Genetics Exam 3

How many different ddNTPs are needed to get a complete sequence of a fragment of DNA?

4

Which of the following is an example of a base analog?

5-bromouracil

Achondroplasia is an autosomal dominant genetic disease. A birth census of a specific country revealed that of 1.6 million births that year, 16 children were born with achondroplasia who had normal parents. At that time, there were 140 people with achondroplasia already living in the population of 20 million. What is the mutation rate for achondroplasia in this population?

5.0 × 10-6 Correct! Mutation rate is expressed as the number of mutations per biological unit, which may be per cell division, per gamete or per round of replication. The number of mutations per gamete in the year of the census would be 16/(1,600,000 × 2) = 5.0 ×´ 10-6. Remember each birth is the product of two gametes.

Which pair of sequences below might be contained at the ends of an insertion sequence in bacteria?

5′-GCGTATAC-3′ and 5′-GTATACGC-3′ Correct! These two sequences are inverted repeats, which are found at the ends of insertion sequences.

What percentage of human genes can be regulated through RNA splicing?

95%

How would the mutations cause the operon to be constitutive?

A mutation in the promoter region of the repressor gene prevents transcription of the repressor. A mutation in the operator region of the operon has altered the binding site of the repressor so that the repressor cannot bind to the operator. The repressor is unable to bind to the operator because a mutation in the repressor gene results in a conformational change.

An interesting mutation is discovered in a species of wasp where the DNA sequence of the genome is unknown. In order to try to determine the molecular nature of this mutation, a geneticist treats mutant wasps with the chemical 5-bromouracil, a chemical mutagen that induces both types of transition mutations at high frequencies, and hydroxylamine, which induces only GC-to-AT transitions. Neither chemical mutagen caused the back mutation or reversion frequencies to increase beyond the low spontaneous values. Which of the following types of mutations is the least likely to be the original wasp mutation?

A-to-G Correct! This is a transition and would be expected to be reverted by mutagens that cause GC-to-AT transitions, and this was not found.

A geneticist is carrying out a pyrosequencing reaction. A solution with deoxyadenosine is passed across the plate and well number 256 emits a flash of light. Then a second solution containing deoxyguanosine is passed across the plate and well number 256 emits three times as much light as previously. Finally, a solution containing deoxythymidine passes across the plate and well number 256 emits no light. What is the DNA sequence of the fragment in well number 256?

AGGG If no light is emitted, the nucleotide in the solution is not present.

Which of the following describes a mechanism for isolating mRNA from a cell?

Add total cellular RNA to a column containing oligo(dT) chains. Correct! The oligo(dT) chains will bind to the poly(A) tails of the mRNA.

_____ is a field that develops databases and computer programs for analyzing DNA and protein sequence information.

Bioinformatics

A geneticist examines an ear of corn that contains mostly yellow kernels. However, a few kernels contain purple spots, which he concludes result from transposition events. In which kernel below did transposition most likely occur the earliest?

Correct! This is a large spot, indicating that many cells were derived from the cell in which transposition occurred because the event occurred early in development.

What chemical modification occurs when DNA is treated with sodium bisulfite?

Cytosine is converted to uracil. Correct! Bisulfite treatment leads to the deamination of cytosine to produce uracil.

Which characteristic of gene regulation is shared between prokaryotes and eukaryotes?

DNA binding proteins influence the ability of RNA polymerase to initiate transcription.

Which process affects gene regulation through alterations in chromatin structure?

DNA methylation

What is the purpose of primers in a PCR reaction?

DNA polymerase requires an existing 3\'-hydroxyl group to which it can add free nucleotides.

Expansion of triplets of nucleotides are "fixed" into the DNA strand by which of the following processes?

DNA replication and DNA repair synthesis

Why are chromatin structure changes essential for transcription in eukaryotic cells?

DNA would not be accessible to regulator proteins without these structural changes.

How can a probe for a gene be obtained when the gene has not yet been isolated or sequenced?

Determine the nucleotide sequence of the probe from the amino acid sequence of the protein encoded by the gene. Use the sequence of a similar gene from another organism. Correct! A probe can be obtained by determining the nucleotide sequence from the amino acid sequence of the protein or from a similar gene found in another organism.

In your lab, you discover and sequence a novel gene isolated from your study organism. What would be the first, and easiest, thing you could do?

Do an online search for homologous genes that may provide clues to your gene's function.

Which of the following is one of the challenges of working at the molecular level?

Each cell contains thousands of genes.

_____ genes have their own promoters and are transcribed separately, while _____ genes are organized into operons and are transcribed into a single RNA molecule.

Eukaryotic, bacterial

Compared to the expression of a normal, wild-type operon, what would be the consequence of a mutation that inactivates the trpR regulatory gene of the trp operon?

Expression of the trp structural genes would be increased in the presence of tryptophan. Correct! An active repressor cannot be made so there will be some gene expression even in the presence of tryptophan.

True or false? A single eukaryotic gene may not be regulated by several different response elements.

False

True or false? Epigenetic effects of early stress are only seen in mice and rats.

False

True or false? Epigenetic inheritance follows the same basic rules as genetic inheritance.

False

True or false? Epigenetic modifications cannot be determined from ancient (30,000-40,000 year old) DNA.

