Question 1

What is the connection between DNA methylation, histone deacetylation, and gene regulation in eukaryotes?

Accepted Answer

DNA methylation and histone deacetylatio

Question 2

List at least two ways that regulation of genes for yeast galactose-metabolizing enzymes is different from regulation of E. coli lactose-utilizing enzymes.

Accepted Answer

One way that regulation of genes for yea

Question 3

A scientist is using crosslinked chromatin immunoprecipitation (XChIP) to determine the DNA sequences to which a protein of interest binds. However, when she attempts to sequence the DNA in the last step of the procedure, she is unable to obtain any DNA to sequence. Which of the following is a likely reason she is getting these results?

Accepted Answer

A)  The antibody she is using to precipitate the protein-DNA complex is not specific enough and binds the protein in question and five other proteins. 
B)  The protein and DNA are not properly crosslinked. 
C)  The antibody she is using is not specific to the DNA sequence to which the protein binds. 
D)  The DNA is too tightly complexed with histone proteins to allow sequencing. 
E)  The cells were lysed during the precipitation stage of the process. 
A)  The antibody she is using to precipitate the protein-DNA complex is not specific enough and binds the protein in question and five other proteins. 
B)  The protein and DNA are not properly crosslinked. 
C)  The antibody she is using is not specific to the DNA sequence to which the protein binds. 
D)  The DNA is too tightly complexed with histone proteins to allow sequencing. 
E)  The cells were lysed during the precipitation stage of the process.

Question 4

In both prokaryotes and eukaryotes, groups of genes can be regulated simultaneously (coordinately expressed). However, each group accomplishes this task differently. Explain how coordinate expression differs in prokaryotes compared with eukaryotes.

Accepted Answer

In prokaryotes, coordinate gene expressi

Question 5

Describe the unusual posttranscriptional control of Drosophila sex determination. How does the cascade of events differ between males and females?

Accepted Answer

In Drosophila, the sex determination pat

Question 6

Given the following figure, what would be the effect of a mutation that occurred in the insulator that prevented the binding of the insulator-binding protein?

Accepted Answer

A)  Both Enhancer 1 and Enhancer II would be able to stimulate the transcription of Genes A and B. 
B)  Enhancer I would no longer be able to stimulate the transcription of Gene B. 
C)  Enhancer I will be able to hypermethylate Gene B. 
D)  As long as the insulator sequence is not deleted, there will be no change in the transcription regulation of Gene A or B. 
E)  Enhancer II will no longer be able to stimulate the transcription of Gene A. 
A)  Both Enhancer 1 and Enhancer II would be able to stimulate the transcription of Genes A and B. 
B)  Enhancer I would no longer be able to stimulate the transcription of Gene B. 
C)  Enhancer I will be able to hypermethylate Gene B. 
D)  As long as the insulator sequence is not deleted, there will be no change in the transcription regulation of Gene A or B. 
E)  Enhancer II will no longer be able to stimulate the transcription of Gene A.

Question 7

Which of the following CANNOT be determined by chromatin immunoprecipitation (ChIP)?

Accepted Answer

A)  the types of modification present on the DNA-binding proteins 
B)  the location of modified histones that activate or repress transcription 
C)  the position of transcription factors and associated regulators on the chromosome 
D)  identification of active promoters on a genome-wide level 
E)  the exact amount of protein expressed from a gene 
A)  the types of modification present on the DNA-binding proteins 
B)  the location of modified histones that activate or repress transcription 
C)  the position of transcription factors and associated regulators on the chromosome 
D)  identification of active promoters on a genome-wide level 
E)  the exact amount of protein expressed from a gene

Question 8

Let us assume that your goal is to determine whether or not the expression of your favorite gene (YFG) is regulated by miRNA. Also assume that the genome sequence is known for the organism from which YFG was isolated. Describe the logical experiment steps to achieve your goal.

