Question 1

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

Accepted Answer

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

Question 2

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

Accepted Answer

A) True 
 B)False  True

Question 3

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

Accepted Answer

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

Question 4

The $\lambda$ and Cro repressors share affinities for the same operators,but they have microspecificies for OR1 or OR3.

Accepted Answer

A) True 
 B)False

Question 5

Protein crystals are used in x-ray diffraction studies because

Accepted Answer

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. 
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 6

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

Accepted Answer

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. 
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 7

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

Accepted Answer

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 
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 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?

Accepted Answer

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. 
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

DNA binding proteins are usually octamers.

Accepted Answer

A) True 
 B)False

Question 10

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

Accepted Answer

A) True 
 B)False

Question 11

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

Accepted Answer

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. 
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 12

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

Accepted Answer

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 
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 13

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

Accepted Answer

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. 
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 14

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

Accepted Answer

A) True 
 B)False

Question 15

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

Accepted Answer

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. 
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.

Question 16

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.

Accepted Answer

A) True 
 B)False

Question 17

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

Accepted Answer

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 
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 18

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

Accepted Answer

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. 
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 19

In x-ray crystallography

Accepted Answer

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. 
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 20

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

Accepted Answer

A) True 
 B)False

Exam 9: Dna-Protein Interactions in Bacteria

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

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

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

The λ\lambdaλ and Cro repressors share affinities for the same operators,but they have microspecificies for OR1 or OR3.

Protein crystals are used in x-ray diffraction studies because

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

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

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?

DNA binding proteins are usually octamers.

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

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

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

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

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

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

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.

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

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

In x-ray crystallography

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

A Brief History

The Molecular Nature of Genes

An Introduction to Gene Function

Molecular Cloning Methods

Molecular Tools for Studying Genes and Gene Activity

The Mechanism of Transcription in Bacteria

Operons: Fine Control of Bacterial Transcription

Major Shifts in Bacterial Transcription

Eukaryotic Rna Polymerases and Their Promoters

General Transcription Factors in Eukaryotes

Transcription Activators in Eukaryotes

Chromatin Structure and Its Effect on Transcription

Rna Processing I: Splicing

Rna Processing II: Capping and Polyadenylation

Rna Processing: Other Post-Transcriptional Events

The Mechanism of Translation I: Initiation

The Mechanism of Translation II: Elongation and Termination

Ribosomes and Transfer Rna

Dna Replication,damage and Repair

Dna Replication II: Detailed Mechanism

Homologous Recombination

Transposition

Introduction to Genomics: Dna Sequencing on a Genomic Scale

Genomics II: Functional Genomics,proteomics and Bioinformatics

Filters

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