False

True or false? Insertion of transposable elements is always detrimental to the cell.

False

True or false? Introns of human genes are much longer than introns of genes from other organisms. Thus, human genes encode more protein domains.

False

True or false? RNA interference is a mechanism that is only present in animal cells.

False

True or false? Spontaneous replication errors occur much more frequently than induced mutations.

False

True or false? The majority of the human genome is noncoding DNA, thus the majority of the human genome has no function.

False

True or false? The regulator gene is part of its respective operon.

False

True or false? Transcriptional activator proteins are capable of binding DNA, but are unable to interact with other proteins.

False

Which genes would likely be part of the same operon? Gene A = defense against other bacteria Gene B = defense against bacteriophages Gene C = carbohydrate metabolism Gene D = cell motility protein Gene E = toxin production

Genes B, E, A

How did the International Human Genome Sequencing Consortium sequence the human genome? Place the below events in the correct order: I. Contigs were positioned on the chromosomes by using genetic markers. II. Copies of the human genome were cut into 150,000 bp fragments. III. Restriction fingerprints were used to assemble BAC clones into contigs. IV. Fragments were inserted into BACs. V. Smaller fragments were sequenced. VI. BAC clones were cut into smaller fragments. VII. Sequences were assembled.

III, I, V, VII

Which next-generation sequencing technique is most similar to the Sanger sequencing method?

Illumina

Prokaryotes commonly use attenuation as a mechanism to control gene expression, but eukaryotes do not. Why do you think that attenuation is more common in prokaryotes than eukaryotes?

In eukaryotes, transcription and translation usually take place in separate physical locations.

What is an advantage of translational control mechanisms?

It allows a cell to rapidly respond to a stimulus.

How does the long, noncoding RNA Xist cause X-inactivation through epigenetics?

It attracts PRC2, which methylates residues on the histone tails.

What is an important characteristic of the strain of S. typhimurium used in the Ames test?

It does not have an active DNA-repair system.

Why is Taq polymerase used in a typical polymerase chain reaction (PCR)?

It is stable at high temperatures.

Which of the following is true of DNA cloning?

It is used to isolate specific sequences of DNA, and it requires the enzyme DNA ligase.

Which is a limitation of traditional polymerase chain reaction (PCR)?

It requires knowledge of at least part of the sequence. Contamination is a significant problem. Taq polymerase tends to make errors. Fragments greater than 2000 bp cannot usually be amplified.

What is the purpose of the hot (usually about 95 °C) portion of the PCR temperature cycles?

It separates or denatures the template strands of DNA.

If a cell is simultaneously starved for most amino acids, including tryptophan, this general starvation affects the trp operon in an unique way. Because the ribosome stalls early in the translation of the leader peptide, region 1 in the mRNA 5′ UTR is able to pair with region 2. What effect will this have on the activity of the trp operon?

It will result in reduced expression of the structural genes compared to when the cell is starved only for tryptophan. Correct! Region 3 will pair with region 4 so attenuation will occur even though tryptophan is not present.

One SR protein, called splicing factor 2 (SF2), stimulates the binding of snRNPs to the 5' splice site. What effect would this likely have on RNA splicing?

It would enhance the use of that splice site.

How is mass spectrometry a useful tool for researchers studying the Human Proteome Project?

It would identify each protein and tell you how much of it was in your sample.

_____ mice are genetically altered animals in which a normal gene has been fully disabled.

Knockout

The are other substrates for β-galactosidase in addition to lactose. One of these substrates is lactobionic acid. The LacY permease made by lacY is able to transport lactobionic acid as well as lactose into the cell, but LacZ (β-galactosidase) made by lacZ cleaves lactobionic acid very inefficiently, such that wild-type cells cannot grow on lactobionic acid as the sole energy source. Mutant forms of LacZ have been found that cleave lactobionic acid efficiently and allow growth on this energy source. However, these cells that carry the mutant form of LacZ will not grow on lactobionic acid unless they also have a lacOc mutation. What would explain this situation?

Lactobionic acid is not a good inducer of the lac operon. Correct! Without the lacOc mutation there is not sufficient expression of the structural genes because induction does not occur.

Which of the following statements about P bodies is correct?

Most of the RNA degradation takes place in P bodies. P bodies can temporarily store mRNA molecules that may later be released. siRNA mediated RNA degradation also takes place in P bodies.

Can nonsense mutations be reversed by hydroxylamine? Why or why not? Use the codon table to help determine the effect of hydroxylamine.

No, treatment with hydroxylamine results in the mutation of two of the stop codons to another stop codon.

Would epigenetic changes brought about by methylation be inherited if methyltransferases were NOT present?

No. DNA is replicated in a semiconservative fashion.

The majority of sequenced genes in the human genome function as _____.

None of the above answers are correct. The majority of sequenced genes do not have a known function.

You are investigating a potential translational control mechanism for your favorite mRNA. You determine that Protein X is binding to the 5' UTR region of your mRNA and initiating translation. However, when you mutate the possible binding site in 5' UTR sequence, you still see Protein X binding. How do you explain this result?

Protein X binds to the secondary structure of the DNA.