Accepted Answer

1. Identify potential miRNA binding site

Question 9

In the nematode roundworm Caenorhabditis elegans, the LIN-14 protein controls the timing of certain cell divisions during development. LIN-14 protein levels are normally high in early development but decrease in the later stages. In a lin-4 mutant, the level of LIN-14 protein stays high throughout development, changing the pattern of cell divisions in the animal and producing defects in the shape of the animal. The lin-4 gene encodes a microRNA that binds to a sequence in the 3'UTR of the lin-14 mRNA.
a. How does the lin-4 microRNA likely regulate LIN-14 protein levels? Explain why the lin-4 mutant has high levels of LIN-14 throughout development.
b. Mutations in the 3' UTR of lin-14 have been identified that alter the sequence to which lin-4 normally binds. What effect would these mutations be expected to have on the expression of LIN-14 protein in the animal?

Accepted Answer

a. The lin-4 microRNA likely regulates L

Question 10

Attenuation occurs in prokaryotes but has not been seen as a gene-expression mechanism in eukaryotes. Why not?

Accepted Answer

Attenuation is a regulatory mechanism th

Question 11

Degradation of a eukaryotic mRNA is generally initiated by:

Accepted Answer

A)  cleavage of the 5' end. 
B)  random cleavages throughout the mRNA strand. 
C)  shortening of the poly(
A)  tail. 
D)  recruitment of the chromosome-remodeling complex. 
E)  removal of the 5' cap. 
A)  cleavage of the 5' end. 
B)  random cleavages throughout the mRNA strand. 
C)  shortening of the poly(
A)  tail. 
D)  recruitment of the chromosome-remodeling complex. 
E)  removal of the 5' cap.

Question 12

DNA sequences that might act as enhancers (regulatory elements) can be attached to the gene for green fluorescent protein (GFP) and the combined DNA sequence can be reintroduced into an organism. If the DNA sequence attached to GFP actually can act as an enhancer, glowing green pigment will be observed in particular regions of the organism. Gene A is expressed in developing nerve cells, muscle cells, and intestinal cells in the fruit fly embryo. The region of DNA around gene A is depicted below. The pieces of DNA indicated with lines 1-5 were attached to GFP and tested for the ability to activate gene expression in the fly embryo. In piece 5, the "X" indicates a deletion of a single base pair.   $$\begin{array} { | l | l | } 
\hline \text { DNA } & { \text { GFP Expression } } \
\hline \text { Piece 1 } & \text { Muscle cells } \
\hline \text { Piece 2 } & \text { Nerve cells, intestinal cells } \
\hline \text { Piece 3 } & \text { No expression } \
\hline \text { Piece 4 } & \text { Nerve cells, intestinal cells } \
\hline \text { Piece 5 } & \text { Intestinal cells } \
\hline
\end{array}$$ a. Based on the pattern of GFP expression when attached to either piece 1 or piece 2, propose a model for how gene A is activated in the different cells of the embryo.
b. Propose an explanation for the difference in GFP expression caused by piece 3 and piece 4.
c. What has the deletion "X" in piece 5 likely affected to cause the change of GFP expression compared to piece 2? How does this result refine the model proposed in (a)?

Accepted Answer

The answer of DNA sequences that might act as enhancers...

Question 13

A genetics student identified a male fly (Drosophila) that had an XX genotype. Which of the following is the MOST accurate plausible explanation?

Accepted Answer

A)  The fly could only have a mutation in its sex-lethal (Sxl) gene. 
B)  The fly could only have a mutation in its transformer (tra) gene. 
C)  The fly could only have a mutation in its double-sex (dsx) gene. 
D)  The fly could have a mutation in either its sex-lethal (Sxl) or transformer (tra) gene. 
E)  The fly could have a mutation in its sex-lethal (Sxl), transformer (tra), or double-sex (dsx) gene. 
A)  The fly could only have a mutation in its sex-lethal (Sxl) gene. 
B)  The fly could only have a mutation in its transformer (tra) gene. 
C)  The fly could only have a mutation in its double-sex (dsx) gene. 
D)  The fly could have a mutation in either its sex-lethal (Sxl) or transformer (tra) gene. 
E)  The fly could have a mutation in its sex-lethal (Sxl), transformer (tra), or double-sex (dsx) gene.

