genetics final part 1

In the beginning of the gene depicted below, what region is represented by "A" and what region is represented by "B"?

"A" represents the regulatory promoter and the activator binding site; "B" - the core promoter;

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.

All of the following are DNA sequencing techniques except _____. Select all that apply.

-Mullis chain-terminating sequencing -DNA fingerprinting

Gene expression may be controlled at the level of _____

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

Some mutations in the trp 5ʹ UTR region increase termination by the attenuator. An example of a mutation that may have this effect is a _____.

-mutation that disrupts the anti-terminator structure -deletion in region 2 that prevents it from pairing with region 3 -mutation in the UGG codons in region 1 -mutation that replaces the two tryptophan codons in the 5ʹ UTR The anti-terminator structure occurs when regions 2 and 3 pair, preventing transcription termination. This can only occur when the ribosome stalls at the UGG codons, which encode tryptophan, in region 1.

Mispairing due to tautomeric shifts in nucleotides may result in _____.

-mutations. -unusual base pairings. -errors in DNA replication. -non Watson and Crick base pairing.

How many promoters are typically found in a four-gene operon

1

To which part of the mRNA sequence does the RISC bind?

3′ UTR

Which part of eukaryotic mRNA would contain AU-rich elements which affect stability by being bound to microRNAs?

3′ UTR

Which of the following is an example of a base analog

5-bromouracil

Which DNA fragment will migrate furthest in a gel when subjected to electrophoresis?

50 bp fragment

The location in the pre-mRNA that small nuclear ribonucleoproteins (snRNPs) bind to in order to perform splicing is the _____.

5′ splice site

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

5′-GCGTATAC-3′ and 5′-GTATACGC-3′

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

95%

In a DNA sequencing reaction, which base would be read out by ddATP?

A

Which of the following statements concerning chromatin remodeling is correct?

Chromatin remodeling complexes require energy to restructure nucleosomes, which may allow exposing certain regions of the DNA to the action of other regulatory proteins.

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

Which one of the statements below accurately describes gel electrophoresis?

DNA moves through the gel toward the positive electrode.

An enzyme called _____ cleaves and processes double-stranded RNA to produce siRNAs or miRNAs.

Dicer

How are siRNAs and miRNAs made?

Dicer processes and cleaves double-stranded RNA to produce 21- to 25-nucleotide-long sequences.

Why is the metabolism of glucose preferred over lactose or other sugars in bacteria?

Glucose requires less energy to metabolize.

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.

Choose the correct description of function for the specific domain of histone proteins.

The globular domain associates with other histone proteins.

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.

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.

What disease occurs as a result of mutations in the genes for DNA-repair systems?

Xeroderma pigmentosum

What is the basal transcription apparatus?

a complex of RNA polymerase, transcription factors, and other transcription proteins

A mutation that prevents the catabolite activator protein (CAP) from binding to the lac operon promoter will result in _____.

a decrease in the ability of RNA polymerase to initiate transcription.

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

a few months

What is a conditional mutation?

a mutation that affects the phenotype only under certain conditions

What is a missense mutation?

a mutation that results in a different amino acid in a protein

What is the regulatory segment of an mRNA that binds a small molecule resulting in a change in the production of the protein encoded by this mRNA called?

a riboswitch

What is a transposable element

a segment of DNA that can move within the genome of a cell

What is chromatin immunoprecipitation?

a technique that determines the specific locations within the genome where proteins interact with DNA

What is the Ames test?

a test to screen for mutagenic chemicals

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

Which of the following matches the modification of histones with the correct effect on the histone?

acetylation of histones-—stimulates transcription

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

affects the rate of mRNA translation

Attenuation occurs when during the process of transcription?

after transcription begins

The lacI gene which makes the lac represson of the lac operon is only expressed under which of the following conditions?

all the time

Which of the following is the true inducer of the lac operon?

allolactose

Proteins that change shape on binding to another molecule are called ____.

allosteric

Gene regulation in bacteria cells _____.

allows the bacteria to respond to environmental changes.

