Homework Problems and Answers(CH 13-CH17)

True or False: Thymine dimers can be replaired by Photoreactivation Repair or Nucleotide Excision Repair

True

In a particular bacterial mutant, a specific gene is not producing a mRNA or the corresponding protein. Researchers sequence the gene and determine that there are no mutations in the coding portion of the gene. Choose the structures that could be mutated to explain these observations.

-35 sequence (TTGACA) - Pribnow box

What are two main types of posttranscriptional modifications that take place in the mRNA of eukaryotes?

The addition of a 7-mG cap at the 5' end of the transcript and the addition of a poly-A sequence at the same 3' end of the message

A researcher is looking at a cellular sample using an electron microscope. They observe that while mRNA is being transcribed from the DNA that ribosomes are binding to the mRNA to make proteins. Is this sample from a bacterial or a eukaryotic cell?

This sample is from a bacterial cells since in bacteria the ribosomes can bind to the mRNA as its being synthesized and initiate translation

Which of the following lists steps of mRNA production in eukaryotes in the correct order? a) Transcription, 5' cap addition, addition of poly-A tail, exon splicing, passage through nuclear membrane b) Transcription, 5' cap addition, addition of poly-A tail, passage through nuclear membrane, exon splicing c) Transcription, addition of poly-A tail, 5' cap addition, exon splicing, passage through nuclear membrane d) 5' cap addition, addition of poly-A tail, exon splicing, passage through nuclear membrane, transcription

Transcription, 5' cap addition, addition of poly-A tail, exon splicing, passage through nuclear membrane

True or False: Many chemicals are more mutagenic after being processed in the liver.

True

True or False: Tautomers of nucleotide bases are isomers that differ from each other in the location of one hydrogen atom in the molecule

True, nucleotide tautomers differ only in the bonding location of one hydrogen atom

Proteins are targeted for degradation as a result of which of the following modifications?

Ubiquitination, an ubiquitin ligase adds a polyubiquitin tag to proteins that need to be degraded in a regulated fashion

All EXCEPT which of the following experiments or discoveries helped to identify the "triplet nature" of the DNA code?

Universality of the genetic code

Generally speaking, which of the following mutations would most severely affect the protein coded for by a gene?

a frameshift deletion at the beginning of the gene

Which of the following is most likely attributable to a base substitution at a 5' splice junction?

a longer than usual final transcript

What are four ways that mRNA can be modified?

adding a modified guanine to the 5' end aplicing of introns adding a polyadenylation tail to the 3' end RNA editing

Which mRNA modification is likely absent if the mRNA is degrading prematurely from the 5 end of the mRNA?

addition of the 7-methylguanosine cap to the 5 end

Which of the following statements about transcription factors is FALSE?

all transcription factors act to increase levels of transcription, this statement is false. Some transcription factors are activators and increase levels of transcription, while others act as repressors and will reduce transcription levels.

A DNA sequence produces a mutant protein in which several amino acids in the middle of the protein differ from the normal protein. What kind of mutation could have occurred?

an addition and a deletion mutation

Which of the following was an outcome of the ENCODE study?

approximately 50% of promoters physically interact with more than one distance enhancer, many promoters are regulated by multiple enhancers

Which of the following events could results in a frameshift mutation?

base deletion

How does DNA methylation regulate gene activity?

by adding methyl groups to the cytosine of CG doublets in DNA. Methylation of 5-methyl-CpG DNA sequences appears to inactivate transcription of the sequences

Which of the following statements about eukaryotic transcription is false? a) the transcripts produced contains both exons and introns b) transcription initiation occurs when RNA polymerase binds to a complex of transcription factors at the TATA box c) A polycistronic mRNA may be transcribed if the gene products are used in the same pathway or needed at the same time d) Eukaryotic promoter regions contain a TATA box and a CAAT box

c) A polycistronic mRNA may be transcribed if the gene products are used in the same pathway or needed at the same time

Which of the following is NOT a process associated with post-transcriptional regulation?

chromatin remodeling

Considering the electromagnetic spectrum, identify likely mutagens from the following list. cosmic rays infrared gamma rays ultraviolet microwaves X-rays radio waves

cosmic rays gamma rays ultraviolet x-rays

Most eukaryotic mRNAs are shorter than the genes that encode them. The reason for this is______

eukaryotic genes contain both introns and exons

Which fo the following is characteristic of transcription in eukaryotes but not in prokaryotes? a) a single transcript may be transcribed and translated simultaneously b) a 5' untranslated leader sequence c) A 3' untranslated trailer sequence d) Exon splicing catalyzed by the spliceosome

exon splicing catalyzed by the spliceosome

Which of the following is a characteristic of RNA splicing in eukaryotes?

exon/intron boundaries are typically characterized by a 5' GU splice junction and a 3' AG splice junction

