Mcp Lect 07-09: Kinetics And Catalysis

Front 1

Boltzmann's constant (h)

Back 1

6.63 X 10-34 Js

Front 2

How is the energy of activation related to rate?

Back 2

The relationship between rate and the energy of activation is INVERSE and EXPONENTIAL (ie. higher energy of activation, the slower the rate)

k=(Kb*T/h)e^-Ea/RT

Front 3

What do catalysts do?

Back 3

The Catalyst:
1) provides a reaction path with a lower activation energy.
2) speeds attainment of, but can not alter, Keq.
3) is unchanged by the reaction, even though it may participate directly.
4) Rate enhancement is a sensitive function of DDG‡cat (DDG‡cat is the reduction in DG‡ aka the energy of activation by the catalyst)

Front 4

What type of reaction is:

2A --->P

Reaction rate?

Back 4

-Second order reaction
-two reactants (may be the same or different)
-V=k[A][A]

*both velocity and halflife are dependent on the concentration of reactant

Front 5

Reaction order

Back 5

The sum of the exponents in the rate equation

Front 6

What type of reaction is:

A --->P

Reaction rate?

Back 6

First order reaction
-one reactant
-V =k[A]

*half life is independent of the concentration of reactant
*many higher order reactions may behave like first order reactions if one component (eg. water) is in vast excess --> many hydrolysis reactions are operationally first order

Front 7

What type of reaction is:

A+B --->P

Reaction rate?

Back 7

-Second order reaction
-two reactants (may be the same or different)
-V=k[A][B]

*both velocity and halflife are dependent on the concentration of reactant

Front 8

Zero order reaction

Back 8

-appears to be independent of reactant concentration (an illusion though!)
-occurs in ENZYME CATALYZED REACTIONS where the reactants are present in great excess over the enzyme!!
-Initially the reaction rate is dependent on the concentration of substrate but eventually rate reaches a point where it is independent of the concentration of substrate

Front 9

Michaelis Menten

Back 9

vo = (Vmax*[S])/(Km + [S])

Front 10

Km

Back 10

= substrate concentration when initial velocity = ½ vmax

refers to the enzyme's intrinsic affinity for specific substrates

Km= (K-1 + k2) / (K1)

Front 11

Kcat

Back 11

refers to enzyme's turnover numbers
*higher Kcat = more efficient enzyme!

Kcat = Vmax / [E]

Front 12

Steady state assumption??

Back 12

d[ES]/dt ~ 0

where ES is the enzyme/substrate complex

Front 13

Back 13

Lineweaver burk
Vo = (Vmax *[S])/(Km +[S])

Front 14

Back 14

Michaelis Menten

Vo = (Vmax*[S])/(Km + [S])

Front 15

Transition state analog

Back 15

-Resembles a substrate/reaction's transition state
-Often bind enzymes with Ki's lower than the Km for the substrate (bind more tightly)

Front 16

Back 16

COMPETITIVE INHIBITION
-A substance that competes with the substrate for binding to the substrate binding site on the enzyme
-NO CHANGE TO VMAX!
-May resemble the substrate or the reaction's transition state (transition state analog)
-Reduces the concentration of free enzyme available for substrate binding

Front 17

Back 17

UNCOMPETITIVE INHIBITION
-binds only to the ES complex!
-effects of inhibitor are not reversed by increasing [S]
-Inhibitors affects both apparent Km and Vmax, but the slope (Km/Vmax) remains unchanged
-**uncompetitive inhibition more effective than competitive for drugs used to target enzymes

Front 18

Back 18

COMPETITIVE INHIBITION
*note that there is an increase in Km but the Vmax is unaffected

Front 19

Back 19

UNCOMPETITIVE INHIBITION

Front 20

Back 20

MIXED INHIBITION
-bind BOTH FREE ENZYME AND ENZYME SUBSTRATE COMPLEX
-Because of this, have two different dissociation constants: Ki (inhibitor + free enzyme) and Ki' (inhibitor + enzyme substrate complex)
-When Ki = Ki', see the lines intersecting on the X axis
-The competitive component affects the apparent Km
-The uncompetitive component affects both Km and Vmax.

Front 21

Inactivators

Back 21

-Molecules that react with an enzyme irreversibly and decrease its activity
-Decreases the effective [E]t at all concentrations of substrate
-Can be a reagant that modifies specific amino acid residues required for catalysis

Front 22

Suicide substrates

Back 22

-Competitive inhibitors that bind irreversibly to the enzyme's substrate binding pocket, usually by covalent modification, thus becoming inactivators

Front 23

What makes enzymes different from chemical catalysts?

Back 23

1. Higher reaction rates
2. Milder reaction conditions
3. Greater reaction specificity
4. Capacity for regulation
5. Formation of ES complex
____
1. Higher reaction rates
-->Enzyme catalyzed reactions are typically 10e6-10e12 times faster than the corresponding uncatalyzed reaction, which is more efficient than chemical catalysts

2. Milder reaction conditions
-->Enzyme catalyzed reactions occur under conditions that we typically think of as being compatible with life, ie. temperatures below 100C, atmospheric pressure, aqueous environments, and nearly neutral pH. Chemical catalysts are often used under extremes.