Restriction enzyme I recognizes a 4 bp restriction site. Restriction enzyme II recognizes a 6 bp restriction site. On average, how does the number of restriction sites recognized by enzyme I compare to the number recognized by enzyme II?

Restriction enzyme I will have more restriction sites than enzyme II. Correct! Enzyme I will have more restriction sites than enzyme II.

The error-prone repair system in bacteria that allows for DNA replication across damaged regions is known as _____.

SOS repair.

Which of the following is NOT a reason why eukaryotic gene regulation is less well understood than bacterial gene regulation?

Scientists have not spent the same amount of time studying eukaryotes compared to prokaryotes.

Spontaneous deamination causes the original C-G pair to be ultimately replaced with _____.

T-A

Which of the following is NOT a mechanism of mRNA degradation?

The 5′ cap of mRNA is removed, followed by 3′-5′ removal of nucleotides. Correct! This statement is incorrect. 5′ cap removal is followed by 5′-3′ removal of nucleotides, NOT 3′-5′ removal.

What would be the result if a cell contained poly(A)-binding proteins (PABPs) that are defective in being able to bind to the poly(A) tail of mRNA?

The 5′ cap of the mRNA would have decreased stability. Correct! PABPs binding to the 3′ end of the mRNA protect the 5′ cap, thereby decreasing the stability of the mRNA.

Acetylation of the Arabidopsis flowering locus C (FLC) plays an important role in suppressing flowering until after an extended period of coldness. The active FLC encodes a protein that represses the activity of other genes that affect flowering. The activity of FLC is controlled by the flowering locus D (FLD) that stimulates flowering by repressing the action of FLC. FLD is a deacetylase enzyme that removes acetyl groups around the chromatin surrounding FLC. What would the predicted result be if FLD is present but has lost its deacetylase activity?

The FLC locus would remain acetylated and active, resulting in continuous suppression of flowering even after exposure to extended periods of coldness. Correct! FLD deacetylates FLC, removing the suppression of flowering. Therefore, FLD that has lost its ability to deacetylate FLC would result in continuous suppression of flowering, even after exposure to extended periods of coldness.

In the absence of tryptophan, what happens in the trp operon when the ribosome stalls at the tryptophan codons?

The attenuator forms and transcription terminates.

A patient exhibits a disease resulting from a lack of a protein that is transcribed by gene X. The protein encoded by gene X cannot be detected in the patient's cells. Furthermore, the mRNA of gene X is absent as well. After genetic testing, it has been determined that gene X in this patient contains an abnormally large amount of cytosine- and guanine-rich repeats near the transcription start site of the DNA. Which of the following hypotheses could be generated from this finding?

The chromatin of gene X is more heavily deacetylated compared to that from normal healthy individuals. Correct! CpG islands are found normally near transcription start sites. In this patient, CpG islands are found where they are normally not. CpG islands contain certain proteins that form complexes with other proteins that act as histone deacetylases. Therefore, the chromatin of gene X would be more heavily deacetylated and inactivated due to this interaction.

What effect on the expression of the trp operon might you expect if there were a deletion of the Shine-Dalgarno sequence prior to the trpD structural gene?

The entire trp operon will always be transcribed unless the cell is able to obtain tryptophan from the external environment.

What effect on the expression of the trp operon might you expect if the stretch of T:A base pairs following region 4 were deleted?

The entire trp operon will be transcribed no matter what the level of tryptophan in the cell.

What effect on the expression of the trp operon might you predict if there was a large deletion in region 3 of the trp operon?

The entire trp operon will be transcribed no matter what the level of tryptophan in the cell.

If the trp operon from E. coli was cloned between a ubiquitous eukaryotic promoter and a strong eukaryotic transcriptional termination sequence, how would this operon function in a eukaryotic cell?

The entire trp operon will be transcribed, but none of the structural genes of the trp operon will be translated no matter what the level of tryptophan in the cell.

What effect on the expression of the trp operon might you predict in the trp operon if the Shine-Dalgarno sequence prior to the leader sequence were deleted?

The entire trp operon would be transcribed no matter what the level of tryptophan in the cell.

Assume that a wild-type strain of E. coli is growing in a medium that contains both glucose and lactose. There is initially a very low level of β-galactosidase synthesis. Suddenly, there is a dramatic increase in the level of β-galactosidase synthesis. What is the most likely explanation for this sudden increase?

The glucose has been fully consumed.

What is the biggest difference between the fluorescently labeled nucleotides of Illumina sequencing and the fluorescently labeled ddNTPs of Sanger sequencing?

The labeled nucleotides of Illumina sequencing do not terminate the sequencing reaction.

What is the role of the protein encoded by the lacZ gene?

The lacZ gene encodes an enzyme that converts lactose to allolactose, and the lacZ gene encodes an enzyme that converts lactose to glucose and galactose.

In E. coli under conditions of high extracellular osmolarity which of the follow occurs?

The micF gene produces an antisense RNA that binds to the mRNA of the ompF gene and blocks its translation. Correct! The micF gene makes an antisense RNA that is complementary to the ompF mRNA.

A mutation in the 5ʹ UTR of the trp operon reduces the ability for region 2 to pair with region 3. What would be the effect of this mutation on the trp operon when tryptophan levels are high?

