Cell Bio Homework Lecture 9-10

In present-day organisms, which trait or gene is commonly acquired by horizontal gene transfer? Choose one: A. antibiotic resistance B. sickle-cell anemia C. antibodies D. β globin E. lactose tolerance

A. antibiotic resistance; In present-day organisms, antibiotic resistance is commonly acquired by horizontal gene transfer. Genes that confer resistance to antibiotics are readily transferred from one bacterial species to another in a process called conjugation.

Which of the following libraries would be expected to be essentially the same? Choose one: A. genomic libraries made from mouse liver and kidney cells B. cDNA libraries made from mouse liver and kidney cells C. cDNA and genomic libraries made from mouse liver cells D. cDNA and genomic libraries made from mouse kidney cells

A. genomic libraries made from mouse liver and kidney cells; Genomic libraries produced from different cell types within the same organism should be the same, as the various cell types within a multicellular organism contain the same genomic DNA.

Which of the following is considered a housekeeping protein? Choose one: A. hemoglobin B. RNA polymerase C. insulin D. cortisol E. an antibody

B. RNA polymerase; Proteins that are common to all the cells of a multicellular organism are called housekeeping proteins. All cells are involved in gene expression and are therefore undergoing transcription, which requires RNA polymerase.

Which of the following statements about exon shuffling is not true? Choose one: A. Exon shuffling allows the generation of hybrid proteins with new functions. B. All human proteins are thought to have arisen from the duplication and shuffling of a few thousand exons. C. Exon shuffling allows bacteria to become antibiotic resistant. D. Exon shuffling requires the presence of introns.

C. Exon shuffling allows bacteria to become antibiotic resistant; Horizontal gene transfer—the movement of genes from one cell to another—allows bacteria to become antibiotic resistant, not exon shuffling.

At any given time, a typical differentiated human cell will express how many of its approximately 19,000 protein-coding genes? Choose one: A. about 200 B. about 20 C. from 5000 to 15,000 D. all 19,000

C. from 5000 to 15,000; Experimental examination of mRNAs in different cell types suggests that differentiated human cells express about this number of genes.

Nucleic acid hybridization, which can be used to detect any given DNA or RNA sequence in a mixture of nucleic acid fragments, relies on what factor? Choose one: a single strand of DNA or RNA forming covalent bonds with the sugar-phosphate backbone of the target nucleic acid A binding to T more tightly than G binds to C in a DNA double helix G binding to C more tightly than A binds to T in a DNA double helix a single strand of DNA or RNA forming a double helix with another nucleic acid strand of an identical nucleotide sequence a single strand of DNA or RNA forming a double helix with another nucleic acid strand of the complementary nucleotide sequence.

a single strand of DNA or RNA forming a double helix with another nucleic acid strand of the complementary nucleotide sequence.; A single strand of DNA or RNA will form a double helix with another nucleic acid strand of the complementary nucleotide sequence.

To determine what makes humans the unique animal that we are, it is most useful to compare our genome with that of which organism? Choose one: E. coli chimp other humans mouse chicken

chimp; Comparing our genome with that of a chimp—or with DNA harvested from fossilized Neanderthal bones—has led to the identification of DNA sequences that have changed particularly rapidly since we diverged from these species. Such human-accelerated regions are thought to reflect characteristics that differentiate us from even our closest relatives.

In eukaryotes, what separate component generally encodes individual protein domains? Choose one: introns codons exons mRNAs genes

exons; This arrangement—with protein domains being encoded by exons that are surrounded by large introns—facilitates the evolution of new genes and proteins by exon shuffling.

The image shows cells from the same organism. Which of the following statements is correct regarding these two human cells? Choose one: A. Both cells contain the same genes, but they are expressed differently. B. The neuron contains fewer genes as compared to the liver cell. C. One human cannot contain both of these diverse cell types. D. The neuron contains more genes as compared to the liver cell.

A. Both cells contain the same genes, but they are expressed differently.; Both cells contain the same genes, but they are expressed differently. If both cells come from the same human organism, then they are both descendants of the initial cell that was created at fertilization and therefore contain the same genome.

Which of the following is not true about noncoding DNA sequences? Choose one: A. They are essentially the same in humans, chimps, and mice. B. Changes in these sequences are likely to be involved in giving rise to new species. C. Their sequences have been shaped by evolution. D. They contain regulatory elements that ultimately dictate each organism's development.

A. They are essentially the same in humans, chimps, and mice. It is the coding sequences that are essentially the same in humans, chimps, and mice.

Which is not an example of epigenetic inheritance? Choose one: A. the inheritance of a single point mutation in a gene B. the inheritance of a regulatory protein that activates its own transcription C. the inheritance of methylation patterns in DNA D. the inheritance of patterns of chromosome condensation

A. the inheritance of a single point mutation in a gene Epigenetic inheritance does not involve changes to the nucleotide sequence of DNA, but a mutation does change the nucleotide sequence.

What happens to the miRNAs that are bound in a RISC? Choose one: A. If they include a sufficiently extensive region of complementarity with an mRNA, they are diverted to a region of the cytosol where they are eventually degraded. B. They are destroyed as soon as they bind to an mRNA. C. They remain bound to the RISC, where they can target the elimination of multiple mRNAs. D. Their translation is blocked.

C. They remain bound to the RISC, where they can target the elimination of multiple mRNAs; This feature allows a single miRNA molecule to inactivate many mRNA molecules.