What is a benefit of a stalled RNA polymerase?

allows the cell to quickly respond to environmental changes

Which of the following forms of gene regulation primarily occurs in eukaryotes?

alteration of chromatin structure

What is the most common result of depurination?

an incorporation error leading to a replication error

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

anti-terminator.

Diseases caused by expanding nucleotide repeats may become more severe in each generation, which may account for the process known as _____

anticipation

All of these methods of regulating gene expression rely on secondary structure, except _____

antisense RNA's -here's what do: attenuators ribozymes riboswitches

In general, DNA repair mechanisms _____.

are present in most organisms

Biotechnology applications include all of the following except _____.

artificial selection for larger fruit size in crops

A mechanism of genetic regulation in which the synthesis of a short RNA is terminated before the structural genes of the operon can be transcribed is called_________.

attenuation

The trp operon exhibits which type of transcription control?

attenuation and repression

Which vector can hold the largest size fragment of DNA?

bacterial artificial chromosome

After separating a complex mixture of DNA fragments according to size, identifying a specific fragment of interest _____.

can be accomplished by Southern blotting

Restriction endonucleases _____.

can be used to create pieces of DNA with cohesive ends

In the trp operon, in the absence of tryptophan, the trp repressor _____.

cannot bind to the operator, so transcription takes place.

A system of gene control in bacterial operons in which glucose is used preferentially and the metabolism of other sugars is repressed in the presence of glucose is called _____.

catabolite repression

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

chromosome walking

Which of the following best describes a cDNA library?

consists of DNA sequences that are expressed

A gene that encodes a protein which is continually expressed to help maintain essential cellular function would be considered _____.

constitutive

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

Which is an important requirement for a cloning vector?

contains an origin of replication

A _____ binds to the repressor and makes it capable of binding to the promoter.

corepressor

Which of the following is not always a typical feature of transposition

creation of an RNA intermediate prior to insertion in target DNA

Which of the following is not always a typical feature of transposition?

creation of an RNA intermediate prior to insertion in target DNA

Which nucleotide base is methylated in DNA methylation?

cytosine

DNA methylation is commonly associated with _____, both of which repress transcription.

deacetylation of histones

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

The part of a regulatory protein that exhibits a discrete function is called a _____.

domain

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

True or false? All siRNA and miRNA degradation of mRNA requires the enzyme Dicer.

false

A set of bacterial colonies or phages that contain all the DNA sequences found in a genome is called a(n) _____.

genomic library

Which of the following is a common DNA-binding motif?

helix-turn-helix

Amino acids in DNA-binding domains typically interact with DNA by forming _____

hydrogen bonds with the nitrogen bases.

The presence of siRNAs and miRNAs _____ the rate at which mRNAs are broken down and _____ the amount of protein produced.

increases, decreases

Antisense RNA molecules typically _____.

inhibit translation.

Which of the following is not a DNA repair mechanism?

insertion sequence repair these are: -nucleotide-excision repair -base-excision repair -direct repair -mismatch repair

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

insulators

Pieces of pre-mRNA that are removed by splicing proteins prior to translation are called _____

introns

CpG islands are regions of DNA with heavy cytosine _____.

methylation

How do mismatch-repair enzymes in E. coli differentiate between the old and new strands of DNA?

methylation of the adenine in the GATC sequence of the old strand

A primary difference between mismatch repair and nucleotide-excision repair (NER) with respect to the type of damage repaired is that mismatch repair will repair _____, while NER will repair _____.

mispaired bases; pyrimidine dimers

Helix-turn-helix, zinc fingers, and leucine zippers are examples of _____ that allow proteins to bind DNA.

motifs

When tryptophan levels are high, transcription terminates at the end of the trp operon because the ribosome can _____.

move quickly through the two UGG codons in region 1 of the 5ʹ UTR -When tryptophan levels are high, the ribosome does not stall when decoding the UGG (trp) codons in region 1 and moves into region 2, allowing a hairpin to form between regions 3 and 4, terminating transcription.

