MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

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1 Practice Question for Prokaryotic and Eukaryotic Gene Regulation Lectures Winter 2009 Name MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question. 1) CREBs and STATs are transcription factors activated by: 1) A) acetylation B) deamination C) methylation D) phosphorylation E) zymogulation 2) Many different minerals are required in trace quantities in the diet. These minerals are found in many different types of molecules that serve a variety of functions. Zinc is found as part of the steroid hormone receptor. The function of the "zinc finger" region of a steroid hormone receptor is to A) Modulate transcriptional activity B) Bind steroid C) Interact with specific DNA sequences D) Control nuclear translocation E) Activate protein kinases 2) 3) Which of the following is an example of gene expression regulation by DNA rearrangement? 3) A) Cassette mechanism of the yeast mating-type switch B) Antibody gene rearrangements (rearrangements of VD & J segments) C) Protein splicing D) Alternative splicing of IgM E) Both A & B 4) The N-terminus tail of the histone protein is able to undergo covalent modification with the addition of an acetyl group. The alteration in tertiary chromatin structure opens the region to interact with transcription factors. Which of the following regions is most likely to show histone acetylation? A) Kinetochore B) Mitotic spindle C) Heterochromatin D) Centromere E) Euchromatin 4) 5) How are proteins targeted for degradation by proteasomes? 5) A) They are linked to ubiquitin B) They are permanently bound to E2 and E3 C) They are hyperphophorylated D) They are glycosylated E) None of the above 6) Which of the following are proteins that regulate transcription initiation? 6) A) Origins of replication B) Promoters C) Enhancers D) Repressors 1

2 7) The corepressor (effector) of tryptophan biosynthesis in E.coli is 7) A) The camp-crp complex B) The product of the trpr gene C) Tryptophan D) trna Trp E) The attenuator 8) Both Prader-Willi and Angelman Syndromes involve deletions of the same region of chromosome 15 (15q11-13). What mode of inheritance best explains this phenomenon? A) Environmental exposure during pregnancy B) Multifactorial inheritance C) Genomic Imprinting D) Mosaicism 8) 9) Which of the following enzymes cleaves lactose to yield glucose and galactose? 9) A) -lactamase B) -galactosidase C) Lactose permease D) -glucosidase E) Lactoperoxidase 10) Genes are regulated on and off during the process of development and aging largely through methylation of which of the following bases? A) thymines B) cytosines C) guanines D) uracils E) adenines 10) 11) The situation in which an active regulatory protein "turns on" expression is an example of 11) A) a mutation. B) negative control. C) positive control. D) constitutive gene elements. E) feedback inhibition. 12) The product of the laci gene 12) A) Binds to the RNA polymerase B) Binds to the operator C) Induces lac operon transcription D) Is cis-dominant E) Transports lactose into the cell 13) Which of the following statements is true about the tryptophan operon in E. Coli? 13) A) The repressor will repress transcription after it interacts with tryptophan B) CRP will stimulate transcription after it interacts with tryptophan C) The repressor will repress transcription when tryptophan levels are scarce D) Allolactose interactions prevent the repressor from interacting with trp operator E) None of the above 2

3 14) A 7-year-old girl is seen in the clinic with developmental delay, behavioral problems and obesity. Upon questioning, it is learned that as an infant, she had trouble feeding and was assisted with special techniques, and that she was also very hypotonic. This improved with age, and around 36 months, she rapidly began to gain weight. She exhibits food-seeking behavior, and has been known to raid the kitchen in the middle of the night. Her appetite is excessive, and she never seems to be satiated. She has temper tantrums and is manipulative when it comes to food issues. Physically, she has a narrow forehead, a down-turned mouth, and small hands and feet for her height. Family history is negative for similar symptoms. High-resolution chromosome analysis is ordered and although 46 chromosomes are present, there is a small deletion in the long arm of chromosome 15. The most probable diagnosis for this child is which of the following? A) Beckwith-Wiedmann syndrome B) Prader-Willi syndrome C) Fragile X syndrome D) Angelman syndrome E) Williams syndrome 15) A transcriptional regulator that decreases transcription of a gene from a vast distance is known as a(n) A) regulator. B) enhancer. C) silencer. D) nonsense mutation. E) upstream control element. 14) 15) 16) Which of the following statements concerning mammalian chromosomes is correct? 16) A) Of the sequences contained in the eukaryotic genome, 37% are copied into RNA B) In higher eukaryotic genomes, cytosine is methylated at cytosine-guanine (CG) islands in inactive segments of DNA C) Chrome can be used to treat chromosomes to determine inactive regions of DNA D) Euchromatin is a term used for inactive DNA, and heterochromatin is a term used for those regions of DNA that are transcriptionally active 17) A genetic abnormality has been detected where the transcript has a problem going from the nucleus to the cytoplasm. What part of this transcript is defective and preventing this transport? A) poly A tail B) promoter region C) start codons D) ribosome binding site 17) 18) You are examining an enzyme associated with glycolysis. As such you would expect 18) A) the protein to be regulated. B) the protein to be constituitively expressed. C) the protein to be expressed only during development. D) the protein to be induced by glucose. E) the protein to be expressed only during mitosis. 19) In E.coli, the product of the regulatory laci gene is the 19) A) -galactsidase B) camp receptor protein C) DNA methylase D) Repressor protein E) Transcriptional activator protein 3

