Cell/Molec Quiz 4 (ch 7-8)
What is the advantage of complex transcription units over simple transcription units?
A complex transcription unit can encode mRNAs processed in multiple ways to generate different proteins. A simple transcription unit can code for only one RNA and one protein. Complex transcription units allow for a greater diversity of proteins from the same number of genes.
Give a functional definition of a gene
A gene consists of the entire DNA sequence required for synthesis of a functional protein or RNA molecule. In addition to the coding regions or exons, a gene includes transcription control regions, such as enhancers, and other critical noncoding regions such as poly(A) sites and splice sites. Sometimes essential control regions can even be located in introns.
Describe the proposed mechanism discussed in this chapter for the origin of gene families.
A gene family consists of a set of duplicated genes that encode proteins with similar but not identical amino acid sequences. An example of a gene family is the genes encoding the b-like globins. The different genes in the gene family probably arose by duplication of an ancestral gene, most likely as a result of an unequal crossover during meiotic recombination. Over time, these duplicated genes accumulated random mutations. In some cases, a protein with a slightly different function emerged; in other cases, the mutations led to a nonfunctional gene known as a pseudogene.
Describe the structure and function of a zinc-finger motif.
A zinc finger is a structural motif found in DNA binding domains; it consists of a short length of the polypeptide chain folded around a Zn2+ ion. The two basic classes of zinc finger domains are the C2H2 and C4 structures. The C2H2 zinc finger domain consists of two cysteine (C) and two histidine (H) residues bound to one Zn2+ ion. The C4 zinc finger contains four cysteines bound to one Zn2+ ion. The three-dimensional structure of the zinc finger forms a compact domain, which can insert its a helix into the major groove of DNA. Question Type: Essay
What is an enhanceosome?
An enhanceosome is a large nucleoprotein complex bound to an enhancer element. This complex is formed by the cooperative assembly of transcription factors to their multiple binding sites in an enhancer.
Why is there a need for a specialized structure at the ends of eukaryotic chromosomes and for the enzyme telomerase?
Because all known DNA polymerases elongate DNA in the 5´ to 3´ direction, all require a RNA or DNA primer to initiate synthesis. As the replication fork approaches the end of the chromosome, DNA synthesis on the leading strand continues to the end of the chromosome without a problem. However, because the lagging strand is synthesized discontinuously, it cannot be replicated in its entirety. When the RNA primer is removed, a short segment of DNA remains single-stranded with no way to make this region double-stranded. If there were no specialized mechanism for replicating DNA at the ends, then the chromosome would shorten with each round of replication. Telomerase is the enzyme that completes DNA synthesis at the telomeres.
Define the terms cis-acting DNA sequences and trans-acting proteins.
Cis-acting DNA elements affect only the expression of genes on the same DNA molecule that are linked to the DNA element. In contrast, trans-acting proteins can diffuse through the cell to bind to their target DNA sequence.
Describe the mechanism of transcriptional control for the heat shock genes. What advantage does this type of control impart to the cell?
During transcription of the heat-shock genes, RNA Pol II pauses after transcribing ≈25 nucleotides. Under stress conditions, where intracellular proteins are denatured or may become denatured, heat shock transcription factor (HSTF) is activated. In this state, HSTF binds to specific regions in the promoter of the heat shock genes, stimulating RNA Pol II to continue chain elongation. Binding also facilitates the rapid re-initiation by other RNA Pol II molecules, leading to a significant up-regulation in heat-shock-gene-expression. Thus, the mechanism of stalling the RNA Pol II and having partially completed transcripts ready to finish elongation and undergo translation when the need arises is a safeguard, protecting cells against unexpected, stressful conditions.
What is the functional difference between enhancers and promoter proximal elements?
Enhancers can stimulate transcription from a promoter tens of thousands of base pairs away. In contrast, promoter-proximal elements are located 100 to 200 base pairs upstream of the start site and usually lose their ability to stimulate transcription from a promoter when moved only several tens of base pairs away.
Describe how lipid soluble hormones, glucocorticoid for example, regulate gene transcription acting through nuclear hormone receptors.