Which of the following always results from transposition

movement of a transposable element within the genome or between genomes

What is an environmental agent that significantly increases the rate of mutation above the spontaneous rate called?

mutagen

Which of the following is not a characteristic of transposable elements?

only found in plants

In the diagram of the lac operon, E represents a(n) _____.

operator

The regulator protein binds the _____ of the operon.

operator

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 -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.

A technique for quickly amplifying DNA fragments is _____.

polymerase chain reaction

A powerful genetic engineering technique used for the amplification of sequences of DNA is _____.

polymerase chain reaction (PCR)

Which of the following is not a mechanism of gene regulation that can take place after transcription is completed in eukaryotes?

polymerase stalling

A DNA or RNA molecule that is complementary to a sequence of interest and that is often used to find the sequence of interest is a called a _____.

probe

In nature, the purpose of the CRISPR-Cas system is to _____.

protect bacteria and archaea from invading DNA elements

Chromatin immunoprecipitation (ChIP) assays identify what interaction?

protein with DNA

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

pyrimidine dimer

What changes does UV light produce in DNA molecules?

pyrimidine dimers

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

recombination after DNA synthesis here's what are: -processing of mRNA -initiation of translation -stability of the mRNA -initiation of transcription

A structural gene encodes proteins involved in essential cellular housekeeping functions, whereas a(n) _____ gene controls the transcription of structural genes of the operon.

regulator

The products of _____ genes are often DNA-binding proteins.

regulatory

Transcriptional activator proteins bind to sequences in the _____ promoter region and affect the rate at which transcription is initiated.

regulatory

Which gene regulation mechanisms affect mRNA?

removal of introns

Which eukaryotic feature functions most like a bacterial operon?

response element

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

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

restriction enzymes

Reverse genetics attempts to determine the function of a gene by changing it, using all of the following techniques except _____.

reverse transcription

The enzymes that are known to degrade cellular RNA are called _____

ribonucleases

Which of the following is not part of the basal transcription apparatus?

ribonucleases

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

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

sex-lethal (Sxl)

Short DNA sequences that are repeated in tandem and that are commonly used in DNA fingerprinting are called _____.

short tandem repeats (STR)

In a common pathway of mRNA degradation, what must happen before the 5' cap is removed?

shortening of the poly(A) tail

A mutation that can affect the individual in which it occurs but not that individual's offspring is a _____ mutation

somatic

What does the control plate measure in the Ames test?

spontaneous mutation of the his- gene

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

Recombinant DNA technology is a set of molecular methods used to isolate, manipulate, and study DNA. What does recombinant mean, in this case?

that the DNA used is often derived from two or more sources and combined

What does the triple methylation of the 4th lysine in an H3 histone tail likely tell you about nearby genes?

that they are transcriptionally active

Transcriptional activator proteins such as GAL4 affect transcription by interacting with _____

the basal transcription apparatus

Mutations in which of the following lac operon genes or regions are cis in their effect on the regulation of the operon?

the lacO operator -The operator is a regulatory region that is bound by the lac repressor and affects the transcription of the lac operon genes on the same piece of DNA; therefore, this region acts in cis.

Mutations in which of the following lac operon genes or regions are trans in their effect on the regulation of the operon?

the laci gene

What next-generation sequencing technique sequences DNA by passing single molecules of DNA through nanopores?

third-generation sequencing

Attenuation refers to the early termination of _____.

transcription.

True or false? Regulatory promoters typically contain binding sites for many different transcriptional activator proteins.

true

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

true

In the trp operon, when does translation keep up with transcription?

when tryptophan levels are low and regions 2 and 3 form a hairpin

Which of the following are used as cloning vectors? Select all that apply.

-plasmids -cosmids -artificial chromosomes

Attenuation of the trp operon involves ____

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

Attenuation of the trp operon involves _____.

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

In yeast cells, the absence of galactose causes GAL80 to bind to GAL4 and prevent transcription activation of galactose metabolizing genes. When galactose is present, it binds to GAL3, causing it to interact with GAL80 and release GAL4 to activate transcription of genes necessary for galactose metabolism. Which of the following hypotheses would be correct to explain the cause of a yeast cell that is unable to properly metabolize galactose?