In our human ancestors, the enzyme lactase, which allows us to digest the milk sugar lactose, was produced only during infancy. Today, many adults can digest lactose, while others cannot. Which group was born with a point mutation in the regulatory DNA of their lactase genes? Choose one: A. all humans who can digest lactose B. babies who can digest lactose C. adults who can digest lactose D. adults who cannot digest lactose E. all humans who cannot digest lactose

C. adults who can digest lactose; Adults who can digest lactose are those that have inherited the point mutation in the regulatory DNA of their lactase genes.

To reinforce cell identity, vertebrate cells can methylate which nucleotide? Choose one: A. any guanine B. any cytosine or guanine C. guanine that falls next to cytosine in the sequence CG D. cytosine that falls next to guanine in the sequence CG E. any cytosine

D. cytosine that falls next to guanine in the sequence CG In vertebrates, this modification occurs on select cytosine (C) nucleotides that fall next to a guanine (G) in the sequence 5'-CG-3'.

Using powerful new sequencing technologies, investigators can now catalog every RNA molecule made by a cell and determine at what quantities these RNAs are present. In an experiment, researchers measured the relative quantities of two different mRNAs—one transcribed from gene A, the other from gene B—in two different cell types. Gene B is expressed in both the liver and the brain whereas gene A is expressed in the brain but not in the liver. Which most likely encodes a housekeeping protein? Choose one: A. both genes B. neither gene C. gene A only D. gene B only

D. gene B only; Because gene B is expressed in both the liver and the brain, it could encode a housekeeping protein, which is the term given to genes that are expressed in all cells of a multicellular organism.

Which of the following cell types, when fully differentiated, does not divide to form new cells? Choose one: A. fibroblasts B. liver cells C. smooth muscle cells D. skeletal muscle cells

D. skeletal muscle cells Skeletal muscle is an example of a terminally differentiated cell.

The nucleotide sequences of which of the following have been used to create a single all-encompassing tree of life? Choose one: A. myosin genes B. rRNA gene C. immunoglobulin genes D. globin genes E. leptin gene

rRNA gene; Because the process of translation is so fundamental to all living cells, the gene encoding the rRNA of the small ribosomal subunit has been highly conserved since the early history of life on Earth.

In clone-by-clone sequencing, individual clones are first placed in order based on what factor? Choose one: their size their sequence their chromosome the amount of repetitive DNA they contain the restriction sites they contain

the restriction sites they contain; Before they are sequenced, individual clones are positioned on a physical map of the genome based on the pattern of restriction sites they contain. This restriction site "signature" can be used to order the fragments and place them on a known restriction map of the human genome.

How does a bacterium protect its DNA from cleavage by its own restriction nucleases? Choose one: A. Proteins attach to the target sequences, preventing restriction nucleases from binding. B. The bacterium sequesters its DNA in an organelle that does not allow restriction nucleases to enter. C. The bacterium chemically modifies its own DNA sequences, thereby preventing recognition by the nucleases. D. The genome of the bacterium does not contain the recognition sequences for the restriction nucleases it produces. E. DNA ligase quickly reseals target sequences when they are cut.

C. The bacterium chemically modifies its own DNA sequences, thereby preventing recognition by the nucleases. By chemically modifying their own DNA sequences, bacteria prevent recognition of their own DNA by their own nucleases. Bacteria methylate their DNA to prevent it from being recognized by restriction nucleases.

What would happen to the helix-3 interaction with DNA if a mutation occurred that altered this adenine (as shown) to guanine? Choose one: A. The integrity of the interaction would increase because the hydrogen bonds would still be able to form and would be stronger. B. The integrity of the interaction would remain the same because the same two hydrogen bonds would still be able to form. C. The integrity of the interaction would decrease because one of the two hydrogen bonds would not be able to form.

C. The integrity of the interaction would decrease because one of the two hydrogen bonds would not be able to form. If guanine replaced adenine, the integrity of the protein-DNA interaction would decrease because one of the two hydrogen bonds would not be able to form. This is because adenine contains an amino group that interacts with the asparagine carbonyl group; however, this interaction would not form if guanine were present in place of adenine.

Which of the following statements is not true about the differences between liver cells and kidney cells in the same organism? Choose one: A. They express different genes. B. They contain different proteins. C. They contain different genes. D. They contain the entire set of instructions needed to form the whole organism.

C. They contain different genes. Specialized cells, such as liver and kidney cells, do contain the same genes. They just express them differently. This is referred to as differential gene expression.

Antibiotic resistance is a serious problem. The U.S. Centers for Disease Control and Prevention estimates that each year 2 million Americans are infected with antibiotic-resistant bacteria and 23,000 people die from their infection. Scientists are searching for new antibiotic drugs that would target the process of conjugation to lessen the spread of antibiotic resistance. Why might a new antibiotic that blocks conjugation be a potentially effective drug? Choose one: A. Blocking conjugation would kill bacteria that already have the antibiotic-resistance genes. B. Blocking conjugation would only be effective against harmful bacteria with antibiotic-resistance genes. C. Blocking conjugation would lead to the removal of antibiotic-resistance genes from drug-resistant bacteria. D. Blocking conjugation would block genetic transfer between two cells, potentially blocking the transfer of antibiotic-resistance genes between bacteria.

D. Blocking conjugation would block genetic transfer between two cells, potentially blocking the transfer of antibiotic-resistance genes between bacteria.; Antibiotic-resistance plasmids are shared among bacteria and blocking this process could lessen the spread of antibiotic resistance.