Glucocorticoid is a lipid soluble hormone that binds to a member of the nuclear hormone receptor family, the glucocorticoid receptor (GR), which regulates gene transcription. In the absence of glucocorticoid, the GR in the cytoplasm is bound to the protein HSP90. When glucocorticoid diffuses through the cell membrane, it binds to the GR ligand-binding domain and causes a conformational change in the GR, releasing HSP90. The GR bound to glucocorticoid is then translocated into the nucleus, where it interacts with glucocorticoid response elements (GRE) and regulates transcription of responsive genes.
Describe the role of histone deacetylation and hyperacetylation in yeast transcriptional control.
Histone deacetylation/hyperacetylation is one mechanism for regulating transcriptional control in yeast. Repressor proteins can cause deacetylation of lysine residues in histone N-termini in nucleosomes. Unacetylated histones contain positive charges due to the N-terminal lysines and interact strongly with DNA phosphates. These strong interactions may restrict access of general transcription factors, thus leading to transcriptional repression. In contrast, histones with hyperacetylated lysines in their N-termini are neutral in charge, eliminating the strong electrostatic interactions with the DNA phosphates. This more open chromatin configuration facilitates access of general transcription factors and induces transcriptional activation.
Describe the similarities and differences between prokaryotic and eukaryotic RNA polymerases.
In prokaryotes, there is only one RNA polymerase, which consists of five subunits. In eukaryotes, there are three RNA polymerases, which are more complex than the bacterial RNA polymerase. RNA polymerase I synthesizes ribosomal RNA; RNA polymerase II synthesizes messenger RNA; and RNA polymerase III synthesizes tRNA and other small RNAs. All three contain two large subunits and 12-15 smaller subunits, which contain some sequence homology to the E. coli RNA polymerase subunits (a, b, and b´).
Describe how the electrophoretic mobility shift assay (EMSA) and the DNase I footprinting techniques are used to identify DNA-protein interactions.
In the electrophoretic mobility shift assay (EMSA), DNA-protein interactions are detected by changes in the mobility of a DNA fragment bound to a protein. A DNA fragment containing a putative protein binding site is first radiolabeled and then incubated in the presence of sequence-specific DNA binding proteins. The DNA fragment containing a bound protein migrates slower in a gel, causing a shift in the location of the radiolabeled DNA detected by autoradiography. In the DNase I footprinting technique, a DNA fragment is first labeled at only one end with 32P. The radiolabeled DNA fragment is incubated with a DNA binding protein and then digested with a limiting concentration of DNase I. The DNase I concentration is set such that on average each DNA molecule is cut only once. The resulting DNA fragments are separated by denaturing gel electrophoresis and visualized by autoradiography. In the absence of a DNA binding protein, a ladder of DNA bands is detected on the autoradiogram. Binding of a protein to the DNA prevents DNase I from digesting the radiolabeled DNA at the site of the DNA-protein interaction, resulting in a blank area (or "footprint") in the DNA ladder.
Describe the general organization of protein coding genes in the yeast and human genomes.
In yeast, the protein coding regions are closely spaced along the DNA sequence. In contrast, in the human genome, only a small fraction of the DNA encodes for protein. Thus, the density of protein coding genes per length of DNA is higher in yeast than it is in humans. Put another way, the human genome contains a much higher proportion of noncoding to coding sequences than does the yeast genome. Question Type: Essay
Describe the two major pathways for transposition of mobile elements.
Mobile elements fall into two major classes. Insertion sequences and transposons move via a DNA intermediate, whereas retrotransposons transpose via an RNA intermediate. DNA elements encode a transposase enzyme, which catalyzes the transposition event. A retrotransposon is first transcribed into RNA, which is then used as a template for synthesis of double-stranded DNA by the action of the retrotransposon-encoded enzyme, reverse transcriptase. The resulting double-stranded DNA is then integrated into the host genome.
How can transcription factors be purified using sequence-specific DNA-affinity chromatography?
Sequence-specific DNA-affinity chromatography is a technique that takes advantage of the binding specificity of a protein to a specific DNA sequence. Once the DNA sequence to which a transcription factor binds is identified, this DNA sequence can be coupled to a bead in a column. A protein mix containing the transcription factor is applied to this column. Proteins that do not bind to the DNA fragment are washed off the column. The bound transcription factor can then be eluted from the column in the presence of a high concentration of a salt.