A mutation in the GAL80 protein results in an inability to undergo conformational changes resulting in constitutive interaction with GAL4.

What are CpG islands?

DNA regions with many cytosine bases adjacent to guanine bases

Which cellular process is most like the Sanger method of DNA sequencing?

DNA replication

What are insulators?

DNA sequences that block the effect of enhancers in a position-dependent manner

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

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

Which of the following is a feature of both prokaryotic and eukaryotic genes?

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

Regions called _____ hypersensitive sites frequently develop approximately 1000 nucleotides upstream of the start site of transcription that indicates "active" sites of chromatin structure.

DNase I

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. -An active repressor cannot be made so there will be some gene expression even in the presence of tryptophan.

A transcriptional activator protein GAL4 and its inhibitor GAL 80 play important roles in the inducible regulation of galactose metabolism in yeast. Which of the following statements incorrectly describe the action of GAL4 and GAL80 in response to galactose?

GAL80 contains several zinc fingers that allow its binding to UASG.

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

Which of the following statements about mutations is incorrect?

Germ-line and somatic mutations are both passed on to offspring. here's what are correct: -Somatic mutations are numerous, occurring at a rate one per every million cell division. -Mutations can be used to examine biological processes. -Mutations are a source of all genetic variation. -Gene mutations affect a single gene, whereas chromosome mutations affect the number or structure of chromosomes.

Assume that a deletion mutation occurs within the trp operon so that the DNA corresponding to the last (distal) part of region 1 and the first (proximal) part of region 2 of the mRNA 5′ UTR is removed. What will be the effect of this deletion on the expression of the trp structural genes?

In the absence of tryptophan, transcription of the structural genes will be reduced compared to a wild-type operon. -Regions 3 and 4 will pair and form the termination structure even in the absence of tryptophan.

What role does the activated form of vitamin B12 (coenzyme B12) have in the regulation of the genes involved in the synthesis of vitamin B12?

It binds to the mRNA for the vitamin B12 structural genes and causes the mRNA to fold into a structure that prevents translation

How does antisense RNA inhibit translation?

It binds to the target mRNA and prevents the ribosome from binding to it.

Which of the following is not true of the Ames test?

It detects forward mutations to his-.

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

How does direct repair return DNA errors to their original sequences?

It removes functional groups or bonds from the altered nucleotide to restore the original structure.

What is the purpose of reverse transcriptase in the creation of a cDNA library?

It synthesizes DNA from mRNA.

_____ 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. -Without the lacOc mutation there is not sufficient expression of the structural genes because induction does not occur.

Which of the following normally happens in the regulation of the trp operon when high levels of tryptophan are present?

Regions 3 and 4 will pair in the attenuation region in the 5' UTR of the RNA.

Why might the trp operon in E. coli be regulated by both negative repression and attenuation?

Repression and attenuation together further reduce expression of the trp structural genes in the presence of tryptophan than either of the two modes do on their own.

Which of the following is NOT a mechanism by which MOST repressors can inhibit eukaryotic transcription

Repressors directly block RNA polymerase. -Only in prokaryotes do most repressors physically block RNA polymerase. In eukaryotes, most repressors do not function by this mechanism.

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

SOS repair.

The alternative splicing of the T-antigen gene of simian virus 40 (SV40) is regulated by the presence of splicing factor 2 (SF2), which is a(n) _____ protein that contains two domains, an RNA-binding region and another domain with alternating serine and arginine amino acids

SR

The alternative splicing of the T-antigen gene of simian virus 40 (SV40) is regulated by the presence of splicing factor 2 (SF2), which is a(n) _____ protein that contains two domains, an RNA-binding region and another domain with alternating serine and arginine amino acids.

SR

Which of the following is a component of chromatin remodeling complexes, which bind directly to particular sites on DNA and reposition the nucleosomes, altering chromatin structure without modifying the chemical structure of the histones directly?

