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Biochem > Exam 3 > Flashcards

Exam 3 Flashcards

1
Q

Catalysts of biochemical reactions

A

Enzymes

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2
Q

Enzymes are _________ of biochemical reactions.

A

catalysts

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3
Q

What is a catalyst’s function

A

Increases the rate or velocity of a chemical reaction without being changed following the reaction

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4
Q

Most biological catalysts are __________

A

Proteins

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5
Q

Only exception currently known for biological catalysts

A

certain types of RNA molecules that can function as enzymes (ribozymes)

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6
Q

Enzyme concentration in cells

A

Very Low

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7
Q

Molecules that modulate enzyme activity

A

Effectors

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8
Q

Number of known enzymes

A

Over 1 million

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9
Q

Different species of organisms produce different __________ ___________ of the same enzymes

A

structural variants

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10
Q

Effectors can be either …

A

Activators or Inhibitors

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11
Q

Each enzyme has a

A

Specificity for a very narrow range of chemically similar substrates

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12
Q

Substrates bind to the enzyme at a region of the enzyme known as the

A

Active Site

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13
Q

The active site occupies

A

less than 5% of the surface area of the enzyme

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14
Q

________________ in the active site determines the type of substrate molecule that can bind and react there

A

The arrangement type of amino acid R-groups

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15
Q

There are usually about __ such R-groups per active site

A

5

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16
Q

Non-covalently bound _______ or covalently bound ____________ are non-protein molecules associated with enzymes at or near the active site

A

Cofactors (ex. Sugars, Lipids, Nucleic Acids)

Prosthetic Groups

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17
Q

Function of cofactors or prosthetic groups

A

Help to determine substrate specificity along with the enzyme’s active site

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18
Q

Enzymes are named according to…

A

the type of reaction they catalyze

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19
Q

Enzyme name =

A

4 integer EC number and a name

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20
Q

EC

A

Enzyme Commission: a group of expert enzymologists from all over the world who come up with the rules of nomenclature

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21
Q

1st integer of the EC number

A

indicates to which of the 6 major enzyme classes and enzyme belongs

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22
Q

2nd integer of the EC number

A

indicates the type of bond acted on

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23
Q

3rd integer of the EC number

A

indicates a subclassification of the bond type or group transferred

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24
Q

4th integer of the EC number

A

serial number

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25
Q

Enzyme that catalyzes the phosphorylation of D-glucose

A

Hexokinase

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26
Q

Why do we have EC numbers?

A

So that when you publish about a specific enzyme, people can use the exact enzyme

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27
Q

Catalyzes oxidation-reduction reactions

A

Oxidoreductase

A Hydrogen or electron donor is one of the substrates

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28
Q

Group Transfer A–X + B–> A + X–B

A

Transferase

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29
Q

Hydrolytic Cleavage of C–C, C–N, C–O, and others

A

Hydrolase

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30
Q

Non-hydrolytic cleavage of C–C, C–N, C–O, and others

A

Lyase

Results in a double bond or the addition to a double bond

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31
Q

Molecular geometrical rearrangement

Transfer of groups within a molecule to yield isomeric forms

A

Isomerase

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32
Q

Ligation (joining) of 2 molecules with accompanying hydrolysis of a high-energy bond (Condensation coupled to ATP hydrolysis)

A

Ligase

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33
Q

Activation energy is

A

the energy required for a reaction to proceed

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34
Q

Energy needed to drive a reaction

A

Energy Barrier

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35
Q

Binding the enzyme to the substrate ______ the activation energy

A

Lowers

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36
Q

If a reaction requires less energy, it is __________ to happen

A

more likely

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37
Q

When the enzyme binds to its substrate

A

Transition state

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38
Q

What is transformed into the transition state?