The mutation would have no effect on the trp operon. Correct! When tryptophan levels are high, regions 2 and 3 never pair, so this mutation would have no effect. Transcription would be terminated.

Vinclozolin is a fungicide that is used on grapes, fruits, and vegetables. It also acts as an androgen receptor antagonist, which prevents testosterone from binding to the receptor. Vinclozolin has also been shown to have epigenetic effects. Why is vinclozolin exposure a potentially larger issue than other environmental chemical exposures that do not cause epigenetic changes?

The negative effects of vinclozolin can be passed down to offspring.

What is the operator?

The operator is a DNA sequence that binds to the lacI repressor protein.

The lac operon is inducible. What does this mean?

The operon is transcriptionally active only in the presence of lactose.

Why is it important that a cloning vector have a unique site for each restriction enzyme?

The presence of several restriction sites will generate multiple DNA fragments that cannot be easily reassembled. Correct! With several sites, the vector will be cut into multiple pieces that will be difficult to reassemble in the correct order.

In the polymerase chain reaction (PCR), the solution is first heated to 90°C, then cooled to 30-65°C, and then heated to 60-70°C. What happens when the solution is cooled to 30-65°C?

The primers anneal. Correct! The primers anneal at 30-65°C.

Which of the following statements about transcriptional repressors is correct?

The repressors may compete with activators for the same DNA binding site.

Typically, DNA repair mechanisms that introduce small insertions and deletions, like nonhomologous end joining, are not ideal for use by researchers because these mutations could harm the gene. Why would this outcome be desired when using the CRISPR-Cas9 system?

The researchers are trying to disrupt genes to study functionality, thus mutations are one way to do this.

What effect on the expression of the trp operon might you expect if a deletion occurred in the leader sequence that removed the trp codons in the trp operon?

The structural genes for the trp operon will not be transcribed no matter what the intracellular levels of tryptophan are.

What effect on the expression of the trp operon might you expect if the trp codons in the leader sequence of the trp operon were replaced by codons for isoleucine?

The structural genes for the trp operon will only be transcribed when isoleucine levels are low.

Fire and Mellow created transgenic worms that expressed GFP. Then they injected double-stranded RNA complementary to the gfp gene. Which of the following results were seen?

The worms were not able to express GFP. Correct! injecting double-stranded RNA complementary to the gfp gene would not allow GFP to be expressed.

What is the mechanism of action of a chromatin-remodeling complex?

They bind directly to the DNA and reposition nucleosomes to make the DNA more accessible.

Which of the following statements about transcriptional activator proteins is INCORRECT?

They bind to the sugar phosphate backbone as they do not require specific consensus base sequence to bind to the DNA.

What is one mechanism by which chromatin-remodeling complexes reposition nucleosomes?

They change the conformation of DNA and/or nucleosomes so that DNA that is bound to nucleosomes assumes a more exposed conformation.

Generally there are four separate sequencing reactions performed to get the sequence of a piece of DNA. How do these four tubes differ from each other?

They contain different ddNTPs.

How do ddNTPs differ from dNTPs?

They do not have a 3\'-hydroxyl group on the sugar.

What is one reason Gregor Mendel and Thomas Hunt Morgan were so successful in their studies of genetics?

They used populations of organisms that had different alleles for particular traits.

If you mutate the demethylases of a cell, rendering them inactive, what effect would that have on gene expression of genes located near CpG islands?

They would continue to be actively repressed.

What would likely happen if poly(A)-binding proteins were irreversibly bound to the poly(A) tail of the mRNA?

This would increase the stability of the mRNA.

A large plasmid that has been used to transfer genes into plant cells is the _____ .

Ti plasmid

Why do eukaryotes have more levels of gene regulation that prokaryotes do?

Transcription and translation are separated by space and time in eukaryotes, so there are more opportunities for regulation.

True or false? Some chemicals are capable of modifying chromatin structure.

True

True or false? The amount of protein synthesized depends on the amount of corresponding mRNA that is available for translation.

True

True or false? The attenuator structure of a hairpin followed by a string of uracil nucleotides is similar to the structure of a bacterial intrinsic terminator.

True

True or false? You find an AU-rich element in the 3' UTR of your favorite mRNA. This suggests that precise regulation of this gene may be critical to cell health.

True

Which gene or genes play a role in making sure Xist is NOT transcribed on the active chromosome?

Tsix and Xite

What procedure can be used to solve the structures of complex proteins?

X-ray crystallography

Which of the genotypes below is correctly matched with the number of X chromosomes that would be inactivated in that genotype?

XXX - 2 Xs inactivated

Is it possible to get any transcription of the lac operon in the absence of lactose? Why or why not?

Yes, some transcription must take place in order to produce the permease to allow lactose to enter the cell, in order to produce β-galactosidase to make allolactose, and because although the repressor protein keeps transcription at a very low basal level, some transcripts will be produced and translated.

If regions 2 and 3 of the 5' UTR trp operon base pair to form a hairpin, will the structural genes be transcribed?

Yes, this hairpin does not prevent transcription.

What is the difference between whole-genome shotgun (WGS) sequencing and map-based (MB) sequencing?

You do not need to use physical or genetic maps in WGS sequencing.

What would you observe in a sequencing reaction with dATP, dCTP, dTTP, dGTP, and ddGTP?

