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BIOL 2421 - Cellular Biochem > 10. Enzyme mechanisms > Flashcards

10. Enzyme mechanisms Flashcards

1
Q

what does an enzymes catalytic activity depend on

A

their native conformation

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2
Q

T or F: an enzymes catalytic activity can function when the enzyme unfolds

A

false; catalytic activity depends on their native conformation and will usually be lost if any degree of unfolding happens

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3
Q

where on the enzyme does the reaction take place

A

the active site

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4
Q

T or F: enzymes often require cofactors/coenzymes

A

true

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5
Q

what is a cofactor

A

a metal ion

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6
Q

what is a coenzyme

A

one or more organic/metalloorganic complexes, usually derived from vitamins

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7
Q

what do the coenzymes carry

A

a specific functional group

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8
Q

when the cofactor/coenzyme is tightly bound to the enzyme, what are they called

A

prosthetic group

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9
Q

what is free energy

A

the energy available to do work

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10
Q

describe the free energy in an exergonic reaction

A

free energy decreases

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11
Q

what does a reaction coordinate diagram look like

A

free energy vs progress of the reaction. There is a peak as S turns into P. There are troughs representing ES and EP

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12
Q

T or F: if a reaction is exergonic, it will be fast

A

false; just because something is spontaneous doesn’t mean it will be fast

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13
Q

what is a transition state

A

it’s the tall peak on a graph, and it represents an energy barrier as we go from S to P

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14
Q

what is the activation energy (Ea)

A

the difference between transition state and ground state of S

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15
Q

T or F; at the transition state, progress towards S or P is equally likely

A

true

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16
Q

explain why progress towards S or P is equally likely at the transition state

A

aligning groups and bond breakage have occurred to a point where decay to the products or decay to the substrates have the same odds

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17
Q

what does ∆Gǂ measure

A

∆Gǂ is the activation energy for the reaction. It measures the difference between the energy levels of the ground and transition states

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18
Q

what does a high activation energy mean

A

slower reaction

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19
Q

in regards to ∆Gǂ, what is the role of the enzyme

A

to decrease ∆Gǂ by lowering the transition state

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20
Q

why is a lock and key a bad analogy for substrates and enzymes

A

if the substrate perfectly fit into the enzyme would stabilize the substrate, and a product would not form. It would increase the activation energy needed to form P

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21
Q

what is binding energy (∆GB)

A

the free energy released from ES interactions in the transition state. It is the difference between the cat. and uncat. reactions

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22
Q

T or F: if there are multiple reaction intermediates, overcoming each barrier may require a dif. activation energy

A

true

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23
Q

which step is the rate limiting step

A

the step with the highest activation energy (has the highest peak)

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24
Q

what are the 6 categories of enzymes

A

oxidoreductases, transferases, hydrolases, lyases, isomerases, and ligases

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25
Q

describe oxidoreductases

A

catalyze redox reactions, most in this group are dehydrogenases, oxidases, peroxidases, oxygenases, or reductases

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26
Q

describe transferases

A

catalyze group transfer reactions (ie kinases)

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27
Q

describe hydrolases

A

catalyze hydrolysis, are special class of transferases with water serving as the acceptor of the group transferred

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28
Q

describe lyases

A

catalyze lysis of a substrate which generates a double bond or a ring

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29
Q

describe isomerases

A

catalyze structural changes within a single molecule to produce an isomer

30
Q

describe ligases

A

catalyze ligation or joining of two substrates (usually linked to the breakage of a pyrophosphate bond)

31
Q

what type of amino acids is the active site lined with

A

hydrophobic ones

32
Q

why is the active site lined with hydrophobic amino acids

A

they help stabilize substrates through hydrophobic interactions

33
Q

which residues in an enzyme are directly involved in the catalysis (there’s 5)

A

His, Asp, Arg, Glu, and Lys

34
Q

what is the role of His, Asp, Arg, Glu, and Lys in catalysis

A

they function as acid, base, and nucleophiles, and they’re more likely to bind and stabilize transition states and cofactors

35
Q

other than binding energy, how do enzymes promote catalysis

A

once an S is bound to E, properly positioned functional groups in E aid in the cleavage and formation of bonds to form P

36
Q

name the 3 mechanisms for catalysis

A
  1. general acid base catalysis
  2. covalent catalysis
  3. metal ion catalysis
37
Q

describe general acid-base catalysis

A

it’s a proton transfer mediated by weak acids and bases (not water). These acids/bases are amino acid residues within the active site

