Biochem Enzymes Lecture 1

Question 1

These are proteins which catalyze biochemical reactions

Answer 1

Enzymes

Question 2

The structure of enzymes are essential to their

Answer 2

Catalytic activity

Question 3

Is the MW of enzymes variable?

Answer 3

Yes, vary from 12,000 to 1,000,000+

Question 4

Some enzymes require and additional chemical component to function, called a

Answer 4

Cofactor

Question 5

Cofactors tend to be one or more ___

They can also be a complex organic or metalloorganic molecule, called a

Or they can be both a

Answer 5

inorganic ions (Fe2+, Mg2+, Mn2+, Zn2+)

(coenzyme

Metal ion and a coenzyme

Question 6

How are enzymes classified?

Answer 6

According the the type of reaction that they catalyze

Question 7

Many enzymes ar enamed by addding _____ to the name describing their activity

Answer 7

“ase”

Question 8

What does an enzyme do?

Answer 8

Provides an environment that speeds up a given reaction

Question 9

This is the term describing a pocket on the enzymes where the enzymes-catalyzed reaction occurs

The surface of the above location is lined with _____ that help bind the substrate and catalyze its chemical transformation

Answer 9

Active Site

AA residues

Question 10

This is the term describing the molecule that is bound in the active site and acted upon by the enzyme

Answer 10

Substrate

Question 11

Does a reaction affect the equilibrium of a reaction? Yes or no?

Answer 11

No

Question 12

What does an enzyme affect about a reaction?

Answer 12

The reaction rate

Question 13

In a reaction diagram, the equilibrium between S and P reflects the difference in ____ of their ground states

Answer 13

Free energies

Question 14

E + S → ES → EP → E + P

If the free energy of the ground state, P is lower than that of S, ΔG is _____ and the equilibrium favors ___ formation

Answer 14

Negative

P formation

Question 15

Does a favorable equilibrium mean a fast conversion of products?

Answer 15

No.

Question 16

The difference between energy levels of the ground state and the transition state is the ________ or ΔG‡

Answer 16

Activation energy

Question 17

A higher activation energy means a faster/slower reaction?

Answer 17

Slower reactions

Question 18

Catalysts increase reaction rates by lowering….

Answer 18

ΔG‡

Question 19

This is the term describing the transient chemical species of a raection

Answer 19

Reaction Intermediates

Question 20

This is the term describing the step in an enzymatic reaction with the highest activation energy, it determines the overall reaction rate

Answer 20

Rate-limiting step

Question 21

E + S → ES → EP → E + P

In the above reaction, the reaction rate is determined by the concentration of ___ and

What is the equation, then, for the rate of the reaction (V)?

What order is it?

What is the unit for the rate constant, k?

Answer 21

Reaction [S] and the rate constant, K

V=k[S]

First order

s^-1

Question 22

If a reaction is dependent upon two different compounds, S1 and S2, k is a _______ rate constant with units ____

What would the rate equation be then

Answer 22

Second Order

M-1s-1

V=k[S1][S2]

Question 23

What is the equation that describes how the rate constant and activation energy are related?

Answer 23

k=(kT/h)e ^-ΔG‡/RT

k=Boltzmann constant and h is Planck’s constant

Question 24

What helps to lower activation energies?

Answer 24

Weak, noncovalent interactions between substrate and enzyme

Question 25

What are the weak interaction between E and S in ES complexes?

Answer 25

H-bonds Hydrophobic interactions Ionic Interactions Some of these weak interactions occur in the reaction transition state and stabilize the transition state

Question 26

The energy obtained from an enzyme substrate interaction is the _____

Answer 26

Binding energy, ΔG

Question 27

The binding energy is used by enzymes to to increase/lower the activation energies of reactions?

Answer 27

Lower the activation energies

Question 28

The binding energy can be used to lower substrate _______ or to cause a ___ change in the enzymes

Answer 28

Entropy Conformational Change (induced fit)

Question 29

To successfully catalyze reactions, the enzye must be complementary the reaction ___ state Weak interactions formed in the transition state make the major contribution to ____

Answer 29

Transition state Catalysis

Question 30

Figure 6-5 describes how the free energy changes that occur depending upon how the enzyme interacts with the substrate When the enzyme fits tightly to the substrate, is the substrate more or less difficult to move to the transition state? What about when the enzyme fits well with the transition state?

Answer 30

More difficult because the substrate is stabilized The substrate is destabilized and catalysis readily proceeds

Question 31

Fig 6-6 shows how the binding energy (ΔGB) lowers the activation energy. The free energy released by the formation of weak interactions between E and S in the transition states partially offsets the __ energy for the reaction

Answer 31

Activation energy

Question 32

Binding energy also gives an enzyme its ______ for a particular substrate

Answer 32

Specificity

Question 33

Enzymes tend to be large. Why?

Answer 33

They provide functional groups located in specific positions to maximize multiple weak interactions in the transition state.

Question 34

The binding energy holds substrates in the proper orientation to react. This lowers the ____

Answer 34

entropy

Question 35

Enzyme-substrate interactions replace virtually all of the ______ bonds between the substrate and water

Answer 35

H-bonds

Question 36

Binding energy compensates kinetically or thermodynamically for the electron redistribution the substrate undergoes in order to react?

Answer 36

Thermodynamically

Question 37

Binding energy may be used to cause a conformation change in the enzyme itself when the substrate binds. This is called an ___ It changes the alignment of specific ___ groups It also is important in the formation of additional ______ interactions in the transition state

Answer 37

Induced fit Functional Weak interactions

Question 38

Additional catalytic mechanisms involve transient ____ interactions with a substrate or group transfer to or from a substrate

Answer 38

Covalent Different from the weak contributions found with the binding energy just discussed

Question 39

When there is no catalyst present, unstable, charged intermediates formed in many biochemical reactions tend to break down immediately to form reactants (and products will not be formed) These charged intermediates can be stabilized by _____ to form a species that breaks down readily to products (instead of reactants)

Answer 39

Proton transfer

Question 40

This is acid-base catalysis that uses only the H+ or OH- ions present in water This is acid-base catalysis of proton transfers facilitated by other classes of molecules

Answer 40

Specific Acid-Base catalysis General Acid-Base Catalysis

Question 41

For nonenzymatic reactions in aqueous solutions, weak organic acids or bases can be proton _____ in addition to water

Answer 41

Donors

Question 42

In an enzyme's active site, amino acid side chains can act as proton ____ and _____ Rate enhancements of ___ to ___ are observed

Answer 42

donors and acceptors 10^2 to 10^5

Question 43

________ are the most common biochemical reactions

Answer 43

Proton transfers

Question 44

This type of catalysis involves the formation of a transient covalent bond between an enzyme and substrate In the uncatalyzed hydrolysis of an A-B bond In the presence of a covalent catalyst (an enzyme with nucleophile X)

Answer 44

Covalent Catalysis ? ?

Question 45

Catalysis occurs when the newer pathway has a HIGHER/LOWER energy than the uncatalyzed reaction Where do the nucleophiles come from?

Answer 45

Lower AA side chains Functional groups of some enzyme cofactors

Question 46

This type of catalysis is ionic interactions between an enzyme bound metal and a substrate It can orient the ___ for reaction Or stabilize the ____

Answer 46

Metal Ion Catalysis Substrate Transition state

Question 47

Metals are involved in ______ reactions about 1/3 of all known enzymes require metal ions for activity

Answer 47

Oxidation/reduction

Question 48

In sum, most enzymes use a combination of catalytic strategies or one catalytic strategy? What two processes does chemotrypsin use?

Answer 48

A combination Covalent and general acid-base catalysis