You would only be able to determine where the cytosines were located in your original DNA template.

What is a partial diploid?

a bacterium that has at least some common genes on both the chromosome and a plasmid

An 'interactome' is _____.

a complete set of protein interactions in a cell

In eukaryotic cells, what is the longest that an mRNA can last before it is degraded?

a few months

A recombinant plasmid contains _________.

a foreign piece of DNA and an origin of replication

What best defines an operon?

a group of bacterial genes that are transcribed together on the same mRNA

Select the definition of a repressor.

a regulatory protein that greatly decreases operon transcription by binding to the operator

A codon that specifies leucine undergoes a single-base substitution, producing a new codon that specifies methionine. The codons that specify leucine are UUA, UUG, CUU, CUC, CUA, and CUG. The only codon that specifies methionine is AUG. Which of the following correctly describes the mutation?

a transversion at the first nucleotide position of a leucine codon Correct! A transversion at the first position can convert either UUG or CUG to AUG.

The vehicle that carries a piece of foreign DNA to be cloned into a bacterial cell is called _________.

a vector

An advantage of using an adenovirus as a gene vector in gene therapy is that _____.

adenoviruses transfer DNA to nondividing cells Correct! Adenoviruses have the advantage that they can be used to transfer DNA to nondividing cells.

How does the availability of molecules such as elongation and initiation factors affect gene expression?

affects the rate of mRNA translation

Proteomics is the study of _____.all the proteins found in a cell

all the proteins found in a cellq

What is the inducer of the lac operon?

allolactose

What is a benefit of a stalled RNA polymerase?

allows the cell to quickly respond to environmental changes

Which molecular mechanism does NOT affect chromatin structure?

alternative splicing

A plasmid vector generally contains which of the following?

an antibiotic resistance gene, a cloning site, and a replication origin

What is a constitutive operon?

an operon that is not regulated and is always transcribed

What is an inducible operon?

an operon that is transcribed when a specific molecule is present

When cellular tryptophan levels are low, regions 2 and 3 of the 5ʹ UTR pair and form the 2+3 structure called _____.

antiterminator.

In prokaryotes, which organism would likely have the most genes?

archaeum D, genome size 8.2 million base pairs

Which of the following is not one of the basic types of gene mutations?

base-pair rearrangements

Which of the following types of mutation probably has the smallest effect on the function of the protein encoded by the mutated gene?

base-pair substitutions

A researcher wants to study the methylation pattern at a specific locus. Which method should be used to do this?

bisulfite sequencing Correct! The treatment of DNA with sodium bisulfite converts unmethylated cytosines to uracil while leaving methylated cytosines unaffected.

In the presence of allolactose, the lac repressor _____.

cannot bind to the operator.

A bacterial cell is grown in the presence of both glucose and lactose. Over time, a researcher measures the amount of glucose and lactose that have been used by the cells. She finds that glucose levels are reduced, but lactose levels have remained constant. She proposes that these bacterial cells are exhibiting _____.

catabolite repression Correct! Glucose requires less energy to metabolize and inhibits transcription of genes involved in metabolizing lactose.

A geneticist inserts a DNA fragment into a restriction site within the lacZ gene of a plasmid that also has an ampicillin-resistance gene. The geneticist then transforms lacZ− bacterial cells with the plasmids and plates the bacteria on a medium containing ampicillin. Which cells will have copies of the recombinant plasmid?

cells that grow and are white, because they did not produce b-galactosidase Correct! The cells that grow and remain white have a plasmid in which the inserted DNA fragment has disrupted the functional lacZ gene.

Which technique uses antibodies to separate chromatin fragments with specific histone modifications?

chromatin immunoprecipitation

A technique in which neighboring genes are used to locate a gene of interest is called _____.

chromosome walking

The area of genomics that studies the similarities and differences in gene content, function, and organization of whole genomes of different organisms is _____ genomics.

comparative

Which of the following best describes a cDNA library?

consists of DNA sequences that are expressed

Many genes in various types of cancer cells are expressed inappropriately, causing the cancer cells to grow unchecked and mutate without repair. Which type of gene is NOT likely to be inappropriately expressed in these cells?

constitutive

A point mutation in region 1 of the 5ʹ UTR converts UGG to UGU. In the absence of cysteine, this mutation would most likely result in _____.

continued transcription of the trp operon in both the absence and presence of tryptophan. Correct! The codon UGU encodes cysteine. This codon, and therefore the ribosome, would not be sensitive to trp levels. In the absence of cysteine, regions 3 and 4 would not pair and premature termination would not occur.

In what organism was paramutation first discovered?

corn

A rare autosomal recessive disease called xeroderma pigmentosum (XP) results in a number of phenotypic traits including abnormal skin pigmentation. People with this disease also exhibit a strong predisposition to skin cancer. This can be best explained by a(n) _____.

decrease in nucleotide-excision repair activity Correct! XP is a disease resulting from defects in the DNA excision repair mechanism. This is one reason XP individuals may exhibit increased skin-cancer rates.

Which of the following is a potential use of a microarray?

determining which genes are likely to be important in brain function Correct! Microarrays are often used to determine which genes are expressed.

