Biochemistry II Quiz 4

Question 1

What is the transport mechanism of SERT?

Answer 1

-dependent on sodium and chloride: binding Na+, serotonin, Cl- causes a conformational change to transport
-membrane potential of Na+ needed (ATPase)

Question 2

What are the conformational changes for transport?

Answer 2

-outward-open: central substrate site accessible to synapse cleft
-occluded: substrate site closed; but access to an allosteric site where drugs bind
-inward-open: structural change for substrate exiting

Question 3

What are Primary Active Transporters?

Answer 3

-transfers solutes against the concentration gradient
-energy from ATP hydrolysis

Question 4

What are two examples of Primary Active Transporters?

Answer 4

P-type: Na/K ATPase
ABC: P-glycoprotein

Question 5

What is the role of ATP-binding cassette (ABC) transporters in eukaryotic cells?

Answer 5

-to be exporters or effluxers (not importers) that function as pumps to extrude toxins/drugs out of the cell

Question 6

What two domains are found in ABC transporters?

Answer 6

-2 Transmembrane domains (substrate binding; changes conformation)
-2 Nucleotide binding domains (ATP cassette; where ATP binds)

Question 7

What type of ABC transporters cause drug resistance?

Answer 7

-multi resistance drug family (Mdr); aka P-glycoprotein

Question 8

What are Topoisomerases?

Answer 8

-function to maintain proper DNA supercoiling; targets for anticancer drugs

Question 9

What are some differences between B-DNA and A-DNA?

Answer 9

B-DNA: elongated, narrow
A-DNA: compressed, wider
-differerent major and minor grooves

Question 10

Which type of DNA is most energetically stable under physiological conditions?

Answer 10

B-DNA

Question 11

What DNA has a wider and shallower major groove?

Answer 11

B-DNA
-makes proteins highly accessible to bind

Question 12

What is the biological role of A-form DNA?

Answer 12

-occurs under dehydrating conditions and protects DNA under desiccating conditions (bacterial spores have A-form DNA)

Question 13

What are intercalators?

Answer 13

-hydrophobic, heterocyclic agents that insert between bases via ring-stacking
ex: TOTO

Question 14

What are minor or major groove binders?

Answer 14

-molecules that selectively bind to the minor/major groove of DNA
ex: Netropsin; lies in minor groove and changes rotation

Question 15

What is supercoiling (Superhelicity)?

Answer 15

created by the underwinding or overwinding DNA
underwinding- negative supercoiling
overwinding- positive supercoiling
occurs in B-form DNA

Question 16

What is formed with underwinding of DNA?

Answer 16

right-handed superhelix (negative supercoiling)
-clockwise as you go up the coil

Question 17

What is formed with overwinding of DNA?

Answer 17

left-handed superhelix (positive supercoiling)
-counterclockwise as you go up the coil

Question 18

What is the topology of supercoiling?

Answer 18

Lk(Linking Number)= Tw(Twist) + Wr(Writhe)
Twist- turns in DNA chain; one turn for every 10 base pairs of DNA
Writhe- superhelical coils
righthandedness- subtract for Wr
lefthandedness -add for Wr

Question 19

What is the role of a prokaryotic topoisomerase?

Answer 19

-introduce negative supercoils
-some bacteria can make supercoils leading to potential targets for antibiotic targets

Question 20

What are some differences between Type 1 and Type 2 topoisomerases?

Answer 20

Type 1: cuts one strand of DNA; no energy source is needed; cut strand is free to rotate around intact
Type 2: cuts both strands of DNA; requires ATP; moves another dsDNA segment through the opening in the cut strand

Question 21

What occurs in the Topoisomerase I mechanism?

Answer 21

-forms a transient covalent bond between a tyrosine residue and a phosphoryl group at the cleavage site
-relaxes by controlled rotation of the free end
-gap is sealed by re-ligating the cleaved strand

Question 22

Topoisomerase drugs
1. are highly selective and used to treat inflammation
2. stall DNA replication
3. are under development for many topoisomerase classes, but only Top1 inhibitors have been approved by the FDA
4. based on the overall drug action mechanism, would probably reduce Km but not Vmax
5. can be highly selective as an antibiotic by targeting a bacterial enzyme not present in humans
6. include ciprofloxacin, which gained media attention for its use in the treatment of anthrax
7. prevents supercoils from being relaxed

Answer 22

5. can be highly selective as an antibiotic by targeting a bacterial enzyme not present in humans
6. include ciprofloxacin, which gained media attention for its use in the treatment of anthrax
7. prevents supercoils from being relaxed