SWI

What is the main organism used in the Ames test?

Salmonella typhimurium

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. here's what are: -The 5′ cap is removed followed by 5′-3′ removal of nucleotides. -The mRNA is randomly cleaved and degraded regardless of the directionality. -Nucleotides are removed starting at the 3′ end and moving to 5′.

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. -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

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.

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

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. -When tryptophan levels are high, regions 2 and 3 never pair, so this mutation would have no effect. Transcription would be terminated.

You have isolated a protein that you hypothesize to be a transcriptional activator. What is one characteristic of the protein that would support your hypothesis?

The protein contains helix-turn-helix and zinc-finger motifs. -Helix-turn-helix, zinc-finger, and leucine-zipper motifs are all characteristic of DNA binding domains of transcription activators.

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 was found about the survivors of the atomic bomb blast on the city of Nagasaki

There was no significant evidence of enhanced germ-line mutations in the exposed individuals.

How do response elements work to regulate transcription?

They are binding sites for transcriptional activators in response to stimuli.

Which of the following is not a characteristic of transcriptional activator proteins?

They are capable of binding DNA at a consensus sequence in the protein-coding part of the gene.

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. here's what is correct: -They stimulate and stabilize the basal transcription apparatus at the core promoter. -The activator may or may not directly interact with the basal transcription apparatus. -Some activators are known to have acetyltransferase activity that can alter chromatin structure. -They typically have one or more DNA-binding motifs such as helix-turn-helix, zinc fingers, and leucine zipper.

Which of the following statements is not true about repressors in eukaryotic cells?

They directly block RNA polymerase.

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.

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.

How does transposition cause mutations?

Transposable elements can insert themselves into other genes and disrupt their function.

A technique for transferring protein from a gel to membrane is _____.

Western blotting

What is the role of the Sxl (sex-lethal) protein in the development of Drosophila?

When it is inactive, male-specific splicing of dsx pre-mRNA occurs.

What is the role of tryptophan in the regulation of the trp operon?

When tryptophan levels are high, tryptophan binds to the inactive trp repressor, making it active.

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 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.

You find an AU-rich element in the 3' UTR of your favorite mRNA. What does this suggest about regulation?

Your mRNA is regulated through Dicer and RISC.

The process by which mRNA can be spliced so that two distinct proteins, such as the large T antigen and small t antigen of T cells, can be produced is called _____

alternative splicing

The process by which mRNA can be spliced so that two distinct proteins, such as the large T antigen and small t antigen of T cells, can be produced is called _____.

alternative splicing

A small RNA that can base pair with an mRNA molecule and affects its functioning is called _____.

an antisense RNA

Which mutagens incorporate into DNA and frequently pair with the wrong base?

base analogs

The mechanism that repairs errors through the removal of modified or abnormal bases is called ___

base-excision repair.

All of the following sequences play a role in promoting or repressing the use of a particular splice site in mRNA processing, EXCEPT ________________.

branch points

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 -Glucose requires less energy to metabolize and inhibits transcription of genes involved in metabolizing lactose.

Long noncoding RNAs (lncRNAs) and competing endogenous RNAs (ceRNAs) are involved in RNA crosstalk and gene expression in all the following ways EXCEPT which?

ceRNAs compete with lncRNAs for mRNA molecules.

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. -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.

When a T cell is exposed to viral antigens, it becomes activated and undergoes rapid proliferation. This rapid proliferation is caused by an increased availability of initiation factors that bind to ribosomes, causing the ribosomes to bind to mRNA and begin translation. When the viral threat has been subdued and proliferation halted, which outcome below for cellular components inside the T cell is NOT observed?

decrease in ribosomal subunits compared to the activated T cell

Gene X is controlled by the heat-shock response element and the serum response element. Gene X encodes a cell surface receptors that bind to serum. Which of the following would NOT be the predicted outcome of a cell undergoing thermal stress such as extreme heat?

decreased mRNA production for gene X -This statement would not be a predicted outcome. In response to heat, it would be expected that mRNA production for gene X would increase because of the presence of the heat-shock response element.