Your lab uses the annelid worm Lumbriculus variegatus as a model organism to study regeneration. Your studies would be helped by knowing which genes are present in this organism, but its genome has not been sequenced. A recent technique for gene determination is RNA-Seq, in which RNAs are directly isolated and sequenced. What is a disadvantage of using RNA-Seq for gene identification? Choose one: A. RNA-Seq works only in mammalian cells and therefore cannot be used with model organisms such as Lumbriculus or Drosophila. B. RNA-Seq relies on genes being homologous across species, but not all genes have homologs. C. RNA-Seq may selectively miss noncoding RNAs as compared to mRNAs. D. RNA-Seq may miss genes transcribed in a very tissue- and temporal-limited fashion.

D. RNA-Seq may miss genes transcribed in a very tissue- and temporal-limited fashion. While all cells of a multicellular organism contain the same DNA, which genes are transcribed differs among cell types. Thus, RNA-Seq may miss genes that are not being transcribed in the tissue from which the RNA was isolated or genes that are only expressed during certain developmental stages.

In bacterial cells, the tryptophan operon encodes the genes needed to synthesize tryptophan. What happens when the concentration of tryptophan inside a cell is high? Choose one: It inactivates the tryptophan repressor, which shuts down the tryptophan operon. It activates the tryptophan repressor, which shuts down expression of the tryptophan operon. It activates the tryptophan repressor, allowing transcription of the tryptophan operon. It activates the tryptophan repressor, which breaks down excess tryptophan. It inactivates the tryptophan repressor, allowing transcription of the tryptophan operon.

It activates the tryptophan repressor, which shuts down expression of the tryptophan operon.; In bacterial cells, when the concentration of tryptophan is high, it activates the tryptophan repressor, which binds to the Trp operator and shuts down expression of the tryptophan operon.

How does automated Sanger sequencing differ from the original method? Choose one: It can run gels that are much larger. It uses a mixture of chain-terminating nucleotides, each with its own label. It can be used to directly determine the amino acid sequence of a protein sample. It does not require DNA polymerase. It does not use chain-terminating nucleotides.

It uses a mixture of chain-terminating nucleotides, each with its own label.; Automated Sanger sequencing differs from the original method in that it uses a mixture of chain-terminating nucleotides, each with its own label. These generate a mixture of DNA products of different lengths, each containing a chain-terminating nucleotide of a different color. These products are separated by electrophoresis and the color of the fluorescent labels is read by a computer.

How or where do most transcription regulators bind? Choose one: to the minor groove of DNA to a DNA sequence called the homeodomain to the major groove of RNA to a DNA sequence called a leucine zipper as dimers

as dimers; Dimerization roughly doubles the area of contact with the DNA, making the interaction tighter and more specific.

In bacteria, what would be the consequence of a protein binding to and blocking the ribosomal binding site on an mRNA? Choose one: A. The small ribosomal subunit will not be able to bind to the mRNA, and translation will be inhibited. B. The protein will recruit the small ribosomal subunit to the mRNA, increasing translation efficiency. C. The protein will be incorporated into the growing polypeptide chain. D. The ribosome will begin translation at a new location on the mRNA.

A. The small ribosomal subunit will not be able to bind to the mRNA, and translation will be inhibited. When the ribosomal binding site is covered by a protein, translation is inhibited.

Which of the following statements about eukaryotic activator proteins is false? Choose one: A. They stimulate transcriptional initiation by opening up the double helix. B. They stimulate transcription initiation by promoting the assembly of a transcription initiation complex at the promoter. C. They stimulate transcription initiation by recruiting proteins that modify chromatin structure. D. They stimulate transcription initiation by aiding in the assembly of general transcription factors and RNA polymerase at the promoter.

A. They stimulate transcriptional initiation by opening up the double helix. Eukaryotic activator proteins do not open up the double helix. Rather, eukaryotic transcriptional activators can recruit chromatin-modifying proteins to help initiate gene transcription.

On your first attempt to run a PCR, you realize you forgot to add one of the two primers. The graduate student you work with suggests you throw away your reaction and start over. Why? Choose one: A. You will get a small amount of product that is not correct. B. You will get half as much product. C. You will get a normal amount of product that is smaller than expected. D. You will get a normal amount of product that is single-stranded.

A. increasing the annealing time when primers hybridize to the template DNA; The product will be a long, single-stranded product in very small amounts. Additionally, only one DNA strand will be copied in each round of PCR, so no amplification will occur.

Which of the following is not true about retrotransposons? Choose one: A. They move via an RNA intermediate. B. They are found only in viruses. C. They are abundant in the human genome. D. They are unique to eukaryotes. E. They are transcribed by the host cell's RNA polymerase.

B. They are found only in viruses. Retrotransposons are not found only in viruses. Retrotransposons are abundant in the human genome. Two types—L1 elements and Alu sequences—together constitute about one-quarter of our entire genome sequence.

One way to identify protein-coding genes is to search a DNA sequence for open reading frames—long sequences of 100 or more codons that lack a stop codon. But this process can be made more difficult by the fact that in higher eukaryotes, genes can stretch over tens of thousands of nucleotide pairs, much of which contain introns. To help find the exons buried within this noise, computers can be used to search for other distinctive features that mark the presence of a protein-coding gene. Which is not considered a feature characteristic of a protein-coding gene? Choose one: A. presence of an initiation codon B. splicing sequences that mark intron-exon boundaries C. presence of mobile genetic elements D. conservation with coding sequences of other organisms E. gene regulatory sequences located upstream

C. presence of mobile genetic elements; Mobile genetic elements tend to be excluded from genes by purifying selection, which most likely eliminated insertions that disrupted gene function.