Describe the functional properties of TFIID and TFIIH.
TFIID is a large, multisubunit complex of approximately 750 kDa. TFIID consists of a 38 kDa TATA box-binding protein (TBP) and 11 TBP-associated factors (TAFs). TBP is the first protein to bind to a TATA box-containing promoter. TFIIH is the last protein to bind to the initiation complex. TFIIH contains helicase activity, which unwinds the DNA duplex at the start site. As the polymerase transcribes from the promoter, a subunit of TFIIH phosphorylates the carboxy terminal domain (CTD) of RNA polymerase II.
Describe the structure of the RNA polymerase II transcription initiation complex.
The RNA polymerase II transcription initiation complex is a multiprotein complex. This complex consists of a DNA promoter element to which general transcription factors (i.e., TFIIA, TFIIB, TFIID, TFIIE, TFIIH) bind along with RNA polymerase II. This multisubunit nucleoprotein complex consists of 60-70 polypeptides with a mass of approximately 3 MDa and is nearly as large as a eukaryotic ribosome.
Describe how modification of histone tails can control chromatin condensation.
The amino termini of histones, which are known as histone tails, extend from the structure of the nucleosome. Positively charged lysine side chains present in the histone tails may interact with linker DNA or other nucleosomes. Acetylation of the lysine side chains neutralizes the positive charges, thereby eliminating the potential interaction with the negatively charged DNA phosphate groups. Thus, acetylation of histones makes the chromatin less likely to form a condensed structure. Deacetylation of the histones once again allows the positively charged lysines to interact with the DNA phosphate groups, leading to chromatin condensation.
Describe the structure and function of the carboxy terminal domain (CTD) of RNA polymerase II.
The carboxy terminal domain (CTD) of RNA polymerase II consists of a heptapeptide repeat, with a consensus sequence of Tyr-Ser-Pro-Thr-Ser-Pro-Ser. Yeast RNA polymerase II contains 26 or more repeats of this sequence, while the mammalian RNA polymerase II contains 52 repeats. The CTD is critical for viability, and at least 10 copies of the repeat must be present for survival. During formation of the transcription initiation complex, the CTD is unphosphorylated. When the RNA polymerase transcribes downstream of the promoter, the CTD is phosphorylated at serine and threonine residues. One hypothesis is that phosphorylation of the CTD causes the release of RNA polymerase from the transcription initiation complex.
What is the underlying mechanism behind why gene mutations that lead to Huntington's disease act as dominant mutations?
The mutations that lead to Huntington's disease are examples of expanded microsatellite repeats. In the case of the gene responsible for Huntington's disease, there is a triplet CAG repeat in the first exon. Expansion of this repeat results in synthesis of long stretches of polyglutamine. Over time, the protein products that contain long stretches of polyglutamine aggregate. Protein aggregation leads to neuronal cell death, which in turn gives rise to the symptoms of Huntington's disease. These microsatellite mutations are dominant because the presence of aggregated proteins causes symptoms, even though some normal proteins are produced from the normal allele.
. How many genes are estimated to be in the human genome? a. 21,000 b. 35,000 c. 75,000 d. 100,000
a
2. Which of the following is a typical feature of prokaryotic genes? a. polycistronic messenger RNAs b. complex transcription units c. introns d. a and c
a
All of the following events play a role in yeast-mating type switching except a. methylation of the silent-mating-type locus. b. transcription of the gene at the MAT locus. c. chromatin condensation at the silent mating type locus. d. a recombination event known as gene conversion.
a
All of the following statements about the essential carboxy terminal domain (CTD) of RNA polymerase are true except: a. The CTD is present in RNA polymerase I, II, and III. b. The CTD can become phosphorylated. c. The CTD is critical for viability. d. The CTD of mammals contains more than 50 repeats of a heptapeptide.
a
An enhancer a. is a DNA element that stimulates transcription of eukaryotic promoters. b. binds to RNA polymerase and stimulates transcription. c. acts as a binding site for RNA polymerase. d. interacts with repressor proteins to enhance transcriptional repression.
