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Biochemistry, genetics, and metabolism > Enzymes > Flashcards

Enzymes Flashcards

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Biology 101 flashcards
1
Q

enzymes definition

A

protein catalysts (usually) that increase the rate of reactions without being changed in the overall process

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2
Q

Roles of enzymes in human biochemistry

A

convert substrates into products and channel them into useful pathways, and so direct all metabolic events

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3
Q

How do enzymes

A

increase the rate at which reactions occur, but do not invent new reactions

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4
Q

is life possible without enzymes?

A

no

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5
Q

Nomenclature

A

-ase at end of substrate name or description of the action performed (lactate dehydrogenase)
Some enzymes retain original trivial name.

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6
Q

What are the 6 major classes of enzymes

A
  1. oxidoreductases
  2. transferases
  3. hydrolases
  4. lyases
  5. isomerases
  6. ligases
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7
Q

oxidoreductases

A

catalyze oxidation-reduction reactions, such as

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8
Q

transferases

A

catalyze transfer of C-, N-, P- containing groups, such as

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9
Q

Hydrolases

A

catalyze cleavage of bonds by addition of water, such as

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10
Q

Lyases

A

catalyze cleavage of C-C, C-S and certain C-N bonds. opposite function as ligases

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11
Q

isomerases

A

catalyze racemization of optical or geometric isomers

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12
Q

Ligases

A

Catalyze formation of bonds between carbon and O, S, N coupled to hydrolysis of high energy phosphates. opposite function of lyases

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13
Q

systemic name

A

divided into the 6 major classes of enzymes, includes the names of all the substrates in the reaction catalyzed + ase. Each enzyme is also assigned a unique number

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14
Q

Synthase

A

No ATP required

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15
Q

Synthetase

A

requires ATP

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16
Q

Phosphatase

A

Uses H2O to remove phosphoryl group

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17
Q

Phosphorylase

A

uses Pi to break a bond and generate phosphorylated product

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18
Q

oxidase

A

uses O2 as acceptor without incorporating it into a reaction

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19
Q

Oxygenase

A

one or both oxygen atoms are incorporated

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20
Q

Dehydrogenase

A

electron acceptor in a redox reaction NAD+/FAD+

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21
Q

Arrows used in reactions

A

indicate the direction of the reaction under the normal physiological range of conditions

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22
Q

If the arrow goes in both directions

A

can catalyze either reaction

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23
Q

if the arrow goes only in one direction

A

it will only catalyze the reaction in the direction indicated by the arrow. Does not mean the opposite reaction cannot occur, just not under that enzyme

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24
Q

Enzyme structure

A

active site, allosteric site

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25
Q

catalytic properties of enzymes

A

efficiency, specificity

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26
Q

some other enzyme properties

A
  1. requirements for non-protein molecule
  2. regulation
  3. subcellular localization
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27
Q

active site

A
  • special ‘pocket’ or ‘cleft’ that binds the substrate (3D shape)
  • formed by folding of the protein molecule that allows specific amino acid side chains to participate in S binding and catalysis
  • Binding of S produces ES complex which induces conformational change in the enzyme that facilitates catalysis (induced model fit)
  • ES is converted into an EP complex, this complex dissociates to enzyme and product
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28
Q

allosteric site

A

any other part of the enzyme molecule that is different from the active site. Binds different regulatory molecules

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29
Q

Efficiency

A
  • 10^3-10^14 faster than uncatalyzed reactions

- turnover number (Kcat) is the number of substrate molecules converted to product per enzyme molecule per second

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30
Q

specificity

A
  • highly specific
  • only one or a few substrates
  • only one type of chemical reaction
  • the set of enzymes present in a cell determines which reactions will occur in that cell
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31
Q

coenzymes

A

organic molecules that are required by certain enzymes to carry out catalysis
vitamin derivatives
NAD+, FAD, NADP+, CoQ, CoA

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32
Q

Cofactors

A

inorganic substances that are required for, or increase the rate of, catalysis
Usually ions
Zn2+, Mg2+, Fe3+, Fe2+

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33
Q

holoenzyme

A

enzyme + nonprotein component = active

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34
Q

apoenzyme

A

enzyme without nonprotein component=inactive

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35
Q

regulation by inhibitors and activators

A

a negative feedback mechanism, the amount of the end product produced is regulated by its own concentration

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36
Q

post translational modifications

A

regulation through covalent modulation of the enzyme molecule such as phosphorlyation, myristoylation, and glycosylation

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37
Q

enzyme protein production

A

transcription and translation of enzyme genes

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38
Q

regulation through specific local environment

A

high pH or temp to low pH or temp

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39
Q

enzyme compartmentalization

A

different metabolic pathways occurring in different cellular compartments

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40
Q

Advantages of the enzyme compartmentalization

A

isolates substrates and products from competing reactions

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41
Q

How enzymes work

A
  1. energy changes occurring during the reaction

2. chemistry of the active site

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42
Q

Free Energy (Gibbs free energy, G)