What is an operon? Choose one: A. a set of genes controlled by the binding of two or more transcription regulators B. a sequence of DNA that produces a variety of mRNAs C. a set of genes that is constitutively active D. a set of genes transcribed as a single mRNA from a single promoter E. a short sequence of DNA to which a transcription regulator binds

D. a set of genes transcribed as a single mRNA from a single promoter; Operons are defined by the coordination of expression of their resident genes under the direction of a single promoter. Each operon produces a single mRNA that encodes multiple proteins.

Which would be the best method for determining which genes are being transcribed in a particular cell type? Choose one: A. DNA sequencing B. electron microscopy C. X-ray crystallography D. NMR spectroscopy E. RNA sequencing (RNA seq)

E. RNA sequencing (RNA seq); RNA sequencing, also commonly called "RNA seq," is a new, powerful technique that allows researchers to catalog all of the RNA molecules present in a cell at a given moment in time.

Most of the genetic variation in the human genome takes what form? Choose one: A. chromosomal rearrangements B. copy-number variations C. DNA duplications or deletions D. the size of short, tandem repeats E. single-nucleotide polymorphisms

E. single-nucleotide polymorphisms; Any two unrelated individuals will differ by approximately 2.5 ×× 106 SNPs across their genomes.

Which form of control directly influences which mRNAs are selected by ribosomes for the synthesis of proteins? Choose one: A. transcriptional control B. mRNA processing and localization control C. protein activity control D. mRNA degradation control E. translational control

E. translational control If an mRNA fails to associate with the ribosome, then that mRNA will not be translated into protein

For a retrotransposon, reverse transcriptase produces DNA copies using which of the following as a template? Choose one: transposase a single-strand viral genome RNA the host cell's RNA polymerase double-stranded DNA

RNA; Reverse transcriptase is an unusual DNA polymerase that can use RNA as its template. The enzyme is so named because it "reverses" the normal flow of genetic information from DNA to RNA.

Which of the following statements most accurately describes the expression of the repressor protein of the tryptophan operon? Choose one: The gene for the tryptophan repressor is turned on in response to high levels of tryptophan in the cell. The gene for the tryptophan repressor is turned off in response to high levels of tryptophan in the cell. The gene for the tryptophan repressor is turned on in response to low levels of tryptophan in the cell. The gene for the tryptophan repressor is turned off in response to low levels of tryptophan in the cell. The gene for the tryptophan repressor is expressed constitutively.

The gene for the tryptophan repressor is expressed constitutively.; The gene for the tryptophan repressor is expressed constitutively. The Trp repressor protein must always be present so as to constantly respond to the levels of tryptophan in the cell.

Which of the following statements is/are true of long noncoding RNAs? Choose one or more: They are involved in X chromosome inactivation. They can regulate the translation and stability of mRNAs. They can silence genes by promoting the formation of euchromatin. They can trigger the activity of histone acetyltransferases.

They are involved in X chromosome inactivation. They can regulate the translation and stability of mRNAs.; Long noncoding RNAs are involved in X chromosome inactivation and can regulate the translation and stability of mRNAs.

Within this tree, humans are most related to which of the following? Choose one: orangutan gorilla chimpanzee

chimpanzee Humans share 99% of their DNA sequence with chimpanzees.

Determine whether the following statement is true or false: Noncoding sequences are never conserved by purifying selection. This statement is ______.

false; the majority of noncoding sequences are not constrained by purifying selection. However, approximately 3% of the noncoding sequences in the human genome appear to be functionally important, as these sequences are highly conserved in many other mammals.

Almost half of the human genome consists of what? Choose one: mobile genetic elements genes that code for proteins regulatory sequences introns

mobile genetic elements; Almost half of the human genome consists of mobile genetic elements. These include retrotransposons and DNA-only transposons.

Although all of the steps involved in expressing a gene can in principle be regulated, what is the most important stage of control for most genes? Choose one: RNA transport and localization RNA processing mRNA translation transcription initiation mRNA degradation

transcription initiation; Because transcriptional control is the first step in gene expression, regulation at this level has the most dramatic effects. If an RNA transcript is never synthesized, there is no way for that gene to ever be expressed.

Many mobile genetic elements encode an enzyme that mediates their movement. What is this enzyme called? Choose one: exonuclease transposase flippase jumping gene transposon

transposase; Transposase recognizes and acts on unique DNA sequences present within each mobile genetic element.

Determine whether the following statement is true or false: Master regulators such as Ey in Drosophila are so powerful that they can even activate their regulatory networks outside the normal location. This statement is ______.

true; In Drosophila, master regulators such as Ey induce the expression of other regulatory genes, which can result in the development of organs such as the eye outside of their normal location.

Which of these statements is consistent with the information presented in the figure? Choose one: A. Mutation A is heritable to offspring because the mutation took place in the germ line. B. Mutation A is heritable to offspring because the mutation took place in a somatic cell. C. Mutation B is heritable to offspring because the mutation took place in the germ line. D. All of the above are correct. E. None of the above are correct.

A. Mutation A is heritable to offspring because the mutation took place in the germ line.; Mutation A is heritable to offspring because the mutation took place in the germ line. A mutation that occurs in a germ-line cell (A) can be passed on to the next generation (green). By contrast, a mutation that arises in a somatic cell (B) affects only the progeny of that cell (orange) and will not be passed on to the organism's offspring.

