Deck 10: Analyzing Genomic Variation

Question 1

The gene products encoded by trans-acting elements perform their function by

A) associating with regulatory sequences distant from the gene from which they were transcribed.
B) regulating the expression of the gene from which they were transcribed.
C) the association of nucleotides with the elongating RNA transcript.
D) physically associating with DNA polymerase.
E) regulating the activity of telomerase.

Answer 1

A

Question 2

In generating a reporter construct to study gene regulation,the reporter gene introduced replaces

A) beta-galactosidase.
B) a random region of DNA.
C) the cis-acting regulatory DNA sequence.
D) X-gal.
E) the coding region of the gene being studied.

Answer 2

E

Question 3

Mutations introduced into reporter constructs are used to study

A) the DNA sequences that are important for regulating gene expression levels.
B) the effects on cell function of expression of heterologous proteins.
C) colorimetric assays.
D) protein-protein interactions.
E) Western blots.

Answer 3

A

Question 4

The __________________________ is the cis-acting DNA sequence that serves as the binding site for RNA polymerase.

A) promoter
B) terminator
C) enhancer
D) regulator
E) initiator

Question 5

Which of the following is not true of enhancer DNA sequences?

A) They contain the TATA box regulatory element.
B) They may be located upstream of a TATA box.
C) They can be more than 10 kilobases from the gene they regulate.
D) They may increase or decrease gene transcription levels.
E) They may contain multiple regulatory elements.

Question 6

Which of these is most important to ChIP (chromatin immunoprecipitation)technology?

A) an antibody that recognizes specific chromatin structures
B) an antibody that recognizes a nucleosome
C) an antibody that recognizes a transcription factor of interest
D) an antibody that recognizes the DNA cis-element of interest
E) an antibody that recognizes the promoter of interest

Question 7

Zinc-finger peptide motifs are responsible for what aspect of protein function?

A) kinase activity
B) DNA binding
C) mRNA splicing
D) DNA replication
E) methylation

Question 8

_______________ motifs function to promote the DNA-binding activity of many transcriptional activator proteins.

A) ABP
B) Zinc-finger
C) Basolateral
D) Leucine zipper
E) Medial cleft

Question 9

Mutations altering the amount of protein synthesized from a reporter construct occur most often in which of the following sequences of DNA?

A) the reporter gene
B) cis-acting DNA elements
C) X-gal coding sequence
D) RNA polymerase II gene
E) the introns of the reporter gene

Question 10

Transcription in prokaryotes and eukaryotes is similar in that

A) transcriptional machinery controls compaction and decompaction of chromatin.
B) the mRNA produced can undergo alternative splicing.
C) both prokaryotic and eukaryotic proteins have identical affinities for DNA.
D) both are contained within the cell nucleus.
E) both are regulated by attachment of proteins to DNA adjacent to the gene being transcribed.

Question 11

Trans-acting proteins that influence transcription are commonly referred to as

A) DNA polymerases.
B) tumor suppressors.
C) enhancers.
D) transcription factors.
E) promoter elements.

Question 12

RNA polymerase I synthesizes _________ using a DNA template.

A) dsRNA
B) mRNA
C) tRNA
D) snRNA
E) rRNA

Question 13

A cis-acting DNA sequence that modulates the basal rate of transcription of a gene is termed a(n)

A) repressor.
B) activator.
C) promoter.
D) enhancer.
E) initiator.

Question 14

DNA sequences that serve as binding sites for proteins regulating transcription and are often found adjacent to a gene are said to be

A) cross-reacting.
B) cis-acting.
C) trans-acting.
D) origins of transcription.
E) transcription factors.

Question 15

______________ are cis-acting DNA sequences that often function at a distance from the gene they are regulating.

A) Promoter elements
B) Terminator elements
C) Enhancer elements
D) Regulator elements
E) Initiator elements

Question 16

tRNA molecules are transcribed by

A) DNA pol II.
B) DNA pol III.
C) RNA pol I.
D) RNA pol II.
E) RNA pol III.

Question 17

_____________ are basal transcription factors that associate with TBP to assist in initiating transcription from eukaryotic class II genes.

A) TATAs
B) DNA-BPs
C) TAFs
D) Jun and Fos
E) Sxl and string

Question 18

Most decisions controlling the amount of gene product synthesized are made during

A) termination of replication.
B) transport of mRNA to the cytoplasm.
C) initiation of transcription.
D) alternative splicing.
E) regulation of translation.

Question 19

A transcription factor that increases initiation of transcription by associating with an enhancer element is termed a(n)

A) initiator.
B) activator.
C) repressor.
D) enhancer.
E) super-repressor.

Question 20

The primary function of basal transcription factors is to

A) repress transcription initiation of a particular gene.
B) assist in associating RNA polymerase with the promoter element.
C) increase transcription by binding enhancer sequences.
D) activate RNA synthesis at origins of replication.
E) regulate activity of DNA polymerase II.

Question 21

_______________ is used to describe a situation in which a gene's expression pattern is dependent upon the parent from whom it was inherited.