Question 14

Eukaryotic genes can be introduced into bacteria by recombinant DNA techniques. If the introduced gene encodes a protein that is also found in bacteria-for example, a universally used glycolysis enzyme-then expression of the eukaryotic gene may produce a protein that functions in the bacterial cell.
The mouse gene for a glycolysis enzyme is introduced into an E. coli cell that has a mutant gene for the bacterial version of the same enzyme. Even though the mouse enzyme should function in the bacterial cell and restore the cell's ability to perform glycolysis, it does not.
Provide two possible reasons why this experiment does not work and propose a solution to overcome one of the problems you suggest.

Accepted Answer

There are two possible reasons why the i

Question 15

A fly (Drosophila) with an XY genotype has a mutation in its sex-lethal (Sxl) gene that renders its protein product nonfunctional. Which of the following describes the sex of this fly?

Accepted Answer

A)  male 
B)  female 
C)  intersex 
D)  male, but it will be sterile 
E)  female, but it will be sterile 
A)  male 
B)  female 
C)  intersex 
D)  male, but it will be sterile 
E)  female, but it will be sterile

Question 16

Which of the following statements about regulation of eukaryotic gene expression is INCORRECT?

Accepted Answer

A)  The presence of a nuclear membrane separating transcription and translation in eukaryotes led to the evolution of additional mechanisms of gene regulation. 
B)  In eukaryotes, most structural genes are found within operons. 
C)  Eukaryotic mRNAs are generally more stable than prokaryotic mRNAs. 
D)  The rate of degradation of mRNAs is important in regulation in eukaryotes. 
E)  Posttranslational regulation of histones is unique to eukaryotes. 
A)  The presence of a nuclear membrane separating transcription and translation in eukaryotes led to the evolution of additional mechanisms of gene regulation. 
B)  In eukaryotes, most structural genes are found within operons. 
C)  Eukaryotic mRNAs are generally more stable than prokaryotic mRNAs. 
D)  The rate of degradation of mRNAs is important in regulation in eukaryotes. 
E)  Posttranslational regulation of histones is unique to eukaryotes.

Question 17

Which of the following statements about CpG islands is CORRECT?

Accepted Answer

A)  CpG islands are commonly found at the 3' UTR regions. 
B)  The CpG island methylation is universal across both prokaryotes and eukaryotes. 
C)  Methylated CpG islands are associated with long-term gene repression. 
D)  Transcriptionally active DNA has a higher frequency of methylated CpG. 
E)  There is an association between DNA methylation at the CpG island and acetylation of histone via recruitment of acetylases. 
A)  CpG islands are commonly found at the 3' UTR regions. 
B)  The CpG island methylation is universal across both prokaryotes and eukaryotes. 
C)  Methylated CpG islands are associated with long-term gene repression. 
D)  Transcriptionally active DNA has a higher frequency of methylated CpG. 
E)  There is an association between DNA methylation at the CpG island and acetylation of histone via recruitment of acetylases.

Question 18

In Arabidopsis, FLD (a deacetylase enzyme) stimulates flowering. Which of the following statements is TRUE?

Accepted Answer

A)  FLD deacetylates histones that bind to regions of the FLC gene and stimulates its transcription. 
B)  FLD deacetylates histones surrounding the FLD gene, causing suppression of FLD transcription. 
C)  FLD deacetylates histones that bind to the FLC gene, causing repression of FLC transcription. 
D)  FLD causes repression of FLC translation. 
A)  FLD deacetylates histones that bind to regions of the FLC gene and stimulates its transcription. 
B)  FLD deacetylates histones surrounding the FLD gene, causing suppression of FLD transcription. 
C)  FLD deacetylates histones that bind to the FLC gene, causing repression of FLC transcription. 
D)  FLD causes repression of FLC translation.

Question 19

Which of the following processes is also known as RNA silencing or posttranscriptional gene silencing?

