Exam 1

Question 1

List the common reactions catalyzed by cytochromes P450

Answer 1

1. Aliphatic hydroxylation
2. Aromatic hydroxylation
3. Epoxidation
4. Dealkylation
5. N-oxidation

Question 2

List the functions of cytochromes P450s

Answer 2

1. oxidize pro-drugs
2. metabolize a large majority of drugs (i.e. steroids + vitamins)
3. make xenobiotics carcinogenic
4. decrease xenobiotics lipid solubility
5. detoxify toxins
6. catalyze steps in a biosynthetic pathway with other P450s

Question 3

Where do sequence specific DNA-binding proteins bind?

Answer 3

the major groove (base specific interactions: creates H bonds between protein and DNA)

Question 4

Where do nonspecific DNA-binding proteins bind?

Answer 4

the minor groove (interactions with phosphate backbone and sugar)

i.e. histones; they interact with DNA sugar-phosphate backbone, and many Arg residues will insert into the minor groove

Question 5

Helix-turn-helix (HTH) motif

Answer 5

two helices connected by a short turn
second helix = recognition helix that binds sequence specific in major groove
first helix = stabilizes structure

Question 6

Zinc fingers

Answer 6

-two stranded B-sheet and short a-helix
-Zn2+ ion stabilized by cysteine and histidine residues

Question 7

Leucine zippers

Answer 7

-Leu every 7th position in a-helix
-basic region: arginine + lysine residues bind to major groove
-basic amino acids interact with phosphate backbone

Question 8

Helix-loop-helix (HLH) motif

Answer 8

-two amphipathic a-helices connected by a loop
-extension of a-helix binds major groove

Question 9

What are transcription factors?

Answer 9

-sequence-specific DNA-binding factors that control the rate of transcription by either promoting (activator) or blocking (repressor) the recruitment of RNA polymerase
-eukaryotic TFs have multiple domains

Question 10

Describe the TATA binding protein (sequence, binding location, function)

Answer 10

-transcription factor
-binding location: b-sheet that binds sequence specific in MINOR groove
-sequence= TATA box = TATA AT A AT
-function = control of which gene gets transcribed
-TBP induces change; bends the TATA box

Question 11

How do COX-1 and COX-2 differ?

Answer 11

1. COX-1 is constitutive; COX-2 needs to be induced and can cause inflammation when induced
2. COX-1 has isoleucine where COX-2 has a valine

Question 12

How are COX-1 and COX-2 similar?

Answer 12

1. 60% of amino acid sequence is identical
2. isozymes = same active site, different function

Question 13

What is BiTE?

Answer 13

Bi-specific T-cell monoclonal antibody; two different binding sites each with a VH and VL domain

Question 14

How does a competitive inhibitor affect an enzyme’s kinetics?

Answer 14

changes Km, Vmax stays the same

Question 15

How does a noncompetitive inhibitor affect an enzyme’s kinetics?

Answer 15

Changes Vmax, Km stay the same

Question 16

How does a uncompetitive inhibitor affect an enzyme’s kinetics?

Answer 16

Changes both Vmax and Km