If one compares the base sequences of related genes from different species, one is likely to find that corresponding ______________ are usually conserved, but the sequences of ______________ are much less well conserved.

exons, introns

Which of the following diseases are caused by an expansion of trinucleotide repeats?

fragile X syndrome

It has been observed that diseases caused by repeat expansions are the result of trinucleotide repeats rather than smaller or larger repeat lengths If non-trinucleotide repeat expansions were present in the coding region of a gene, which type of mutation would you expect to be the most likely?

frameshift

Which type of mutation helped lead to the understanding that the genetic code is based on triplets?

frameshift mutation

The Ames test is used to determine whether or not a compound causes _______________.

gene mutations

The relationship among a gene, a messenger RNA, and a protein is that__________

genes make mRNA, which then make proteins

Huntington's disease occurs when a CAG repeat expansion in the coding region of the HTT gene becomes too long. The CAG repeat is also in frame. (...CAG...CAG...CAG....) Which amino acid is coded for in this repeat?

glutamine

Which nucleotide will base-pair with the enol form of 5-broouracil?

guanine

A true reversion occurs when the wild-type DNA sequence is restored to encode its original message by a second mutation at the same site or within the same codon. Which of the following isoleucine codon(s) could be mutated once to orm a methionine codon, and then mutated at a second site to restore an isoleucine codon? Select all that apply (Note that two different positions in the codon must be mutated) AUC AUA AUU none of these codons

none of these codons

For which codon(s) could a single base change account for this amino acid change? GCG GCC GCU GCA none of these codons

none of these codons

Suppose that the top strand is the coding (nontemplate) strand and the three bases shown represent a single in frame codon in a gene. What will be the effect of the tautomeric shift-induced mutation on the amino acid sequence?

nonsense mutation

In which cellular organelle do the three posttranscriptional modifications often seen in the maturation of mRNA in eukaryotes occur?

nucleus

The chromosome of phase X174 encodes nine proteins consisting of a total of more than 2300 amino acids, even though the size of its genome predicts that it should be able to code for only 1795 amino acids. The reason for this discrepancy is????

overlapping reading frames

Which of the following elements function specifically in eukaryotic transcription and gene expression?

promoters and enhancers, promoters are the sites of assembly of the basic transcription complex, and along with enhancers, control transcription in eukaryotes

What are transcription factors?

regulatory proteins that bind to specific DNA sequences, Transcription factors are proteins that bind to specific DNA recognition sequences in the promoter or enhancer elements of a gene.

A bacterial protein factor called rho factor binds to an mRNA at the ______________. It moves along the ______________ in a _____________ direction chasing after the _______________. When it reaches the _____________ it removes it and then proceeds to break through the hydrogen bonds holding the _________________ together, which successfully removes the RNA polymerase.

rut site, mRNA, 5' to 3', RNA polymerase, hairpin loop, RNA-DNA

Which subunit of RNA polymerase establishes template binding to a promoter in prokaryotes?

sigma subunit

Which is the most common type of alternative splicing in animals?

skipping cassette exons

A snRNP is best described as _________________.

small RNAs associated with protein complexes in the nucleus

In the Ames Test, the appearance of his+ revertants in his presence of a non-mutagenic control compound indicates that___________

some of the reversion mutations are not caused by the mutagen being tested

An mRNA that is being produced comes off of the ____________.

template strand in both bacteria and eukaryotes

The purpose of the Ames test is to____________.

test the mutagenic effects of chemicals

What are two main types of posttranscriptional modifications that take place in the mRNA of eukaryotes?

the addition of a 7-mG cap at the 5' end of the transcript and the addition of a poly-A sequence at the 3' end of the message

Which fluctuated in the fluctuation test of Luria and Delbruck?

the number of resistance cells from different independent cultures

Which of the following initially determines which DNA strand is the template strand and therefore in which direction RNA polymerase II moves along the DNA?

the specific sequence of bases along the DNA strands

What are the consequences of having pyrimidine dimers?

these dimers distort the DNA structure and results in errors during DNA replication

The mutagen 5-bromouracil is an analog of ____________, whcih anomalously pair ___________ Ultraviolet light causes________

thymine, guanine thymine dimers

Which of the following best describe(s) the function of the 5' mRNA cap? a) to protect the transcript from degradation b) termination of transcription c) it provides a site for ribosome binding in the cytoplasm d) to provide a binding site for poly(A) polymerase

to protect the transcript from degradation it provides a site for ribosome binding in the cytoplasm

RNA synthesis from a DNA template is called??

transcription

RNA synthesis from a DNA template is called________

transcription

A point mutation occurs such a codon is changed from AGA to AGC. Which term describes this mutation?

transverse mutation

Which bacteria grow on the Agar plate if the Ames test is positive?

his+ prototrophs

Somatic cell mutations can only affect the individuals they occur in and _________________ their offspring. If the mutation is recessive, then it is ____________________ likely to affect the individuals unless the wild-type allele also becomes mutated or if the recessive mutation occurs on a ______________________. If the mutation is dominant, then it is ____________________ likely to affect the individuals. It should be noted that an accumulation of several mutations in a single cell could lead to _____________.

will not affect, less, male's X-chromosome, more, cancer

Ultraviolet light causes pyrimidine dimers to form in DNA. Some individuals are genetically incapable of repairing some dimers at "normal" rates. Such individuals are likely to suffer from__________

xeroderma pigmentosum

Which DNA sequence(s) would be present in the sister chromatids after this second round of replication? Select all that apply

5' TAA 3' 3' ATT5' 5'CAA3' 3'GTT5'

How many different codons code for amino acids?

