Enzymes

Question 1

What are the 2 main components of enzymes?

Answer 1

protein structure - scaffold to provide support

active site - composed of binding and catalytic sites

Question 2

How do enzymes control metabolism?

Answer 2

The breakage and formation of covalent bonds

Question 3

What are the only enzymes not composed of proteins?

Answer 3

Riboenzymes

Question 4

What is an allosteric site?

Answer 4

A site other than the active site on the enzyme

Question 5

What is a coenzyme?

Answer 5

Small non-protein organic compounds e.g Coenzyme A

Question 6

Name 4 differences between enzymes and chemical catalysts

Answer 6

• Higher reaction rates
• Work under milder conditions
• Greater reaction specificity
• Capacity for regulation

Question 7

What do enzymes affect?

Answer 7

Only the kinetics, NO CHANGE IN FREE ENERGY

Question 8

How can unfavourable reactions be catalysed?

Answer 8

By pairing them with favourable ones

Question 9

What is the optimal pH for most enzymes?

Answer 9

6-8 (beyond which electrostatic forces break them down)

Question 10

What are the 6 classifications of enzymes?

Answer 10

1) Oxidoreductases
2) Transferases
3) Hydrolases
4) Lysases
5) Isomerases
6) Ligases

Question 11

What can act as a cofactor?

Answer 11

• Can be inorganic or organic

- Organic group can be permanently associated with the active site or loosely/reversibly bound

Question 12

Name 3 ways in which an enzyme can form a complex with a substrate

Answer 12

1. Interaction of charged groups
2. Formation of H bonds
3. Hydrophobic groups fit into enzyme hydrophobic pockets

Question 13

What is the difference between an apoenzyme and a holoenzyme?

Answer 13

holoenzyme - A catalytically active enzyme-cofactor complex

apoenzyme - The enzymatically inactive protein resulting from removal of the cofactors

Question 14

What is the two-step model of catalysis

Answer 14

Enzyme works by forming a complex with a substrate and acting on it for a finite period of time

Question 15

What is the lock and key model?

Answer 15

Where there is 1 active site per molecule which is a perfect fit

Question 16

What is the induced fit model?

Answer 16

Where the protein changes its structure around the substrate in order to induce a fit

Question 17

What is the conformational selection model?

Answer 17

Where the protein exists in an equilibrium between different conformers to which one a substrate binds

Question 18

What does the affinity between between a substrate and enzyme depend upon?

Answer 18

Interaction strength, cooperativity and allostery

Question 19

What does the affinity refer to?

Answer 19

Strength of the interaction (greater decrease in free energy)

Question 20

What does specificity refer to?

Answer 20

The relative strength of interactions made between one protein and alternative ligands

Question 21

How is protein (P) and ligand (L) binding quantified?

Answer 21

In terms of the association (ka) and dissociation (kd) constant. At saturation equilibrium is reached (kA where kA =(P.L)/(P)(L) or 1/k)

Question 22

Give an equation for change in free energy of binding in terms of dissociation constant

Answer 22

ChangeGbinding = +RT ln kd 
R= gas constant

Question 23

How does kD affect change in Gbind

Answer 23

lower kd decreases (negative) Gbind

Question 24

Define kA and kD

Answer 24

kA = ka/kd
kD= kd/ka

Question 25

How is kD experimentally determined?

Answer 25

Fixed low concentration of receptor and vary the ammount of substrate, measure fraction of bound receptor
In this case the KD is the ligand concentration at which the half of the protein concentration is bound to L

Question 26

How is KD determined when protein concentration is not directly measurable?

Answer 26

Use statchard analysis (see statchard equation)
slope = -1/KD
intercept = Ptotal/KD

Question 27

What happens when we try to measure a high affinity system?

Answer 27

• can no longer assume that total ligand concentration and free ligand concentration are the same
• kD no longer represents half occupancy
• Use a more general quadratic equation

Question 28

What is cooperativity?

Answer 28

Where receptors are multimetric and binding of the first ligand can affect binding of subsequent ligands to other subunits of the complex

Question 29

What is the Hill equation?

Answer 29

f = [L]n/Kd+[L]n
n = Hill coefficient 
n>1 positive cooperativity 
n = 1 no cooperativity 
n <1 negative cooperativity

Question 30

What are the 5 catalytic strategies?

Answer 30

1. Acid-base
2. Covalent catalysis
3. Metal ion catalysis
4. Proximity and orientation effects
5. Preferential binding of the transition state

Question 31

Describe acid-base catalysis

Answer 31

Where the partial proton donation (acid) or
extraction (base) lowers the activation energy and
accelerates the reaction

Question 32

Describe covalent cataysis

Answer 32

usually a nucleophile group on the enzyme which forms a covalent bond with an electrophile group on the substrate, good cataylsis involves a highly nucleophile species and a good leaving group

Question 33

How can metal ions act as catalysts?

Answer 33

electrostatically stabilize negative charges formed during Intermediate states of the reaction

Question 34

By which 4 methods do enzymes catalyze reactions through proximity and orientation effects?

Answer 34

1. Bring substrates close to catalytic residues
2. Allow binding of substrate in proper orientation
3. Stabilization of transition state by electrostatic interactions
4. Freezing out translational and rotational mobility of the substrate (up to 10^7 fold)