In the mid-1980s, Walter Gilbert, a physicist-turned-biologist, suggested that humans could have 100,000 genes. On what did he base this ballpark estimate? Choose one: A. a calculation based on the size of the genome and the average size of the genes that had been sequenced B. a computer program that scanned segments of two human chromosomes for potential protein-coding sequences C. a study that found that a slime mold possesses some 10,000 genes—and humans are at least 10 times as complex D. a technique called RNA-Seq that catalogued all the RNAs produced in a human zygote—a fertilized egg

A. a calculation based on the size of the genome and the average size of the genes that had been sequenced; The average size of the few genes that had been sequenced at the time was 3 ×× 104 nucleotide pairs, and the human genome contains about 3 ×× 109 nucleotide pairs. Gilbert used these two numbers to calculate his estimate.

Which of the following would be most likely to accumulate changes to its sequence? Choose one: A. a gene that has recently been duplicated in the genome B. a regulatory DNA sequence C. a gene encoding DNA polymerase D. a gene that codes for a highly optimized essential protein or RNA molecule E. a gene that is highly conserved among a wide diversity of organisms

A. a gene that has recently been duplicated in the genome When genes are duplicated, each of the copies can accumulate mutations as long as one of the copies retains the original function of the gene. In this way, duplicated genes can evolve new functions over time.

Scientists are working to develop the CRISPR-Cas9 system to treat human disease. One of the first clinical trials in humans will use CRISPR to treat β thalassemia. People with β thalassemia have low levels of hemoglobin and cannot get enough oxygen to all their tissues. The treatment is designed to cleave the gene BCL11A that is important for repressing fetal hemoglobin, which is usually only produced in infancy. Cleaving this gene will prevent expression of the inhibitor BCL11A so that fetal hemoglobin can be produced even in adults, alleviating the symptoms. Which of the following are important components added to cells from β thalassemia patients in order to treat the disorder? Choose one or more: A. a guide RNA that recognizes the BCL11A gene B. a guide RNA that recognizes the Cas9 gene C. the Cas9 enzyme D. the BCL11A protein

A. a guide RNA that recognizes the BCL11A gene C. the Cas9 enzyme; To edit the BCL11A gene, a guide RNA that recognizes the gene and the Cas9 enzyme are needed.

The CRISPR-Cas9 system was discovered in bacteria, which use it as a defense mechanism against viral infections. Scientists have experimentally modified this system to work in other organisms. Which of the following statements correctly describe an application of the CRISPR system? Choose one or more: A. activation of transcription of a specific gene B. gene editing of a specific gene C. editing of the mRNA of a specific gene D. repression of transcription of a specific gene

A. activation of transcription of a specific gene B. gene editing of a specific gene D. repression of transcription of a specific gene; CRISPR can be used to edit a gene and activate or repress a specific gene.

The exons that encode protein domains can be moved without becoming damaged. Why is this? Choose one: A. because recombination tends to occur in introns, not exons B. because exons are so similar in size C. because the recombination process that moves exons is precise and carefully regulated D. because exons are so plentiful E. because recombination enzymes recognize special sequences that mark the beginnings and ends of exons

A. because recombination tends to occur in introns, not exons; Because introns are so large, and their sequence is for the most part unimportant, introns can be broken and rejoined by chance recombination without introducing functional damage.

Conjugation occurs through a series of steps. Scientists are searching for new antibiotic drugs that could block different parts of the conjugation pathway. Predict the molecular pathways that could be targeted by a new drug to block conjugation and reduce the sharing of antibiotic-resistance genes. Choose one or more: A. block the DNA polymerase that replicates the plasmid DNA B. block nicking of the DNA plasmid C. block formation of the cytoplasmic bridge between the two cells D. block formation of the sex pilus

A. block the DNA polymerase that replicates the plasmid DNA B. block nicking of the DNA plasmid C. block formation of the cytoplasmic bridge between the two cells D. block formation of the sex pilus; All four of these steps are critical for conjugation to occur. Formation of the sex pilus is the first critical event. Formation of a cytoplasmic bridge, nicking of the DNA, and replication of the plasmid with DNA polymerase are also critical steps.

What are homologous genes? Choose one: A. genes that are similar in their nucleotide sequence because of a common ancestry B. genes that encode proteins that perform similar functions C. genes that encode proteins that fold into the same shapes D. genes that occupy the same position on different chromosomes E. genes that are present in the same organism

A. genes that are similar in their nucleotide sequence because of a common ancestry The key to homologous genes is not just their similarity, but that they are similar because they share a common evolutionary origin. Around half of our genes have clear homologs in flies and worms.

Which of the following mutations would be least likely to disrupt the function of the leucine zipper protein in the animation? The structures of relevant amino acids are provided below. Choose one: A. mutation of a leucine to valine in the dimerization domain of the protein B. mutation of a leucine to aspartic acid in the dimerization domain of the protein C. mutation of the guanine nucleotide to a thymine nucleotide in the binding site on the DNA D. mutation of the DNA-binding arginine to alanine in the DNA-binding domain of the protein

A. mutation of a leucine to valine in the dimerization domain of the protein; Dimerization between the two subunits requires hydrophobic amino acids like leucine to pack tightly. Mutation of the hydrophobic leucine to another hydrophobic amino acid would be less disruptive than the other listed mutations. Changing the hydrophobic leucine to a charged amino acid in the dimerization domain will very likely disrupt dimerization, which is required for protein function. Changing the polar, charged arginine to a hydrophobic alanine will likely disrupt the ability of the protein to form hydrogen bonds and bind to the DNA, again disrupting protein function. Finally, altering the sequence of the binding site in the DNA will alter the bonds that can be formed and disrupt the sequence-specific interaction between the protein and DNA, disrupting function.

