Deck 9: Dna-Protein Interactions in Bacteria

Question 1

Which of the following techniques would you use if you were designing an experiment to look at cooperativity of repressor binding to DNA?

A)S1 mapping
B)DNAase I footprinting
C)in vitro mutagenesis
D)S1 mapping and in vitro mutagenesis
E)none of the choices are correct.

Answer 1

B

Question 2

Looking at the binding of proteins to DNA in terms of entropy,it appears that

A)the level of entropy decreases in monomeric proteins promoting binding to DNA.
B)the DNA-protein complex is more ordered than the DNA or protein alone.
C)binding of two protein subunits,independently of each other,causes an increase in entropy.
D)the level of entropy decreases in monomeric proteins promoting binding to DNA and the DNA-protein complex is more ordered than the DNA or protein alone are correct.
E)the DNA-protein complex is more ordered than the DNA or protein alone and binding of two protein subunits,independently of each other,causes an increase in entropy are correct.

Answer 2

B

Question 3

Select the correct statement about enhancers

A)They are proteins that promote transcription of RNA.
B)They stimulate the binding of repressor to DNA.
C)They bind protein factors and stimulate transcription.
D)They are nonpromoter protein elements.
E)None of the choices is correct.

Answer 3

C

Question 4

Which of the following is true about repressor interaction with the gal operator?

A)The repressor binds the operator and causes looping of the DNA.
B)Binding of the operator does not prevent transcription.
C)There is no contact with the major grooves.
D)The repressor binds the operator and causes looping of the DNA and binding of the operator does not prevent transcription are correct.
E)Binding of the operator does not prevent transcription and there is no contact with the major grooves are correct.

Question 5

Predict the outcome of addition of DMS to the open complex formed when polymerase binds to a promoter.

A)Repressors will bind more tightly to the operator.
B)Methylation may occur on some nucleotides.
C)Polymerase will be displaced.
D)Phosphodiester bonds in the operator region will be broken.
E)All of the choices are correct.

Question 6

Protein crystals are used in x-ray diffraction studies because

A)the molecules of proteins in a powder or solution are too loose.
B)the diffraction power of a single protein molecule is too low.
C)several molecules of proteins are in a crystal leading to strong diffraction patterns.
D)the molecules of proteins in a powder or solution are too loose and the diffraction power of a single protein molecule is too low only.
E)the molecules of proteins in a powder or solution are too loose,the diffraction power of a single protein molecule is too low,and several molecules of proteins are in a crystal leading to strong diffraction patterns.

Question 7

Compared to x-rays,greater resolution can be obtained with light due to its longer wavelength.

Question 8

In an experiment to study the interaction of polymerase with the promoter region of the gal4 gene,heparin was added to the assay after the open complex was formed.What is the expected outcome of this?

A)The open complex will melt.
B)Some nucleotides will be ethylated.
C)Polymerase will be displaced.
D)Polymerase binding will be inhibited.
E)None of the choices is correct.

Question 9

Which of the following contributes to the specificity of binding between DNA and a repressor protein?

A)specificity of the interaction between bases and amino acids
B)the ability of DNA to assume certain shapes
C)the ability of DNA to base pair
D)specificity of the interaction between bases and amino acids and the ability of DNA to base pair
E)specificity of the interaction between bases and amino acids and the ability of DNA to assume certain shapes

Question 10

In x-ray crystallography

A)x-ray density maps are used to calculate structure.
B)diffraction patterns are generated from crystal structure of molecules.
C)x-ray is used because of its short wavelength.
D)x-ray density maps are used to calculate structure and diffraction patterns are generated from crystal structure of molecules only.
E)x-ray density maps are used to calculate structure,diffraction patterns are generated from a crystal structure of a molecule and x-ray is used because of its short wavelength.

Question 11

The specificity of repressors and activators binding to DNA depends on certain amino acids residing in the recognition helix making specific contact with the major groove.

Question 12

Which of the following techniques can be use to study the interaction between repressors and operators?

A)x-ray diffraction
B)EMSA
C)Southern blotting
D)immunoblotting
E)Both x-ray diffraction and EMSA

Question 13

Which of the following provided further evidence of the importance of specific amino acids in repressor binding?

A)ethylation
B)methylation
C)DNA sequence data
D)genetic analysis
E)all of the choices are correct.

Question 14

High-resolution analysis of the l repressor-operator complex shows that

A)the DNA is contacted by amino acid residues of the repressor through the major groove.
B)the DNA wraps around the helix but makes no contact with the major and minor grooves.
C)the amino acids are covalently bonded to DNA.
D)the DNA is contacted by amino acid residues of the repressor through the major groove and the DNA wraps around the helix but makes no contact with the major and minor grooves are correct.
E)the DNA is contacted by amino acid residues of the repressor through the major groove,the DNA wraps around the helix but makes no contact with the major and minor grooves,and the amino acids are covalently bonded to DNA are correct.

Question 15

Compared to binding of monomeric proteins to DNA,which of the following is true regarding the binding of a dimeric protein?

A)requires twice the energy
B)entropy increases
C)requires less energy
D)disorder increases
E)none of the choices are correct.

Question 16

All of the following contain helix-turn-helix motifs except

A) $\lambda$ repressor.
B)tryptophan.
C)Cro.
D)CAP.
E)All of the choices are correct.

Question 17

Which of the following could alter the specificity of binding of a repressor with an operator?

A)nucleotide deletion at the operator
B)nucleotide addition at the operator
C)site directed mutagenesis at the operator
D)nucleotide deletion at the operator and nucleotide addition at the operator only
E)nucleotide deletion at the operator,nucleotide addition at the operator,and site directed mutagenesis at the operator

Question 18

Predict what may occur when two separate operators are bound to molecules of a specific repressor.

A)attraction of other repressors to the site
B)cooperative binding of a second repressor
C)looping out of the intervening nonoperator sequence
D)attraction of other repressors to the site and cooperative binding of a second repressor
E)cooperative binding of a second repressor and looping out of the intervening nonoperator sequence

Question 19

The array of spots in a diffraction pattern cannot be used to construct an electron density map because

A)the phase angles are not included in a diffraction pattern.
B)the protein is coated with heavy atoms.
C)heavy atoms bind to reactive amino acids.
D)the proteins are coated with mercury.
E)none of the choices are correct.

Question 20

Enhancers are usually quite a distance away from promoters.Which of the following best explains the interaction of such enhancers with promoters?

A)The enhancer is brought closer by sliding.
B)Promoter and enhancer region are brought closer by DNA looping.
C)Promoter and enhancer regions are bought together by the complete removal of supercoils.
D)The enhancer is brought closer by sliding and promoter and enhancer region are brought closer by DNA looping are correct.
E)Promoter and enhancer region are brought closer by DNA looping and promoter and enhancer regions are bought together by the complete removal of supercoils are correct.

Question 21

The $\lambda$ and Cro repressors share affinities for the same operators,but they have microspecificies for O_R1 or O_R3.

Question 22

The tryptophan repressor is composed of tryptophan and an aporepressor.

Question 23

The procedure of making heavy-atom derivative crystals of protein is called multiple isomorphous replacement (MIR).

Question 24

Hydrogen bonds are formed between the amino acids in the repressor and the bases in the DNA.

Question 25

The interaction of DNA-binding proteins to DNA is enhanced by the cooperative association of the protein subunits.

Question 26

There are potential van der Waals forces between some glutamines of the repressor and bases in the operator.

Question 27

DNA binding proteins are usually octamers.