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BioChem Exam 2 > Enzymes Review > Flashcards

Enzymes Review Flashcards

1
Q

biochemical strategies to drive an unfavorable rxn? (2)

what has a higher activation energy?

A
  1. maintain Q
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2
Q

what do enzymes do?

A

lower activation nrg

stabilize transition state

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3
Q

what do enzymes not do?

A

change Gibbs nrg

irreversibly change shape

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4
Q

a catalyst is something that ?

A

increases speed of a rxn

but does not undergo any permanent chemical changes as a result

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5
Q

how do we speed up a rxn?

A
  1. raise temp

2. stabilize transition state via enzyme

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6
Q

describe the induced fit model

A

when a substrate binds, the enzyme changes shape so that the substrate is forced into the transition state

this is reversible

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7
Q

catalysis is achieved through? (4)

A
  1. substrate orientation
  2. straining substrate bonds
  3. creating a favorable microenvironment
  4. covalent/noncovalent interactions between enzyme and substrate
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8
Q

name the 4 catalysis strategies and how they’re achieved

A
  1. covalent catalysis – transfer e-
  2. acid-base catalysis – transfer protons
  3. approximation – proximity and orientation
  4. electrostatic catalysis – noncovalent interactions

(between ions or proteins)

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9
Q

covalent catalysis

A

enzyme covalently binds the transition state

e- transfer

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10
Q

acid-base catalysis

A

partial proton transfer to the substrate

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11
Q

approximation catalysis

A

if e- or H+ must be exchanged spatial orientation and close contact of the reactant molecules must occur

both pieces of the puzzle must be in proximity and proper orientation

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12
Q

electrostatic catalysis

A

stabilize unfavorable charges of transition state by using polarizable side chains in the enzyme or metal ions

and/or noncovalent interactions to lower transition state nrg

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13
Q

name an example of a catalytic triad

A

active site of chymotrypsin

serine 195 = nucleophile
histidine 57 = base
aspartic acid 102 = acid

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14
Q

chymotrypsin - oxyanion hole

A

stabilizes the tetrahedral intermediate/transition state

serine 195
glycine 193

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15
Q

______ pocket determines placement of cut

A

specificity pocket

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16
Q

amino acids that fit into chymotrypsin’s specificity pocket

A

phenylalanine is best

aromatic AAs

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17
Q

trypsin specificity pocket

A

has D, so wants aa’s that are positive and bigger

arginine and lysine

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18
Q

elastase specificity pocket

A

has valines so wants something small and nonpolar

alanine, glycine

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19
Q

carbonic anhydrase – active site

A

–contains zinc ion

coordinated w/ 3 histidines and a water

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20
Q

carbonic anhydrase – water

A

water facilitates the transition state when deprotonated

catalytic strategy = approximation

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21
Q

the entry channel of carbonic anhydrase determines ?

A

size of the substrate

CO2 is small and weakly polar

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22
Q

rxn mechanism of carbonic anhydrase

A
  1. water binds to Zn
  2. water loses H+
  3. substrate enters active site
  4. nucleophilic addition of CO2
  5. release of product and regeneration of enzyme via histidine proton shuffle
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23
Q

first order kinetics

A

V = k[S]^1

linear graph
ln[S] x time

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24
Q

second order kinetics

A

V = k[S]^2

linear graph
1/[S] x time

25
Q

zero order kinetics

A

V = k[S]^0 = k

linear graph
[S] x time

26
Q

define Km

A

michaelis constant

[S] where rxn rate is half max or half the active sites are full

27
Q

michaelis-menten enzymes follow ?

