PL befg: Protein structure; enzyme catalysis & kinetics; molecular recognition

Question 1

Name and describe the 3 levels of protein structure.

Answer 1

• Primary: ordering of amino acids
• Secondary: coiling of parts of chain into helix/sheet
• Tertiary: further folding of secondary structure

Question 2

Describe the bonding which occurs in a protein’s secondary structure.

Answer 2

• Hydrogen bonds between -NH group on one peptide link and -C=O groups on another
• Alpha helices or beta pleated sheets formed

Question 3

List the types of bonding which occur in a protein’s tertiary structure.

Answer 3

• Intermolecular bonding
  
  • Instantaneous dipole-induced dipole
  • Hydrogen
• Ionic bonding
• Covalent bonding

Question 4

Describe how id-id bonding occurs in the tertiary structure of proteins.

Answer 4

• Any group may become a spontaneous dipole
• Induces a dipole on any other group
• Electrostatic attraction occurs between the 2 groups (e.g. non-polar R groups)

R groups occur more commonly in the centre so that they don’t interfere w/ H bonding with surrounding water molecules

Question 5

Describe how hydrogen bonding occurs in the tertiary structure of proteins.

Answer 5

Attraction may occur between polar R groups:

• δ⁺ hydrogen engaged in a polar bond with an electronegative atom, e.g. in N-H, O-H (also S-H since S can be treated like O)
• a lone pair on an electronegative atom, e.g. in C-O, C-N

Attraction may also occur between a peripheral, polar R group and water:

• δ⁺ hydrogen engaged in a polar bond
• Lone pair on O in H₂O

Question 6

Describe how ionic bonding occurs in the tertiary structure of proteins.

Answer 6

• Electrostatic attraction occurs between ionisable/ionised side chains
• E.g. -NH₂ → -NH₃⁺, -SO₃H → SO₃^-, -COOH → COO^-

Question 7

Describe how covalent bonding occurs in the tertiary structure of proteins.

Answer 7

• Occurs by oxidation of -SH groups on neighbouring side chains
• Forming -S-S- link: disulfide bridge

Question 8

Compare the structures of structural and globular proteins.

Answer 8

• Structural: fibrous, consist mainly of helices (structural functions)
• Globular: both sheets + helices (metabolic functions)

Question 9

What is meant by “an enzyme’s receptor/binding site”?

Answer 9

A group in the active site which forms a bond with the substrate (i.e. a single bonding site).

These bonds are weak (usually hydrogen or ionic)

Question 10

Explain how an enzyme breaks down its substrate molecule.

Answer 10

• Tertiary structure of enzyme gives active site which is specific + complementary to substrate
• Substrate binds to active site (at receptor sites)
• Enzyme weakens bonds / lowers E_a / acts as biological catalyst
• Substrate reacts
• Products leave active site

Question 11

How is the enzyme-substrate complex represented shorthand?

Answer 11

ES

Question 12

Draw an enthalpy diagram to show how an enzyme lowers the activation enthalpy of an exothermic biological reaction.

Answer 12

Question 13

In one situation, all enzymes can have a substrate bound to their active site.

• What is the order of reaction with respect to the substrate?
• What is the rate-determining step?

Answer 13

• 0 order
• EP → E + P or ES → EP (never E + S → ES)

Which of those 2 steps it is depends on: a) how easily enzyme can alter substrate; b) how easily product dissociates from enzyme

Question 14

In one situation, not all enzyme active sites are occupied by a substrate.

• What is the order of reaction with respect to the substrate?
• What is the rate-determining step?

Answer 14

• First order
• E + S → ES

Question 15

Explain the shape of the following graph.

Answer 15

• At first, not all active sites are occupied by a substrate, so increasing the substrate concentration increases the rate of reaction
• The graph is 1st order with respect to the substrate
• One all active sites are occupied by a substrate, increasing the substrate concentration has no effect on the rate of reaction
• The graph is 0 order with respect to the substrate

Question 16

How do competitive inhibitors affect enzyme activity?

Answer 16

• Inhibitor has similar shape (+ electron distribution) to substrate
• So it also binds to active site
• It blocks active site / cannot be catalysed
• Substrate cannot bind + react
• Fewer active sites available to substrate
• Decreased rate of reaction

Type of interaction between inhibitor + enzyme determines extent of effect: weak bonds (hydrogen) → impermanent → rate decreased. Strong bonds (ionic, covalent) → permanent → reaction stopped

Question 17

Explain how pH affects enzyme activity.

Answer 17

Small changes:

• Protonation/deprotonation of ionisable groups: -COOH, NH₂, O^δ-
• Can’t interact w/ substrate in same way

Larger changes:

• Ionisation breaks permanent bonds in 3ary structure: ionic + covalent (i.e. disulfide bridges)
• Active site changes shape
• R groups meant to bond to substrate are in wrong place
• Enzyme rendered dysfunctional

Question 18

Explain how temperature affects enzyme activity.

Answer 18

Temperature rises approaching optimum temperature:

• More molecules have sufficient energy to collide with at least activation energy
• Frequency of successful collisions increases
• Rate increases

Further rises:

• Weak instantaneous dipole-induced dipole + hydrogen bonds in tertiary structure are weakened / broken
• Enzyme can’t interact with substrate in same way
• Rendered dysfunctional

Question 19

Answer 19

Need to relate general ideas to structures of molecules given in order to score full marks

General description of how enzyme works:

• Substrate has complementary shape to active site
• Substrate binds to active site
• Enzyme weakens bonds / lowers E_a / acts as biological catalyst
• Substrate reacts
• Products leave active site

General description of how inhibitor works:

• Inhibitor has similar shape to substrate
• So it also fits into active site
• It blocks active site
• Substrate cannot bind + react
• Fewer active sites available to substrate so decreased rate of reaction

Comments specific to these molecules:

• Examples of structural similarity (could annotate diagram), e.g. middle part of molecule
• Example of intermolecular interaction between molecules + enzyme:
  
  • Substrate has amide bond that can be hydrolysed, so products leave
  • Inhibitor has no amide bond in this position, so does not react + leave

Question 20

Define pharmacophore.

Answer 20

The part of a drug which is biologically active.

When deducing a drug’s pharmacophore by comparing it to the biological molecule whose function it mimics, draw the whole region that they have in common, even if some of it seems likely to be inactive.

Question 21

Define molecular recognition.

Answer 21

The structure and action of a pharmacologically active material.

I.e. interactions between specific sites on molecules, involving non-covalent bonds

Question 22

Give two reasons why the pharmacophore of a drug might be modified.

Answer 22

• To increase efficacy
• To reduce side effects

Question 23

List the types of weak interactions of pharmacophores with receptor sites.

Answer 23

• Hydrogen bonding
• Ionic bonding
• Instantaneous dipole-induced dipole interactions
• Metal coordination (molecules bound to central metal atom)