A

quantitative measure of the energy transfers between chemical reactions

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43
Q

energy barrier

A

energy difference between that of reactants (A) and high energy intermediate (T*) that occurs during formation of a product (B)

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44
Q

Free energy of activation

A

the difference in free energy between the reactants and T*

45
Q

How do enzymes work

A

lowering the free energy of activation without affecting the energies of the reactants and products

46
Q

chemistry of active site

A

active site is a dynamic molecular machinery.

the enzyme is returned to its unaltered state before the release of the product

47
Q

stabilization of the transition state

A
  • creates a microenvironment in which the bonds in the intermediates are not like the ones in the substrates and products
  • this greatly increases the concentration of the reactive intermediates that can be converted to products
48
Q

provide chemical groups that

A
  • participate in reactions with the substrate

- enhance the probability of transition state formation

49
Q

factors affecting reaction velocity

A
  1. substrate concentration
  2. temperature
  3. pH
50
Q

rate of velocity (v)

A

number of substrate molecules converted to product per unit time (micromole of product formed per minute)

51
Q

Maximal velocity (Vmax)

A

the rate of an enzyme catalyzed reaction increases with substrate concentration until Vmax is reached.

it represents the saturation of all available binding sites on enzyme molecules in the reaction

52
Q

hyperbolic curve

A

most enzymes show michaelis-menten kinetic when initial reaction velocity (Vo) is plotted against substrate concentration ([S]), which results in a hyperbolic curve.

53
Q

sigmoidal curve

A

some enzymes that are allosterically regulated or demonstrate cooperativity

54
Q

Increase of V with temp

A

reaction velocity increases with increasing temp until a peak is reached. An increase in temp would increase the number of molecules that have the energy to overcome the energy of activation

55
Q

decrease of V with higher temperature

A

further increase in temp beyond the peak velocity results in a decrease in velocity usually as a result of denaturation of the enzyme

56
Q

what is the temp optimum for humans

A

37 C

57
Q

what temp does denaturation of enzymes being in humans?

A

40 C, why high fevers are potentially life threatening

58
Q

Effect of pH on the ionization of the active site

A

E and S usually have to have certain groups in a protonated or un-protonated form to interact optimally for catalytic activity. Any change in pH may influence this state resulting in decreased reaction rate

59
Q

effect of pH on enzyme integrity

A

protein structure itself require specific ionic interactions that are influenced by the pH, hence, higher or lower pH can denature the enzyme

60
Q

variable pH optimum

A

the pH optimum is specific characteristic of each enzyme and often reflects the pH of the environment in which the enzyme functions in the body.
digestive enzyme

61
Q

reaction model for michaelis-menten

A
  • a simple model that accounts for most of the features of enzyme-catalyzed reactions
  • E reversibly combines with its S to form an ES complex that subsequently yields the P and regenerates the free E
62
Q

Michaelis-menten equation

A

describes how reaction reaction velocity varies with substrate concentration at a given concentration of enzyme
vo=(Vmax[S])/(Km + [S])

63
Q

Assumptions about the MM equation

A
  • the concentration of S is much greater than the concentration of E
  • [ES] does not change with time
  • the initial velocity (vo) is used in the analyses
64
Q

Km

A
  • characteristic of an enzyme and its particular substrate and reflects the affinity of the enzyme for that particular substrate
  • defined as the amount of substrate needed to half maximal velocity (1/2 Vmax)
65
Q

small Km

A

high affinity, as it takes a low concentration of substrate to reach 1/2Vmax

66
Q

high Km

A

low affinity, as it takes a high cxn of substrate to reach 1/2 Vmax

67
Q

relationship of velocity to [E]

A

reaction rate is directly proprtional to [E] at all cxns of [S]

68
Q

When [S] is much lower than Km

A

velocity is appx proportional to the substrate cxn, and the rate is said to be first order with respect to the substrate

69
Q

when [S] is much greater than Km

A

the velocity is appx constant and equal to Vmax, and independent od [S], and the rate is said to be zero order with respect to the substrate

70
Q

lineweaver-burk plot

A
  • uses 1/vo vs 1/[S], which results in a straight line, which allows us to determine both the Km and the Vmax
  • intercept on x-axis is equal to -1/km
  • the intercept on the Y-axis is equal to 1/Vmax
  • very useful for determining the mechanism of action of enzyme inhibitors
71
Q