3. Greater reaction specificity
-->The high specificity of enzymes for their substrates, described by their Kms, means that enzyme catalyzed reactions rarely have non-productive side products, like chemical reactions.

4. Capacity for regulation
-->The rates of reactions vary in response to the concentrations of their substrates and inhibitors. The complexity of enzymes allows for multiple additional layers of regulation. This is key to their fulfilling their biological functions, as spatially or temporally inappropriate enzymatic activity can be as disastrous as no activity at all.

5. Formation of specific enzyme/substrate complex

Front 24

Oxoreductases

Back 24

Transfer of electrons (hydride ions of H atoms)

Front 25

Transferases

Back 25

Group-transfer reactions
eg. methyl-transferase or phospho-transferase (kinase)

Front 26

Hydrolases

Back 26

Hydrolysis reactions (transfer of functional groups to water)

Front 27

Lyases

Back 27

Addition of groups to double bonds, or formation of double bonds by removal of groups

Front 28

Isomerases

Back 28

Transfer of groups within molecules to yield isomeric forms
**changes the configuration of the substrate

Front 29

Ligases

Back 29

Formation of C-C, C-S, C-O, and C-N bonds by condensation reactions coupled to ATP cleavage

Front 30

Rate Enhancement Mechanisms of Enzymes

Back 30

1. Proximity and Orientation
2. Transition State Binding
3. Acid Base Catalysis
4. Covalent Catalysis
5. Metal Ion Catalysis
__
1. Proximity and Orientation
-->proper orientation of reactant, arrest of relative motions (entropy trap), suitable reaction surface

2. Transition State Binding
-->Binding of transition state to an enzyme with greater affinity than the substrate or products

3. Acid Base Catalysis
-->Partial proton transfer from a Bronsted acid to a Bronsted Base

4. Covalent Catalysis
-->transient formation of a catalyst-substrate bond

5. Metal Ion Catalysis
-->Orienting substrates, shielding or stabilizing negative charges, mediating oxidation-reduction reactions

Front 31

Bronsted Acid/Base

Back 31

Bronsted acids donate protons
Bronsted bases extract protons

Front 32

Proenzymes

Back 32

Enzyme precursors in which the active portion of the protein is expressed in frame with additional regulatory sequences that prevent enzyme activity. These regulatory regions must be protolytically cleaved to activate the enzyme. Activation of this type is irreversible.

Front 33

Coenzymes

Back 33

Complex organic molecules required to help certain enzymes carry out their catalytic functions

Front 34

Cofactors

Back 34

Metal ions required by certain enzymes to carry out their catalytic functions

Front 35

Apoenzyme

Back 35

An enzyme lacking its accessory (coenzyme/cofactor) factor

Front 36

Holoenzyme

Back 36

Complete, active assemblage of an enzyme including all necessary protein subunits, cofactos, and coenzymes

Front 37

The rate of a catalyzed reaction should be increased by a factor of __?

Back 37

e^(ddG ‡)/(RT)

Front 38

Transition state analogue

Back 38

– resembles transition state (in size/shape/charge) but it’s STABLE
-Analogs of the proposed transition state act as powerful competitive inhibitors, and are therefore good lead compounds in drug design. For example, “statins” are competitive inhibitors of HMG-CoA reductase

Front 39

General acid catalysis

Back 39

A process in which partial proton transfer from a Bronsted acid lowers the free energy of the transition state

Front 40

General base catalysis

Back 40

Occurs when the rate of a reaction is stimulated by partial proton abstraction by a Bronsted base

Front 41

Specific acid base catalysis

Back 41

Occurs when the catalytic effects are due SOLELY to the ions produced by the solvent (ie. water); this is not the case for enzyme catalysis discussed in the context of proteins

Front 42

Side chains that often participate in NUCLEOPHILIC COVALENT CATALYSIS include:

Back 42

Histidine
Cysteine
Serine
Threonine
Asparagine

Front 43

Metalloenzymes

Back 43

Contain tightly bound metal ions

Front 44

Metal-activated enzymes

Back 44

Loosely bind metal ions from solution

Front 45

How can metal ions participate in catalysis

Back 45

1. By binding to substrates in order to orient them properly
2. To mediate REDOX reactions through reversible changes to the metal ions oxidation state
3. By electrostatically stabilizing (ie. SHIELDING) negative charge

Front 46

Distributive enzyme

Back 46

Binds to substrate, undergoes catalysis, lets go
eg. lysozyme

Front 47

Processive enzyme

Back 47

Carries out polymerization rxn. Binds to substrate and carries out number of catalyzations before letting go.
Eg. DNA polymerization, other polymerases

Front 48

Homotropic modulator

Back 48

A substrate for its target enzyme, as well as a regulatory molecule of the enzyme's activity. Typically an ACTIVATOR of the enzyme.

listed at homotropic (allosteric) modulator