Enzymes

Question 1

What are enzymes

Answer 1

Biological catalysts (not consumed/changed), globular proteins (1,2,3 sometimes 4 structure).

Question 2

Apoenzyme vs Holoenzyme

Answer 2

Apoenzymes have no prosthetic groups

Question 3

How do you increase speed of chemical reactions

Answer 3

Heat or a catalyst

Question 4

Which non-covalent interactions stabilize enzymes

Answer 4

Hydrophobic interactions, H-bonds, ion pairs, VDW, disulphide bridges

Question 5

Differences between enzymes and non-biological catalysts

Answer 5

Higher rxn rates, milder rxn conditions, greater rxn specificity, capacity for REGULATION

Question 6

Why can enzymes regulate

Answer 6

Conformational change in protein structure is possible

Question 7

Why is ATP a high energy molecule

Answer 7

Decreased electrostatic repulsion, resonance stabilization

Question 8

When is a reaction “thermodynamically favourable” (rxn proceeds)

Answer 8

At negative delta G = spontaneous =free E released

Question 9

What determines the speed of a reaction

Answer 9

Size of the activation energy barrier

Question 10

What do enzymes affect

Answer 10

Activation energy/reaction rates = speed up reactions

Question 11

What don’t enzymes affect

Answer 11

Free energy change (deltaGrxn)

Question 12

What does the design of the active site contribute to

Answer 12

Affinity, specificity

Question 13

What is the correct substrate binding model

Answer 13

Induced fit, binding changes shape of active site

Question 14

What is desolvation / why is it advantageous

Answer 14

Removing substrates from aqueous solutions. Prevents interference by water, formation of H-bonds more effective, eliminates energy barrier imposed by ordered solvent molecules (water)

Question 15

What is the proximity and orientation effect

Answer 15

orientation and movement of the substrate molecules when binding to enzyme active sites. Thousand-fold increase in rxn rates

Question 16

How do catalysts lower the activation energy barrier

Answer 16

1. Desolvation
2. Proximity and orientation effect
3. Taking part in the reaction mechanism
4. Stabilizing the TS

Question 17

How do enzymes take part in reaction mechanisms

Answer 17

positioning aa side chains in the active site so they can react with substrates (acid-base catalysis), provide other chemical substances at the active site (cofactors)

Question 18

How do enzymes stabilize the transition state

Answer 18

Active site binds TS better than it binds the substrate. Free E of TS lowered

Question 19

What are the mechanisms for the regulation of enzyme activity

Answer 19

Competitive inhibition, allostery, reversible covalent modification, regulation of gene expression

Question 20

What is competitive inhibition

Answer 20

The inhibitor is similar to the substrate in shape/size but differs chemically and cannot react, binds to site before substrate

Question 21

What do competitive inhibitors do to the enzyme/substrate Km?

Answer 21

Increase it (decrease affinity)

Question 22

Describe allosteric enzymes

Answer 22

Sigmoidal curve, conformational change in response to effector, quaternary structure. Molecule binds at site other than active site and either improve binding (+ive cooperation/homoallostery) or decrease binding (negative effector). They have a T and R (relaxed, high activity) state

Question 23

What is the role of kinases

Answer 23

Transfer phosphate from one group to another

Question 24

Addition of phosphate group results in…

Answer 24

Increase in size, polarity, hydrophilicity. Addition of two negative charges, capability of making new H bonds