If we increase Km or Vmax on Lineweaver Burk plot…

A

they will be closer to zero

72
Q

if we decrease km or Vmax on a lineweaver burk plot…

A

they will be further from zero

73
Q

inhibitors

A

any substance that can diminish the velocity of an enzyme-catalyzed reaction

74
Q

Irreversible inhibitor

A

bind to E through cavalent bonds anf the only eay to recover E-activity is to synthesizea new molecule

75
Q

suicide inhibitor-E

A

converts I into a reactive form in its active site

76
Q

reversible inhibitors

A

bind through non-caovalent bonds, which allow for recovery of E-activity

77
Q

competitive reversible inhibitor

A

I competes with S for the active site of the E

78
Q

noncompetitive reversible inhibitors

A

I binds to a different (allosteric) site of the E molecule
Binds reversibly to a different site on the enzyme than the substrate. It may bind to either the free enzyme of the ES complex

79
Q

Competetive inhibition on Vmax

A

the effect of a competitive I can be overcome by high [S], therefore the same Vmax can be obtained, no effect on Vmax

80
Q

competitive inhibition effect on Km

A

a competitive I increases the apparent Km for a given substrate and more substrate is needed to achieve 1/2 Vmax, therefore the apparent affinity is lower. Km is increased

81
Q

HMG CoA-reductase

A

the rate-limiting enzyme in cholesterol biosynthesis

82
Q

statin drugs are

A

structural analogs of HMG-CoA reductase substrate that: compete for the active site of the enzyme. By inhibiting de novo synthesis of cholesterol, they help lower plasma cholesterol levels

83
Q

noncompetitive inhibition effect on Vmax

A

effect cannot be overcome by increasing [S], therefore they lower the apparent Vmax of the reaction. Vmax is decreased

84
Q

noncompetitive inhibition effect on Km

A

do not interfere with binding of the substrate to the enzyme (affinity). No effect on Km

85
Q

Noncompetitive inhibition of purine degradation

A

noncompetitive inhibitor which reduces the production of uric acid, used for treatment of hyperuricemia and related medical conditions

86
Q

what regulates enzymes

A

effectors (modifiers) that bind to the sites other than the active site not he enzyme non-cavalently

87
Q

What can effectors do?

A
  • alter the affinity of the enzyme for its substrate (affect Km)
  • alter the maximal catalytic activity (affect Vmax)
  • alter both
  • be negative
  • be positive
88
Q

How does an effector altering the affinity of the enzyme for its substrate have an affect?

A

it has an affect on Km

89
Q

What does an effector altering the maximal catalytic activity do?

A

affect Vmax

90
Q

negative effector

A

inhibit enzyme activity

decrease Vmax and/or increase Km

91
Q

positive effector

A

increase enzyme activity

increase Vmax and/or decrease Km

92
Q

Homotropic effector

A

substrate itself serves as an effector

usually +, so enhances the catalytic properties of the active site, also called “cooperativity effect

93
Q

What kind of curve does cooperatively show?

A

sigmoidal, does not follow MM kinetics

94
Q

What kind of curve would you see for a homotropic effector?

A

sigmoidal

95
Q

heterotropic effectors

A

effector is different from the substrate molecule

feed-back inhibition

96
Q

feed back inhibition

A

an end-product of a metabolic pathway inhibits upstream step

97
Q

phosphofructokinase-1

A

rate limiting enzyme in glycolysis
allosterically inhibited by high levels of substrate
this inhibition redirects glucose towards the synthesis of glycogen

98
Q

What is the most commonly encountered type of enzyme regulation by covalent modification?

A

phosphorylation/dephosphorylation

99
Q

what AA can be phos/dephos?

A

serine, threonine, tyrosine

100
Q

What kind of enzymes phos/dephos

A

protein kinases - phosphorylate, use ATP as phosphate donor

Protein phosphatases-dephosphorylate or remove a phosphate group

101
Q

the amount of enzyme present can be controlled by altering the rate of

A

synthesis (altering gene expression-increase/decrease)

degradation (targeting for proteolysis

102
Q

timing: gene expression regulation

A

takes from hours to days to see an effect on reaction rates (effects of steroid drugs are not immediate)

103
Q

timing: covalent changes

A

immediate to minutes

104
Q

timing: allosteric changes

A

immediate

105
Q

plasma

A

physiological fluid part of the blood without the cells (contains coagulating factors)

106
Q

serum

A

plasma without the coagulating facts (prepared from blood in laboratory)

107
Q

actively secreted plasma enzymes

A

have certain function in plasma
small group
do not play role in diagnosis

108
Q

plasma enzymes not actively secreted

A 
function intracellularly not in plasma
released from cell lysis during normal turnover
fairly constant
increase=tissue damage
109
Q

alanine aminotransferase

A

released from damaged liver cells, it is part of the liver function

Biochemistry, genetics, and metabolism (11 decks)

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