38
Q

describe covalent catalysis

A

a transient covalent bond is formed between E and S. The side chain of the involved amino acid in the active site is either a nucleophile or an electrophile

39
Q

describe metal ion catalysis

A

metals can either be tightly bound as cofactors or taken up from the solution along with the substrate. Ionic interactions between the metal and S can help orient S for the reaction

40
Q

what are serine proteases

A

a class of enzymes that cleave peptide bonds. They’re characterized by the presence of catalytic serine residues within their active sites

41
Q

give 3 examples of serine proteases

A

chymotrypsin, trypsin, and elastase

42
Q

where are the serine proteases synthesized

A

in the pancreas

43
Q

in what form are the serine proteases stored

A

stored as zymogens

44
Q

list the names of the serine proteases when they’re in their zymogen form

A

chymotrypsinogen, trypsinogen, and proelastase

45
Q

why are the serine proteases stored as zymogens

A

so they’re not degrading protein when they’re not supposed to

46
Q

T or F: trypsin, chymotrypsin, and elastase are homologs

A

true

47
Q

explain how the serine proteases are homologs

A

all 3 have a two-lobed structure with the active site in a cleft between the two domains. The positions of the catalytically active side chains (Ser, His, and Asp) are almost identical

48
Q

describe how chymotrypsin’s active site differs from the others

A

it catalyzes cleavage of peptides on the carbonyl side of uncharged residues with aromatic or bulky hydrophobic side chains

49
Q

describe how trypsin’s active site differs from the others

A

catalyzes cleavage of peptides on the carbonyl side of Arg and Lys

50
Q

describe how elastase’s active site differs from the others

A

catalyzes the cleavage of elastin, a fibrous protein rich in Gly and Ala residues

51
Q

describe the structure of chymotrypsin

A

3 polypeptide chains linked by disulfide bonds. Has a hydrophobic pocket where the bulky amino acid side chain of S will bind

52
Q

what are the 2 reaction phases of chymotrypsin

A

acylation phase

deacylation phase

53
Q

what is the acylation phase

A

peptide bond is cleaved and an ester linkage is formed between the peptide carbonyl carbon and the enzyme (specifically serine)

54
Q

what is the deacylation phase

A

the ester linkage is hydrolyzed and a non acylated enzyme is regenerated

55
Q

what are the 3 catalytic residues of chymotrypsin

A

His57, Asp102, Ser195

56
Q

what do the 3 catalytic residues of chymotrypsin form

A

a hydrogen bonding network called the catalytic triad

57
Q

describe the location of the H bonds within the catalytic triad

A

Asp with His, which is bonded to Ser

58
Q

T or F: Gly is in the catalytic triad

A

false

59
Q

since Gly isn’t in the catalytic triad, what is it’s role

A

it has a backbone N that contributes to an H bond to the tetrahedral intermediate

60
Q

what nucleophile starts the chymotrypsin mechanism

A

the deprotonated oxygen of the serine OH group

61
Q

where will the substrate be cleaved

A

on the carboxyl side of the residue in the middle

62
Q

what is an oxyanion hole

A

an oxyanion is an oxygen anion (O-) so O- will go in the hole

63
Q

describe what happens when a substrate binds to chymotrypsin

A

causes a conf. change, bringing Asp and His closer together, compressing the H bond between them. Now, His REALLY wants a proton, and it will get it from the OH group of Ser. Also, the side chain of the residue adjacent to the pep bond nestled in a hydrophobic pocket

64
Q

what effect does deprotonation have on Ser

A

it makes it a really strong nucleophile

65
Q

see notes for the rest of chymotrypsin mechanism

A
66
Q

why do enzymes have a pH range where their activity is maximal

A

as pH varies, dif. R groups may change their ionization status

67
Q

what pH is chymotrypsin’s peak velocity around

A

8

68
Q

T or F: both kcat and Km will be affected by pH changes

A

true

69
Q

what affect will a protonated His have on kcat

A

it will lower the kcat because when it’s protonated it no longer needs to steal protons from Ser

70
Q

Km is ___ at low pH values

A

low

71
Q

what changes as Km increases as pH increases

A

polypeptide B of chymotrypsin has Ile16 at the N term, and it normally forms a salt bridge with Asp194 when charged. The salt bridge stabilized the active site, so when you protonate you lose the bridge and therefore stabilization (this collapses the hydrophobic pocket)

BIOL 2421 - Cellular Biochem (21 decks)

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