True or false: Regulation of gene expression in prokaryotes is characterized by a greater diversity of mechanisms than those of eukaryotic gene expression

false

True or false? Chromatin-remodeling complexes alter the chemical structures of the histones directly in order to make the DNA more accessible to regulator proteins

false

True or false? During attenuation, translation does not influence transcription.

false

True or false? Enhancers are typically found close to the gene they affect.

false

True or false? Histone methyltransferases and demethylases bind to specific DNA binding sites to add or remove methyl groups respectively

false

True or false? In both prokaryotes and eukaryotes, pre-mRNAs are processed before being translated

false

What secondary structure forms in the 5' UTR of the trp operon when tryptophan levels are high?

hairpin between regions 3 and 4

Proteins that are synthesized to prevent damage from stressing agents such as extreme heat are referred to as _____.

heat-shock proteins

Which of the following sets of conditions will lead to the highest expression of the lac structural genes?

high levels of lactose and low levels of glucose

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 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

Pieces of pre-mRNA that are removed by splicing proteins prior to translation are called _____.

introns

All of the following are required for genome editing with the CRISPR-Cas9 system except _____.

invading DNA protospacers

Breaks in double-stranded DNA molecules are most likely to result from exposure to _____.

ionizing radiation.

Which of the following E. coli strains with the lac genotypes will synthesize β-galactosidase in the absence of lactose?

lacI- lacP+ lacO+ lacZ+ lacY- -Here, the lac repressor gene is mutated and nonfunctional; constitutive expression would occur if the rest of the operon is wild type. Therefore, no induction is required to activate transcription.

Which of the following genotypes will result in a lac operon that produces β-galactosidase, both when lactose is present and when it is absent?

lacIs lacP+ lacOc lacZ+ lacY- -β-galactosidase will be constitutively produced because of the lacOc mutation.

A mutation in the lac promoter region that causes this region to no longer function would lead to which of the following?

lack of expression of the lac structural genes in the presence of lactose

The first structural gene of the trp operon, trpE, contains a 5ʹ UTR which is also known as a(n) _____ that has four regions.

leader

Small DNA fragments that contain one or more restriction sites and can be attached to the end of a DNA molecule are termed _____.

linkers

High concentrations of cAMP in the cell is a direct result of _____

low concentrations of glucose.

When glucose and lactose are present, β-galactosidase levels are ____

low.

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 Ames II test uses auxotrophic strains of bacteria to detect base pair substitutions and frameshift mutations. The test identifies a chemical as a mutagen when _____.

more his+ colonies appear on chemically treated plates than on control plates.

In E. coli, the mismatch repair system is able to distinguish the template DNA strand from the newly synthesized DNA strand by _____.

more methylations at sites in the template strand compared with the new strand.

The trp operon is an example of a _____ and _____ operon.

negative; repressible

What is one benefit of next-generation sequencing technologies over Sanger sequencing?

next-generation sequencing technologies are faster

Genes encoding proteins with related functions that are all under the control of a single promoter are called a(n) _____.

operon

Trans acting genes can control expression of genes on _____ DNA molecules, while cis acting genes can control expression of genes on _____ DNA molecules.

other; the same

If researchers have not yet isolated the protein product of a gene, what method can they use to isolate that gene?

positional cloning

Utilizing a genetic library requires all of the following except _____.

positional cloning here's what are required -All the steps listed are required when utilizing genetic libraries. -transforming cells so that, in the pool of cells, all genes are represented -cloning a large number of DNA fragments including the one of interest -screening the library with a probe for a gene of interest

If you wanted to increase the level of transcription of the trp operon, which type of control, when mutated and rendered ineffective, would give you a larger effect?

repression

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

repression of transcription

Mutations due to small insertions and deletions can arise spontaneously during DNA replication due to _____.

strand slippage.

Genes that encode proteins which are used in metabolism or biosynthesis are called _____ genes.

structural

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

the Ames test.

