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MCAT Biochem > Biochem #2 > Flashcards

Biochem #2 Flashcards

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MCAT flashcards
1
Q

enzymes

A

a substance produced by a living organism which acts as a catalyst to bring about a specific biochemical reaction

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2
Q

catalyst

A
  • do not impact the thermodynamics of a biological reaction (the ΔHrxn and equilibrium position do not change) but help the reaction proceed at a faster rate
  • The enzyme is also not changed during the course of a reaction.
  • specific enzymes are used for specific reactions
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3
Q

describe the key points of enzymes

A

 Lower the activation energy
 Increase the rate of the reaction
 Do not alter the equilibrium constant
 Are not change or consumed in the reaction (which means that they will appear in both the reactants and products)
 Are pH- and temperature-sensitive, with optimal activity at specific pH ranges and temperatures.
 Do not affect the overall ΔG of a reaction.
 Are specific for a particular reaction or class of reactions

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4
Q

enzyme specificity

A

a given enzyme will only catalyze a single reaction or class of reactions with specific substrates (molecules upon which an enzyme acts)

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5
Q

oxidoreductase

A

Catalyze oxidation-reduction reactions, the transfer of electrons between biological molecules.
• Often have a cofactor that acts as an electron carrier (NAD+ or NADP+)
• Reductant: electron donor
• Oxidant: electron acceptor
• Trends:
o Enzymes with dehydrogenase or reductase in their names
o Enzymes in which oxygen is the final electron acceptor

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6
Q

transferase

A

: Catalyze the movement of a functional group from one molecule to another.
• Kinases: catalyze the transfer of a phosphate group, generally from ATP, to another molecule.

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7
Q

hydrolase

A

Catalyze the breakdown of a compound into two molecules using the addition of water.
• Commonly named for their substrate

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8
Q

lyase

A

catalyze the cleavage of a single molecule into two products. They do not require water as a substrate and do not act as oxidoreductases.

they can also catalyze the reverse reaction and it is common for them to be referred to as synthases

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9
Q

isomerase

A

catalyze the rearrangement of bonds within a molecule
• Stereoisomers and constitutional isomers.
• Some can also be classified as oxidoreductases, transferases, or lyases.

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10
Q

ligase

A

catalyze addition or synthesis reactions, generally between large similar molecules, and often require ATP.
• Lyases are for smaller molecule reactions
• Most often coupled with DNA synthesis and repair.

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11
Q

synthase

A

when catalyzing the reverse reaction and making two molecules into a single molecule.

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12
Q

thermodynamics of a reaction

A

: relates to the relative energy states of a reaction in terms of its products and reactants.

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13
Q

endergonic

A

one that requires energy input (ΔG>0)

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14
Q

exergonic

A

: one in which energy is given off (ΔG<0)  spontaneous

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15
Q

activation energy

A

the minimum quantity of energy which the reacting species must possess in order to undergo a specified reaction
• Energy required for a substrate to reach the transition state in a reaction

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16
Q

substrate

A

molecule on which an enzyme acts

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17
Q

enzyme-substrate complex

A

the physical interaction between the substrate and enzyme

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18
Q

active site

A

the location within the enzyme where the substrate is held during the chemical reaction.
o Hydrogen bonding, ionic interactions, and transient covalent binds within the active site stabilize the interaction.

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19
Q

lock and key theory

A

the enzyme’s active site (lock) is already in the appropriate conformation for the substrate (key) to bind.
o Like hand in glove
o No alteration of the tertiary or quaternary structure is necessary upon binding.

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20
Q

induce fit model

A

the substrate induces a change in shape of the enzyme, which changes the shape of the substrate as well. When the substrate is present and ready to interact, the induced form (transition state) is more comfortable for both
o Shape of active site become complementary when the substrate begins to bind.
o More widely accepted

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21
Q

cofactor

A

inorganic molecules or metal ions, ingested as dietary minerals

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22
Q

coenzymes

A

small organic groups, the vast majority of which are vitamins or derivatives of vitamins such as NAD+, FAD and coenzyme A (nonprotein factor)

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23
Q

apoenzyme vs. holoenzyme

A

apoenzyme: enzymes without their cofactors
Holoenzymes: enzymes with their cofactors

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24
Q

saturation

A

Saturation: a point in the reaction in which it will not go any faster no matter how much more substrate is added. All of the active sites of the enzyme are full.
o At this rate, the enzyme is working at a maximum velocity Vmax
 Only way to increase Vmax is to increase enzyme concentration,

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25
Q

As the amount of substrate increase, the enzyme is able to increase its rate of reaction until it reaches a maximum enzymatic reaction rate (___); once it is reached, adding more substrate will not increase the reaction rate.

A

vmax

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26
Q

what is held constant for michaelis-menten kinetics

A

enzyme concentration

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27
Q

Km

A

Km (Michaelis Constant): the substrate concentration at which half of the enzyme’s active sites are full.
 Intrinsic property
 The higher the KM, the lower the binding affinity of the enzyme for the substrate.

