Chapter 11 (Part 1)

Question 1

Define what an enzyme is, and what it does.

Answer 1

Enzymes are proteins that catalyze reactions in biology.

Question 2

(T/F) Enzymes can enhance some reaction rates by up to 14 orders of magnitude.

Answer 2

True.

Question 3

Thermodynamically, when is a reaction in the direction of product formation favorable? Be specific in terms of the energy of the reactants, products, and reference the overall ΔG value.

Answer 3

When the free energy of the products is less than the reactants, a reaction is favorable in the direction of product formation. Overall ΔG value is negative.

Question 4

How do enzymes allow reactions to proceed to equilibrium more quickly?

Answer 4

By lowering the activation energy needed to move through the transition state.

Question 5

(T/F) Enzymes alter the overall ΔG of a reaction.

Answer 5

False. Enzymes only make equilibrium easier to achieve by lowering the activation energy required to go through the transition state.

Question 6

How is the reaction rate expressed (which term derived from the Arrhenius equation)?

Answer 6

e^(-ΔG‡/RT)

Question 7

How is the rate enhancement expressed mathematically?

Answer 7

e^(ΔΔG‡/RT)

Question 8

There are 5 common mechanisms employed by an enzyme to lower the energy of the transition state. Name them.

Answer 8

1. Acid-base catalysis
2. Covalent catalysis
3. Metal ion catalysis
4. Proximity/orientation effects
5. Preferential binding of the transition state

Question 9

How does acid-base catalysis lower the energy of the transition state (in basic no pun intended terms)?

Answer 9

By either donating a proton from an acid or abstracting a proton using a base.

Question 10

With regard to acid-base catalysis, what are the acids and bases?

Answer 10

Acids and bases in this case are the side chains of amino acid residues that have pKa values in the physiological range

Question 11

When proton donation and abstraction occur at different points in a multistep reaction, the acid-base catalysis reaction is said to be ______.

Answer 11

Concerted

Question 12

(T/F) The concerted acid-base catalysis mechanism is uncommon in enzymes.

Answer 12

False. It is very common.

Question 13

Describe the digestion process of RNase A, a digestive enzyme used to degrade dietary RNA in the small intestine. Mention key residues. What kind of catalysis mechanism is used?

Answer 13

Acid-base catalysis.

1. His12 acts as a base catalyst to remove a proton from the 2’-OH group of the RNA substrate, converting the oxygen into a strong nucleophile that attacks the phosphorus atom nearby.
2. His119 acts as an acid catalyst, donating a proton to the leaving group oxygen to promote bond breakage. The first product has been released with the phosphodiester bond cleavage
3. His12 acts as an acid catalyst, protonating the oxygen bound to the phosphorus atom
4. His119 acts as a base catalyst by deprotonating a water molecule from the solvent to activate it for hydrolysis of the cyclic nucleotide intermediate.
5. This results in conversion of the cyclic nucleotide structure into a more normal 3’phosphate, and also resets each His residue to its starting form

Question 14

When does covalent catalysis occur? Reference which element of the reaction is the nucleophile and which is the electrophile.

Answer 14

Occurs when there is transient bond formation between the substrate (electrophile) and enzyme (nucleophile). A nucleophile on the protein attacks an electrophilic group on the substrate.

Question 15

Name 3-4 important nucleophiles for covalent catalysis that are found as part of amino acid residues in proteins

Answer 15

Hydroxyl, sulfhydryl, amino, and imidazole groups

Question 16

Why must covalent catalysis be transient?

Answer 16

The covalent bond cannot be so stable that it fails to decompose during formation of the final product

Question 17

In metal ion catalysis, what kind of metals are used most often?

Answer 17

First row transition metals.

Question 18

How many enzymes are estimated to be metalloenzymes?

Answer 18

Up to 1/3

Question 19

How is metal bound by the enzyme in the active site?

Answer 19

Using amino acid side chains to coordinate it (especially cysteine thiols and histidine imidazoles)

Question 20

Describe 3 ways that metal ion catalysis can occur?

Answer 20

1. Can bind substrates and orient them for the reaction
2. Some metals (like copper and iron) can mediate Red/Ox reactions where they accept or donate an electron to or from the substrate
3. Because metal ions are often cations, they are good at shielding or stabilizing negative charges that might form on the substrate during the reaction

Question 21

(T/F) The charge on metal ions cannot be used to make any bound water molecule much more acidic than a free water molecule.

Answer 21

False. The charge on metal ions allows bound water molecules to become a nucleophilic hydroxide ion.

Question 22

The enzyme carbonic anhydrase takes advantage of which means of enzyme catalysis?

Answer 22

Metal ion

Question 23

Carbonic anhydrase catalyses the conversion of ____ and _____ into ______.

Answer 23

Aqueous CO2 and H2O into bicarbonate

Question 24

Carbonic anhydrase utilizes which metal ion?

Answer 24

Zinc (2+)

Question 25

In the carbonic anhydrase reaction, zinc is bound to ____ [how many] active site ___ residues.

Answer 25

3 active site Histidine residues

Question 26

Describe the mechanism of the carbonic anhydrase reaction.

Answer 26

1. The zinc ion coordinates water at its open 4th coordination site
2. The Zn-bound water ionizes to OH-, a nucleophile
3. The hydroxide group attacks the CO2 to form bicarbonate
4. The remaining proton from the water molecule is shuffled to the enzyme surface, and released by His64 (which acts as a base)
5. The enzyme is reset when a new water molecule comes into the active site to bind the Zn

Question 27

Describe how proximity/orientation effects assist in enzymatic catalysis.

Answer 27

Using binding sites with high specificity results in correct positioning of reacting groups, which reduces degrees of freedom of substrates and enhances concentration of substrates (by effectively increasing the “effective molarity” of substrates)

Question 28

(T/F) Proximity/orientation effects increase entropy (energetically favorable)

Answer 28

False. The reaction is not energetically favorable, but the other 2 advantages (reduction of degrees of freedom & increase of “effective molarity” of substrates”) prevail, and reaction rates are accelerated.

Question 29

How do enzymes achieve substrate constraint with regard to proximity/orientation effects? What kinds of motion are reduced?

Answer 29

By binding the substrates in structurally well-defined active sites. Helps to freeze out rotational and translational motion in the substrate to promote the desired reaction pathway.

Question 30

(T/F) Enzymes often bind the substrate of a reaction with a much higher affinity than the transition state or product.

Answer 30

False. Enzymes bind the transition state with a much higher affinity.

Question 31

How much more tightly can enzymes bind a transition state than a substrate?

Answer 31

10^10 to 10^15 times more tightly

Question 32

Why are inhibitors that mimic the transition state of a reaction usually more potent enzyme inhibitors?

Answer 32

The inhibitor binds and blocks the active site more tightly than the intended substrate, but cannot itself be converted into a useful product