Accepted Answer

A)  protein degradation 
B)  transcriptional stalling 
C)  RNA splicing 
D)  transcriptional repression 
E)  RNA interference 
A)  protein degradation 
B)  transcriptional stalling 
C)  RNA splicing 
D)  transcriptional repression 
E)  RNA interference

Question 20

A scientist created transgenic C. elegans worms that expressed a gene that made the worms glow green under fluorescent light. Then she injected double-stranded RNA complementary to this gene. Which of the following results was MOST likely to be seen?

Accepted Answer

A)  The worms glowed green under fluorescent light. 
B)  The worms were not able to glow green under fluorescent light. 
C)  The injection of double-stranded RNA was lethal and the worms died. 
D)  The worms had an increased life span. 
E)  The CpG islands near the promoter of the gene became demethylated. 
A)  The worms glowed green under fluorescent light. 
B)  The worms were not able to glow green under fluorescent light. 
C)  The injection of double-stranded RNA was lethal and the worms died. 
D)  The worms had an increased life span. 
E)  The CpG islands near the promoter of the gene became demethylated.

Exam 17: Control of Gene Expression in Eukaryotes

What is the connection between DNA methylation, histone deacetylation, and gene regulation in eukaryotes?

List at least two ways that regulation of genes for yeast galactose-metabolizing enzymes is different from regulation of E. coli lactose-utilizing enzymes.

In both prokaryotes and eukaryotes, groups of genes can be regulated simultaneously (coordinately expressed). However, each group accomplishes this task differently. Explain how coordinate expression differs in prokaryotes compared with eukaryotes.

Describe the unusual posttranscriptional control of Drosophila sex determination. How does the cascade of events differ between males and females?

Given the following figure, what would be the effect of a mutation that occurred in the insulator that prevented the binding of the insulator-binding protein?

Which of the following CANNOT be determined by chromatin immunoprecipitation (ChIP)?

Let us assume that your goal is to determine whether or not the expression of your favorite gene (YFG) is regulated by miRNA. Also assume that the genome sequence is known for the organism from which YFG was isolated. Describe the logical experiment steps to achieve your goal.

Attenuation occurs in prokaryotes but has not been seen as a gene-expression mechanism in eukaryotes. Why not?

Degradation of a eukaryotic mRNA is generally initiated by:

A genetics student identified a male fly (Drosophila) that had an XX genotype. Which of the following is the MOST accurate plausible explanation?

A fly (Drosophila) with an XY genotype has a mutation in its sex-lethal (Sxl) gene that renders its protein product nonfunctional. Which of the following describes the sex of this fly?

Which of the following statements about regulation of eukaryotic gene expression is INCORRECT?

Which of the following statements about CpG islands is CORRECT?

In Arabidopsis, FLD (a deacetylase enzyme) stimulates flowering. Which of the following statements is TRUE?

Which of the following processes is also known as RNA silencing or posttranscriptional gene silencing?

A scientist created transgenic C. elegans worms that expressed a gene that made the worms glow green under fluorescent light. Then she injected double-stranded RNA complementary to this gene. Which of the following results was MOST likely to be seen?

Introduction to Genetics

Chromosomes and Cellular Reproduction

Basic Principles of Heredity

Sex Determination and Sex-Linked Characteristics

Extensions and Modifications of Basic Principles

Pedigree Analysis, Applications, and Genetic Testing

Linkage, Recombination, and Eukaryotic Gene Mapping

Chromosome Variation

Bacterial and Viral Genetic Systems

DNA: the Chemical Nature of the Gene

Chromosome Structure and Organelle Dna

DNA Replication and Recombination

Transcription

Rna Molecules and Rna Processing

The Genetic Code and Translation

Control of Gene Expression in Prokaryotes

Gene Mutations and Dna Repair

Molecular Genetic Analysis and Biotechnology

Genomics and Proteomics

Epigenetics

Developmental Genetics and Immunogenetics

Cancer Genetics

Quantitative Genetics

Population Genetics

Evolutionary Genetics

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