A

The substrate

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39
Q

Less energy is required for the reaction to proceed when

A

the substrate is in the transition state

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40
Q

The rate of a chemical reaction depends on

A

how efficiently the reactants can reach a transition state

If it does it easily we will have a high rate enhancement

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41
Q

The transition state is an ____________ ___________ arrangement of atoms in which bonds are being formed or broken

A

Unstable energized

Electrons are shifting when bonds are being formed and broken

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42
Q

The transition state is NOT a

A

reaction intermediate
Rection intermediates are stable structures formed as a result of a reaction series, so when it forms it is a stable molecule

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43
Q

Reactants are normally in the _______ ________ and have ________ potential energy for reacting

A

Ground State
Little
(Energy must be added to allow a reaction to occur)

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44
Q

The energy required to reach the transition state from the ground state is called the

A

Energy of Activation, or Activation Barrier, or Energy Barrier, or Activation Energy

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45
Q

Enzymes _______ the activation energy required to reach the transition state

A

Lower

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46
Q

The reaction is more likely to occur, thus the reaction rate is _______ if you lower the energy

A

increased

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47
Q

Circumstantial evidence comes from the use of molecules known as

A

Transition State Analogs

48
Q

Stable structures that resemble the postulated (what we think) transition state structure

A

Transition State Analogs

49
Q

Transition state analogs are _____ inhibitor enzymes

A

Powerful

50
Q

If an enzyme has an analog stuck in the active site, the enzyme is now permanently bound to the analog and inactive, which makes the analogs such

A

Powerful Inhibitors

51
Q

If we find a molecule that’s an analog of our transition state and we add that analog to our substrate the enzyme is going to…

A

bind to that transition state analog
Structurally the enzyme believes the analog is substrate. So now nothing happens because the analog is stable (there’s nothing left to happen) so the enzyme does not work.

52
Q

The enzyme doesn’t release the substrate until

A

the product is formed (NOT when the transition state hits)

53
Q

How to test to see if you have the correct transition state?

A

Look for molecules that are stable and are similar to the proposed transition state

54
Q

Enzymes bind to analog and are no longer able to bind which…

A

inhibits enzyme activity

55
Q

Mechanisms by which enzymes increase reaction rates

A

Facilitation of proximity, Covalent catalyst, Acid-base catalysis, and Molecular Distortion/Strain

56
Q

Also known as the Propinquity Effect

A

Facilitation of Proximity

57
Q

Reaction rate between 2 molecules is enhanced when the enzyme removes them from dilute solution and holds them in close proximity to each other in the enzyme active site

A

Facilitation of Proximity

This raises the effective concetration of reactants

58
Q

An enzyme can increase the reaction between two molecules when…

A

an enzyme binds to them and takes them out of solution and holds them together
(Facilitation of Proximity)

59
Q

A means to artificially raise reactive concentration so the reaction is faster

A

Facilitation of Proximity

60
Q

Amino acids in the active site with nucleophilic R-groups attack electrophilic parts of the substrate forming covalent bonds between the enzyme and substrate

A

Covalent Catalyst

61
Q

Nucleophilic groups include

A

COO- NH2, Aromatic OH, Histidyl groups, R-OH, S-

62
Q

This mechanism is particularly evident in transferases (enzymes that most often use this mechanism)

A

Covalent Catalyst

63
Q

Transfer of a proton in the transition state

A

Acid-Base Catalysis

64
Q

Rate enhancement is only about a factor of 100 in this mechanism

A

Acid-Base Catalysis

65
Q

Clu, His, Asp, Lys, Tyr, and Cys act as acid catalysts when they are protinated during this mechanism

A

Acid-Base Catalysis

When unprotinated the same amino acids can act as base catalysts

66
Q

This mechanism is dependent on pKa of the R-groups that are in the active site and on pH optimum of the enzyme

A

Acid-Base Catalysis

67
Q

Strain is induced in the bond system of the reactants and the release of the strain as the transition state converts to products provides the rate enhancement

A

Molecular Distortion/Strain

When the substrate is removed and converts into products

68
Q

When the enzyme binds to the active site, strain is placed on the reactant

A

Molecular Distortion/Strain

69
Q

Substrate in highly energized state, stressed state, enzyme lets go and that releases the energy in the transition state which helps push the substrate into product in this mechanism

A

Molecular Distortion/Strain

70
Q

Discipline that describes the properties and characteristics of enzymes in mathematical terms

A

Enzyme Kinetics

71
Q

When an enzyme is first mixed with a large excess of substrate there is an initial periods during which the concentration of ES complex builds up. It then…

A

finds substrate molecules and binds to them:ES

72
Q

The enzyme complexed with the substrate

A

ES

73
Q

The initial period where ES builds up is called

A

The pre-steady state

74
Q

Usually too short to be easily observed

A

Pre-steady state

75
Q

The reaction quickly achieves a ____________ in which the concentration of ES and the concentration of any other intermediates remains approximately constant overtime

