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LDSCI211 (Biochem 1) > Enzymes and Kinetics > Flashcards

Enzymes and Kinetics Flashcards

1
Q

What are enzymes?

A

proteins that increase rate of reaction (accelerate transformation of substrate into product). Most are globular proteins.

Strict specificity by weak interactions by the ES

they are characterized according to reactions they catalyze

“ase”

don’t alter chemistry of reactions

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2
Q

What is a cofactor?

A

non protein compound that is bound to a protein and required for the protein’s activity. It completes the active site of the enzyme by binding to one or more of the amino acid side chains)

metal ions from minerals in food have various functions in catalysis

ex: Fe and Cu are used by oxidases in REDOX reactions

“helper molecules”

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3
Q

what are coenzymes?

A

Acts as carriers of functional groups.

one of the types of organic cofactors (loosely-bound cofactors)

vitamins

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4
Q

What are the 6 enzyme classifications?

A
  1. Oxidoreductase
  2. Transferases
  3. Hydrolases
  4. Lyases
  5. Isomerases
  6. Ligases
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5
Q

What are oxidoreductase?

A

catalyzes REDOX (transfer of e-)

ex: dehydrogenase, oxidase, reductase, catalase

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6
Q

What are transferases

A

catalyzes transfers of groups (ie. methyl, acetyl, phosphate)

ex: methylase, polymerase, protein kinase

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7
Q

What are hydrolases?

A

catalyzes hydrolysis reactions where a molecule is split into two or more smaller molecules by adding h20

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8
Q

What are histone acetyl transferases?

A

enzymes that acetylate conserved lysine amino acids on histone proteins by transfering an acetyl group from acteyl CoA to form E-N-acetyl lysine

linked to transcriptional activation

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9
Q

What are lyases?

A
  1. enzymes that catalyzes the addition of groups across a double bond
    OR
  2. elimination of groups to generate DB
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10
Q

What is Enoyl-CoA hydratase

A

enzyme that hydrates the DB between the second and third carbon on acyl-CoA

essential to metabolizing fatty acids to produce acetyl CoA and energy

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11
Q

What do isomerases do?

A

catalyze atomic rearragements within a molecule.

Ex: Prolyl isomerase is an enzyme that interconverts cis and trans isomers of peptide bonds

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12
Q

What do Ligases do?

A

catalyze the rxn which joins two molecules

uses energy derived from ATP

ex: peptide synthase, DNA ligase

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13
Q

What are the 2 ways a cofactor can bind to the apoenzyme?

A
  1. via a non-covalent bond. Can dissociate from the apoenzyme
  2. interact via covalent bond. Can’t dissociate from enzyme even after denaturation
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14
Q

what are prosthetic groups?

A

tightly bound cofactors

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15
Q

Difference between apoenzyme and holoenzyme? Which has low or high enzyme activity?

A

apoenzyme: inactive enzyme without the cofactor. Has low activity
holoenzyme: complete enzyme with cofactor. Has max activity

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16
Q

What are the 2 classes of cofactors?

A
  1. inorganic: metal ions (ie. Na+, Fe2+)

2. organic: coenzymes or prosthetic groups. Also referred to as vitamins

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17
Q

Use of vitamin C (ascorbic acid)?

A

vital for collagen synthesis

cofactor for prolyl hydrolase and lysyl hydroxylase

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18
Q

Use of folic acid?

A

cell growth and multiplication

required for nucleic acid synthesis

deficiency results in anemia

sources: leafy greens, liver, yeast, wheat germ

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19
Q

Use of Thiamine (B2)?

A

found on membranes of neurons

muscle disease (heart)

used in the breakdown of energy molecules

deficiency causes beriberi

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20
Q

Use of vit K?

A

needed for prothrombin formation, posttranslational modification of proteins, blood coagulation

deficiency leads to increased clotting time

deficiencies are rare

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21
Q

how do enzymes accelerate reactions?

A

they stabilize the unstable transition state intermediate of the rxn.

Reactants are positioned in the reactive conformation in the active site which facilitates the bond making/breaking when substrate becomes product

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22
Q

what is the active site?

A

pocket on enzyme where rxn occurs

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23
Q

what is the substrate?

A

molecule bound to active site. It is acted upon by the enzyme

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24
Q

What is the energy of activation?

A

amount of energy needed to acheive the transition state.

Requires heat input

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25
Q

which is higher? enzyme activation energy or chemical activation energy?

