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Biochem > Test 2 > Flashcards

Test 2 Flashcards

1
Q

What are some general properties of enzymes?

A
  • accelerate the rate of reaction of a chemical reaction by factors of 10^3 to 10^20
  • Enzymes will not induce a reaction that is unfavorable due to a positive free energy change
  • high specificity for the reaction substrate
  • High rxn specificity
  • enzyme is unchange in the reaction and can undergo rapid turnover
  • subject to regulation to alter their substrate binding affinity or activity
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2
Q

What was the first Enzyme?

A

RNA

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3
Q

What is the largest class of enzymes?

A

protein -ribozymes are another class

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4
Q

E+S -> ES -> E + P

Label the enzyme, substrate, enzyme-substrate complex, and the product

List important points about this reaction

A

E= Enzyme

S= Substrat

E-S= Enzyme-substrate complext

P= Product

  • the first step in this reaction (E+S-> E-S) is your slow/rate-determining step. This rate is dependent on the substrate concentration and is limited by the diffusion rate
  • the second step of the reaction (ES-> E+P) is the rapid step. Once the ES complex forms the reaction takes place very rapidly thus the ES comlex does not remain long
  • The second step is generally irreversible. Thus only K2 is included in the overall reaction scheme
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5
Q

How do enzyme change the reaction rate?

A
  • progress of a rxn is dependent on the free energy changes as the reaction proceeds
  • The enzyme lowers the activation free energy which is needed to get to the transition state, which increases the forward Rate constant
  • DOES NOT change the overall Delta G of the reactoin
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6
Q

Transition State

A

an unstable arragnement of atoms with the chemical bonds in the process of being formed or broken

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7
Q

Activation Energy

A

the energy barrier of the reaction that must be overcome for the reaction to occur

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8
Q

Oxidoreductases

A

One of the 6 classes of enzymes

  • catalyze oxidation-reduction (electron transfer) reactions
  • typically utilize NAD-NADH and NADP-NADPH for the oxidation-reducation and electron transfer
  • most frequently characterized by the gain or loss of a proton when electrons are also transfered
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9
Q

Oxidation

A

Loss of electrons

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10
Q

Reduction

A

Gain of electrons

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11
Q

Transferase

A
  • one of the 6 classes of enzymes
  • these enzymes transfer a chemical group from one molecule to another
  • often involve coenzymes
  • often involve the covalent attachment of the substrate to the enzyme
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12
Q

Hydrolases

A

these enzymes catalyze hydrolysis reactions-

-transfer functional groups to water with the cleavage of a single or double bond

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13
Q

What are some examples of hydrolases?

A

esterase, phophatase, peptidase

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14
Q

Lyases

A

enzymes catalyze (lysis) breakage of a bond,

  • NO water involved
  • No change in oxidation state
  • Generate double bond in product
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15
Q

Isomerases

A

catalyze structural changes in a single molecule (isomerization reactions)

-always reversible but does not absolutely require stereoisomers

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16
Q

Ligases (synthetases)

A

Catalyze ligation (joining) of two substrates

  • usually requires ATP as a energy source for the reaction
  • ATP or its parts are not part of the product
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17
Q

For a reaction that needs an enzyme, what would happen to the initial velocity?

A

the initial velocity would depend on the amount of enzyme added as long as there is a lot of substrate for all of the enzyme concentrtions used

-Plot of V0 vs [E] should be linear as long as their is enough substrate to keep all of the enyzme molecules occupied

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18
Q

Initial Rate of a rxn formula?

A

v= k[S]

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19
Q

What does Vmax tell us about the enzyme properties?

A

the enzyme is working as fast as it can.

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20
Q

Vmax formula and definition

A

Vmax= Kcat[E]tot

  • max reaction rate
  • occurs when all enzyme is bound, Vmax=Kcat[E]tot
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21
Q

Km

A

Michaelis Constant

defined by the ratio of rate constants that dissociate (k1 and K-2) over what associates teh substrate (k1) but usually K2 is small compared to K-1 thus:

Km=(k2+k-1)/k1=k-1/k1

dissociation constant between the enzyme and the substrate

***concentration of S when half Etot is bound

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22
Q

What two parameters characterize the strength of an enzyme?

A

Kcat and strength of the enzyme (Km)

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23
Q

Kcat

A

Turnover number

  • indicates how fast the enzyme can work under conditions in which their is saturating amount of substrate
  • STRONG ENZYME =large Kcat
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24
Q

A small Km corresponds to what?