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28
Q

kcat

A

measures the # of substrate molecules converted to product, per enzyme molecule, per second. Larger the Kcat the greater the turnover rate

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29
Q

catalytic efficiency

A

how efficient an enzyme is. The larger the catalytic efficiency, the more efficient the enzyme (Kcat/Km)

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30
Q

lineweaver-burk plot

A

double reciprocal plot of the MM equation
o Actual data in the upper right quadrant
o Y intercept: 1/vmax
o X intercept: -1/km
o Slope: km/vmax

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31
Q

cooperativity

A

o Certain enzymes show sigmoidal rather than hyperbola MM plot  when enzymes have multiple subunits and multiple active sites.
o Subunits and enzymes are in one of two states:
 T state: low affinition tense state
 R state: high affinity relaxed state
 Binding of the substrate encourages the transition of other enzyme subunits from the TR, increase likelihood of substrate binding by other subunits.
o Often regulatory enzymes in pathways.
o Subject to activation and inhibition, both competitively and through allosteric sites.

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32
Q

describe Hill’s coefficient

A

quantifies cooperativity, indicates the nature of binding of the molecule
 >1: positively cooperative binding is occurring; one ligand is bound the affinity of the enzyme for further ligands increases
 <1: negatively cooperative binding is occurring; one ligand is bound the affinity of the enzyme for further ligands decreases
 =1: enzyme does not cooperatively bind

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33
Q

what is body temperature

A

37 C, 98.6 F

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34
Q

describe the effects of temperature on enzyme activity

A

o With increasing temperature, enzyme velocity increases until lit hits a certain optimum temperature but then it begins to decrease
o Some proteins can regain their function after denaturing but some cannot

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35
Q

describe the effects of pH on enzyme activity

A

o effects ionization of the active site and also can lead to denaturation of the protein
o certain enzymes function better in certain pH. Ex: stomach, pepsin, pH 2

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36
Q

describe the effects of salinity on enzyme activity

A

o In vitro, changing salt concentration can affect the protein

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37
Q

feedback regulation

A

enzymes are subject to regulation by products further down a given metabolic pathway.

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38
Q

feedback inhibition

A

helps maintain homeostasis, once we have enough of a product, we want to turn off the pathway that creates the product.

39
Q

what are the 4 types of reversible inhibition of feedback regulation

A

competitive, noncompetitive, mixed, uncompetitive

40
Q

competitive inhibition

A

occupancy of the enzyme active site
o Can be overcome by adding more substrate
o Does not affect Vmax (can add a lot more substrate than inhibitor so you can still hit the Vmax value), does affect Km (have to add more substrate to get to half saturated point)

41
Q

vmax

A

maximum velocity that an enzyme is working at

42
Q

noncompetitive inhibition

A

bind to an allosteric site instead of the active site, which induces a change in enzyme confirmation.
o Allosteric site: non catalytic part of the enzyme that binds regulators.
o Bind equally well to the enzyme and enzyme-substrate complex (unlike mixed)
o No effect to Km (active enzyme copies have same affinity), but does effect Vmax (less enzyme available to react)
Once the enzyme active site is altered via the binding of the noncompetitive inhibitor, no matter how much substrate is added it will not be conducive to forming the enzyme-substrate complex.

43
Q

allosteric site

A

non catalytic part of the enzyme that binds regulators.

44
Q

mixed inhibition

A

inhibitor can bind to either the enzyme or ES complex but has different affinity for each
o Bind at allosteric site
o Km
 If binds to E: Km increases
 If binds to ES: Km decreases
o Vmax decreases
o LB plot: curves intersect at a point that is not an intercept

45
Q

irreversible inhibition

A

 Irreversible Inhibition: the active site is made unavailable for a prolonged period of time, or the enzyme is permanently altered.
• Not easily overcome or reversed, must make a new enzyme
• Prime drug mechanism

46
Q

feedforward regulation

A

enzymes are regulated by intermediates that precede the enzyme in the pathway

Feed forward activation is rare in metabolism. It is a term used to describe a metabolic product (such as F1,6BP above) that ACTIVATES an enzyme that catalyzes a reaction further ahead of it in a metabolic pathway

47
Q

allosteric enzymes

A

alternate between an active and inactive form

48
Q

allosteric activators or inhibitors

A

molecules that bind to the allosteric site, binding causes a conformational shift in the protein.

49
Q

phosphorylation and dephosphorylation can ____

A

can activate or deactivate an enzyme

50
Q

glycosylation

A

covalent attachment of sugar moieties/carbohydrate, can tag an enzyme for transport within the cell or modify the protein for activity

51
Q

zymogen

A

contain a catalytic (active) domain and regulatory domain. The regulatory domain must be removed or altered to expose the active site
o Most have suffix -ogen
o Ex: caspases enzymes that are involved in apoptosis

52
Q

what is a substrate?