A

chemical activation energy is higher. (because enzymes lower the amount of energy needed)

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26
Q

what does -delta G mean?

A

rxn is favourable and spontaneous.

This does tell how fast the rxn goes

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27
Q

What does every of activation tell you?

A

high EA = slow rxn

low EA = fast rxn (accelerates faster)

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28
Q

what does +delta G mean?

A

rxn is not favourable and not spontaneous

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29
Q

how do you accelerate a rxn?

A

increase thermal energy/ temp or pressure (this increases movement which increases # of collisions)

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30
Q

what are the 5 proteases?

A 
chymotrypsin
trypsin
elastase
thrombin
substilisin
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31
Q

What is the serine protease family?

A

consists of aspartic acid (asp102), histidine (his57) and serine (ser195) residues

participate directly in the cleavage of the peptide bond

“charge transfer relay network”

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32
Q

What is the amino acid preference of cymotrypsin?

A

Phe, Trp, Ile, Try, bulky sidechain

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33
Q

What does delta G = 0 mean?

A

equilibrium (no net change)

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34
Q

what is the rate limiting step

A

highest energy point in rxn.

determines the rxn rate

varies with rxn conditions

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35
Q

what are catalytic pockets on the active site?

A

they are lined with amino acid residues that bind to the substrate

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36
Q

Wht is the amino acid preference of trypsin?

A

lys
arg
long sidechain
positive charge

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37
Q

amino acid preference of elastase?

A

ala
gly
val
small side chain

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38
Q

what is a scissile bond in polypeptides?

A

a covalent chemical bond that can be broken by an enzyme

39
Q

what happens if you change one amino acid in the catalytic triad mechanism?

A

the negative charge will not move down

the length of the side chains would change which changes the specificity pockets

40
Q

what is the importance of the shape of binding pockets?

A

the shape of binding pockets determines the types of substrate that can bind and be cleaved

41
Q

how many aceyl intermediates are formed in the serine proteases?

A

2

42
Q

where does chymotrypsin cleave?

A

cleaves on the carboxy terminal of the amino acid.

Preference for phenylalain, tryptophan, tyrosine, isoleucine

43
Q

where does trypsin cleave?

A

cleaves specifically on carboxy terminal of lysine and arginine ONLY

44
Q

where does elastin cleave?

A

cleaves on carboxy terminal of small side chain amino acid (glycine,alanine,valine)

45
Q

what are the 3 factors that affect rxn rates?

A

temp
ph
enzyme concentration

46
Q

How does temperature affect rxn rate?

A

increasing temp = increase rxn rate

q10 rule

47
Q

What is the Q10 rule?

A

enzyme activity doubles with every 10deg C increase until approx 40deg C when proteins start to denature

48
Q

what is the temperature for max activity of most enzymes?

A

25-37deg C

49
Q

define reaction rate

A

the measure of how fast a product is generated

can look at how fast the substrate is depleted

50
Q

What is the effect of pH changes on rxn rate?

A

extreme ph denatures proteins (the pH optimum reflects the enzymes biological environment)

amino acid required for catalysis are ionized

substrates become ionized and no longer bind to the enzyme

51
Q

how doe enzyme concentration affect rxn rate?

A

rxn rate increase linearly with amount of enzyme (as long as the enzyme concentration is much lower than the substrate concentration)

52
Q

what conditions do you need for molecules to react with each other?

A

need to have correct orientation and enough energy to crash into one another

53
Q

rate = ?

A

rate = k [reactants] = Kf [A] [B] = V0 = totalproductformed/time

54
Q

what is k

A

rate constant

55
Q

what were michaelis and menten’s observations?

A
  1. at constant substrate conc and variable enzyme conc: rxn velocity increases with the enzyme concentration
  2. at constant enzyme concentration and variable substrate concentration: non linear hyperbolic relationship
56
Q

what is the michaelis-menton equation?

A

v0 = (vmax [S]) / (Km + [S])

57
Q

what are the two parts of enzymatic rxns?

A

binding (formation of ES complex) and catalysis (breakdown of ES to products)

58
Q

what are the 2 meanings of Km (michaelis-menton constant)

A
  1. substrate concentration at which 1/2 the active sites are filled

[S]&raquo_space; KM when v0=vmax
[S] = KM when v0=1/2 vmax

  1. dissociation constant for ES when k2»K3

km = k2/k1 = k3

59
Q

what is the km equation in normal circumstances?

A

km=(k3+k2)/K1

60
Q

what does a lower km mean?