4 20) Molecular analysis of the fibrillin gene in a family identified the mutation associated with Marfan's syndrome as a single base substitution at the 5' end of exon 3. The result of this substitution was a deletion of the entire exon 3 from the mrna, and consequently 41 amino acids from the fibrillin protein. The mutation was most likely a A) nonsense mutation B) frameshift mutation C) missense mutation D) splice-donor mutation E) splice acceptor mutation 21) DNA packaging into nucleosomes is an important aspect of eukaryotic gene regulation. Gene activator proteins that result in DNA restructuring A) recruit histone deacetylases causing DNA to unbind to histones B) recruit histone deacetylases causing DNA to bind tightly to histones C) recruit histone acetylases causing DNA to bind tightly to histones D) recruit histone acetylases causing DNA to unbind to histones 20) 21) 22) Regulatory domains of most activators interact with 22) A) the regulatory factor complex B) RNA polymerase C) the DNA binding domain D) the transcription factor complex E) repressors 23) Of the enzymes associated with the metabolism of lactose with the lac operon, the one associated with transport of lactose into the cell is A) transacetylase. B) lactose translocase. C) lactase. D) galactoside permease. E) galactosidase. 24) How are most eukaryotic gene regulatory proteins able to affect transcription when their binding sites are far from the promoter? A) By directly unwinding the DNA between their binding site and the promoter B) By attracting RNA polymerase and modifying it before it can bind to the promoter C) By looping of the DNA between their binding site and the promoter D) By binding to their binding site and sliding to the site of RNA polymerase assembly 25) The coding strand of the DNA has a sequence whose job is to bind the general transcription factor TFIID which then initiates the process of recruiting RNA polymerase to bind to the promoter. This sequence is: A) AAATGAGC B) TATA box C) AATAAA D) CAAT box E) GC box 23) 24) 25) 4

5 26) Angelman syndrome or Prader-Willi syndrome may occur following inheritance of a small 15q deletion from the mother or the father, respectively, of the affected child. Why are these children abnormal? A) They suffer from haploinsufficiency (one functional gene is not enough) for products encoded by genes in the region. B) The remaining genes produce excessive product in an effort to compensate for the deletion. C) This region of chromosome 15 is critical for the X inactivation process D) They lack critical functional genes in the region. E) Cells with the deletion frequently develop trisomy ) 27) Proteins that block the passage of RNA polymerase are called: 27) A) operons B) promoters C) repressors D) enhancers E) activators 28) Identify the below mutation in the cis-acting DNA element of a typical human gene appropriately 28) AATAAA > ACTAAA A) A splicing (acceptor site) mutation B) A polyadenylation signal mutation C) A promoter mutation D) A splicing (donor site) mutation E) A Cap site mutation 29) During the fourth year of medical school, you engage in a research project studying mammalian embryonic development. You discover a microrna that plays a critical role in influencing the regional identity along the axis of the developing limbs. Mutational analysis of the microrna gene reveals that the product regulates protein levels of a key transcription factor (HOXD9). In vitro analysis confirms that the microrna can specifically interact with the HOXD9 mrna, but that it is only partially complementary to the mrna. What is the most likely mechanism of action by which the microrna regulates the HOXD9 levels? A) Inhibiting translation of the HOXD9 mrna B) Increasing the rate of translation of the HOXD9 protein C) Activating transcription of the HOXD9 gene D) Inhibiting transcription of the HOXD9 gene E) Promoting HOXD9 mrna degradation 29) 30) A lac Y- mutant would 30) A) no longer be induced by the presence of lactose. B) be constitutive. C) not have galatosidase activity. D) not metabolize lactose. E) transport lactose into the cell effectively. 31) You are studying a biochemical pathway. Preliminary results suggest that this pathway is subject to end product repression. This pathway is therefore most likely to be a(n) pathway. A) induced B) constitutive C) unregulated D) anabolic E) catabolic 31) 5