A

Steady-state

76
Q

Concerned themselves with the steady-state rate, and analysis of this type (referred to as Steady-State Kinetics)

A

Michaelis and Menten

77
Q

Steady-state rate and analysis of this type

A

Steady-state Kinetics

78
Q

Every time E converts S to a product, the enzyme binds to a new

A

substrate

79
Q

Pioneer of science for women

A

Maude Menten

80
Q

Enzyme + Substrate –>

A

ES–> E+P

81
Q

E + S–>

A

ES k1

82
Q

ES–>

A

E + S k1

83
Q

Rate constant

A

k

84
Q

The catalytic rate

A

Product formation rate = k2

85
Q

Measures the number of S molecules turned over per enzyme molecules per second; number of substrates that get used for each enzyme in given time

A

k2

86
Q

(Michaelis-Menton Equation) Vo=

A

Vmax[S] / Km + [S]

87
Q

Every enzyme in the reaction is bound to a substrate

A

Enzyme saturation

If just on enzyme wasn’t bound to a substrate you would not achieve maximum product

88
Q

Combined rate constant (Michaelis-Menten Constant)

A

Km

89
Q

Total enzyme in reaction

A

Et

90
Q

Maximum Velocity

A

Vmax

91
Q

Initial velocity

A

Vo

92
Q

k2[ES] =

A

Vo

93
Q

Velocity increases with

A

increased substrate

94
Q

A direct measure of _______ _________ can be judged by k2/Km

A

Reaction Efficiency (Enzyme Efficiency)

95
Q

The theoretical maximum efficiency would fall between 10^8-10^9 s/mol/L assuming

A

every possible collision between E and S gives ES

96
Q

Can also be directly assessed by k2/Km

A

Substrate specificity

97
Q

Higher value for k2/Km if

A

enzyme is in solution with substrate it likes to bind with

98
Q

Lower value for k2/Km if

A

Enzyme is in solution with substrate it doesn’t prefer to bind with

99
Q

Almost a zero value for k2/Km if

A

enzyme can’t bind with substrate

100
Q

Michaelis-menten Equation

A

Vo=Vmax[S]/Km + [S]

101
Q

When Vo is 1/2 Vmax

A 
Vmax/2 = Vmax [S]/ Km +[S]
Km= [S]
102
Q

A direct measure of _________ _________ can be judged by k2/Km

A

Reaction efficiency or enzyme efficiency

103
Q

Theoretical maximum efficiency would fall between

A

10^8-10^9 assuming every possible collision between enzyme and substrate gives ES

104
Q

Can also be directly assessed by k2/Km

A

Substrate specificity

105
Q

Higher value for k2/Km if enzyme is in solution with…

A

Substrate it likes to bind with

It would be almost zero if it can’t bind with the substrate

106
Q

Allows for a more accurate determination of Vmax using reciprocals and does not effect Km accuracy

A

Double reciprocal plots

107
Q

Most popular double reciprocal plot

A

Lineweaver-Burk Plot

108
Q

Reciprocal transformation of Michaelis-Menten equation

A

Double reciprocal plots

109
Q

1/[S] on x-axis and 1/Vo on y-axis

A

Double reciprocal plots

Slope = Km/Vmax
Y-int = 1/Vmax
X-int = 1/Km
110
Q

Reactions that usually involve the transfer of one atom or a group from one substrate to the other substrate

A

Bi substrate reactions

111
Q

2 common mechanisms for bi substrate reactions

A

Ternary complex formation (random and ordered binding)

Ping-pong (aka double displacement)

112
Q

Random or ordered binding mechanism

A

Ternary complex formation

113
Q

Enzyme catalyzed before substrate comes in. Enzyme can only bind to S2 in its modified form. When enzyme binds to S2 it modifies it back to original enzyme.

A

Ping pong mechanism

114
Q

Bi substrate reactions can be analyzed using

A

Steady state kinetics

115
Q

Bi substrate graph with three separate starting points

A

Ternary complex formation

116
Q

Bi substrate graph with parallel lines

A

Ping pong

Biochem (11 decks)

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