A

lower km means tighter substrate binding

km tells affinity between enzyme and substrate

61
Q

what is the km range? (what is considered weak or tight binding?)

A

10^-2 is weak

10^-7 is tight

62
Q

when is vmax reached?

A

when [s] is very high

[E] is very low (enzyme is saturated with substrate)

all enzyme is in ES complex

63
Q

what is v0 when [s]=km?

A

v0=1/2vmax

64
Q

what is v0 when [s]&raquo_space; km?

A

v0=vmax

65
Q

what is the rate determining step?

A

slowest step in the rxn

determines the rate of the overall rxn

overall rate of rxn is proportional to the concentration of [ES]

ES E+P (product formation)

66
Q

what does low [S] mean?

A

most enzyme is uncombined (high [E]).

As [S] increases, equilibrium is pushed towards ES formation

67
Q

what happens as [s] increases?

A

equilibrium is pushed towards ES formation

68
Q

what is the presteady state?

A

when the enzyme is first mixed with substrate and [ES] builds up

E+S –> ES

this is a very short period

69
Q

what is the steady state?

A

when [ES] and [intermediate] remains constant

this is when [ES] is formed and broken down at an equivalent rate

equilibrium: E+S ES

70
Q

what does Vmax describe?

A
  1. the efficiency of catalysis

ES –> E+P

vmax = k3 [E]

  1. turnover rate

Vmax/[E] = K3 = Kcat

71
Q

what does Km describe?

A

how tight the enzyme binds to substrate

affinity between enzyme and substrate

72
Q

when is the steady state assumption valid?

A

when [s]» [E]

73
Q

what does a higher km mean?

A

high km means looser substrate binding

74
Q

what is the turnover rate?

A

of substrate molecules converted to product when [E]«

75
Q

how do you determine km and vmax experimentally?

A
  1. have a fixed amount of enzyme
  2. add into test tubes in increasing substrate conc
  3. incubate
  4. measure product formed (gives the initial velocity
  5. plot velocity vs substrate
76
Q

what is the relationship between v0 and [s]?

A

directly porportional

77
Q

what are the axis’ in the lineweaver-burk graph?

A

1/v0 vs 1/[s]

78
Q

what is the linewear-burk equation?

A

1/vo = (Km/Vmax) (1/[s]) + (1/Vmax)

79
Q

what is the x intercept on the lineweaver-burk graph?

A

x int = intercept on 1/[s] axis = -/Km

80
Q

what is the y-intercept on the lineweaver-burk graph?

A

y int = intercept on 1/Vo axis = 1/Vmax

81
Q

what is the slope on the lineweaver-burk graph?

A

slope = km/vmax

82
Q

what are the four types of enzyme inhibition?

A

competitive
noncompetitive
uncompetitive
irreversible inhibition

83
Q

what are the types of reversible inhibition?

A

competitive noncompetitive uncompetitive

84
Q

whats the difference between reversible and irreversible enzyme inhibition

A

reversible: inhibitor doesnt covalently bond to enzyme
irreversible: inhibitor covalently binds to enzyme

85
Q

what is enzyme inhibition

A

interference with the catalysis

86
Q

describe competitive inhibition?

A

inhibitor competes with substrate for the enzyme’s active site.

the inhibitor is structurally similar to the substrate and occupies the active site. This prevents the binding of substrate to the enzyme

EI complex is formed. No catalysis occurs

87
Q

In competitive inhibition, does KM and Vmax increase, decrease or stay the same?

A

Km increases

Vmax is the same

88
Q

In noncompetitive inhibition, does KM and Vmax increase, decrease or stay the same?

A

Km is the same

Vmax decreases

89
Q

In uncompetitive inhibition, does KM and Vmax increase, decrease or stay the same?

A

Km and Vmax decreases

90
Q

What is non competitive inhibition?

A

the inhibitor binds at a different site from the substrate active site (binds to E or ES)

K3 doesn’t occur

91
Q

What is uncompetitive inhibition?

A

inhibitor binds at a site distinc from substrate active site (binds only to ES)

doesn’t bind to E

works best when [S] is high

92
Q

What is irreversible inhibition?

A

inhibitor binds covalently or noncovalently to the enzyme.

The enzyme is permanently inactived (ie. confirmation is changed)

E + I –> EI (can’t go reverse direction)

93
Q

when does uncompetitive inhibition work best?

A

when [s] is high

LDSCI211 (Biochem 1) (8 decks)

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