A) Genomic imprinting
B) Spermatogenesis
C) Heterodimerization
D) Homodimerization
E) Gender-specific RNA stability

Question 22

Hypercondensation of heterochromatin results in

A) hyperactivation of transcription.
B) suppression of progression through metaphase.
C) DNA replication.
D) transcriptional silencing.
E) reduced cell size.

Question 23

Regions of DNA are most sensitive to DNase digestion when

A) they are free of histones.
B) they are maintained as chromatin.
C) the nuclei in which they are contained enter prophase.
D) a cell is in G₀.
E) found at a recombination hotspot.

Question 24

Which of the following is not a mechanism employed by repressor proteins to decrease transcription of a specific gene?

A) The repressor associates with a promoter element,blocking RNA polymerase from binding promoter element.
B) The repressor binds to the activation domain of an activator,eliminating its ability to increase transcription.
C) The repressor binds to DNA-binding domain of an activator,eliminating its ability to associate with enhancer.
D) The repressor binds to a DNA sequence in an enhancer,eliminating access to sequence by activator.
E) The repressor binds to RNA polymerase II,blocking its ability to associate with promoter element.

Question 25

Which of the following would be suggested by a DNase hypersensitive site?

A) No transcription occurs in this region of the chromosome.
B) The chromatin is in an open state and available for transcription.
C) Transcription terminates at this site.
D) It indicates a region devoid of (lacking)genes.
E) The DNA is highly methylated.

Question 26

Why do Max/Max homodimers convert to Myc/Max heterodimers in the presence of Myc protein?

A) Myc has a higher affinity for Max than Max has for Max.
B) Myc more tightly associates with DNA,thus recruiting Max monomers to the enhancer.
C) The enhancer element being regulated only associates with Myc/Max heterodimers.
D) Max is rapidly degraded in the presence of Myc.
E) Myc/Myc homodimers are rapidly degraded in the presence of Max.

Question 27

Proteins that consist of two identical polypeptide subunits are classified as

A) monomers.
B) oligomers.
C) heterodimers.
D) homodimers.
E) diplomers.

Question 28

In yeast,the SIR protein complex physically interacts with histones H3 and H4 to cause

A) mRNA folding.
B) transcriptional silencing.
C) transcriptional activation.
D) basal transcription.
E) initiation of replication.

Question 29

A variation that does not involve a change in DNA sequence but can be passed from one generation to another is a(n)

A) enhancer trap.
B) replication origin.
C) Mendelian enhancer.
D) mutant chromosome.
E) epigenetic condition.

Question 30

The ________________ is the repeating structural unit of chromatin,consisting of approximately 200 base pairs of DNA and associated histone proteins.

A) transcriptosome
B) regulosome
C) nucleosome
D) enhanceosome
E) spliceosome

Question 31

Which of the following protein dimers are unable to associate with a DNA enhancer element?

A) Jun/Jun
B) Fos/Jun
C) Max/Max
D) Myc/Myc
E) Myc/Max

Question 32

DNA regions that are transcriptionally silenced by hypercondensation have often undergone a modification of their cytosine residues termed

A) hyperoxidation.
B) methylation.
C) dephosphorylation.
D) phosphorylation.
E) integration.

Question 33

The leucine zipper motif functions to

A) mediate the physical association of two polypeptides.
B) anchor transcriptional activator proteins to enhancer sequences.
C) release leucines from misfolded transcription factors.
D) integrate leucines and isoleucines into newly translated transcriptional activators.
E) open up proteins after transcription.

Question 34

The Myc protein is synthesized only in cells that are

A) in G₀.
B) virally infected.
C) proliferating.
D) cancerous.
E) dormant.

Question 35

In Drosophila females,Sxl protein associates with RNA transcribed from the ________________ gene,altering its splicing pattern.

A) sax
B) max
C) sxl
D) myc
E) SIR

Question 36

The DNase enzyme can be used in assays to identify regions of DNA that are

A) unable to undergo transcription.
B) associated with DNA polymerase.
C) unable to undergo replication.
D) of the Z-DNA form.
E) free of associated proteins.

Question 37

_________________ are transcription factors that decrease transcriptional activity by associating with specific enhancer elements or activator proteins.

A) Deregulators
B) Depleters
C) Regulators
D) Repressors
E) TBPs

Question 38

Mutations in the GAL80 gene in yeast result in the continuous expression of the GAL1,GAL7,and GAL10 genes,even in the absence of galactose.This genetic evidence suggests that the GAL80 gene product acts as a(n)

A) transcriptional repressor.
B) promoter element.
C) enhancer element.
D) transcriptional activator.
E) RNA polymerase.

Question 39

The association of DNA with histones to form chromatin affects transcription by

A) increasing basal transcription rates.
B) decreasing basal transcription rates.
C) increasing transcription of a few genes,while not influencing most others.
D) decreasing transcription of a few genes,while not influencing most others.
E) increasing transcription of some genes and decreasing transcription of others.

Question 40

The Myc transcription factor functions to increase transcription in specific cell types by

A) associating with Ras to form heterodimers.
B) forming Myc-Myc homodimers.
C) associating with Max to form heterodimers.
D) dissociating with Fos Jun heterodimers.
E) enhancing formation of Max-Max homodimers.

