Topic 5

Question 1

Enzyme Catalysis

Answer 1

• biological catalysts
• perform nearly all chemical transformations in cells
• accelerate , but are unchanged by a reaction
• most enzymes are proteins
• name most often ends in ‘ase’

Question 2

Substrate Definition

Answer 2

• the molecule on which an enzyme acts

Question 3

Enzymes are Amazing Moleculat Machines

Answer 3

1. Specificity
2. Fidelity
3. Rapidity
4. Ability to Work Under Mild Conditions

Question 4

Specificity

Answer 4

• many enzymes will recognize only 1 or a few of the hundreds kinds of molecules

Question 5

Fidelity

Answer 5

• enzymes almost never make a mistake (result in close to 100% yield)

Question 6

Rapidity

Answer 6

• can accelerate reactions alot over the rate of uncatalyzed reactions

Question 7

Ability to Work Under Mild Conditions

Answer 7

• low temps (37°C) , pressure, neutral pH

Question 8

Enzymes Speed Up Biochemical Reactions

Answer 8

• need to hydrolyze peptide bonds

Question 9

Post- Translation Modifications

Answer 9

• enzymes are regenerated during the reaction
  1. Phosphorylation
  2. Glycosylation
  3. Kinase

Question 10

Phosphorylation

Answer 10

• alters stability or signaling

Question 11

Glycosylation

Answer 11

• affects protein folding
• secretion
• solubility
• binding to other molecules

Question 12

Kinase

Answer 12

• transfers a phosphoull group from ATP to another molecule

Question 13

Active Site of Enzymes

Answer 13

1. part of the enzyme where the reaction takes place
   - small part of enzyme surface
   - often a cleft or crevice between domains
2. substrate bindsin active site
   - multiple weak bonds
   - binding is reversible

Question 14

Transition State

Answer 14

• not stable-bondsbreaking (A–B) + bonds forming (B–c)
• lower energy barrier = faster reaction

Question 15

The Transition State Continued

Answer 15

• intermediate forms between the reactants/products
• point of highest free energy
• a form that is different from both reactants/products
• conceptualized to have bonds in the process of forming + breaking

Question 16

Proximity + Orientation Effects:

Answer 16

• 2 groups must cometogether collide with correct orientation to react
• reactants must overcome translational/ rotational motions
• When reactants bind to an enzyme their motion is limited

Question 17

Mechanisms to Lower Activation Energy

Answer 17

1. enzyme binds to 2 substrate molecules - orients them precisely to cause a reaction between them
2. binding of substrate to enzyme rearranges electrons in the substrate that favour a reaction
3. enzyme strains the bound substrate molecule - forcing it toward a transition state to favour a reaction

Question 18

Transition State Analogues

Answer 18

• compounds that resemble the transition state
• similar geometry, charge distribution
• do not undergo a chemical reaction
• excellent inhibitors
  ( since they bind tightly, blocking the active site (competitive inhibitors))

Question 19

Cofactors

Answer 19

• some enzymes require a partner (cofactor) to function
• can either be essential or simply increase the rate of reaction
• can either be proteins , metal ions (iron/zinc or “co enzymes”

Question 20

Chymotrypsin

Answer 20

• member of the serine protease family (each member contains a critical serine residue inthe active site)
• secreted by the pancreas that allows breakdown of dietary protein during digestion
• hydrolyze peptide bonds

Question 21

Feature Characteristic

Answer 21

• catalytic triad

Question 22

Specificity Pocket

Answer 22

• a pocket located near the catalytic triad that interacts with the residue on the N-terminal side of scissile bond

Question 23

Serine Proteases Synthesized as Inactive Precursors

Answer 23

• active: trypsin
• inactive: trypsinogen
• one enzyme can activate another
• trypsin activates the inactive form (chymotrypsinogen) + creates chymotrypsin

Question 24

Enzyme Kinetics

Answer 24

• how rate of the reaction is influenced by substrate concentration , inhibitors , etc
• can help discover how an enzyme works
• rate of reaction will depend on various factors
• affinity of enzyme for substrate/ substrate concentration

Question 25

Michaelis- Menten Equation

Answer 25

• describes how substrate (s) concentration + rate of the reaction relate to eachother
• not as simple as protein-ligand binding

Question 26

Km Value

Answer 26

• Michaelis constant
• equal to substrate concentration at hald Vmax
• allows determination of km+Vmax from velocity vs . substrate data
• reflects affinity of the enzyme for substrate and its efficiency
• independent of enzyme concentration

Question 27

Enzyme Inhibtion

Answer 27

• theraputic drugs, natural inhibitors of metabolism, herbicides + pesticides

Question 28

2 Types of Enzyme Inhibition

Answer 28

1. Reversible
2. irreversible

Question 29

Type 1. Reversible

Answer 29

• binding to inhibitor to enzyme non-covalently
• inhibitor can be removed

Question 30

Type 2. Irreversible

Answer 30

• covalent bond formed with enzyme
• permanently blocks activity

Question 31

Reversible Inhibitor

Answer 31

• major category of reversible inhibitors : competitive
• inhibitor binds to the active site
• structure similar to substrate or product
• blocks access to substrate
• affects km of the reaction but not Vmax ( because the enzyme will have lower afiintiy for the substrate)
• large excess of substrate overcomes inhibition

Question 32

Allostery in Enzymes

Answer 32

• process by which proteins transmit the effect of binding at one site to another
• often distal , functional site , allowing for regulation of activity
• Hemoglobin is Allosteric but not an enzyme!!!

Question 33

Two Phenomena in Allostery in Enzymes

Answer 33

1. binding of substrate at 1 active site influences binding at other sites (cooperativity)
2. binding of regulatory molecule changes conformation of enzyme and affects its activity

Question 34

T-state

Answer 34

• low activity
• lower affinity for fructose-6-phosphare phosphenolpyruvate binding

Question 35

R-state

Answer 35

• high activity