02b: Enzyme Catalysis

Question 1

Enzymes can accelerate reactions by factor of:

Answer 1

10^6 or more

Question 2

Are cofactors proteins?

Answer 2

No

Question 3

Enzyme with cofactor is (active/inactive) and called:

Answer 3

Active

Holoenzyme

Question 4

Enzyme without cofactor is (active/inactive) and called:

Answer 4

Inactive

Apoenzyme

Question 5

Inorganic cofactors are:

Answer 5

Metal ions

Question 6

Organic cofactors are:

Answer 6

Coenzymes

Question 7

(X) are derived from vitamins and facilitate enzymatic activity.

Answer 7

X = coenzymes

Question 8

Co-substrate is a type of (X) that’s (loosely/tightly) bound to enzyme.

Answer 8

X = coenzyme

Loosely

Question 9

Prosthetic group is a type of (X) that’s (loosely/tightly) bound to enzyme.

Answer 9

X = coenzyme

Tightly/covalently

Question 10

(X) are coenzymes changed by the reaction.

Answer 10

X = co-substrates

Question 11

T/F: an enzyme can only catalyze one specific reaction.

Answer 11

False - can also catalyze other closely related reactions

Question 12

T/F: enzymes differ in degree of substrate specificity.

Answer 12

True

Question 13

Free energy change for reaction depends on:

Answer 13

Only free E of products (minus) free E of reactants

Question 14

What can change in free E tell us about the reaction rate?

Answer 14

Nothing

Question 15

What can change in free E tell us about the reaction’s spontaneity?

Answer 15

If reaction is endergonic, exergonic, or at equilibrium

Question 16

What are P, [X], pH, and T at standard conditions?

Answer 16

P = 1 atm
[X] = 1 M
pH = 7

No real standard for T

Question 17

What’s the basis for reaction coupling (in terms of free energy change)?

Answer 17

In non-equilibrium conditions, (delta)G sign can differ from (delta)Go sign.

Question 18

How do enzymes alter free energy change?

Answer 18

They don’t! Can’t alter thermodynamic laws (free energy or equilibrium)

Question 19

Transition state has (high/low) stability and (high/low) free energy.

Answer 19

Low; high

Question 20

T/F: Enzymes enhance both forward and reverse reaction rates.

Answer 20

True

Question 21

Transition state theory assumes equilibrium between:

Answer 21

Substrate and transition state

Question 22

Enzyme active site is most responsible for:

Answer 22

Lowering activation energy (by promoting formation of transition state)

Question 23

T/F: active site makes up large portion of enzyme volume.

Answer 23

False

Question 24

Formation of (reversible/irreversible), non covalent interactions, such as (X), in active site cause:

Answer 24

Reversible

X = H bonds, van der waals

Cause release of free (binding) E

Question 25

How is binding E used by enzyme?

Answer 25

Facilitates transition state formation

Question 26

List catalytic strategies of enzymes.

Answer 26

1. Covalent catalysis 2. General acid-base catalysis 3. Catalysis by approximation 4. Metal ion catalysis

Question 27

Describe covalent catalysis.

Answer 27

Transient covalent bond forms between substrate and enzymes

Question 28

Nucleophilic attack is what type of catalytic strategy by enzyme to (X) the transition state.

Answer 28

X = form and stabilize Covalent catalysis

Question 29

In chymotrypsin protease activity, general base catalysis is seen when (X) (accepts/donates) proton.

Answer 29

X = His Accepts

Question 30

Describe general acid-base catalysis.

Answer 30

Molecule becomes proton donor or acceptor.

Question 31

T/F: Water is the typical molecule involved in acid-base catalysis of enzymes.

Answer 31

False - molecule involved here cannot be water

Question 32

Describe metal ion's function in metal ion catalysis.

Answer 32

``` 1. Promotes nucleophile formation OR 2. Acts as electrophile (stabilizes negative charge on intermediate) OR 3. Serves as E-S bridge ```

Question 33

Chymotrypsin is what type of enzyme?

Answer 33

Serine protease

Question 34

Chymotrypsin catalyzes:

Answer 34

cleavage of peptide bonds (via hydrolysis)

Question 35

Describe specific location that chymotrypsin works on polypeptide.

Answer 35

Cleaves on C-terminal side of aromatic and large hydrophobic AA

Question 36

T/F: A process that's kinetically unfavorable is also thermodynamically unfavorable.

Answer 36

False

Question 37

Peptide hydrolysis is thermodynamically (favorable/unfavorable).

Answer 37

Favorable

Question 38

Peptide hydrolysis is kinetically (favorable/unfavorable).

Answer 38

Unfavorable

Question 39

Why would peptide hydrolysis be (thermodynamically/kinetically) unfavorable?

Answer 39

Kinetically; Due to partial double-bond character of peptide bond

Question 40

(X) uses the catalytic triad to overcome (Y).

Answer 40

X = chymotrypsin Y = kinetically unfavorable nature of peptide hydrolysis

Question 41

Which AA are involved in catalytic triad?

Answer 41

1. His 57 2. Ser 195 3. Asp 102

Question 42

What's (formed/degraded) in stage 1 of peptide hydrolysis by chymotrypsin?

Answer 42

Formation of covalent acyl-enzyme intermediate

Question 43

Step 1 of peptide hydrolysis by chymotrypsin is formally termed:

Answer 43

Acylation

Question 44

What is held in chymotrypsin's specificity pocket?

Answer 44

Aromatic ring of AA side chain

Question 45

The first complex to form in peptide hydrolysis by chymotrypsin is:

Answer 45

E-S complex

Question 46

T/F: There's a nucleophile involved in peptide hydrolysis by chymotrypsin.

Answer 46

True

Question 47

Describe steps in formation of tetrahedral intermediate during peptide hydrolysis by chymotrypsin.

Answer 47

1. General acid-base catalysis - His accepts proton from Ser (-OH group) 2. Covalent catalysis - Nucleophile (alkoxide ion) generated on substrate