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Biochemistry > Chapter 6: Introduction to Enzymes > Flashcards

Chapter 6: Introduction to Enzymes Flashcards

1
Q

Enzyme

A

a biomolecule, often a protein but sometimes RNA, that catalyzes a specific chemical reaction

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2
Q

Substrate

A

a specific component acted on by an enzyme(reactant)

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3
Q

Cofactor

A

an additional chemical component that binds to the protein and aids in substrate binding and/or catalysis
- may be metal ions or coenzymes

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4
Q

Enzyme with cofactor(s)

A

Holoenzyme
- active

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5
Q

enzyme without cofactor(s)

A

Apoenzyme
- inactive

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6
Q

Active site

A

the pocket on the enzyme where the substrate binds and catalysis happens
- cleft or hollow
- water is often excluded
- small part of protein structure

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7
Q

Coenzyme

A

an organic cofactor, often derived from vitamins
ex: heme, ubiquinone, FAD
-subtype of cofactor

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8
Q

Prosthetic Group

A

coenzyme or metal ion that is very tightly or covalently bound to the enzyme protein
- permanently bound

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9
Q

How do enzymes work?

A

accelerate a chemical reactions but do not change the equilibrium
- reduce the activation energy

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10
Q

transition state

A

: fleeting molecular moment, often mid bond break or form

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11
Q

What does the enzyme rate depend on?

A
  • concentration of substrates
  • rate constant
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12
Q

First Order Rate Equation

A

V=k[S]
k units=s-1

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13
Q

Second Order Rate Equation

A

V=k[S1][S2]
k units=s-1M-1

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14
Q

Substrate Specificity

A

ability to discriminate between substrate and related compounds

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15
Q

Enzymes that lack specificity

A

called promiscuous

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16
Q

Enzyme Catalysis Strategies

A
  • desolation from the substrate
  • orientation and approximation (stabilizing transition state)
  • (Temporary) covalent interactions between the enzyme and the substrate
    -Metal-ion assisted
  • General Acid-base catalysis
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17
Q

Stabilizing the Transition State

A
  • the enzyme is complementary to the transition state, not the substrate
    - favoring/ pushing substrate towards desired transition state and product
  • binding is often favorable, free energy of binding can drive reaction
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18
Q

General Acid-Base Catalysis

A
  • H+ transfer
  • A H+ transfer can be used to stabilize a charged intermediate or transition state
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19
Q

What is enzyme kinetics the study of?

A

Enzyme kinetics is the study of the rate of an enzyme-catalyzed reaction under various conditions
-provides quantitative information

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20
Q

What is modern enzyme-kinetics based on?

A

steady-state condition i.e. when the [ES] is constant

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21
Q

Enzyme kinetics graph axis’s

A
  • product concentration vs time
  • y-axis, x-axis
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22
Q

Why do we only use initial velocity?

A

We use initial velocity because the concentration of the substrate hasn’t changed very much and the situation gets more complicated as we decrease [S] and increase [P]

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23
Q

What happens to velocity with increasing [S]?

A

velocity increases to a maximum (Vmax)

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24
Q

Michaelis Menton Equation

A

an equation to describe the kinetic plot of the rectangular hyperbola produced by plotting Vo vs [S]

Vo=(Vmax[s]/Km+[S])

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25
Q

Enzymes that display a rectangular hyperbola graph are said to have __________.

A

Michaelis-Menten Kinetics

26
Q

Vmax

A

the maximum velocity at near saturating [S] (all E exists as ES)

27
Q

Km

A
  • Michaelis Constant
  • [S] at 1/2 Vmax
  • combination of rate constants
    Km=(K2+K-1)/(K1)
28
Q

What two assumptions are made in Michaelis Menten Kinetics?

A
  • Steady State Assumption: the concentration of [ES] is constant
  • Rapid Equilibrium: the formation of the ES complex is fast and product formation is slow (rate limiting)
29
Q

When can Km be equal to Kd (binding affinity of E+S)?

A

If k2«««k-1
- this means ES->E+P is much slower than E+S->ES

30
Q

What is Kd?