a
DNA that is transcriptionally active a. is more susceptible to DNase I digestion. b. is tightly packed into a solenoid arrangement. c. contains nonacetylated histones. d. is more condensed than nontranscribed DNA.
a
How does binding of the lac repressor to the lac operator block transcription initiation? a. lac repressor binding blocks RNA polymerase from interacting with DNA at the start site. b. lac repressor binding induces a DNase that cleaves the DNA at the transcription start site. c. lac repressor binding causes a conformational change in RNA polymerase. d. lac repressor binding induces a protease that degrades the sigma subunit of RNA polymerase.
a
In bacteria, an operon: a. is a region of DNA that is transcribed as a single mRNA encoding several proteins. b. encodes for miRNAs. c. contains a promoter unique for each individual gene in the operator. d. none of the above
a
In eukaryotes, tandemly repeated genes encode a. rRNAs. b. cytoskeletal proteins. c. b-globin. d. all of the above
a
There are five major types of histone proteins, but only four of them are considered as core histones. Which one of the following is NOT considered a core histone protein? a. H1 b. H2B c. H3 d. H4
a
To examine the folding and compaction of chromatin during mitosis, you will need to isolate and stain chromosomes at a particular stage using a special spreading preparation technique. For the best analysis, the chromosomes must be at which one of the following stages? a. metaphase b. interphase c. telophase d. anaphase
a
Which of the following is the correct order of binding of general transcription factors to initiate transcription at RNA polymerase II promoters? a. TFIID, TFIIB, Pol II, TFIIH b. PolII, TFIID, TFIIB, TFIIH c. TFIIB, PolII, TFIIH, TFIID d. TFIID, TFIIH, TFIIB, PolII
a
Which of the following mobile elements is a retrotransposon? a. yeast Ty element b. bacterial IS sequence c. Drosophila P element d. maize activator (Ac) element
a
Which of the following pairs of proteins are considered to be paralogous? a. yeast a-tubulin and yeast b-tubulin b. yeast a-tubulin and worm a-tubulin c. fly b-tubulin and human b-tubulin d. worm b-tubulin and human a-tubulin
a
Which protein domains are found in nuclear-receptor family members? a. variable region, DNA-binding domain, ligand-binding domain b. acetylase domain, DNA-binding domain, ligand-binding domain c. variable region, acetylase domain, ligand-binding domain d. variable region, DNA-binding domain, acetylase domain
a
"3C" or chromosome conformation capture methods, used to determine the three-dimensional spatial organization of chromatin within nuclei of interphase cells, rely on a series of steps where the end result is the sequence analysis of purified DNA fragments. Which one of the following presents the correct order of steps you as an investigator need to follow in a 3C method strategy? a. shear DNA to 200-600 bp; cross-link proteins and DNA with formaldehyde b. ligate linkers marked with biotin onto DNA fragments; dilute and ligate the fragments c. cross-link streptavidin to DNA; purify and shear biotin-labeled fragments d. none of the above
b
. Which of the following terms describes when a chromosome is replicated everywhere except the telomeres and centromere, but the daughter chromosomes do not separate? a. hybridization b. polytenization c. polymerization d. heterochromatization
b
1. Which one of the following regarding pseudogenes is NOT true? a. They are present in the eukaryotic genome. b. They encode miRNAs. c. They mark the region of gene duplications. d. They always encode functional products.
b
13. Which of the following classes of repetitive DNA is most abundant in the human genome? a. simple-sequence DNA b. non-LTR transposons c. LTR transposons d. DNA transposons
b
A leucine-zipper motif contains a. a stretch of five leucine residues in a row. b. a leucine residue at every seventh position. c. a leucine residue complexed with a zinc ion. d. an alternating leucine-alanine-proline structure.
b
All the following statements about heterochromatin except: a. It is a dark-staining area of a chromosome. b. It is usually transcriptionally active. c. It is often simple sequences of DNA. d. It is a region of condensed chromatin.
b
Bromodomains are found in chromosome-associated proteins that contribute to transcriptional activation. To facilitate this activation, the bromodomains bind to histones, specifically their lysine residues that have been post-translationally modified by: a. methylation. b. acetylation. c. phosphorylation. d. ubiquitination.