A

Strong binding (strong enzymes)

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25
Q

A large Km corresponds to what?

A

weak binding

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26
Q

If [S]

A

V0= Kcat/Km[E][S]

  • the rate constant for this condition is kcat/Km
  • same as the second order rate constant for the reaction
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27
Q

Kcat/Km

A

enzymatic rate constant

-measures the overall efficiency of the enzyme (combination of binding strength and catalytic rate)

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28
Q

Diffusion Controlled limit

A

caused by the fact that the ES complex is formed by the diffusion S to E

-determines how small the Km can be, because the rate of the association rxn, k1, cannot be larger than the rate of diffusion of the S to E

Thus the value of Kcat/Km could not be larger than about 10^8-10^9 M-1S-1

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29
Q

Michaelis Menton Equation

A

v0=Kcat[E][S]/Km +[S]

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30
Q

When dealing with the Michaelis Mentin Equation, what does it mean when reactions are a Low[S]

A

Km>>[S]

dependence on both the enzyme and substrate thus

‘v0=(kcat/km)[E][S] fits the limiting slope

Kcat/Km can be determined

31
Q

When dealing with the Michaelis Mentin equation, what does it mean when there is high [S] Values?

A

since all of the E are saturated at a very high [S]

V0=Kcat[E] and Kcat can be determined

32
Q

Competitive Inhibition

A

inhibitor and substrate compete for the same binding site on the enzyme

-two versions: class and nonclassic

**in both versions, binding of inhibitor prevents the binding of the substrate

33
Q

Uncompetitive Inhibitor

A

inhibitor binds to the ES comlex and prevents reaction

  • Inhibitor decreases the Vmax/Kcat
  • [ES] is lowered
  • resulting in a decrease of Km/equilibrium shifts to the right
34
Q

Noncompetitive Inhibition

A

inhibitor binds to either E or to ES complex, does not interfere with S binding but prevents reaction

  • inhibitor binds to both E and Es
  • Km is not changed since the biding of S is not inhibited
  • Vmax and kcat is decreased
35
Q

Competitive Inhibition

A

the inhibitor and substrate compete for the same binding site on the enzyme.

-two versions classic and nonclassic

***both versions the binding of the inhibitor prevents binding of substrate

**inhibitor lowers concentration of available E, resulting in an increase of Km/equilibrium shifting to the left

36
Q

If there is a high concentration of [S] in competitive inhibition what results?

A

high [S] overcomes the effect of the inhibitor, thus Vmax is not chagned

37
Q

What type of inhibition is this?

A

Simple End product inhibition

  • the final product inhibits the first enzyme in the pathway
  • Frequently called FEEDBACK INHIBITION
38
Q
A

Sequential End-product inhibition

  • E and G individually control their own synthesis so they will not interfere with synthesis of each other
  • The arrangement of this pathway allows the continuing synthesis of either E or G, if either of those substances are specifically needed.
39
Q

What type of inhibition is this?

A

Concerted End-product inhibition

-synthesis of the common precursor D for the E and G pathways is slowed down whenever either pathway is inhibited

40
Q
A

DIfferential Inhibition of multiple Enzymes

41
Q
A

Substrate Activation

  • accumulation of substrate A induces activation of the enzyme to increase synthesis of B and activating the following pathway
  • Typically Allosteric activation involving a multi subunit enzyme exhibitying cooperative substrate binding and alteration of enzyme structure to increase substrate binding interaction with the enzyme
42
Q

Enzyme structure and activity can be influenced by what?

A

interaction with small molecules called effectors

43
Q

What can be an effector?

A

enzyme’s substrate

enzymes products

often other effector molecules that do not resember substrate

44
Q

Allosteric Enzymes

A

multi-subunit enzymes

-Do not exhibit Michaelis Mentin Kinetics instead exhibits a sigmoid kinets (s shaped)

45
Q

Multi-Subunit Enzyme

A

binding of the first (and subsequent) effector to a subunit:

induces structural changes in the subunit and in other subunits
this alters the binding strength of the substrate (a measure of this is an altered Km in the subunits)

46
Q

Allostery

A

the capability of one ligand to bind and affect the binding of the second ligand at a distant site

47
Q

Positive Coopertivity

-Draw a relative graph of what would happen

A

binding of the first ligand increases the affinity of subsequent ligands

48
Q

Negative cooperativity

-Draw a relative graph of what would happen

A

binding of the first ligand decreases teh affinity of subsequent ligand

49
Q

Allosteric Activator

A

ligand that increases activity of the enzyme

50
Q

Allosteric Inhibitor

A

is a ligand that decreases the activity of the enzyme

51
Q

If the effector is in an inhibitor what will happen?

