Molecular Catalysis and Energetics

Question 1

Chemical systems tend to _ free energy

Answer 1

minimize

Question 2

What is free energy?

Answer 2

the amount of energy available to do work

Question 3

What direction does the reaction proceed if G<0?

Answer 3

toward the products

Question 4

What direction does the reaction proceed if G=0?

Answer 4

at equilibrium

Question 5

What direction does the reaction proceed if G>0?

Answer 5

toward the reaction

Question 6

What are most biosynthetic reactions?

Answer 6

thermodynamically unfavorable, but are driven forward by coupling to a more strongly favorable reaction

Question 7

The second reaction _ the products of the first reaction, _

Answer 7

consumes; preventing reversal of the first reaction which would otherwise be favored

Question 8

How does a peptide bond form?

Answer 8

results from a condensation reaction between the carboxyl group of one amino acid and the amino group of another

Question 9

What are the N-terminus and C-terminus?

Answer 9

exposed amino grup and carboxyl group

Question 10

What forms the peptide backbone?

Answer 10

a repeating series of C and N atoms

Question 11

How are residues in a polypeptide numbered?

Answer 11

from the N-terminus

Question 12

Peptide bond formation requires _

Answer 12

activated amino acid precursors; formation of high energy bond with AMP, using ATP as the donor

Question 13

What cannot be used directly for synthesis of DNA or RNA?

Answer 13

nucleoside monophosphates nor nucleoside diphosphates because G>0

Question 14

What must nucleoside monophosphates and diphosphates first convert to?

Answer 14

nucleoside triphosphates using ATP as a phosphate donor

Question 15

What can be used directly for synthesis of DNA or RNA?

Answer 15

nucleoside triphosphates can be joined in a reaction that releases pyrophosphate, which is rapidly converted to two phosphates because G<0.

Question 16

DNA/RNA polymerization requires _

Answer 16

energy

Question 17

What happens in DNA/RNA polymerization

Answer 17

1. hydrolysis of a nucleoside triphosphate generates a nucleoside monophosphate and energy, both needed for the reaction
2. pyrophosphate hydrolysis to monophosphate (by pyrophosphatase) releases additional energy and is coupled to bond formation

Question 18

What does a favorable free energy change tell us?

Answer 18

whether a reaction will occur spontaneously

Question 19

What is an activation energy?

Answer 19

the threshold that must be overcome for a reaction to proceed

Question 20

What is the function of enzymes?

Answer 20

work by lowering the activation energy barrier

Question 21

Can a favorable reaction still occur if activation energy is high?

Answer 21

very few molecules will be able to proceed, making the reaction slow

Question 22

What is the transition state?

Answer 22

the highest point on the energy scale between substrate and product; short lived

Question 23

Where are metal ions and cofactors bound?

Answer 23

in the active site and are required for function

Question 24

Active sites are usually _ among different organisms, even if the rest of the protein is more _

Answer 24

conserved; diverged

Question 25

How can enzymes catalyze reactions?

Answer 25

1. by bringing two reactive substrates together (proximity catalysis)
2. by destabilizing the substrate, increasing its free energy (ground-state destabilization)
3. by stabilizing the transition state, lowering the barrier to the reaction
4. by leading the reaction through an alternative set of stages that have a smaller energy barrier than the uncatalyzed reaction; transient reaction intermediates

Question 26

What is nucleophilic displacement?

Answer 26

involves the movement of an electron from an electron-rich atom (nucleophile) to an electron-poor atom (electrophile)

Question 27

What is a nucleophilic attack?

Answer 27

encouraged when a proton is removed by a general base on an enzyme - here the H+ on the ‘ OH is removed

Question 28

What do enzymes provide?

Answer 28

groups that act as acids or bases and encourage proton movements

Question 29

What are intermediates?

Answer 29

transition state structures that have additional bonds and can interact favorably with other molecules in the reaction

Question 30

What are the steps of RNAse A degradation of RNA?

Answer 30

1. histidine 12 removes a proton from the 2’ OH of one ribose and histidine 119 donates a proton to the 1’ O of a second sugar
2. breaks the bond holding the nucleotides together, and a cyclic phosphate intermediate is formed
3. histidine 12 donates a proton to the 2’ O, re-forming the 2’ OH. histidine 119 accepts a proton from a water molecule and the remaining OH binds to P