Question 41

Recessive mutations in the sxl gene in Drosophila are lethal in XX females because

A) sxl functions as a repressor of male-specific dosage-compensation genes.
B) recessive mutations indicate an increase in sxl activity.
C) these mutations are the result of a loss of both X chromosomes.
D) sxl is required for transcription of male-specific genes.
E) recessive mutations are always lethal.

Question 42

The Sxl protein triggers a cascade of splicing affecting other transcripts besides its own.

Question 43

Enhancers are regulatory sites that are next to the promoter.

Question 44

In repressor quenching,a repressor protein binds directly to an activator protein.

Question 45

One function of chromatin is to increase transcription to a high basal level.

Question 46

Which of the following is true in twin studies of imprinting and epigenetics?

A) Monozygotic twins have identical CpG methylation patterns
B) CpG methylation patterns are more similar in dizygotic twins than in monozygotic twins
C) Twin studies are not useful in methylation because environment overwhelms heritability in epigenetics
D) Dizygotic twins have identical CpG methylation patterns
E) CpG methylation patterns are more similar in monozygotic twins than in dizygotic twins

Question 47

All of the following are associated with the formation of a functional miRNA except

A) lack of an open reading frame (ORF).
B) 5' GTP cap and 3' poly A tail.
C) stem-loop structures.
D) translation on ribosomes.
E) RNA pol II promoter.

Question 48

In a process known as _____________,many tissues exposed to hormones for a long time lose their ability to respond to the hormone.

A) dephosphorylation
B) phosphorylation
C) degradation
D) sensitization
E) deamination.

Question 49

Trans-acting elements are genes located somewhere other than at the target gene and encode proteins that regulate another gene.

Question 50

RNA interference is a process that regulates gene expression at the time of transcription.

Question 51

What would be the most likely result of transferring the UTR (untranslated region)from one gene to another?

A) the binding of transcription factors may change
B) the posttranslational modification may change
C) the ubiquitination of the protein may change
D) the half-life of the mRNA may change
E) the rate of transcription may be decreased

Question 52

The max gene is expressed at all times.

Question 53

Cis-acting elements are DNA sequences that serve as attachment sites for DNA-binding proteins that regulate the initiation of transcription.

Question 54

Which of the following is not true of the mouse agouti A^vy allele?

A) it is recessive to all other alleles
B) it is metastable
C) it is an epiallele
D) it is caused by a retrotransposon
E) it is responsible for phenotypic variation

Question 55

Which of the following is not true of pri-miRNA?

A) It is transcribed by RNA polymerase II.
B) It is exported from the nucleus.
C) It contains stem-loop structures.
D) It may contain introns.
E) It is a substrate for Drosha in animal cells.

Question 56

Which of the following is not a mechanism for posttranslational modification controlling gene function?

A) ubiquitination
B) methylation
C) phosphorylation
D) dephosphorylation
E) covalent attachment of small molecules to protein.

Question 57

Which of the following is not involved in RNA interference processes?

A) RISC
B) Drosha
C) RNA polymerase I
D) Dicer
E) pre-miRNA.

Question 58

RNA polymerase III transcribes all protein-encoding genes.

Question 59

Basal transcription factors bind to the promoters of all protein-encoding genes.

Question 60

Genomic imprinting is an example of epigenetic alteration of DNA.

Question 61

What is an enhanceosome?

Question 62

Why is genomic imprinting considered an epigenetic alteration?

Question 63

Gene expression can be modulated posttranscriptionally through micro RNAs (miRNAs)in eukaryotes.

Question 64

You have cloned and sequenced a new mouse gene and wish to know whether chromatin structure may affect its transcription.You DNase treat and then run Southern analysis.In the mouse strain with hypothetical phenotype A you detect your gene,but it is not detected in DNase treated samples from the mouse strain with phenotype B.What do you suspect as the cause?

Question 65

Unlike prokaryotes,eukaryotes have three RNA polymerases.What are they and what does each do?

Question 66

Reporter constructs are used to identify and characterize DNA sequences that regulate the expression levels of specific genes.What two DNA sequences are linked together to generate a reporter construct?

Question 67

RNA interference is a posttranscriptional process for modulating gene expression in prokaryotes.

Question 68

You are studying a brain region-specific mouse gene.You have cloned and sequenced the gene but wish to identify the DNA sequences that direct the regional specificity.Describe an experimental technique that would allow you to test this.

Question 69

All somatic cells in an individual have the same genetic content.Yet different cell types have different functions.What allows two cells with identical DNA content to function differently?

Question 70

Describe two modes of action by which RNA interference can modulate gene expression.

Question 71

How does chromatin structure regulate gene transcription?

Question 72

Gene A is maternally imprinted while Gene B is paternally imprinted.A mother with Genes A and B imprinted and a father with an imprinted Gene A have a daughter and a son.The children then marry individuals known not to be imprinted for either gene.What is the imprint status of the daughter and son respectively? If each marriage results in the birth of a daughter and a son,what would you expect the imprint status of genes A and B to be for the grandchildren?

Question 73

Each eukaryotic class II gene contains two kinds of essential DNA sequences.What are they?