A

it will increase the tendency to the T state(low affinity for substrate)

52
Q

If the effector is an activatory what will happen?

A

it will increase the tendency to the R state (high affinity for substrate)

53
Q

ATC

A

aspartate transcarbamoylase

  • classic example of allosteric regulation of an enzyme in a key metabolic pathway
  • catalyzes the synthesis of the pyrimidine ring needed for all the pyrimidine nucleosides in the cell.
  • ATC is 12 subunits – 6 regulatory, 6 catalytic

-

54
Q

when dealing with ATC, if there is excess CTP what will happen?

A

ATC will be inhibited

55
Q

When dealing with ATC, if there is excess ATP what will happen?

A

ATC will be activated to make CTP to catch up to [ATP]

56
Q

Enzyme Regulation by Covalent Modifications

  • most common types are methylation, phosphorylation, and acetylation
  • regulate enzymatic activity by changing the R to T equilibirum
A

-

57
Q

Pyruvate Dehydrogenase

A
  • involved in glycolysis and is subject to many control mechs
  • Pyruvate Dehydrogenase is deactivated when phosphate is attached and the enzyme specifically carries out the phosphate addition
58
Q

Pyruvate Dehydrogenase Phosphatase

A

specifically removes the phosphate from pyruvate dehydrogenase

59
Q

How can an enzyme increase the reaction rate?

A

by lowering free energy of transition state

  • binding the substrates A and B (this raises the free energy, so it makes the activation free energy smaller)
  • bind A and B and also bind to the transition state to reduce its free energy
60
Q

Limit to binding strength (Km) values for enzyme

A

enzymes need to have low Km values to have good affinity to their substances and good specificity to prevent inappropriate products

61
Q

Why shouldn’t enzymes bind to their substrates to tightly?

A
  • tight binding could prevent reaction, substrates bound in very tight binding pockets will be incompatible with reaction
  • strong binding could result in a E-S intermediate which would have an even harder time reaching the transition state than the uncatalyzed reaction
  • Very tight binding pockets could prevent product release
62
Q

Significance of Induced Fit Binding Mechanism

A

Enzymes are flexible and the ability to collapse on a suitable substrate offers several advantages

  • the substrate changes the enzyme structure and this can be connect with the enzyme activity (ex: the enzyme is not active unless the correct substrate is present)
  • the enzyme structure is fairly open and accessible to the substrate, until it binds; this allows access but prevents water and other undersirable molecules from the active site
  • after reaction, the enzyme can reversibly change its structure and release product
63
Q

Organization of enzyme active sites

A

active sites for enzyme catalysis will generally be in interior locations

–Many reactions will need to exclude water, or carefully control it, at the reaction site

-Want to have a large area of contact between substrates and enzyme for substrate specificity

Many amino acids lining an active site will be nonpolar

  • this will help exclude water from the active site
  • nonpolar enviroment will hlep raise electrostatic effects in active site

***However, there will be key polar and charged amino acids at the active site that will be involved in binding the substrates and in the reaction mechanism;

64
Q

Nucleophile

A

a functional group rich in, and capable of, donating electrons

65
Q

Electrophiles

A

a functional group that seeks electrons

66
Q

What are the amino acids that act as bases

A

His, Asp, Glu

67
Q

What are the amino acids that act as acids

A

His, Lys

68
Q

How does base catalysis happen?

A

Directly

-extraction of proton from the substrate to activate the reaction indirectly through water-extraction of proton from water generates OH

69
Q

When does acid catalysis happens

A

happens usually through direct protonation (addition of H+) to the substrate to activate the reaction

70
Q

Covalent Catalysis

A
  • an intermediate is formed by the covalent joining of the substrate and the enzyme
  • This intermediate goes on further
71
Q

Effect of pH changes on reaction rates

A

pH of the solvent can significantly impact the activity of the enzyme

  • as the pH increases or decreases the ionization states of the amino acid side groups change
  • If critical side groups are in the active site, changes in ionization will alter the strength of substrate binding or the catalytic acitivty

-

72
Q

Transition state stabilization

A

very tight binding between the reactant and the enzyme in the transition state which helps lower the transition state energy

73
Q

Transition State Analog

A

a chemical compound that resembles a transition state arrangement

74
Q
A

Biochem (23 decks)

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