The Sanger method of DNA sequencing uses a special substrate that causes DNA synthesis to terminate. This special substrate is a _____.

dideoxyribonucleotide

Which type of DNA repair mechanism does not replace the altered nucleotide but rather restores it to its original structure?

direct repair

Regions of proteins that have specific functions or shapes are called protein _____.

domains

A very common type of DNA damage that stalls DNA replication and sometimes leads to chromosomal rearrangements is called a(n) _____.

double-strand break.

The amount of target DNA _________.

doubles after each cycle of PCR

The DNA sequences that are capable of affecting transcription at distant promoters, sometimes tens of thousands of base pairs away are referred to as _____.

enhancers

cDNA from cancer cells is labeled with red fluorescent nucleotides; cDNA from normal cells is labeled with green fluorescent nucleotides. The cDNAs are hybridized to a microarray that contains probes from a number of different genes. What does a yellow spot on the microarray indicate?

equal expression of the gene in cancer and normal cells Correct! Yellow indicates equal expression in the two cell types.

A genome consists of 500 million bp, the density of genes varies across the genome, and a large fraction of the genome consists of repetitive sequences derived from transposable elements. This genome is most likely from which organism?

eukaryote Correct! Eukaryotic genomes vary in size, but they are larger than prokaryotic genomes, vary in their density of genes, and often contain many repetitive sequences.

A man whose father died in his late fifties of an unknown but debilitating degenerative disease had two children with a woman who has no history of this type of disease in her family. On his fortieth birthday, the man decided to get tested for symptoms of this still-unidentified disease. The results revealed that the man did in fact have the disease and it was progressing at a rate faster than it did in his father. The couple's physician told them it appeared the phenomenon of "anticipation" was occurring in their family. Of the mutations listed below, which one is most likely to explain the possible anticipation that may be occurring?

expanding nucleotide repeat Correct! The phenomenon of "anticipation" relates to an increase in the severity of diseases that are caused by an increase in the number of copies of particular trinucleotide sequences.

Researchers studied inheritance of Huntington's disease within a family for three generations and found that both the age of onset and time to death decreased each generation. This increase in severity of the disease from generation to generation can best be explained by _____.

expansion of nucleotide repeats.

The traditional approach to genetics that begins with a phenotype and proceeds to find the gene responsible for that phenotype is called _____ genetics.

forward

Functional genomic approaches are favored over biochemical approaches to determine the function of a gene for all the reasons below, except that _____.

functional genomic approaches are more accurate

Gene expression may be controlled at the level of _____.

gene structure. transcription initiation. RNA stability. RNA processing.

Another name for recombinant DNA technology is _____.

genetic engineering

The International HapMap Project has greatly facilitated which type of study?

genome-wide association studies Correct! The HapMap project identified over 4 million single nucleotide polymorphisms, which have been used extensively in genome-wide association studies.

The differential expression of a gene which depends on the sex of the parent who transmitted that gene is called _____.

genomic imprinting

Long stretches of which of the following amino acids are known to be highly toxic to cells?

glutamine

Which of the following is not found in a PCR reaction?

helicase

DNA methylation promotes what other chemical alteration of chromatin to suppress gene expression?

histone deacetylation

Which of the following might be used to help determine the function of a DNA sequence?

homology search Correct! Homology searches locate similar sequences whose function may be known.

Where is the repressor encoded?

in a regulatory gene, which is separate from the operon

A geneticist wants to determine how the expression of a gene varies among different tissues. What technique should the geneticist use?

in situ hybridization Correct! In situ hybridization can be used to detect the presence of a particular RNA molecule in a tissue sample.

Where might mutations that cause the operon to be constitutively expressed occur?

in the operator region of the operon in the repressor gene

Some compounds are not active carcinogens until they are converted into cancer-causing compounds in the body. To identify potential carcinogens using the Ames test, how should a compound be treated before being tested on bacteria?

incubated in mammalian liver extract

A mutation at the operator site prevents the regulator protein, which acts as a repressor, from binding. Constitutive expression results from the operon. This is an example of a(n) _____ operon.

inducible Correct! In an inducible operon, transcription is off due to a repressor binding, and an inducer must be present to relieve the repression.

The DNA sequences that block or negatively regulate the effect of enhancers in a position-dependent manner are referred to as _____.

insulators

A mutation in a gene results in a protein that disrupts a protein-protein interaction. A second mutation in a different gene that results in a protein that restores this interaction is called _____.

intergenic suppressor mutation.

Normally, purple people-eaters are purple. Researchers isolated a mutant that is pink and bred a large population of pink people-eaters for sale to the public as exotic (and dangerous) pets. Geneticists showed that pink is recessive. After many generations, a purple mutant appeared within the pure-breeding pink population. The enzyme that is supposed to convert pink pigment to purple was isolated from members of the original purple population (enzyme 1), from members of the pure-breeding pink population (enzyme 2), and from the new purple mutant (enzyme 3). The amino acid sequence of a portion of each enzyme is shown below: Enzyme 1: ...Leu-Pro-Val-Ala-Pro... Enzyme 2: ...Leu-Leu (truncated) Enzyme 3: ...Leu-Leu-Leu-Ala-Pro Which of the following mechanisms would best account for the production of the normal phenotype in the purple mutant that appeared among the pink population?

intragenic suppression Correct! The amino acid sequence of enzyme 2 indicates that the first mutation was a frameshift, and the sequence of enzyme 3 indicates that a second frameshift just downstream of the first one restored normal function by restoring the original reading frame.

