Question 1

Which statement is FALSE regarding the mediator protein in eukaryotic gene regulation?

Accepted Answer

A) It contains multiple subunits. 
B) It is involved in the formation of complexes with multiple additional proteins. 
C) It forms protein:protein interactions with RNA polymerase II. 
D) It enhances dephosphorylation of the RNA polymerase carboxy-terminal domain. 
E) It is required for transcription of multiple different mRNA species. 
A) It contains multiple subunits. 
B) It is involved in the formation of complexes with multiple additional proteins. 
C) It forms protein:protein interactions with RNA polymerase II. 
D) It enhances dephosphorylation of the RNA polymerase carboxy-terminal domain. 
E) It is required for transcription of multiple different mRNA species.

Question 2

Allolactose is an important molecule in regulation of the lac operon. How does allolactose differ from lactose?

Accepted Answer

A)  Lactose contains galactose and glucose, while allolactose contains two glucose units. 
B)  Lactose is a reducing sugar, while allolactose is not. 
C)  Lactose contains a $\beta$-glycosidic bond, while allolactose contains an $\alpha$-glycosidic bond. 
D)  Lactose contains a 1$\rightarrow$4 glycosidic bonds, while allolactose contains a 1$\rightarrow$6 glycosidic bond. 
E)  None of these statements describes differences between lactose and allolactose. 
A)  Lactose contains galactose and glucose, while allolactose contains two glucose units. 
B)  Lactose is a reducing sugar, while allolactose is not. 
C)  Lactose contains a $\beta$-glycosidic bond, while allolactose contains an $\alpha$-glycosidic bond. 
D)  Lactose contains a 1$\rightarrow$4 glycosidic bonds, while allolactose contains a 1$\rightarrow$6 glycosidic bond. 
E)  None of these statements describes differences between lactose and allolactose.

Question 3

Briefly explain (a) why there is a lag in cell growth when bacteria are switched from a medium containing glucose to one containing lactose. (b) When the growth medium contains both lactose and glucose, what proteins will be bound to the lac operon regulatory region? (c) If only lactose is in the growth medium, what proteins will be bound to the lac operon regulatory region?

Accepted Answer

(a) When bacteria are switched from a me

Question 4

Protein structural motifs often have general functions in common. Which motif is known to be involved in protein dimer formation but not in direct protein-DNA interactions?

Accepted Answer

A) $\beta$ barrel 
B)  helix-turn-helix 
C)  homeodomain 
D)  leucine zipper 
E)  zinc finger 
A) $\beta$ barrel 
B)  helix-turn-helix 
C)  homeodomain 
D)  leucine zipper 
E)  zinc finger

Question 5

Which base pair can form a hydrophobic interaction with a protein in the major groove?

Accepted Answer

A)  A-T 
B)  G-C 
C)  T-A 
D)  C-G 
E)  both A-T and T-A 
A)  A-T 
B)  G-C 
C)  T-A 
D)  C-G 
E)  both A-T and T-A

Question 6

Define each in one to two sentences: (a) heterochromatin; (b) euchromatin; (c) chromatin remodeling.

Accepted Answer

(a) Heterochromatin: Heterochromatin ref

Question 7

What is the functional complex that leads to proteolysis of LexA?

Accepted Answer

A)  RecA:dsDNA 
B)  LexA:dsDNA 
C)  RecA:ssDNA 
D)  LexA:ssDNA 
E)  LexA:RecA:ssDNA 
A)  RecA:dsDNA 
B)  LexA:dsDNA 
C)  RecA:ssDNA 
D)  LexA:ssDNA 
E)  LexA:RecA:ssDNA

Question 8

Which statement is FALSE?

Accepted Answer

A)  Unipotent cells can develop into only one type of cell or tissue. 
B)  Pluripotent cells can develop into a complete organism. 
C)  Multipotent bone marrow cells can develop into different types of blood cells. 
D)  Totipotent cells can develop into any kind of tissue. 
E)  Totipotent, unipotent, multipotent, and pluripotent are all types of stem cells. 
A)  Unipotent cells can develop into only one type of cell or tissue. 
B)  Pluripotent cells can develop into a complete organism. 
C)  Multipotent bone marrow cells can develop into different types of blood cells. 
D)  Totipotent cells can develop into any kind of tissue. 
E)  Totipotent, unipotent, multipotent, and pluripotent are all types of stem cells.