61

Which three statements correctly describe the processing that takes place before a mature mRNA exits the nucleus?

A poly-A tail (50-250 adenine nucleotides) is added to the 3' end of the pre-mRNA Noncoding sequences called introns are spliced out by molecular complexes called spliceosomes A cap consisting of a modified guanine nucleotide is added to the 5' end of the pre-mRNA

For which codon(s) could a single base change account for this amino acid change?

AAG and AAA

For which codon(s) of isoleucine could a single base change account for an aminoi acid change to methionine?

AUA, AUU, AUC

Which of the following statements regarding Nucleotide Excision Repair (NER) and Base Excision Repair (BER) is true?

Both NER and BER involve the removal of one or more damaged bases by a nuclease

Trinucleotide repeat disorders are hereditary diseases caused by mutant genes containing an increased number of repeats of a DNA trinucleotide sequences

CACGGAGAA

For which codon(s) could a single base change account for this amino acid change?

CUG, CUA

Now consider a single base mutation in a codon for leucine that creates a codon for phenylalanine. A true reversion changes the phenylalanine codon back to a codon for leucine. Which of the following leucine codon(s) could be mutated once to form a phenylalanine codon, and then mutated at a second site to restore a leucine codon? Select all that apply. (Note that two different positions in the codon must be mutated)

CUU, UUG, CUC, UUA

Which of the following modifications is NOT associated with changes in eukaryotic gene expression?

DNA acetylation. Cytosine methylation is the only covalent modification of DNA that is known to contribute to transcriptional regulation

Which enzyme is responsible for proofreading during replication?

DNA polymerase

True or False: All compounds that have been found to be mutagenic in the Ames test are also carcinogenic

False

True or False: The genetic code varies by organism and must be determined for each

False

True or False: The genetic code is degenerate, meaning that a codon can specify more than one amino acid.

False, the degeneracy of the genetic code means that an amino acid may be coded for by more than one codon. However a single codon can only ever specify one amino acid.

True or False: Transcription and translation are NOT coupled in eukaryotic cells, although both processes take place in the cytoplasm.

False. In eukaryotes, transcription and translation are not coupled because transcription occurs in the nucleus and translation in the cytoplasm

Which trinucleotide repeat disorder would not be consistent with the hairpin formation part of this model?

Friedreich ataxia (GAA repeat)

How do we know that DNA repair mechanisms detect and correct the majority of spontaneous and induced mutations?

Individuals that have defective DNA repair pathways have an increased mutation rate

Why are liver extracts used in the Ames test?

Liver enzymes may activate some innocuous compounds, making them mutagenic

Numerous studies, beginning with those of __________________showed that the occurrence of mutations could be associated with X-rays Since that time, various chemicals and radiation have been tested by a number of screening strategies. If the __________________ in a test organism ___________________ when exposed to a given agent, that agent is classified as a mutagen.

Muller (1927) and Stadler(1928) frequency of mutation, increases

Which of these concepts that affect gene mutations in eukaryotes would apply to bacteria???

Mutations comprise any change in the nucleotide sequence of an organisms genome Mutations have a wide range of effects on organisms depending on the type of base-pair alteration, the location of the mutation within the chromosome, and the function of the affected gene product Mutations can occur spontaneously as a result of a natural biological and chemical processes, or they can be induced by external factors, such as chemicals or radiation Mutations are a source of genetic variation and provide the raw material for natural selection

How do we know that mutations occur randomly?

No agents are involved The mutation appears to occur naturally No indication of a mutation in the "family line"

An intron is a section of __________

RNA that is removed during RNA processing

Suppose that a transient tautomeric shift occurred in the guanine base to produce a rare tautomer in the partial DNA sequence just prior to a round of DNA replication

T

When considering the initiation of transcription, one often finds consensus sequences located in the region of the DNA where RNA polymerase(s) binds. Which of the following is a common consensus sequence?

TATA

Which of the following cis-acting elements of focused promoters serves as the binding site for TFID?

TATA Box, The TATA box is the binding site for TFIID and TBP

Which general transcription factors assist RNA polymerase II at a core promoter region?

TFIID, TFIIB, TFIIA, TFIIE, TFIIF, and Mediator