b
Chromosome painting involves a. staining chromosomes with Giemsa reagent. b. hybridizing fluorescent probes to chromosomes. c. hybridizing radioactive probes to chromosomes. d. a and b
b
Regulation of transcription by steroid hormones a. involves hormone receptors only found in the nucleus. b. involves cytoplasmic hormone receptors that can move to the nucleus. c. involves two ligase domains. d. always activates transcription.
b
The DNA and protein sequences of the a-tubulin genes in humans and in fish are similar, and because each arose due to speciation, these genes would be considered: a. homologous. b. orthologous. c. paralogous. d. autologous.
b
The nuclear-receptor superfamily consists of several proteins that bind to consensus sequences of DNA response elements. Which of the following is NOT considered a member of this superfamily? a. retinoic acid receptor b. acetylcholine receptor c. glucocorticoid receptor d. progesterone receptor
b
What is the function of TFIIH in the transcription initiation complex? a. binding to the TATA box b. unwinding the DNA duplex c. catalyzing the synthesis of RNA d. all of the above
b
Which of the following is a fundamental difference between gene regulation in bacteria compared with eukaryotes? a. In bacteria, but not eukaryotes, there is a specific sequence that specifies where RNA polymerase binds and initiates transcription. b. In eukaryotes, but not bacteria, transcription can be influenced by how effectively the DNA sequence of a promoter region interacts with histone octamers. c. Transcription regulation is the most widespread form of control of gene expression in bacteria but not in eukaryotes. d. Gene regulation is readily reversible in eukaryotes but not bacteria.
b
Which of the following is an algorithm designed to compare the sequence of a newly identified protein with sequences already stored in the GenBank database? a. LINES b. BLAST c. HATs d. 3C
b
Which of the following is not a mobile DNA element? a. transposon b. long terminal repeats (LTR) c. long interspersed elements (LINES) d. insertion sequence (IS) elements
b
Which of the following proteins does not "footprint" the lac operon control region? a. lac repressor b. b-galactosidase c. RNA polymerase d. cAMP-CAP
b
Which one of the following techniques would be best suited to follow how a thyroxine-bound receptor translocates from the cytoplasm to its DNA response element? a. in situ hybridization and a radioactive fragment of the DNA response element b. fluorescence microscopy and a GFP-tagged receptor fusion protein c. pulse-chase radiolabeling d. none of the above
b
X chromosome inactivation in mammals is mediated by a. micro RNAs (miRNA). b. long non-coding RNAs (ncRNA). c. messenger RNA (mRNA). d. short RNA-directed methylation of histones and DNA.
b
You are studying the effects of α-amanitin, a poisonous cyclic octapeptide, on eukaryotic cells and have noticed that following treatment, there is no miRNA transcription. Based on this evidence you conclude that α-amanitin must be inhibiting: a.RNA polymerase I. b. RNA polymerase II. c. RNA polymerase III. d. RNA polymerase I and RNA polymerase III.
b
You have identified a transcription factor and hypothesize that it binds to the promoter region of a gene that encodes a protein that causes cells to stop dividing. In order to test the interaction between the transcription factor and the DNA you will need to do a specific assay. Which one of the following would you use to test your hypothesis? a. fluorescent in situ hybridization b. chromatin immunoprecipitation c. immunocytochemistry d. high-throughput DNA sequencing
b
11. Which of the following organisms has the greatest amount of DNA per cell? a. chicken b. fruit fly c. tulip d. human
c
After a diagnostic sequencing analysis of an individual's DNA, you find that this person has a number of microsatellite triplet repeats within a region of their huntingtin gene. Specifically, these CAG repeats code for long stretches of: a. glycines. b. prolines. c. glutamines. d. stop codons.
c
All of the following can be found in chromatin except a. DNA. b. histones. c. RNA. d. transcription factors.
c
All the following statements are true about a nucleosome except: a. It contains an octamer core of histones. b It is about 10 nm in diameter. c. It is the "string" of the "beads-on-a-string" appearance. d. It contains approximately 150 base pairs of DNA.