Which are the structural genes of the lac operon?

lacZ, lacY, and lacA

The lac operon would produce the greatest amount of β-galactosidase when _____.

lactose is present but glucose is absent.

The comparative approach to finding genes uses which method?

looking for sequence similarity between a new sequence and known genes

When glucose and lactose are present, β-galactosidase levels are _____.

low.

When used with cDNA, a microarray can provide information about active gene expression in that cell. Based on this, what is cDNA a 'complementary' sequence of?

mRNA

In your experimental system, you notice that translation of the eukaryotic gene you are working with yields three different proteins. What might be the cause of this observation?

mRNA processing

The purpose of the polymerase chain reaction (PCR) is to _________.

make many copies of a single DNA segment

Which technique is being used to characterize the proteome?

mass spectrometry

siRNA transcriptional silencing can happen through _____.

methylation of the DNA directly or of histone tails

What mechanism is likely responsible for most replication errors?

mispairings through wobble

The random induction of mutations and the mapping of those mutations is referred to as a _____.

mutagenesis screen

Which is the correct order of steps in a mutagenesis screen?

mutagenesis, identification of mutants, verification of genetic basis, positional cloning Correct! The steps are: mutagenesis, identification of mutants, verification of genetic basis, and then positional cloning.

A scientist is studying the effects of a chemical she believes to be a mutagen in Drosophila. Her treatment results in a forward mutation phenotype. To understand the molecular nature of this mutation, she attempts to reverse the mutation by treating the Drosophila mutant with hydroxylamine. However, this treatment has no impact on the mutant phenotype. Among the possibilities given below, the type of forward mutation her new mutagen most likely caused is a _____.

nonsense mutation. Correct! In a stop or nonsense codon, CG-to-TA changes result only in a different stop codon. Therefore, the original mutation could be a nonsense mutation.

Somatic mutations _____.

only affect non-reproductive tissues.

A mutant strain of E. coli produces β-galactosidase in the presence and in the absence of lactose. The mutation in this operon lies in the _____.

operator Correct! This is where the lac repressor binds to prevent RNA polymerase from binding. If the lac repressor cannot bind, then RNA polymerase will always be able to bind and stimulate transcription.

Homologous genes found in two different species that evolved from the same gene in a common ancestor are _____.

orthologs

Homologous genes found in the same organism that arose when a single gene underwent a duplication are _____.

paralogs

An interaction between two alleles that leads to a heritable change in expression of one of the alleles is called _____.

paramutation

SNPs are useful in the study of _____.

paternity or maternity genome-wide associate studies susceptibility to disease evolutionary relatedness

Which kind of map has better resolution of gene location?

physical

Which of the following regions does not seem to affect the stability of the mRNA?

poly(A) tail 5′ cap 5′ UTR 3′ UTR

An approach to finding a gene of interest based on first mapping the location of the gene in relation to other genes or genetic markers is called _____.

positional cloning

DNA fingerprinting can be used for all the applications below EXCEPT _____.

predicting disease risk

Why are eukaryotic genomes typically larger than prokaryotic genomes?

presence of introns in genes multiple copies of genes noncoding DNA transposable elements

Which choice below is NOT a mechanism by which DNA methylation suppresses gene expression?

prevents DNA methyltransferases from recognizing CpG islands

Restriction enzymes are used during DNA cloning to _________.

produce sticky ends on the vector and target DNA

Chromatin immunoprecipitation (ChIP) assays identify what interaction?

protein with DNA

What is the best characterized mutagenic DNA lesion induced by UV light?

pyrimidine dimer

Which of the following is a next-generation sequencing technique?

pyrosequencing

Which of the following is not recognized as an important level of gene regulation?

recombination after DNA synthesis

Which gene regulation mechanisms affect mRNA?

removal of introns

Many copies of a recombinant plasmid are produced by _________.

replication of the plasmid DNA using the host enzymes and cell division of the host cell

Heavily methylated DNA is usually associated with _____.

repression of transcription

Which of the following effects on transcription would histone deacetylation generally have?

repression of transcription

Genes that are coordinately expressed in eukaryotic cells are able to respond to the same stimulus due to short common regulatory sequences built into their promoters or enhancers called _____.

response elements

Enzymes that make double-stranded cuts in DNA at specific nucleotide sequences are called _____ enzymes.

restriction

Which of the following is NOT a component used in a sequencing reaction?

restriction enzymes Correct! Restriction enzymes are not used in a sequencing reaction.

Some mRNA molecules contain regulatory sequences called _____, where molecules can bind and affect gene expression by influencing the formation of secondary structures in the mRNA.

riboswitches

Attenuation of the trp operon involves _____.

secondary structure formation in RNA molecules. untranslated regions of RNA. high tryptophan levels. 5ʹ UTR.