Question 9

RecA protein provides the functional link between DNA damage and the SOS response by displacing the LexA protein from its operator sites on the SOS genes. RecA does so by:

Accepted Answer

A)  associating with polymerase holoenzyme to help it remove LexA from operator. 
B)  bending LexA operator DNA to force dissociation of LexA repressor. 
C)  binding to LexA protein to weaken directly its affinity for operator sites. 
D)  causing self-cleavage of LexA, thus inactivating its binding to operator. 
E)  competitively binding to LexA operators and serving as an activator. 
A)  associating with polymerase holoenzyme to help it remove LexA from operator. 
B)  bending LexA operator DNA to force dissociation of LexA repressor. 
C)  binding to LexA protein to weaken directly its affinity for operator sites. 
D)  causing self-cleavage of LexA, thus inactivating its binding to operator. 
E)  competitively binding to LexA operators and serving as an activator.

Question 10

By mutating selected bases in sequence 3 in the leader peptide of the trp operon of E. coli, attenuation compared with the normal sequence is:

Accepted Answer

A)  unchanged. 
B)  only increased in the presence of Trp. 
C)  always increased. 
D)  decreased. 
E)  It cannot be determined from the information given. 
A)  unchanged. 
B)  only increased in the presence of Trp. 
C)  always increased. 
D)  decreased. 
E)  It cannot be determined from the information given.

Question 11

Draw a simple map of the lactose operon indicating the relative positions of promoter, operator, CRP-binding site, repressor gene (I), and the structural genes of the operon (A, Y, Z). Indicate where the CRP protein binds within this operon. When it is bound to this site, does the CRP protein have a positive or negative effect on gene expression in this system?

Accepted Answer

The lactose operon is a genetic system i

Question 12

When tryptophan binds to the Trp repressor, what is the effect on the repressor:operator interaction?

Accepted Answer

A)  The Kd for the repressor:operator complex increases, lowering affinity. 
B)  The Kd for the repressor:operator complex decreases, increasing affinity. 
C)  The Kd for the repressor:operator complex increases, increasing affinity. 
D)  The Kd for the repressor:operator complex decreases, lowering affinity. 
E)  There is no change in Kd. 
A)  The Kd for the repressor:operator complex increases, lowering affinity. 
B)  The Kd for the repressor:operator complex decreases, increasing affinity. 
C)  The Kd for the repressor:operator complex increases, increasing affinity. 
D)  The Kd for the repressor:operator complex decreases, lowering affinity. 
E)  There is no change in Kd.

Question 13

"All secondary structures formed in the trp operon attenuator can act as transcription terminators." Is this statement true or false, and if it is false, why is it false?

Accepted Answer

A)  The statement is true. 
B)  It is false because domains 3 and 4 will act as an antiterminator. 
C)  It is false because domains 2 and 3 will act as a terminator. 
D)  It is false because domains 3 and 4 will act as a terminator. 
E)  It is false because domains 2 and 3 will act as an antiterminator. 
A)  The statement is true. 
B)  It is false because domains 3 and 4 will act as an antiterminator. 
C)  It is false because domains 2 and 3 will act as a terminator. 
D)  It is false because domains 3 and 4 will act as a terminator. 
E)  It is false because domains 2 and 3 will act as an antiterminator.

Question 14

GCN5 is a histone acetyltransferase from S. cerevisiae. Given this, what can reasonably be stated about GCN5?

Accepted Answer

A)  GCN5 functions as a monomer in vivo. 
B)  GCN5 will convert euchromatin into heterochromatin. 
C)  GCN5 will reduce the positive charges on histone substrates. 
D)  GCN5 will have a single histone target. 
E)  GCN5 could be described as a histone chaperone. 
A)  GCN5 functions as a monomer in vivo. 
B)  GCN5 will convert euchromatin into heterochromatin. 
C)  GCN5 will reduce the positive charges on histone substrates. 
D)  GCN5 will have a single histone target. 
E)  GCN5 could be described as a histone chaperone.

Question 15

The tryptophan operon of E. coli is repressed by tryptophan added to the growth medium. The tryptophan repressor probably:

Accepted Answer

A)  binds to RNA polymerase when tryptophan is present. 
B)  binds to the trp operator in the absence of tryptophan. 
C)  binds to the trp operator in the presence of tryptophan. 
D)  is a DNA sequence. 
E)  is an attenuator. 
A)  binds to RNA polymerase when tryptophan is present. 
B)  binds to the trp operator in the absence of tryptophan. 
C)  binds to the trp operator in the presence of tryptophan. 
D)  is a DNA sequence. 
E)  is an attenuator.

Question 16

Which type of eukaryotic regulatory proteins interacts with enhancers?