A

Dissociation constant= affinity/binding

31
Q

kcat

A

the rate constant for the rate limiting step at saturating [S]
- assuming Michaelis Menten kinetics, k2=kcat

32
Q

turnover number (aka kcat)

A

the number of substrate molecules catalyzed per second
- units of s-1 (first order)

33
Q

Lineweaver-Burk Plots

A
  • also called double-reciprocal plots
  • plots the reciprocal of Vo and [S]
34
Q

How do we look at enzyme kinetics if the enzyme has two substrates?

A

We place one substrate in great excess over the other substrate so that the rate only depends on one of the substrates.

35
Q

Km(apparent)

A
  • The Km measured in the presence of an inhibitor
    = alpha x Km
36
Q

How do competitive inhibitors work?

A

they bind to the active site and compete with the substrate
- increase Km
- no effect on Vmax because as high [S], natural substrate can outcompete inhibitor

37
Q

How do uncompetitive inhibitors work?

A

they do not bind at the active site, they only bind to the ES complex, not E alone
- decrease the Km
- decrease the Vmax

38
Q

How does mixed inhibition work?

A

Mixed inhibitors do not bind at the active site and can bin either the E or the ES complex
- May increase or decrease the Km
- Decrease Vmax

39
Q

Irreversible Enzyme Inhibition

A

Enzymes can be irreversibly inhibited by covalent modification that destroys critical function groups OR by binding a molecule so tightly, it is essentially irreversible

40
Q

Suicide Substrate/ Inactivators

A

are modified by the enzyme and then become covalently bound to the active site

41
Q

Transition State Analogs

A

molecules that resemble the substrate transition state and bind with his affinity

42
Q

Regulatory Enzymes

A

enzymes at key steps in a metabolic pathway
- heavily regulated
- exists an an equilibrium between an active and inactive conformation

43
Q

How can enzyme activity be controlled?

A
  • substrate availability
  • allosteric modulators/effectors
  • reversible covalent modification
  • post translational modification (PTM)
  • Proteolytic cleavage
44
Q

Allosteric Effectors/ Modulators

A

generally small molecules that bind away from the active site and change the enzymes activity (can have a negative or positive effect)
- with Hb, 2,3-BPG is a negative allosteric modulator (favors T state)

45
Q

Kinetics of allosteric enzymes?

A
  • will not display Michaelis Menten kinetics, but instead will have sigmoidal plot of Vo vs [S]
46
Q

What are Post-Translational Modifications?

A
  • include the addition of various function groups to the side chains or termini of proteins
47
Q

How do post translational modifications affect enzymes?

A
  • can alter intermolecular forces, changing the enzyme structure and activity
  • can activate or inhibit
48
Q

Kinases

A

the enzymes that transfer a phosphate from ATP to a target protein (Ser, Thr, or Tyr residues)

49
Q

Protein Phosphatases

A

cleave and remove phosphate groups

50
Q

What does chymotrypsin do?

A

It is a protease, cleaves peptide binds adjacent to large aromatic side chains: Phe, Trp, Tyr

51
Q

What are chymotrypsins substrate?

A

peptide and water

52
Q

What class of enzyme does chymotrypsin belong to?

A

hydrolase

53
Q

What is the structure of Chymotrypsin?

A

monomer (multiple chains), soluble and globular
- initially translated from RNA as one continuous polypeptide chain

54
Q

Zymogen

A

inactive precursor

55
Q

Chymotrypsinogen

A

inactive/not cut form of chymotrypsin

56
Q

What happens when chymotrypsin is delivered to the digestive tract?

A

When delivered to the digestive tract, it is cleaved into three chains that are held together by disulfide bonds

57
Q

What role does Ser195 play in the reaction mechanism of chymotrypsin?

A

-contains a strong nucleophilic O (alkoxide, stabilize His57) that attacks carbonyl carbon of substrate
-forms the covalent bond with substrate, facilitating peptide bond cleavage

58
Q

What role does His 57 play in the mechanism

A

-multiple general acid-base mechanism
- protonated and deprotonated multiple times
- stabilizing the alkoxide of Ser195, also generating hydroxide (-OH) from H2O

59
Q

What role does Asp102 play in the reaction mechanism

A

positioning His 57 in the right location and the negative charge helps stabilize the protonations of the His side chain

60
Q

What common strategies does chymotrypsin use to catalyze the peptide cleavage?

A

General-acid base, covalent catalysis, approximation and orientation

61
Q

What is the catalytic triad?

A
  • Ser195, His 57, Asp102

Biochemistry (8 decks)

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