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Biochemistry > Biochem Exam #2 Study Guide > Flashcards

Biochem Exam #2 Study Guide Flashcards

1
Q

Enzymes

A

proteins that catalyze specific reactions

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2
Q

Each Enzyme is

A

unique
catalyze specific reactions
speed up reactions

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3
Q

What attracts an enzyme to a substrate?

A

intermolecular forces

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4
Q

Active Site

A

catalytic center where the substrate fits into the enzyme

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5
Q

What happens when the enzyme undergoes a conformational change?

A
  • creates tighter induced fit

- bring chemical groups in position to catalyze the reaction

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6
Q

When S binds to E

A
  • there is a conformational change
  • transition state is stabilized
  • create environment for rxn
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7
Q

cofactor

A

any organic or inorganic molecule that aids in catalysis

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8
Q

What are the 2 types of cofactors? Protein or Non-protein?Organic or inorganic?

A

coenzyme & prosthetic group
nonprotein
organic

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9
Q

How do the 2 cofactors bind?

A

coenzyme: binds with IMFs

prosthetic group: bind with covalent bond

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10
Q

Holoenzyme vs. Apoenzyme

A

holoenzyme: has cofactor
apoenzyme: does not have cofactor

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11
Q

Oxidoreductase (dehyrogenase)

A

cataylze redox reactions

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12
Q

Transferases

A

transfer functional group

G+ATP->G6P+ ADP

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13
Q

Hydrolase

A

use H20 to break covalent bonds

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14
Q

Lyase

A

adds or removes covalent bond without H2O

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15
Q

Isomerase

A

creates an isomer (molecule with same EF but arranged differently)

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16
Q

Ligase

A

make covalent bond and use energy (ATP)

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17
Q

What does enzyme kinetics give us? (5)

A 
info on:
purity of enzyme
catalytic efficiency
specificity
inhibition
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18
Q

Lock & Key Theory

A

Enzyme binds S like a lock fits a key

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19
Q

Induced Fit

A

S binds to E, but “fit” to accommodate transition state

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20
Q

The conformational change during cataylsis allows for what?

A

Stabilization of the transition state

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21
Q

How does an enzyme speed up a reaction?

A

by lowering its activation energy

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22
Q

What are the 2 things we need to know about the enzyme?

A
  1. how good the substrate binds (km)

2. Production of product

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23
Q

k1 is; k-1

A

the association of S to E; disassociation of S from E

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24
Q

Rate=____: which is?

A

Velocity: the quantity of S that disappears and quantity of P that appear in a specific time

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25
Q

1st order rate

A

exponential

rate depends on substrate concentration

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26
Q

Zero order rate

A

horizontal line

rate does not depend on substrate concentration; there is no difference

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27
Q

ka

A

rate constant

indicator of strength of acid

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28
Q

2nd order rate

A

sigmodial

rate depends on concentration of both substrate 1 and 2

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29
Q

Steady State Assumption was created by?

A

Briggs Haldene

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30
Q

Steady State

A

As the [S] decrease the [P] increases, but the ES complex is still the same

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31
Q

Vmax

A

theoretical max rate of an enzyme that is never reached

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32
Q

Km

A

“affinity”

concentration of S at 1/2 Vmax

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33
Q

Small Km=

High Km=

A

small=tight fit (better affinity)

high=weak fit

34
Q

Kcat;equation

A

“turnover number”
-number of S molecules converted to P
the bigger the number the more product made
-Kcat=Vmax/[Et]

35
Q

Kcat/Km

A

catalytic efficiency

36
Q

Types of Inhibition

A

Competitive
Noncompetitive
Uncompetitive

37
Q

Competitive Inhibition: reversible?

A

-inhibitor binds the to the same place that the substrate binds
reversible
-can be overcome by adding more substrate

38
Q

Affects of competitive inhibitor

A

Lowers the Km, but Km will appear to increase

39
Q

Noncompetitive Inhibition:reversible?