Researchers have created plasmids that only allow expression of inserted genes in response to a metabolite. Researchers can add these plasmids to E. coli cells and increase the expression of the inserted gene by adding the appropriate metabolite to the culture media. Plasmids containing which combination of operator and promoter allow activation of gene expression in response to an added metabolite? Choose one or more: A. operator recognized by Lac repressor protein B. operator recognized by Trp repressor protein C. weak promoter D. strong promoter

A. operator recognized by Lac repressor protein D. strong promoter; Effective transcription relies on strong binding of RNA polymerase to promoters. This can occur if the promoter itself is strong because it is a good match for the consensus DNA sequences recognized by RNA polymerase or if RNA polymerase is recruited to a weak promoter by an activator binding to a regulatory site. Normally, robust transcription from the Lac operon requires both the presence of lactose (to remove the repressor protein) and the binding of the CAP activator protein (see image below). The requirement for the CAP activator can be overridden with a strong promoter.

Investigators are attempting to clone a gene that is bracketed by the following 5'-to-3' sequence: ATGAAATCTACGTTTCAC......CCCCCAGTACCCCCCTTA Which of the following pairs of primers could be used to direct the amplification of this gene? (All sequences are written 5' to 3'.) Choose one: TACTTTAGATGCAAAGTG and ATTCCCCCCATGACCCCC TACTTTAGATGCAAAGTG and CCCCCAGTACCCCCCTTA ATGAAATCTACGTTTCAC and ATTCCCCCCATGACCCCC ATGAAATCTACGTTTCAC and TAAGGGGGGTACTGGGGG TACTTTAGATGCAAAGTG and GGGGGTCATGGGGGGAAT

ATGAAATCTACGTTTCAC and TAAGGGGGGTACTGGGGG; The first primer would hybridize with the 3' end of the strand that is complementary to the sequence shown. This "forward" primer (with a sequence ATGAAATCTACGTTTCAC) would be extended to the right (in the 5'-to-3' direction). The second primer would hybridize to the 3' end of the sequence shown. This "reverse" primer, which would have the sequence TAAGGGGGGTACTGGGGG, would be extended to the left (also in the 5'-to-3' direction).

Which of the following statements concerning leucine zipper protein dimerization and DNA binding is correct? Choose one: A. Leucine zipper protein dimerization is facilitated by polar amino acids in the dimerization domains. B. Leucine zipper proteins function as a dimer with both subunits making contact with the sequence-specific DNA site. C. Leucine zipper proteins use ionic bonds to bind with the sequence-specific DNA site. D. Leucine zipper proteins contain many leucine amino acids in the DNA-binding region that facilitate sequence-specific DNA binding.

B. Leucine zipper proteins function as a dimer with both subunits making contact with the sequence-specific DNA site. The leucine and other hydrophobic side chains in the first portion of the helices dimerize along the length of the two helices. The second portion of the helices forms the DNA-binding domain, where amino acid side chains hydrogen-bond with specific bases in the DNA, leading to sequence-specific binding.

You are a new hire at a bioinformatics company and are helping to annotate the genome of a recently sequenced organism. A co-worker indicates that the software used to detect potential genes finds protein-coding genes more easily than genes for noncoding RNAs. What difference between coding and noncoding genes explains why genes coding for proteins are easier to identify than genes for noncoding RNAs? Choose one: A. Only protein-coding genes contain homologs in other organisms. B. Only genes coding for proteins contain open reading frames (ORFs). C. Only genes for noncoding RNAs contain introns. D. Only genes coding for proteins have promoter regions preceding their genes.

B. Only genes coding for proteins contain open reading frames (ORFs). ORFs are long sequences of nucleotides without stop codons and hence may encode proteins. Noncoding RNAs cannot be detected with this method because they don't code for proteins.

If two distantly related organisms have regions of conserved synteny, what does this mean? Choose one: A. The genes examined in the two species are on different chromosomes, but in their last common ancestor, the genes were on the same chromosome. B. The genes examined in the two species are present in the same order as in their most recent common ancestor. C. The genes examined in the two species are under the control of the same transcription regulators. D. The genes examined in the two species are identical in sequence to each other. E. The genes examined in the two species are nonhomologous to each other.

B. The genes examined in the two species are present in the same order as in their most recent common ancestor. If two distantly related organisms have regions of conserved synteny, then the genes examined in the two species are present in the same order as in their most recent common ancestor. Comparison of the mouse and human sequences reveals that more than 90% of our genome can be partitioned into such regions of conserved synteny.

Humans differ from one another by how much? Choose one: A. an average of 1 nucleotide in 10 B. an average of 1 nucleotide in 1000 C. an average of 1 nucleotide in 100 D. an average of 1 nucleotide in 1,000,000

B. an average of 1 nucleotide in 1000; As individuals, our nucleotide sequences differ by about 0.1%, or about 3 million differences between one genome and another.

Researchers assayed the activity of enzyme F in three different types of tissue from the same mouse by determining the amount of enzyme product produced per milligram of tissue per unit time. As shown in the graph below, results indicate more product generation in the liver compared to the kidney and muscle samples. Which of the following factors might explain the different results among the three tissues? Choose one or more: A. differences in the DNA content among the tissue types B. differences in the transcription of the gene encoding the enzyme among the tissue types C. differences in the translation of the mRNA encoding the protein among the tissue types D. differences in the post-translational modifications of the enzyme among the tissue types

B. differences in the transcription of the gene encoding the enzyme among the tissue types C. differences in the translation of the mRNA encoding the protein among the tissue types D. differences in the post-translational modifications of the enzyme among the tissue types Control of gene expression can happen at any step along the pathway from DNA to protein, including transcription, mRNA processing and localization, protein production and degradation, and protein activity control.