6 32) Which of the following mechanisms is primarily responsible the generation of the vast number of different antibodies the body produces? A) DNA rearrangement B) Cassette mechanism C) Protein splicing D) mrna rearrangement E) Altered polyadenylation 32) 33) When tryptophan is present in the environment of E. coli, the tryptophan binds to the 33) A) trp operon B) trp promoter C) trp polymerase D) trp operator E) trp repressor 34) Which of the following processes allows activation of transcription by changing the accessibility of chromatin to transcription factors? A) Extensive methylation of DNA B) Binding of protamines to DNA C) Action of ATPase chromatin remodeling complexes D) Formation of a Barr body E) Deacetylation of histones 34) 35) The "calico" pattern of coat coloration in female cat is a result of 35) A) X-chromosome inactivation B) Turner syndrome C) Unequal crossing-over D) Endoreduplication E) Fragile X syndrome 36) Steroid hormones modify protein synthesis primarily by affecting 36) A) DNA synthesis B) Post-transcriptional processing C) Post-translational processing D) Transcription E) Translation 37) E. coli is able to use foods other than glucose in the absence of available glucose, because falling levels of glucose cause an increase of A) lactase B) trna C) camp D) glu operons E) CAP 37) 38) The leucine zipper motif involves the cooperation of two subunits. 38) A) polymerase B) RNA C) leucine D) histone E) protein 6

7 39) Attenuation of the trp operon in E.coli is the result of 39) A) Rapid mrna turnover B) Production polycistronic rrna C) Ability to synthesize amino acids D) Programmed DNA rearrangements E) Coupled transcription-translation 40) The situation in which an active regulatory protein "turns off" expression is an example of 40) A) positive control. B) negative control. C) a mutation. D) constitutive gene elements. E) unique regulation. 41) Of the following statements about messenger RNA (mrna) transcription, the most accurate is that it A) may be regulated by hormones B) involves the removal of internal regions of DNA from the genome C) occurs only in the cytoplasm of the human cell D) involves the posttranscriptional addition of adenylate nucleotides to the 5' end of the molecule E) proceeds by synthesis of the RNA in the 3' to 5' direction 41) 42) Heavy methylation is associated with 42) A) Programmed DNA rearrangements B) Low transcription rate C) mrna stability D) High transcription rate E) Initiation of translation 43) Genes associated with embryonic development are known as 43) A) homeotic genes. B) heterologous genes. C) hopanoids. D) sigma factors. E) homologous genes. 44) Cortisol, a steroid hormone, will most likely bind to: 44) A) G-protein membrane receptor B) Cytoplasmic receptor C) Membrane ion channel D) Tyrosine kinase growth factor receptor E) Ras 7

8 45) Which of the following are eukaryotic regulatory DNA sequence able to function in either orientation and at many locations in or near a gene, which acts to help recruit transcriptional activator proteins to the genes? A) attenuators B) silencers C) operators D) enhancers E) core promoters 46) The trp operon in E. coli is regulated in such a manner as to allow expression of the genes only when cellular levels of tryptophan are low. When tryptophan levels are adequate, the secondary structure of the mrna halts translation. This form of regulation is known as A) attenuation. B) repression. C) positive regulatory control. D) negative regulatory control. E) transcriptional regulation. 47) A gene is heavily methylated within and around its promoter. What does this methylated state tell you about the activity of this gene? A) The gene is most likely expressed at a high level. B) The gene most likely encodes a transfer RNA (trna). C) The gene cannot be replicated. D) The gene is most likely transcriptionally silent. E) The gene most likely encodes a protein found in microtubules. 48) RNA polymerase will read in direction which produces an RNA polymer in the direction. A) 5' to 3', 5' to 3' B) 5' to 3', 3' to 5' C) 3' to 5', 3' to 5' D) 3' to 5', 5' to 3' 45) 46) 47) 48) 49) A person with the genotype XXXY would be expected to have how many Barr bodies? 49) A) 0 B) 1 C) 2 D) 3 E) 4 50) The role of methylation of DNA is now viewed as 50) A) irrelevant to gene transcription B) prevention of mutation C) insuring that genes that are turned off, stay off D) complexing with enhancers to prevent transcription E) interfering with DNA transcription by blocking base pairing between cytosine and guanine 51) Regarding Duchene's muscular dystrophy, an X-linked recessive disorder, genetic analysis show a mutation on dystrophin at the promoter region, what is the most likely effect of the mutation? A) Initiation of dystrophin mrna will be defective B) Defective capping of dystrophin mrna C) Over expression of dystrophin gene D) Inabitilty to add poly A tail to the dystrophin mrna 51) 8