A
  • inhibitor binds to a spot on the enzyme other than the active site
  • can not be overcome by adding more substrate
40
Q

Affects of noncompetitive inhibitor

A

Vmax is decreased; Km is unchanged

41
Q

Uncompetitive Inhibitor

A

inhibitor binds to ES only

prevents S from detaching or become P

42
Q

Affects of uncompetitive inhibitor

A

Km & Vmax are decreased

43
Q

Cleland Notations

A

for enzymes with 2 substrates

44
Q

What are the 2 types of notations for cleland diagrams

A

sequential & double displacement

45
Q

Ordered Sequential

A

S1:S2:P1:P2

order matters

46
Q

Double Displacement

A

S1:P1:S2:P2

47
Q

catalytic residue (2)

A
  • amino acid side chains in active site that are involved in the mechanism
  • alter pka
  • stabilize transitional state
48
Q

Acidic Residue

A

want charge: pka decrease (-)

not want charge: pka increases (+)

49
Q

Basic Residue

A

want charge: pka increase (+)

not want charge: pka decreases (-)

50
Q

Nu

A

nucleus loving
has extra electrons
reacts with + or partial +

51
Q

E+

A

electron loving
has lack of electrons
react with - or partial -

52
Q

proteases

A

enzyme the cut peptide bonds

53
Q

Acid Catalysis

A

uses a strong E+
a molecule other than water acts as an acid
positive charge pulls on oxygen

54
Q

Base Catalysis

A

uses a strong Nu
a molecule other than water acts as a base
negative charge pulls on hydrogen

55
Q

Acid/Base Catalysis

A

uses both strong E+ and Nu

56
Q

Carboxypeptidase A

A

CPA
metalloprotease
cuts off C-terminal residue
uses Zn+2 for catalytic activity

57
Q

MetalloPR

A

uses a metal for catalytic mechanism

metal acts as E+

58
Q

Mechanism of CPA (6)

A
  1. Substrate binds to active site
  2. Zn attacks the double bonded oxygen
  3. Glu takes H+ from water
  4. Attack N-term leaves
  5. Tetrahedral intermediate forms
  6. Enzyme resets
59
Q

CPA: substrate binds active site

A

Arg attacks the C term

60
Q

CPA:Zn attacks double bonded oxygen

A

makes carbon better E+(acts as an acid)

61
Q

CPA:Glu take H+ from water

A

water acts as a base

62
Q

CPA:Tetrahedral intermediate form

A

Transition state stabilized by Tyr

Tyr acts as an acid

63
Q

CPA: Enzyme reset

A

Tyr accepts H from Glu

64
Q

Chymotrypsin

A

Serine PR
has a catalytic triad
cuts after WMFYL

65
Q

What amino acids are in the catalytic triad?

A

aspartic acid
histidine
serine

66
Q

Mechanism of Chymo (9)

A
  1. substrate binds active site and activates catalytic triad
  2. Asp takes H+ from His, then His takes from Ser
  3. Nu attack bu Ser
  4. Tetrahedral intermediate formed
  5. Reform pi bond
  6. 2nd Nu attack
  7. Shiff N of His gives es to water
  8. Attack on tetrahedral intermediate
  9. N term released
67
Q

Cutting locations of chymo

A

WMFYL

68
Q

Cutting locations of trypsin

A

K and R

69
Q

Cutting locations of elastase

A

A and G

70
Q

Feed forward activation

A

ATP binds Enz to make go

71
Q

Feedback inhibition

A

E binds Enz to make slow

72
Q

Enzyme catalyze with step in the pathway

A

rate limiting step-committing step

73
Q

T State

A

Active site is blocked; little S bind

74
Q

R State

A

Active site open; S bind readily

75
Q

What types of domains do enzymes have?

A

active site domain

regulatory domain

76
Q

Effector binds the _____ domain
w/ + effector=
w/ - effector=

A

regulatory domain
activator (more in R)
inhibitor (more in T)

77
Q

Isozymes

A

2 enzymes

78
Q

Zymogen

A

inactive precusor

ex.chymotrypsiongen

79
Q

post translational modifications

A

“after protein made change”

80
Q

Kinase

A
  • enzyme that catalyze the transfer of a phosphate from ATP to an aa side chain in an enzyme
  • reversed by phosphatases

Biochemistry (14 decks)

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