Chapter 9: DNA-Protein Interactions in Prokaryotes

Question 1

434 repressor protein recognition helix (x2)

key amino acids? they bind…?

Answer 1

carries partial positive charge

forms H-bonds with DNA to create slight structural bend inhibiting transcription (compacts minor groove, opens major groove)

glutamine 28/24/33; adenine, guanine, & thymine/adenine

Question 2

helix-turn-helix

allows protein to fit within DNA strands

Answer 2

repressor supersecondary structure

function?

Question 2

form dimers

directly bind operator O_R2 w/in major DNA groove using hydrgoen bonding of recognition helices (between DNA bases and specific amino acids)

DNA-bound proteins can associate/dimerize with other repressor proteins at distant sites –> DNA looping (what does this do?)

Answer 2

Lambda repressor proteins (x3)

-blocks transcription or makes DNA susceptible to cutting by DNases

Question 3

both contain polar & nonpolar hydrophobic amino acids (but tend to be hydrophobic)

Answer 3

helices from phages 434 & P22

Question 5

Ptashne et el

Answer 5

ID’d and mapped the key amino acids within the helices of 434 & P22

Question 6

glutamine 33/34 & serine 45

asparagine 55 & lyrine 4

Answer 6

crucial lambda repressor amino acids to recognition helix

additionals?

Question 7

Acceptor and Donor Sites

1. AT: major
2. AT: minor
3. CG: major
4. CG: minor

Answer 7

Acceptor and Donor Sites

1. 2 A’s, 1 D
2. 2 A’s, 0 D’s
3. 2 A’s, 1 D
4. 2 A’s, 1 D

Question 7

Cap binding to DNA

Answer 7

requires DNA kinking

Question 8

crucial lambda repressor amino acids to recognition helix

additionals?

Answer 8

glutamine 33/34 & serine 45

asparagine 55 & lyrine 4

Question 9

carries partial positive charge

forms H-bonds with DNA to create slight structural bend inhibiting transcription (compacts minor groove, opens major groove)

glutamine 28/24/33; adenine, guanine, & thymine/adenine

Answer 9

434 repressor protein recognition helix (x2)

key amino acids? they bind…?

Question 9

contains 2 operators, one internal, one near promoter

Trxn stopped with protein binding to both operators and dimerization –> DNA looping

Answer 9

Gal operon

Question 10

Asparagine, Valine, Serine, & Arginine

Answer 10

P22 DNA-binding amino acids

Question 11

Cro protein (x2)

Answer 11

uses helix-turn-helix DNA binding motif and binds same operators as the lambda repressor

Question 12

helices from phages 434 & P22

Answer 12

both contain polar & nonpolar hydrophobic amino acids (but tend to be hydrophobic)

Question 13

Enhancer

• stabalizes or recruits polymerase to promoter
• e.g.?

Answer 13

DNA-protein binding complexes that trigger transcription from a distant site or separate DNA molecule using DNA looping (how?)

e.g.= E. coli glnA

Question 15

Gal operon

Answer 15

contains 2 operators, one internal, one near promoter

Trxn stopped with protein binding to both operators and dimerization –> DNA looping

Question 16

repressor supersecondary structure

function?

Answer 16

helix-turn-helix

allows protein to fit within DNA strands

Question 17

uses helix-turn-helix DNA binding motif and binds same operators as the lambda repressor

Answer 17

Cro protein

Question 18

Acceptor and Donor Sites

1. 2 A’s, 1 D
2. 2 A’s, 0 D’s
3. 2 A’s, 1 D
4. 2 A’s, 1 D

Answer 18

Acceptor and Donor Sites

1. AT: major
2. AT: minor
3. CG: major
4. CG: minor

Question 19

requires DNA kinking

Answer 19

Cap binding to DNA

Question 21

ID’d and mapped the key amino acids within the helices of 434 & P22

Answer 21

Ptashne et el

Question 22

DNA-protein binding complexes that trigger transcription from a distant site or separate DNA molecule using DNA looping (how?)

e.g.?

Answer 22

Enhancer

• stabalizes or recruits polymerase to promoter
• e.g. E. coli glnA

Question 23

P22 DNA-binding amino acids

Answer 23

Asn, Val, Ser, & Arg

Question 24

Lambda repressor proteins (x3)

-blocks transcription or makes DNA susceptible to cutting by DNases

Answer 24

form dimers

directly bind operator O_R2 w/in major DNA groove using hydrgoen bonding of recognition helices (between DNA bases and specific amino acids)

DNA-bound proteins can associate/dimerize with other repressor proteins at distant sites –> DNA looping (what does this do?)