In DNA sequencing, gel electrophoresis is used to _________.

separate the newly synthesized DNA molecules by size

Several examples of antisense RNA regulating translation in bacterial cells have been discovered. If you wanted to design a construct to artificially control the expression of a bacterial gene with antisense RNA, what sequences might the antisense RNA contain? c sequence identical to the DNA region that contains the operator of an operon

sequence complementary to a 5ʹ UTR of mRNA target

This protein is not produced in male Drosophila; in females, it regulates the splicing of sex determination genes.

sex-lethal (Sxl)

During RNA interference, _____ tend to base pair perfectly with mRNA, whereas _____ often form less-than-perfect pairings.

siRNAs; miRNAs

Which insertion or deletion mutation would likely not lead to a frameshift mutation?

six base pairs

Insertion of additional repeats in repetitive segments of DNA often involves which of the following?

slippage

In the dideoxy method of sequencing DNA the term "dideoxy" refers to _________.

special nucleotides

These types of proteins may get held up on certain genes in the absence of stress, but are then quickly released when stress is encountered, allowing for rapid transcription of genes that facilitate adaptation to the stressful environment.

stalled RNA polymerases

If you were to move an enhancer site further away from the gene it affects, what would be the likely effect on the level of transcription of that gene?

stays the same

Which of the options below is NOT an application of CRISPR-Cas9?

targeting RNA of a specific gene for degradation

DNA is the _____________________ for in vitro synthesis.

template

In a dideoxy sequencing reaction the incorporation of a ddNTP into the growing DNA strand _________.

terminates the polymerization reaction

The principal that mutagenesis in bacterial DNA can serve as an indicator of carcinogenesis in humans is the basis for _____.

the Ames test.

A high-resolution structure of a protein can provide all the information below, except _____.

the DNA sequence of the protein-encoding gene

Malaria is one of the most pervasive and destructive of all infectious diseases transmitted by mosquitos. About 300 million people worldwide are infected by malaria, which results in upward of a million deaths every year. The causative agents of malaria are protozoan parasites of the genus Plasmodium. The surface antigen is encoded by the var gene family, which consists of about 60 genes whose DNA sequences vary slightly. Expression of the type of var protein is known to change continuously, which allows parasites to evade the immune system. The var genes are located near the telomeres that are typically in heterochromatin state. The studies from 2006 revealed that the var genes are expressed when chromatin structure is disrupted via chemical changes in the histone proteins. Which of the following may serve as a plausible explanation that links var gene expression to chromatin changes?

the H3K4me3 type modification on histone H3 The H3K4me3 modification is frequently found in promoters of transcriptionally active genes in eukaryotes.

When speaking of gene regulation, regulatory elements are often described as cis- or trans-regulatory elements. A cis-regulatory element is a nucleic acid sequence that regulates the expression of genes located on the same molecule of DNA. In contrast, a trans-regulatory element is a diffusible factor, usually a protein, that may modify gene expression at distant sites on the same or different molecule of DNA. In the lac operon, which of these is a trans-regulatory element?

the lacI repressor

Blood samples were collected from 19,000 children of people who were within 2000 meters of the atomic blast in Nagasaki, Japan. Amino acid substitutions were investigated in 28 proteins and any variants detected led to an analysis of the child's parents' blood proteins to determine if the variant was an inherited or new mutation. Of the 289,868 genes examined, only one mutation was found in the children of parents exposed to the blast. None were found in the control group. This surprised the researchers, as animal studies clearly show that radiation causes mutations. In addition, the exposed parents did exhibit an increased incidence of leukemia and other types of cancers relative to unexposed people. These data suggest that _____.

the mutations in the parents were mostly somatic Correct! These types of cancers represent induced somatic mutations that will not be inherited by offspring.

The _____ is based on the assumption that information about the parental environment may be useful to the offspring.

thrifty hypothesis

For what purpose would one use a bacterial artificial chromosome?

to clone a large DNA fragment (larger than 100,000 bp) Correct! Bacterial artificial chromosomes can be used to clone DNA fragments up to 300,000 bp.

Why is ampicillin added to the agar medium upon which transformed bacterial cells are grown?

to select for cells containing the vector

Since eukaryotic gene expression is separated by space and time, _____ occurs first in the nucleus and _____ happens after in the cytoplasm.

transcription, translation

All of the RNA molecules transcribed from the genome comprise the _____.

transcriptome

Functional genomics includes determining which of the following?

transcriptome Correct! Functional genomics includes determining the transcriptome, all of the DNA sequences that are transcribed into RNA.

The process by which a plasmid vector is introduced into a bacterial cell is called _________.

transformation

What is the movement of a transposable element from one location to another called?

transposition

Trinucleotide repeat expansions involve all of the following except _________.

triplets of base pairs repetitive DNA segments replications hairpins

Which of the following processes is most likely to create deletions and insertions?

unequal crossing over

The Genetic Information Nondiscrimination Act prohibits _____.

use of genetic information in decisions about health insurance and employment.

What would be the result of a partial diploid with a bacterial chromosome containing a super repressor (lacIS) mutation but otherwise wild type, and a plasmid containing a wild- type lacI gene and lacI promoter but also containing both a nonfunctional lac operon promoter mutation and a lacOC mutation? P lacIS......P lacO lacZ lacY lacA / P lacI ...P-lacOC lacZ lacY lacA

β-galactosidase would not be produced whether or not lactose was present.