A

it is a molecule on which an enzyme acts

53
Q

what is the name of the electron donor in an oxidoreductase reaction?

A

reductant

54
Q

what is the name of the electron acceptor in an oxidoreductase reaction?

A

oxidant

55
Q

dehydrogenase

A

type of oxidoreductase enzyme that removes electrons and oxidizes a molecule

56
Q

reductase

A

type of oxidoreductase that catalyzes a reduction reaction

57
Q

kinase

A

type of transferase. Transfers a phosphate group from one molecule to another (adds the phosphate group)

58
Q

what are the names of some common hydrolases?

A

peptidase, nuclease, lipase (break down proteins, nucleic acids, and lipids via the addition of water)

59
Q

lyases vs. ligases

A

lyases are usually for synthesis reactions with smaller molecules

60
Q

enzyme affect the _____ a reaction gets to equilibrium but not the actual _____ itself

A

rate

equilibrium state

61
Q

what is the consequence of enzymes not being consumed by the reaction?

A

they can be re-used and one enzyme can act in the conversion of many substrates.

62
Q

what are biochemical ways that enzymes increase the rate of a reaction?

A

they provide a stable micorenvironment for the reaction: pH, stabilize transition state, bring reactive groups nearer to one another.

63
Q

Holoenzymes

A

enzymes with their cofactors

64
Q

apoenzyme

A

enzymes without their cofactors

65
Q

prosthetic groups in relation to enzymes are _____

A

cofactors or coenzymes that are necessary for enzyme function

66
Q

Name of vitamin: B1

A

thiamine

67
Q

Name of vitamin: B2

A

riboflavin

68
Q

Name of vitamin: B3

A

niacin

69
Q

Name of vitamin: B5

A

pantothenic acid

70
Q

Name of vitamin: B6

A

pyridoxal phosphate

71
Q

Name of vitamin: B7

A

biotin

72
Q

Name of vitamin: B9

A

folic acid

73
Q

Name of vitamin: B12

A

cyanocobalamin

74
Q

what are the water soluble and fat soluble vitamins?

A

water soluble: b complex vitamins and ascorbic acid (vitamin C)
fat soluble: ADEK

75
Q

in the induced fit model, the ______ of the enzyme is modified for it to function properly

A

tertiary and quaternary structure

76
Q

in the michaelis-menten equation, ___ is held constant

A

enzyme concentration

77
Q

the enzyme with the higher Km has the ___ affinity for its substrate because ____

A

lower

it requires a higher substrate concentration to be half saturated

78
Q

the Km value is an ____ property of the enzyme-substrate system

A

intrinsic

it cannot be changed by changing the substrate or enzyme concentration

79
Q

what is are the units of vmax?

A

moles of enzyme per second

80
Q

what are the units for Kcat?

A

substrate molecules converted per second (s^-1)

81
Q

in cooperativity, what is the T state and what is the R state and how is the curve shifted?

A

T: tense state, low affinity
R: relaxed state, high affinity

82
Q

binding of the substrate encourages the transition of other subunits from the ___ state to the ___ state

A

T state to the R state

83
Q

enzyme-catalyzed reactions tend to ___ in velocity every _____ degrees C until the ____ is reached

A

double
10
optimum temperature

84
Q

what is the ideal temperature for enzymes in the human body?

A

37 degrees C, 98.8 F

85
Q

what is the optimum pH for humans blood?

A

7.4

86
Q

the pepsin enzyme in the stomach works best at a pH of ____ and pancreatic enzymes work best at a pH of ____

A

2

8.5

87
Q

how do temperature, pH, and salinity mess up enzymes when not normal?

A

temperature: denature
pH: denature and messes with ionization of active site
salinity: messes with tertiary and quaternary structure

88
Q

how do noncompetitive and mixed inhibitors differ?

A

noncompetitive inhibitors bind equally well to the enzyme and the enzyme-substrate complex.

89
Q

describe the Km for mixed inhibition?

A

if binds to enzyme preferentially, Km increases because less affinity
if binds to enzyme-substrate complex preferentially, Km decreases because bound enzyme-substrate is stuck so it looks like affinity has increased.

90
Q

why can’t uncompetitive inhibitors bind until the enzyme-substrate complex forms?

A

they only bind to this complex which slightly changes the confirmation of the enzyme (allowing the inhibitor to bind)

91
Q

what are two types of enzyme covalent modification?

A

phosphorylation (adding a phosphate group) and glycosylation (adding a sugar moiety/carbohydrate)

92
Q

what can glycosylation do?

A

tag an enzyme for transport within a cell or modify protein activity and selectivity.

93
Q

most zymogens have the suffix _____

A

-ogen

94
Q

what are examples of transient or covalent enzyme modifictions?

A

transient: allosteric inhibitors or activators
covalent: glycosylation or phosphorylation

MCAT Biochem (12 decks)

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