9 52) Which of the following areas in a eukaryotic cell is a site of RNA processing? 52) A) Peroxisomes B) Endosomes C) Golgi complex D) Mitochondria E) Rough endoplasmic reticulum 53) A 15-year-old male presents to your family practice complaining of delayed onset of puberty. He is 48 inches tall and shows no secondary sex characteristics. He requests testosterone injections. In general, testosterone mediates its effect by which of the following mechanisms? A) Activates a receptor that increases the permeability of the membrane to cations B) Activates an intracellular enzyme when combined with a membrane receptor C) Activates genes by binding with an intracellular receptor D) Activates the phosphatidylinositol system E) Increases camp levels by activating a second messenger 54) In some eukaryotic cells an increase in cyclic AMP regulates the transcription of specific genes. The action of cyclic AMP involves: A) Transport of cyclic AMP to the nucleus and binding to the regulatory region of the gene B) Activating protein kinase A, which phosphorylates CREB C) Binding to JAK and stimulating it to phosphorylate STAT which, in turn binds to the regulatory region of the gene D) Binding to CREB and causing it to dissociate from DNA, thus depressing transcription E) Binding to CREB which, in turn, binds to the regulatory region of the gene and activates transcription 53) 54) 55) Nucleosomes inhibit 55) A) RNA methylation B) translation C) enhancer duplication D) assembly of transcription factors 56) In the process of isolating DNA for transcription and translation, you digest the DNA with BamHI and ligate the gene into a plasmid vector. However, even though all of the controls work, no transcription is obtained using your fragment. Working backward, you note that restriction digestion has removed approximately 250 base pairs from the 5' end of the gene. It is possible that during restriction digestion A) primase could not bind. B) the termination signal was removed. C) the RNA polymerase became inactivated. D) the promoter was removed. E) none of the above 56) 57) The process that occurs at the 5' position of cytosine and often correlates with gene inactivation is? 57) A) phosphorylation B) acetylation C) methylation D) deamination 9

10 58) A transcriptional regulator that decreases transcription of a gene from a vast distance is known as a(n) A) upstream control element. B) silencer. C) enhancer. D) regulator. E) nonsense mutation. 58) 59) The observed "puffs" in the polytene chromosomes of Drosophilia are sites of 59) A) translation. B) induction. C) condensation. D) attenuation. E) transcription. 60) Nucleosomes require a chemical modification in order to make them more transcriptionally active. This chemical modification is: A) acetylation B) nucleation C) hydroxylation D) oxidation E) proteolytic cleavage 60) 61) Transcription factors appear to be unable to bind to a nucleosome because 61) A) nucleosomes are especially vulnerable to repressors B) operators are placed in an inaccessible position C) of inhibition of RNA polymerase D) activators are inhibited by the configuration E) of histones positioned over promoters 62) Which of the following is an example of translational regulation? 62) A) protein degradation B) protein folding C) mrna degradation D) RNA splicing E) DNA methylation 63) In order for cytokines to mediate their biologic effects on target cells, they must generate intracellular signals that result in the production of active transcription factors and, ultimately, gene expression. Binding of a cytokine to its cellular receptor induces polymerization of receptor polypeptides at the cell surface. Signaling is initiated by the activation of JAK kinases, which results in the phosphorylation of tyrosine residues present on a family of transcription factors known as A) CREBs B) RAS C) MAPKs D) STATs E) NFKBs 64) A male is tested for cellular abnormalities. Within each of his cells, the technician notes that there are two Barr bodies present within his cells. As a result he has the genotype A) XY. B) XXY. C) XXX. D) XXXY. E) XO. 63) 64) 10

11 65) In S.cerevisiae, the genetic basis of mating-type interconversion is 65) A) Methylation of the HMR cassette B) Expression of haploid-specific genes C) Repression of haploid-specific genes by a1/ 2 complex D) DNA rearrangement E) Methylation of MATa allele 66) The helix-turn-helix and zinc finger are structural motifs found in 66) A) DNA binding proteins B) Spiceosomes C) Catabolic enzyme complexes D) Shine-Dalgarno sequences 67) The graph below shows a growth curve of E. coli growing in defined medium containing equal amounts of glucose and lactose. 67) Based on your knowledge of the regulation of the lac operon, the best explanation of these results is that A) the bacteria are utilizing both sugars simultaneously. B) early on, due to the presence of lactose, the bacteria utilize the lac operon. Glucose is used later. C) the presence of glucose causes the formation of camp catabolic repressor protein (CRP) complexes, which shut down the lac operon until the glucose is used up. D) glucose is used first. Once glucose becomes limiting, intracellular camp increases, forming camp CRP complexes that activate the lac operon to use lactose. E) none of the above 68) Which of the following endogenous small RNAs requires a two-step cleavage of hairpin precursors by Drosha and Dicer? A) transfer RNA (trna) B) MicroRNA (mirna) C) messenger RNA (mrna) D) Short interfering RNA (sirna) E) ribosomal RNA (rrna) 69) Which term best desribes a nucleus that contains the complete set of genes needed to create a new organism of the same type as the organism from which the nucleus was taken? A) monogenomic hybrid B) totipotent C) differentiated D) unipotential E) uniploidy mosaicism 68) 69) 11