Topic 5 Flashcards
1
Q
Enzyme Catalysis
A
- 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’
2
Q
Substrate Definition
A
- the molecule on which an enzyme acts
3
Q
Enzymes are Amazing Moleculat Machines
A
- Specificity
- Fidelity
- Rapidity
- Ability to Work Under Mild Conditions
4
Q
Specificity
A
- many enzymes will recognize only 1 or a few of the hundreds kinds of molecules
5
Q
Fidelity
A
- enzymes almost never make a mistake (result in close to 100% yield)
6
Q
Rapidity
A
- can accelerate reactions alot over the rate of uncatalyzed reactions
7
Q
Ability to Work Under Mild Conditions
A
- low temps (37°C) , pressure, neutral pH
8
Q
Enzymes Speed Up Biochemical Reactions
A
- need to hydrolyze peptide bonds
9
Q
Post- Translation Modifications
A
- enzymes are regenerated during the reaction
1. Phosphorylation
2. Glycosylation
3. Kinase
10
Q
Phosphorylation
A
- alters stability or signaling
11
Q
Glycosylation
A
- affects protein folding
- secretion
- solubility
- binding to other molecules
12
Q
Kinase
A
- transfers a phosphoull group from ATP to another molecule
13
Q
Active Site of Enzymes
A
- part of the enzyme where the reaction takes place
- small part of enzyme surface
- often a cleft or crevice between domains - substrate bindsin active site
- multiple weak bonds
- binding is reversible
14
Q
Transition State
A
- not stable-bondsbreaking (A–B) + bonds forming (B–c)
- lower energy barrier = faster reaction
15
Q
The Transition State Continued
A
- 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
16
Q
Proximity + Orientation Effects:
A
- 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
17
Q
Mechanisms to Lower Activation Energy
A
- enzyme binds to 2 substrate molecules - orients them precisely to cause a reaction between them
- binding of substrate to enzyme rearranges electrons in the substrate that favour a reaction
- enzyme strains the bound substrate molecule - forcing it toward a transition state to favour a reaction
18
Q
Transition State Analogues
A
- 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))
19
Q
Cofactors
A
- 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”
20
Q
Chymotrypsin
A
- 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
21
Q
Feature Characteristic
A
- catalytic triad
22
Q
Specificity Pocket
A
- a pocket located near the catalytic triad that interacts with the residue on the N-terminal side of scissile bond
23
Q
Serine Proteases Synthesized as Inactive Precursors
A
- active: trypsin
- inactive: trypsinogen
- one enzyme can activate another
- trypsin activates the inactive form (chymotrypsinogen) + creates chymotrypsin
24
Q
Enzyme Kinetics
A
- 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
25
Michaelis- Menten Equation
- describes how substrate (s) concentration + rate of the reaction relate to eachother
- not as simple as protein-ligand binding
26
Km Value
- 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
27
Enzyme Inhibtion
- theraputic drugs, natural inhibitors of metabolism, herbicides + pesticides
28
2 Types of Enzyme Inhibition
1. Reversible
2. irreversible
29
Type 1. Reversible
- binding to inhibitor to enzyme non-covalently
- inhibitor can be removed
30
Type 2. Irreversible
- covalent bond formed with enzyme
- permanently blocks activity
31
Reversible Inhibitor
- 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
32
Allostery in Enzymes
- 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!!!
33
Two Phenomena in Allostery in Enzymes
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
34
T-state
- low activity
- lower affinity for fructose-6-phosphare phosphenolpyruvate binding
35
R-state
- high activity