What type of molecule triggers RNA interference (RNAi)? Choose one: A. single-stranded RNAs B. foreign, double-stranded RNA C. double-stranded DNA D. double-stranded miRNAs E. foreign, single-stranded DNA

B. foreign, double-stranded RNA; Double-stranded RNAs are produced by many viruses and transposable elements, and are thus recognized as "foreign." This makes them valid targets for elimination by RNAi.

Which technique or reagent would be least likely to reveal whether a patient has been infected by a virus? Choose one: A. DNA microarray B. green fluorescent protein C. RNA-Seq D. in situ hybridization E. polymerase chain reaction

B. green fluorescent protein; Green fluorescent protein is a "signal" molecule but does not have any inherent specificity. To detect a particular virus, it would need to be linked in some fashion to another molecule that would identify the presence of the virus.

You have now added both PCR primers and successfully run the PCR, but you notice that the quantity of product generated is low. The graduate student you work with mentions that your expected product is quite long and that you may want to alter your PCR conditions to increase efficiency of product generation. Which of the following would help increase the amount of long PCR product generated? Choose one: A. increasing the annealing time when primers hybridize to the template DNA B. increasing the elongation time when DNA polymerase synthesizes the new DNA C. increasing the annealing temperature when primers hybridize to the template DNA D. increasing the elongation temperature when DNA polymerase synthesizes the new DNA

B. increasing the elongation time when DNA polymerase synthesizes the new DNA Increasing the elongation time during DNA synthesis could allow more time to synthesize the longer strands of DNA and could increase product generation.

Where do transcription regulators usually bind on a DNA double helix? Choose one: A. 3' end B. major groove C. minor groove D. 5' end E. single-stranded regions

B. major groove It is the binding of a transcription regulator to the major groove of DNA in a regulatory sequence that acts as the switch to control transcription.

What is the most general term for a change in a single nucleotide pair? Choose one: A. neutral mutation B. point mutation C. missense mutation D. nonsense mutation E. frameshift mutation

B. point mutation; point mutation is one that changes a single nucleotide pair.

The long noncoding RNA Xist silences genes on the X chromosome by doing what? Choose one: A. acting as an antisense transcript that binds to mRNAs B. promoting the formation of heterochromatin C. producing miRNAs D. encoding a repressor protein E. producing siRNAs

B. promoting the formation of heterochromatin; Although the molecular mechanisms are not entirely clear, it is thought that Xist recruits enzymes and chromatin-remodeling complexes that promote the formation of a highly condensed form of heterochromatin.

Which of the following describes the Lac operon in E. coli when lactose, but not glucose, is present in the culture medium? Choose one: A. Neither CAP nor the Lac repressor is bound to the Lac operon's regulatory DNA, and the Lac operon is expressed. B. CAP and the Lac repressor are both bound to the Lac operon's regulatory DNA, and the Lac operon is not expressed. C. CAP, but not the Lac repressor, is bound to the Lac operon's regulatory DNA, and the Lac operon is expressed. D. Neither CAP nor the Lac repressor is bound to the Lac operon's regulatory DNA, and the Lac operon is not expressed. E. The Lac repressor, but not CAP, is bound to the Lac operon's regulatory DNA, and the Lac operon is not expressed.

C. CAP, but not the Lac repressor, is bound to the Lac operon's regulatory DNA, and the Lac operon is expressed. The expression of the Lac operon is tightly regulated by the type of carbohydrate present in the environment. Glucose is the preferred carbohydrate source and only in its absence will the necessary small molecule, cAMP, be found. cAMP binding to the CAP activator is necessary but not sufficient for the expression of the Lac operon. In addition to low glucose levels, there must also be lactose present in the environment. If this is the case, allolactose, a derivative of lactose, can bind to the Lac repressor and cause it to release from the promoter. Therefore, as outlined in the figure below, the Lac operon is only expressed when glucose is absent and lactose is present because the CAP activator is bound to the promoter, but the Lac repressor is not. This ensures that the genes in the Lac operon are expressed only in the conditions where lactose is the only carbohydrate source available.

More than 500 human genetic diseases are caused by haploinsufficiency, a heterozygotic condition in which the wild-type allele cannot produce enough normal protein to make up for the loss of functional protein expression from the mutated allele to get a normal phenotype. What might be an approach for treating haploinsufficiency disorders in non-human disease models? Choose one: A. Cre recombinase conditional knockout of the mutated gene B. polymerase chain reaction of the wild-type allele DNA sequence to amplify the gene C. CRISPR targeting wild-type gene with inactive Cas9 fused to a transcription activator D. siRNA targeted to the mutated gene sequence to reduce mutated mRNA levels

C. CRISPR targeting wild-type gene with inactive Cas9 fused to a transcription activator; This would boost production of the wild-type gene, leading to more protein production as shown in the image below. This approach was recently used to treat a genetic cause of obesity in a mouse model (Matharu et al. 2019, Science vol. 363). Catalytically inactive Cas9 fused to a transcriptional activator can increase gene expression from a gene specified by the guide RNA (in blue).

The maltose operon contains genes that code for proteins that catabolize the disaccharide maltose. Similar to the Lac operon, which is only efficiently transcribed in the presence of lactose, the maltose operon is only efficiently transcribed in the presence of maltose. How might induction of the maltose operon in response to maltose be achieved? Choose one or more: A. Maltose causes a repressor to bind an operon with an efficient promoter. B. Maltose removes an activator from an operon with an inefficient promoter. C. Maltose removes a repressor from an operon with an efficient promoter. D. Maltose causes an activator to bind an operon with an efficient promoter. E. Maltose causes an activator to bind an operon with an inefficient promoter.