A scientist wishes to investigate if a region of DNA within a pancreas cell is being actively transcribed in response to insulin. What would she look for as evidence of active regions of DNA transcription?

the ability of DNase I to cleave specific sites within the DNA

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

Reverse genetics would likely utilize all mutagenesis technique below EXCEPT _____.

transposable elements

Barbara McClintock is known for her discovery of _____.

transposons

One of the codons that specifies the amino acid Gly (GGU, GGC, GGA, and GGG) undergoes a single-base substitution to become a nonsense mutation (UAA, UAG and UGA). This mutation is a _____.

transversion at the first position of the GGA codon. -A nonsense mutation is a stop codon (UAA, UAG, UGA). A G-to-U transversion at the first position of the GGA codon would produce a UGA stop codon.

True or false? Although the precise mechanism is unknown, SR proteins influence the choice of splice sites.

true

What determines whether the addition of a methyl group to a histone tail activates or represses transcription?

which histone is modified and the amino acid in the tail that gets methylated

A strain of E. coli with the lac genotype lacI- lacP+ lacO+ lacZ+ lac Y- / lacI+ lacP+ lacOc lacZ+ lacY- will be expressed in which of the following ways, assuming that glucose is not present?

β-galactosidase will be produced whether or not lactose is present; permease will not be produced regardless of whether lactose is present or not.

Riboswitches can influence gene expression by _____. Choose all that apply.

-stabilizing a terminator -stabilizing a secondary structure that masks the ribosome-binding site -eliminating a premature terminator when not bound by a regulatory molecule -making the ribosome-binding site available when not bound by a regulatory molecule

What is the function of the lac operator?

It is bound by the lac repressor protein.

A plasmid carries a copy of the lac operator region (lacO) but no other part of the lac operon (the lac repressor can bind to single operator regions). This plasmid is placed in an E. coli cell which has a normal copy of the lac operon in its chromosome. When this strain is grown, the number of plasmids reaches about 40 copies per bacterial cell. What is the expected phenotype of such a strain in the absence of glucose?

The lac operon will be turned on even in the absence of lactose. -Almost all the lac repressor molecules will be bound to operators carried by copies of the plasmid and not bound to the lac operator so the presence of lactose is not needed for the lac operon to be expressed.

The type of transcriptional control in operons in which a regulatory protein is an activator and stimulates transcription is called _____.

positive control

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.

The DNA that follows the DNA corresponding to region 4 in the mRNA 5′ UTR in the trp operon is AT-rich. What is the role of this AT-rich region in the functioning of the trp operon?

It facilitates the termination of transcription when region 3 pairs with region 4 in the mRNA 5′ UTR.

Which of the following is the most accurate description of gene expression regulation by riboswitches?

It involves a regulatory sequence within a mRNA that binds to some small molecule and alters mRNA secondary structure.

The lacI gene is placed on a multi-copy plasmid. Only the lacI gene without the rest of the lac operon is present on the plasmid. In E.coli, this plasmid exists in 30 to 40 copies per cell and genes carried on it are expressed. In an E.coli strain that contains a wild-type lac operon on its chromosome and also carries this plasmid, what will be the effect on expression of the chromosomal lac operon?

The structural genes of the lac operon will not be fully expressed even in the presence of lactose and absence of glucose.

An operon that is transcriptionally inactive until an activator protein associates with the DNA is called a(n) _____.

positive inducible operon.

Which level of gene control is matched appropriately to a regulatory mechanism?

post-translation modification - activation of a protein by cleaving it

A key factor controlling attenuation in the trp operon is the number of tRNA molecules charged with _____.

tryptophan.

When tryptophan levels are high, regions 3 and 4 of the 5ʹ UTR pair, followed by a string of _____ nucleotides.

uracil

What is the function of lacI in the regulation of the lac operon?

It encodes a repressor that, in the absence of lactose, binds to the lac operator and blocks expression of the structural genes.

An operon that is transcriptionally active and must be turned off is called a(n) _____.

repressible operon.

Cloning a gene after isolating it requires which of the following? Select all that apply.