Accepted Answer

A)  basal transcription factors 
B)  coactivators 
C)  repressors 
D)  TATA-binding proteins 
E)  transactivators 
A)  basal transcription factors 
B)  coactivators 
C)  repressors 
D)  TATA-binding proteins 
E)  transactivators

Question 17

The operators in the lac operon include two 6-base-pair sequences that are palindromes separated by approximately nine residues. What is the significance of that in terms of binding of the repressor protein?

Accepted Answer

The lac operon is a well-studied example

Question 18

Usually, a mutation in the promoter region of an operon causes reduced levels of synthesis of the proteins encoded by that operon. Occasionally, a mutation in the promoter region actually causes increased levels of synthesis. Can you suggest a plausible explanation?

Accepted Answer

Certainly! The promoter region of an ope

Question 19

Which factor does NOT contribute to the activation of transcription in eurkaryotes?

Accepted Answer

A)  SWI/SNF chromatin remodeling proteins 
B)  histone acetyltransferases 
C)  histone methylases 
D)  histone deacetylases 
E)  alterations in histone content 
A)  SWI/SNF chromatin remodeling proteins 
B)  histone acetyltransferases 
C)  histone methylases 
D)  histone deacetylases 
E)  alterations in histone content

Question 20

Which effect is NOT expected from changing the sequence in the -10 region of an E. coli promoter for a protein-coding gene?

Accepted Answer

A)  decreased binding of $\sigma$ subunits 
B)  decreased transcription of the mRNA 
C)  decreased binding of ribosomes to the mRNA 
D)  lower concentrations of the protein product in the cell 
E)  All of these effects would be expected. 
A)  decreased binding of $\sigma$ subunits 
B)  decreased transcription of the mRNA 
C)  decreased binding of ribosomes to the mRNA 
D)  lower concentrations of the protein product in the cell 
E)  All of these effects would be expected.

Exam 28: Regulation of Gene Expression

Which statement is FALSE regarding the mediator protein in eukaryotic gene regulation?

Allolactose is an important molecule in regulation of the lac operon. How does allolactose differ from lactose?

Protein structural motifs often have general functions in common. Which motif is known to be involved in protein dimer formation but not in direct protein-DNA interactions?

Which base pair can form a hydrophobic interaction with a protein in the major groove?

Define each in one to two sentences: (a) heterochromatin; (b) euchromatin; (c) chromatin remodeling.

What is the functional complex that leads to proteolysis of LexA?

Which statement is FALSE?

RecA protein provides the functional link between DNA damage and the SOS response by displacing the LexA protein from its operator sites on the SOS genes. RecA does so by:

By mutating selected bases in sequence 3 in the leader peptide of the trp operon of E. coli, attenuation compared with the normal sequence is:

When tryptophan binds to the Trp repressor, what is the effect on the repressor:operator interaction?

"All secondary structures formed in the trp operon attenuator can act as transcription terminators." Is this statement true or false, and if it is false, why is it false?

GCN5 is a histone acetyltransferase from S. cerevisiae. Given this, what can reasonably be stated about GCN5?

The tryptophan operon of E. coli is repressed by tryptophan added to the growth medium. The tryptophan repressor probably:

Which type of eukaryotic regulatory proteins interacts with enhancers?

The operators in the lac operon include two 6-base-pair sequences that are palindromes separated by approximately nine residues. What is the significance of that in terms of binding of the repressor protein?

Usually, a mutation in the promoter region of an operon causes reduced levels of synthesis of the proteins encoded by that operon. Occasionally, a mutation in the promoter region actually causes increased levels of synthesis. Can you suggest a plausible explanation?

Which factor does NOT contribute to the activation of transcription in eurkaryotes?

Which effect is NOT expected from changing the sequence in the -10 region of an E. coli promoter for a protein-coding gene?

The Foundations of Biochemistry

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Amino Acids, Peptides, and Proteins

The Three-Dimensional Structure of Proteins

Protein Function

Enzymes

Carbohydrates and Glycobiology

Nucleotides and Nucleic Acids

DNA-Based Information Technologies

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Biological Membranes and Transport

Biosignaling

Bioenergetics and Biochemical Reaction Types

Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway

Principles of Metabolic Regulation

The Citric Acid Cycle

Fatty Acid Catabolism

Amino Acid Oxidation and the Production of Urea

Oxidative Phosphorylation and Photophosphorylation

Carbohydrate Biosynthesis in Plants and Bacteria

Lipid Biosynthesis

Biosynthesis of Amino Acids, Nucleotides, and Related Molecules

Hormonal Regulation and Integration of Mammalian Metabolism

Genes and Chromosomes

DNA Metabolism

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