C. Maltose removes a repressor from an operon with an efficient promoter. E. Maltose causes an activator to bind an operon with an inefficient promoter. There are two ways to accomplish operon induction: (1) the inducer can remove a repressor from an operon with an efficient promoter, or (2) the inducer can cause an activator to bind to an operon with an inefficient promoter.

c-Met is an oncogene that contributes to the development of certain cancers by triggering cell division and tumor growth. In a 2009 article, Yan and colleagues found regions in the 3' untranslated region of c-Met mRNA complementary to microRNA-1/206. In addition, higher levels of microRNA-1/206 were associated with slower cell proliferation. What is a likely explanation for the inverse correlation between microRNA-1/206 and cell proliferation? Choose one: A. MicroRNA-1/206 codes for a protein that directly binds to and inhibits c-Met protein. B. MicroRNA-1/206 codes for a tumor suppressor protein that directly inhibits cell proliferation. C. MicroRNA-1/206 targets c-Met mRNA for destruction via RISC. D. MicroRNA-1/206 stabilizes c-Met mRNA, leading to enhanced translation.

C. MicroRNA-1/206 targets c-Met mRNA for destruction via RISC.; MicroRNAs are noncoding regulatory RNAs that regulate gene expression by binding complementary mRNAs, leading to the destruction of the targeted mRNAs.

Which of the following describes the Lac operon in E. coli when both lactose and glucose are present in the culture medium? Choose one: A. CAP, but not the Lac repressor, is bound to the Lac operon's regulatory DNA, and the Lac operon is expressed. B. The Lac repressor, but not CAP, is bound to the Lac operon's regulatory DNA, and the Lac operon is not expressed. C. Neither CAP nor the Lac repressor is bound to the Lac operon's regulatory DNA, and the Lac operon is not expressed. D. CAP and the Lac repressor are both bound to the Lac operon's regulatory DNA, and the Lac operon is not expressed. E. CAP binds to the Lac repressor, preventing it from binding to the Lac operon's regulatory DNA, and the Lac operon is expressed.

C. Neither CAP nor the Lac repressor is bound to the Lac operon's regulatory DNA, and the Lac operon is not expressed.; Under these conditions, neither CAP nor the Lac repressor is bound to the Lac operon's regulatory DNA, and the operon is not expressed.

Based on all data presented in the stained agarose gel, which of the following statements is correct? Choose one: A. The original piece of DNA was linear and was cut by EcoRI twice and HindIII only once. B. The original piece of DNA was linear and was cut by EcoRI once and not at all by HindIII. C. The original piece of DNA was circular and was cut by EcoRI once and not at all by HindIII. D. The original piece of DNA was circular and was cut by EcoRI twice and HindIII only once.

D. The original piece of DNA was circular and was cut by EcoRI twice and HindIII only once. The original piece of DNA must have been circular and was cut by EcoRI twice because there are two different-sized fragments of DNA observed on the gel. Similarly, the circular DNA was cut by HindIII only once, which is why there is only one size DNA fragment observed on the gel. The fourth lane provides the conclusive nature of this result, as there are three bands present: EcoRI cut twice and HindIII only once in the middle of one of the two EcoRI-released fragments.

You are a virologist. A friend asks you how reverse transcriptase inhibitors help treat HIV. You explain that inhibition of reverse transcriptase directly prevents the following step of the HIV viral life cycle. Choose one: A. packaging of viral genome into coat and envelope proteins B. transcription of new RNA genomes from integrated viral DNA C. integration of viral DNA into host cell genome D. production of DNA from RNA genome

D. production of DNA from RNA genome; HIV is a retrovirus with a single-stranded RNA genome. This RNA genome is reverse-transcribed into DNA via the enzyme reverse transcriptase.

In comparing the genomes of mammals to the relatively small genome of the pufferfish (about one-tenth the size of a mammalian genome), what tends to be missing in pufferfish? Choose one: A. genes only B. introns only C. exons only D. repetitive DNA in noncoding sequences, including that of introns

D. repetitive DNA in noncoding sequences, including that of introns; Compared to the human genome, the pufferfish (Fugu rubripes) genome lacks repetitive DNA in noncoding sequences, including that of introns. Fugu introns—and other noncoding sequences—lack the repetitive DNA (and mobile genetic elements) that make up such a large portion of most mammalian genomes.

What do both retroviruses and retrotransposons do? Choose one: integrate into the host cell genome use DNA as a template for DNA synthesis surround themselves with a protein coat escape from cells and move to other cells

integrate into the host cell genome; Both retroviruses and retrotransposons integrate into the host cell genome. Retrotransposons normally reside within a host cell's genome. Retroviruses, too, can integrate into a host cell's DNA. They can persist in this latent state within host cells for decades. This ability to "hide" in host cells makes retroviruses, such as HIV, very difficult to eliminate.

Determine whether the following statement is true or false: Viruses do not encode all of the enzymes necessary to replicate themselves. This statement is _______.

true; Viruses do not encode all of the enzymes necessary to replicate themselves. Viruses require the host's molecular machinery to replicate. Because of this reliance, viruses are generally not considered to be "alive."

The transcription initiation site of a eukaryotic gene is found at which location? Choose one: where general transcription factors bind where RNA polymerase first binds where transcription regulators bind where RNA synthesis begins

where RNA synthesis begins; The transcription initiation site of a eukaryotic promoter is where RNA synthesis first begins, and this location is "downstream" of the core promoter region.