Chapter 9. Catalytic Strategies

Question 1

In general, an enzyme that attaches a methyl group to a molecule. Methylases modify the recognition sites for restriction enzymes in bacterial DNA in order to prevent digestion by the bacteria&#39s own restriction enzymes.

Answer 1

Methylases

Question 2

catalysis in which a metal acts as an electrophilic catalyst by stabilizing a negative charge on a reaction intermediate, generates a nucleophile by increasing the acidity of nearby molecules, or increases the binding energy of the enzyme-substrate interaction by binding to substrates.

Answer 2

Metal ion catalysis

Question 3

the free energy released in the formation of the weak interactions between enzyme and substrate.

Answer 3

Binding energy

Question 4

catalysis in which a molecule other than water plays the role of a proton donor or acceptor.

Answer 4

General acid-base catalysis

Question 5

A reaction in which a molecule modifies a specific amino acid residue in a protein.

Answer 5

Chemical modification reaction

Question 6

a constellation of three residues, found in many proteolytic enzymes, in which two of the residues convert the remaining residue, usually a serine or cysteine, into a potent nucleophile.

Answer 6

Catalytic triad

Question 7

The modification of the shape of an active site in an enzyme after the substrate is bound.

Answer 7

Induced fit

Question 8

A hydrolysis reaction, characteristic of restriction enzymes, in which the incoming nucleophile attacks the phosphorus atom. The transition state has a trigonal bipyramidal geometry centered at the phosphorus atom, with the incoming nucleophile at one apex of the two pyramids and the group that is displaced (the leaving group) at the other apex, in line with the incoming nucleophile.

Answer 8

In-line displacement

Question 9

region on certain proteolytic enzymes that stabilizes the oxyanion constituent of the tetrahedral intermediate of the reaction.

Answer 9

Oxyanion hole

Question 10

enhancing the rate of a reaction by bringing multiple substrates together along a single binding surface of the enzyme.

Answer 10

Catalysis by approximation

Question 11

catalysis in which the active site contains a reactive group that becomes temporarily covalently modified in the course of catalysis.

Answer 11

Covalent catalysis

Question 12

the passing of pieces of DNA (plasmids) between species that provide a selective advantage in particular environment.

Answer 12

Horizontal gene transfer

Question 13

a component of the NTP binding domain that interacts with the phosphoryl groups of the bound nucleotide. Such loops are characteristic of nucleotide-binding proteins.

Answer 13

P-loop

Question 14

Enzymes that catalyze the hydrolysis of adenosine triphosphate (ATP) to form adenosine diphosphate (ADP) and inorganic phosphate (Pi) and use the energy released to power otherwise endergonic reactions.

Answer 14

ATPase

Question 15

A substrate analog that forms a colored product.

Answer 15

chromogenic substrate

Question 16

A means to allow buffer components from solution to participate in the reaction catalyzed by carbonic anhydrase II. The primary component of this shuttle is histidine 64. This residue transfers protons from the zinc-bound water molecule to the protein surface and then to the buffer.

Answer 16

Proton shuttle

Question 17

a system such that for each restriction enzyme that a prokaryote produces, the cell also produces a corresponding methylase that marks the host DNA and prevents its degradation.

Answer 17

Restriction-modification system

Question 18

The particular base sequences recognized by DNA binding proteins, such as restriction enzymes.

Answer 18

Recognition sequence

Question 19

A drug or protein that specifically inhibits a particular proteolytic enzyme. Chemical protease inhibitors are clinically important drugs.

Answer 19

Protease inhibitor