A

first order kinetics

28
Q

define Vm

A

max velocity

max rate possible for a given conc of enzyme

29
Q

define Kcat

A

turnover number

number of substrate molecules converted per active site per time
–first order rate constant

30
Q

define Ks

A

no name

dissociation constant for substrate binding

31
Q

define Kcat/Km

A

specificity constant

measure of enzyme performance by predicting the fate of E*S

32
Q

types of reversible inhibition

A
  1. competitive
  2. noncompetitive – allosteric
  3. uncompetitive
33
Q

irreversible group-specific inhibitor

A

targets a specific amino acid to inactivate the enzyme

low specificity for active site

34
Q

irreversible substrate analog inhibitor

A

mimics the substrate to bind to the enzyme and modify it into inhibition

high specificity for active site

35
Q

irreversible suicide inhibitors

A

mimic the substrate to inhibit enzyme
and unable to form products

very high specificity for active site

36
Q

important michaelis-menten model values gained from lineweaver-burk plots

A
  1. [S]0 = amount of substrate initially added to rxn
  2. V0 = recorded initial rxn rate for given [S]0
  3. y-intercept = 1/Vmax
  4. x-intercept = -1/Km
37
Q

enzyme regulation - HOW? - what rxn is influenced ?

A
  1. substrate level control acts on a single rxn

2. feedback control targets a step in the pathway (dif from the one targeted above)

38
Q

enzyme regulation - HOW? - what is the effect on product formation?

A

activators vs inhibitors

act = promote more products

inh = prevent more products

39
Q

how are metabolic enzymes regulated ?

A

compartmentalization
conc
activity/vol control
hormone signals or 2nd messenger sys

40
Q

isozymes - WHO?

A

enzymes that catalyze the same rxn but w/ dif efficiency

41
Q

LDH - isozymes

A

participates in lactic acid fermentation pathway

lactate dehydrogenase rxn

has 5 dif isozymes
each one works in a dif area of the body

LDH-1 can be used to detect is heart attacks have occurred

42
Q

reversible covalent modification - WHAT?

A

how can we modify the enzyme to activate/inactive

what can we add?

note post-translational modifications = non-proteinogenic amino acids

43
Q

list the common modifications

A
  1. phosphorylation
  2. acetylation
  3. methylation
  4. carboxylation
  5. sulfation
  6. ubiquitination
44
Q

kinases and phosphatase

A

kinases = add pi
–are named to indicate which aa the pi will be added

phos = remove pi

45
Q

acetylation

A

adding an acetyl group to histones w/ acetyl CoA

46
Q

methylation

A

can activate or inhibit histones by adding a methyl group

47
Q

allostery - WHERE?

A

allosteric binding does not occur at the active site

heterallostery = effect binds allo site

Homoallostery = cooperativity

48
Q

ACTase

A

aspartate carbamoyl-transferase

it is inhibited by CTP

49
Q

ACTase – binding of CTP vs ATP

A

CTP prefers T/inactive state
–inhibits ACTase

ATP activates
R/active state

T= tense, R = relaxed

50
Q

what is the on/off switch for enzymes? and what are the 2 levels of control for this? - WHEN?

A

protein synthesis regulation

  1. transcription reg at promoters
  2. translation reg at UTRs
51
Q

histone acetylation _______ transcription, phosphorylation _______ transcription, and histone methylation will ?

A

promote
prevent

both/ either or

52
Q

UTR

A

untranslated regions

UTRs and miRNAs can control translation

53
Q

define zymogen

A

the inactive form

54
Q

proteolytic activation - WHY? - irreversible covalent modification

A

most enzymes/substrates are inactive until proteolytically cleaved into the active state

ex. chymotrypsin

55
Q

proteolytic activation of chymotrypsin

A

chymotrypsinogen to chymotrypsin – cleaved by trypsin

must be cleaved twice to become active

makes the oxyanion hole oriented properly

56
Q

cleavage of chymotrypsinogen

A

first. between Ile, Arg, Ser, Leu
2nd. between tyr, thr, asp, ala

cuts are made between 1-2 and 3-4
so aa’s 2 and 3 are lost

57
Q

trypsin activates 5 molecules, name them

A
  1. itself, trypsinogen to trypsin
  2. Chymotrypsinogen to chymotrypsin
  3. proelastase to elastase
  4. procarboxy-peptidase to carboxypeptidase
  5. prolipase to lipase
58
Q

if trypsin is capable of activating itself, what must first activate it before it can further attenuate itself?

A

enteropeptidase first cleaves trypsinogen to trypsin

BioChem Exam 2 (6 decks)

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