c
Drosophila is considered a model system because it is quite easy to create transgenic lines harboring a variety of different genes. As a Drosophilageneticist, which one of the following is a DNA transposon that you would exploit to create a transgenic line? a. copia element b. N element c. P element d. Ty element
c
In mammals, X-chromosome inactivation a. occurs in half the diploid cells of the adult female. b. results from the ionization of the X-chromosome. c. is considered an epigenetic event. d. b and c
c
Lipid soluble hormones activate transcription by a. binding to specific cell-surface receptors. b. phosphorylating a protein kinase. c. binding to a nuclear receptor. d. inhibiting a histone deacetylase.
c
Open reading frame (ORF) analysis is not effective in identifying genes in higher eukaryotes because of the presence of a. promoters. b. enhancers. c. introns. d. repetitious DNA.
c
Operator constitutive mutants of the lac operon would a. express the lac repressor constitutively. b. block the binding of RNA polymerase to the promoter. c. express b-galactosidase constitutively. d. prevent the inducer from binding to the repressor.
c
Short micro RNAs (miRNAs) a. code for proteins. b. are common in bacteria but not eukaryotes. c. are involved in regulation of gene expression. d. have no known function.
c
Sigma factors present in bacteria are proteins required to: a. allow translation to proceed. b. terminate DNA replication. c. initiate transcription. d. terminate DNA replication and initiate transcription.
c
The chicken lysozyme gene is considered to be a solitary gene because a. it contains no introns. b. it is not present on a chromosome. c. it is represented only once in the haploid genome. d. none of the above
c
The human genome encodes transcription factors that contain an acidic activation domain that is phosphorylated in response to increased levels of the second messenger cAMP. Which one of the following contains one of these activation domains? a. CBP b. CDK9 c. CREB d. CTD
c
The mediator complex a. can form a molecular bridge between activators of transcription and DNA replication machinery. b. can function to maintain a promoter in a hypoacetylated state. c. has histone acetylase activity. d. none of the above
c
This serves as the promoter for 70% of eukaryotic genes and typically serves as a control region for genes that are transcribed at relatively low rates. a. TATA box b. enhancers c. CpG islands d. UAS (upstream activating sequences)
c
Transcriptionally inactive genes a. are always located within euchromatin. b. are not located within nucleosomes. c. often are methylated. d. are not resistant to DNase I.
c
What family of proteins plays an essential role in the repression of genes that help to direct the formation of specific tissues and organs in a developing embryo? a. Retinoblastoma b. Trithorax c. Polycomb d. Pax
c
Which of the following is NOT a functional element required for any eukaryotic chromosome to replicate and segregate correctly? a. replication origin b. centromere c. kinetochore d. telomeres
c
Which of the following terms describes the phenomenon of genes occurring in the same order on a chromosome in two different species? a. heterochrony b. neoteny c. synteny d. phylogeny
c
Which one of the following terms is used to describe the protein: DNA complex containing several transcription factors bound to a single enhancer? a. nucleosome b. chromosome c. enhanceosome d. proteasome
c
You are studying the expression of the gene that appears to be under the control of three different transcription-control regions during mouse embryonic development. Which one of the following is the BEST method to use to determine when each of these regions are active in the developing mouse embryo? a. DNA affinity chromatography b. polymerase chain reaction c. reporter gene assay d. DNAse 1 footprinting
c
You are studying the regulation of a group of genes and have determined that the full activation of transcription of these genes occurs when histone acetyl transferases have made post-translational modifications specifically to which one of the following amino acids? a. glycine b. glutamine c. lysine d. proline
c
. Blood samples were retrieved from a crime scene, and three suspects were arrested on suspicion of committing the crime. Which of the following techniques could be used to identify the suspect(s) responsible for crime? a. DNA fingerprinting b. polymerase chain reaction c. in situ hybridization d. DNA fingerprinting and polymerase chain reaction
d
. Reporter genes employ fragments of DNA encoding proteins that when translated do not have any obvious effects in the cells and tissues. Which one of the following is NOT a reporter protein? a. luciferase b. green fluorescent protein c. β-galactosidase d. RNA polymerase 1
d
12. All the following statements about microsatellite DNA are true except: a. It consists of a repeat length of 1-13 base pairs. b. It can cause neurological diseases such as myotonic dystrophy. c. It can occur within transcription units. d. all of the above
d
4. All the following statements about complex transcription units are true except: a. They can have multiple poly(A) sites. b. They can generate multiple mRNAs. c. They can generate multiple polypeptides. d. They are common in bacteria.
