobin.
Leftward shifts indicate increased affinity, making it easier to bind oxygen in the lungs but increasing the difficulty to release oxygen to respiring tissues. A lower partial pressure of oxygen is therefore required by respiring tissues to release the oxygen from oxyhaemoglobin.

39. 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.

40. Effects of temperature and pH
Cells that work hard (e.g. muscle cells) create more carbon dioxide that will lower the pH (converted to carbonic acid). They also have a higher temperature.
This will make them more likely to release oxygen at lower saturations (graph moves to the right).
The opposite happens at lower temperatures and high pH (graph moves to the left).

41. As cells respire aerobically they increase the concentration of carbon dioxide in their surrounding environment.
Respiration also increases temperature as a result of the heat produced.
Carbon dioxide causes the blood and immediate environment around respiring cells to become acidic as carbonic acid forms.
Both an increase in temperature and a decrease in pH cause a right shift in the oxyhaemoglobin dissociation curve.
This ensures that oxyhaemoglobin releases oxygen to respiring body cells more easily.
As the haemoglobin returns to the lungs the carbon dioxide concentration decreases and as a result the affinity for oxygen increases. This ensures that maximal oxygen uptake can be achieved.

42. 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?

43. Red blood cell disorders
Sickle cell anaemia
Thalassaemia

44. High-altitude conditions
High-altitude medicine
High-altitude effects: BBC Horizon, ‘How to Kill a Human Being’

45. Allosteric enzymes Key Concepts
In _______ enzymes, modulators bind at secondary binding sites. The conformation of the enzyme changes and this alters the _______ of the active site for the _____.
_______ modulators increase the enzyme affinity whereas ______ modulators reduce the enzyme’s affinity for the substrate.
Some proteins with _________ structure show cooperativity in which changes in binding at one subunit alter the ______ of the remaining ______.
Cooperativity is involved in the binding and release of oxygen in __________.
_________ and ____ influence affinity.

46. Allosteric enzymes Key Concepts
In allosteric enzymes, modulators bind at secondary binding sites. The conformation of the enzyme changes and this alters the affinity of the active site for the substrate.
Positive modulators increase the enzyme affinity whereas negative modulators reduce the enzyme’s affinity for the substrate.
Some proteins with quaternary structure show cooperativity in which changes in binding at one subunit alter the affinity of the remaining subunits.
Cooperativity is involved in the binding and release of oxygen in heamoglobin.
Temperature and pH influence affinity.

47. 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?
Think about these questions again and answer them as part of a discussion in class based on what you have learned in this section.

48. Key Area 1.2 Protein structure
Past Paper Practice
Advanced Higher
Key Area 1.2
Protein structure

51. Give an account of enzyme activity under the following headings:
induced fit; (4 marks)
enzyme activation. (5 marks)

52. Induced fit (maximum of 4 marks):
The active site is where a substrate binds to an enzyme.
The shape of the active site is specific/complementary to the substrate
When the correct substrate starts to bind, a temporary change in shape of the active site occurs.
The change in shape increases the binding and interaction with the substrate.
The chemical environment that is produced lowers the activation energy required for the reaction.
Once catalysis takes place, the original enzyme conformation is resumed.

53. Enzyme activation (maximum of 5 marks):
Modulators change the rate of reaction/activity.
Modulators bind at secondary binding sites.
Causes a conformation/shape change in the enzyme.
Alters the affinity of the active site for the substrate.
Positive modulators increase the enzyme affinity for the substrate.
Negative modulators reduce the enzyme's affinity for the substrate.
Phosphorylation/addition of a phosphate can alter enzyme activity.
Kinase enzymes carry out phosphorylation/adds phosphate.