-transformation of the recipient cells with the vector with the gene of interest -ligation into a vector -identification of the transformants that have the gene of interest

Which of the following is an example of a transversion mutation?

Adenine is replaced by thymine.

Many bacterial mRNAs including the lac mRNA are degraded within minutes after being synthesized. This may appear to be inefficient since a more stable mRNA could be used in translation over and over again. What is the most likely explanation for the lac mRNA being so unstable?

An unstable lac mRNA allows the expression of the lac structural genes to be turned off quickly when lactose is no longer available.

how CAP and lac work

Bacterial cells will metabolize glucose preferentially in the presence of other sugars. When glucose is available, genes that participate in the metabolism of other sugars are repressed. This is called catabolite repression, which results from positive control in response to glucose. CAP facilitates RNA polymerase binding to the lac operon promoter. CAP levels are inversely affected by glucose levels. Therefore, low glucose levels result in CAP binding, and then RNA polymerase binding and transcription from the lac operon. Prevention of CAP binding will decrease transcription from the lac operon.

What determines whether the addition of a methyl group to a histone tail activates or represses transcription

which histone is modified and the amino acid in the tail that gets methylated

Why are transcriptional regulator proteins necessary?

The basal transcription apparatus can only produce minimal levels of transcription without them.

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. -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.

The formation of chemical bonds between nucleotides on the same strand of DNA resulting from UV light exposure may cause all of the following except _____.

guanine dimers

An additional level of operon control that results in premature termination of transcription is called _____.

attenuation.

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 histone code refers to the direct modification of DNA nucleotides to encode information that affects how genes are expressed.

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

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

forward

Traditional analysis of mutants (natural or induced) to determine gene function is known as _____.

forward genetics

A forward mutation resulting in a green-eyed phenotype was generated in fruit flies by UV exposure. A second UV exposure, however, reversed that mutation as measured by the return of the wild-type phenotype. A researcher conducted a DNA analysis of these mutations. To her surprise, it revealed that the original "green-eye" mutation, which she identified as a nonsense mutation, was still retained in the now normal organism. Moreover, she identified a second mutation within a second gene, which was a tRNA gene. This researcher found evidence of a(n) _____

intergenic suppressor mutation. -There are two mutations occurring in two different genes (intergenic). The first mutation is suppressed by the second mutation in a tRNA gene.

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 -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

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

lactose is present but glucose is absent.

A mutagen that causes the loss of an amino group from a nucleotide is _____

nitrous acid.

Which of the following DNA repair mechanism is most likely to correct double-strand DNA breaks in eukaryotes?

nonhomologous end-joining repair

The repair mechanism that recognizes gross distortions in the helical DNA structure is called _____

nucleotide-excision repair.

Which type of transposition results in multiple copies of the transposable element?

replicative transposition

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

siRNAs; miRNAs

Some eukaryotic regulatory proteins can inhibit transcription as repressor. Which of the following regions do repressors bind?

silencer

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

What is the purpose of the antibody in a crosslinked ChIP (xChIP) assay?

to separate the DNA fragments bound to the protein of interest from the DNA fragments that are not bound

What does the chromatin-remodeling complex expose on the DNA that affects transcription?

transcription factor binding sites

What would be an example of what chromatin immunoprecipitation assays (ChIPs) would identify?

transcription factor interacting with DNA

An organism that has been permanently altered by the addition of a foreign DNA sequence to its genome is said to be _____.

transgenic

Attenuation depends on the fact that in prokaryotes, transcription and _____ are coupled.

translation

True or false? Antisense RNA molecules have been found in a wide range of bacterial species.

true

True or false? Gene regulation and protein modification are important mechanisms to increase protein diversity.

true

True or false? Heavily methylated DNA is associated with the repression of transcription.

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? The goal of the Ames test is to see if a particular chemical is mutagenic enough to cause the his- gene to mutate to the his+ gene.

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 of the following is not a mechanism of action of RNA inference?

ubiquitination of proteins

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

unequal crossing over