d
All the following elements can function as eukaryotic promoters except a. a TATA box. b. an initiator element. c. CpG islands. d. an enhancer.
d
All the following statements about heterochromatin are true except: a. DNA dyes stain heterochromatin more darkly than euchromatin. b. The DNA of heterochromatin is more highly condensed than that of euchromatin. c. Heterochromatin is associated with inactive genes. d. Heterochromatin is more susceptible to DNaseI than is euchromatin.
d
All the following steps are performed by the enzyme transposase during transposition of bacterial insertion sequences except a. excision of the IS element from the donor DNA molecule. b. introduction of staggered cuts into the target DNA molecule. c. ligation of the IS element to the target DNA. d. synthesis of DNA to fill in the single-stranded gaps.
d
Enhancers are considered transcription-control elements that regulate the expression of eukaryotic genes. Which one of the following is true regarding these elements? a. They are only found upstream of the transcription start site. b. They are never found more than one kilobase away of the transcription start site. c. They are only found in introns. d. They generally range in length from about 50-200 base pairs.
d
Epigenetics marks refer to modifications to DNA and proteins that in turn regulate gene expression. Which statement is true regarding these specific types of modifications? a. They have the ability to both silence and activate genes. b. They can involve the methylation of cytosine bases. c. They are linked to the acetylation of histones. d. All of the above
d
Histone modifications play integral roles in chromatin condensation and function. Which of the following is NOT considered to be a histone modification? a. acetylation b. methylation c. phosphorylation d. prenylation
d
Mobile DNA elements likely contributed to the evolution of higher organisms by the a. generation of gene families by gene duplication. b. creation of new genes by exon shuffling. c. formation of more complex regulatory regions. d. all of the above
d
SINES (short interspersed elements) a. are approximately 300 base pairs long. b. are LTRs containing retrotransposons. c. are present in over 1 million copies in the human genome. d. a and c
d
Telomeres a. consist of repetitive sequences with high G content. b. are a few hundred base-pairs long in vertebrates. c. have specific proteins bound at the DNA ends. d. a and c
d
The TATA box a. serves as a promoter sequence for genes transcribed by RNA polymerase III. b. is located approximately 100 base pairs upstream of the start site for mRNAs. c. is present in all eukaryotic genes. d. acts to position RNA polymerase II for transcription initiation.
d
The karyotype for any particular species is characterized by a. the number of metaphase chromosomes. b. the size and shape of the metaphase chromosomes. c. the banding pattern of the metaphase chromosomes. d. all of the above
d
Which of the following is NOT true regarding the chromatin-remodeling SWI/SNF complex? a. It acts as tumor suppressor. b. It serves as a co-activator of transcription. c. It has homology to DNA helicases. d. It can stabilize DNA-histone interactions.
d
Which of the following is not a structural motif found in a DNA-binding domain? a. homeodomain b. zinc-finger c. helix-loop-helix d. random-coil acidic domain
d
Which of the following is not used in the electrophoretic mobility shift assay (EMSA)? a. a radiolabeled DNA fragment b. a polyacrylamide gel c. a DNA binding protein d. DNase I
d
Which of the following lines of evidence is indicative of the presence of a gene in an unknown DNA sequence? a. alignment to a partial cDNA sequence b. sequence similarity to genes of other organisms c. ORF consistent with the rules for exon and intron sequences d. all of the above
d
Which of the following statement(s) is (are) true of a eukaryotic chromosome? a. It is a linear structure. b. It consists of a single DNA molecule. c. It can contain greater than a billion base pairs of DNA. d. all of the above
d
Which of the following statement(s) regarding transcription initiation and RNA Pol III is (are) true? a. ATP hydrolysis is not required for initiation. b. Pol III is responsible for synthesizing tRNAs and 5S-rRNA. c. The promoter elements of tRNA genes lie entirely within the transcribed sequence. d. all of the above
d
of tulips and yeast and humans, which organisms has the greatest amount of DNA per cell
tulips