Name: _______________________________________________________ BIOL2800 Exam#2 (70 points + 5 points for timely submission) Answers need not to be descriptive, but need to be precise and specific to get full points. SECTION A: Highlight/ Underline/bold/change the color for the correct option (1X25=25 pts) 1. Which of the following is not a constituent of deoxyribonucleotides? a. phosphate moieties b. deoxyribose c. ribose d. organic bases 2. Which base pair(s) typically occur(s) in double-stranded DNA? a. G·C b. G·T c. G·A d. G·G 3. The ability of DNA to denature is important for which process? a. DNA synthesis b. nucleic acid hybridization experiments c. RNA synthesis d. all of the above 4. Which of the following are removed from mRNAs during processing? a. exons b. noncoding sequences c. RNA cap structure d. poly(A) tail 5. DNA replication begins at sequences called a. promoters. b. initiators. c. origins. d. Okazaki fragments. 6. An enzyme that breaks DNA, dispels the tension, and reseals the strand ahead of a DNA replication growing fork is called a(n) a. topoisomerase. b. DNA polymerase. c. phosphodiesterase. d. aminoacyl-tRNA synthetase. 7. 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. 8. In eukaryotes, tandemly repeated genes encode a. rRNAs. b. cytoskeletal proteins. c. b-globin. d. all of the above 9. 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. 10. Which of the following events are catalyzed by a RNA? a. polyadenylation b. transcription c. splicing. d. none of the above 11. The consensus sequence for poly(A) addition is a. the site of poly(A) tail addition. b. AAUAAA. c. downstream of the cleavage site. d. none of the above 12. Which process involves two transesterification reactions? a. splicing b. RNA editing c. capping d. nuclear transport 13. Splice sites in pre-mRNA are marked by two universally conserved sequences contained a. in the middle of the intron. b. at the ends of the exons. c. at the ends of the introns. d. none of the above 14. Splicing joins a. two intron sequences. b. two polypeptides. c. two DNA molecules. d. two exon sequences. 15. This type of RNA functions in the removal of introns from pre-RNAs. a. snRNA (small nuclear RNA) b. snoRNA (small nucleolar RNA) c. siRNA (small interfering RNA) d. miRNA (micro RNA) 16. RNA editing is a. post-transcriptional alteration of sequences in mRNAs. b. pretranscriptional alteration of sequences in RNAs. c. post-transcriptional joining of two RNA molecules. d. none of the above 17. Which type of RNA participates in nuclear export of mRNA? a. snRNA b. hnRNA c. tRNA d. rRNA 18. Which of the following does not part in the degradation process of eukaryotic mRNAs? a. capping b. endonucleolytic cleavage c. exonucleolytic decay d. poly(A) shortening 19. 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. 20. All the following elements can function as eukaryotic promoters except a. a TATA box. b. an initiator element. c. CpG islands. d. an enhancer. 21. 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 22. This serves as the promoter for 60–70% 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) 23. 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. 24. 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. 25. Which of the following is not a structural motif found in a DNAbinding domain? a. homeodomain b. zinc-finger c. helix-loop-helix d. random-coil acidic domain SECTION B: Descriptive section (20 pts): 1. (2 pts) Give two differences between DNA and RNA. DNA consists of the sugar deoxyribose, while RNA consists of the sugar ribose. The difference is the ribose has one more -OH group then deoxyribose. Under alkaline conditions DNA is stable but RNA is not stable. DNA is a molecule that is double stranded, while RNA is a molecule that is single stranded. 2. (2 pts) What is the difference between splicing and trans-splicing? In splicing there is a modification done to the nascent pre-messenger RNA transcript. This results in introns being removed and exons being joined. In trans splicing exons from the two separtate primary RNA transcripts are joined together and ligated. 3. (2 pts) What is a reporter gene? Give two examples of it commonly used in laboratory A gene attached to a bacteria, cell culture, animals or plants of interest in by researchers to make certain characteristics easily recognizable or measurable. A green fluorescent protein is a frequently used reporter gene encode, this protein can be visualized under a fluorescence microscopy. Coli β-galactosidase, when incubated with the colorless soluble lactose analog X-gal, generates an intensely blue insoluble precipitate. 4. (2 pts) What is the difference between a transcription factor and a promoter element? A transcription factor is a protein that will bind to a specific DNA sequence and control the rate of transcription. They may do this by promoting thus being an activator or by blocking thus being a repressor. Promotor elements play a key role in initiation of gene transcription by RNA polymerase II, one example is the downstream promoter element. In order for a core promoter element to initiate transcription there is a minimal proportion of the promoter required. 5. (2 pts) What does TBP do in eukaryotic transcription? TBP is part of a larger molecule know as TFIIF. In depth, TFIIF consists of 38-kDa TATA box binding protein (TBP) along with 13 TBP-associated factors (TAFs). TBP’s binding initiates transcription complex assembly at many genes. TBP is involved in assembly of the preinitation complex. TFIIF is basically the bridge that joins the TATA-bound TBP and polymerase. To the right is a visual description of TBP’s transformation and how it contributes to eukaryotic transcription. As you can see TAFs TFIID and TBP are replaced by ISWI and DREF. 6. (3 pts) Write down the steps of initiation stage of transcription (no schematic is needed). The RNA polymerase is bound to the DNA at a specific sequence of nucleotides called the promoter. The promoter has an initiation site where transcription of the gene will commence. RNA polymerase then unwinds DNA at the beginning of the gene. 7. (1+3 pts) Write the three pathways for mRNA degradation and describe the steps for any one of them. The three pathways for mRNA degradation are the following: deadenylation dependent pathway, deadenylation independent pathway or decapping pathway, and the endonucleolytic pathway. Several pathways exist in mammals but the most common is the deadenylation dependent pathway. This initiates with the removal of the poly (A) tail. After the process of deadenylation two events can transpire; the mRNA is degraded by 3’ 5’ with the exosome, or the mRNA will be decapped and 5’ - 3’ mediated by XRN1. 8. (3 pts) Write down the steps of miRNA processing (no schematic is needed). RNA polymerase II transcribes the primary miRNA. The double-stranded RNA-binding protein DGCR8 and the nuclear double-stranded RNA-specific endoribonuclease Drosha start by making the initial cleavage in the pri-miRNA. Next the nuclear transporter Exportin-5 transport the ~70-nucleotide miRNA to the cytoplasm. In the cytoplasm the pre-miRNA is processed into a double strand with two-base single-stranded 3′ end by Dicer at the same time with the double stranded RNA binding protein TRBP. Lastly, they are incorporated into a RISC pretend and bound to Argonaute protein. SECTION C: Use of concept (25 pts) 1. (3 pts.) Assuming that all three exons can be alternatively spliced, how many distinct mRNAs can be generated from the gene below? (Circle the correct option). a. 1 b. 3 c. 6 d. 7 2. (3 pts) What will happen to the target RNA, upon binding the short complementary miRNA as shown below? 3. (3 pts) Arrange the following components of the eukaryotic transcriptional machinery in the sequence in which they bind to the promoter to assemble the transcriptional preinitiation complex. a. Polymerase II b. TBP c. TFIIB d. TFIIE e. TFIIF a. TBP binds the promotor, creating a sharp bend in the promoter DNA. b. TBP-TFIIB interactions recruit TFIIA to the promoter. c. TFIIB-RNA polymerase II and TFIIB-TFIIF interactions recruit RNA polymerase II and TFIIF to the promoter. d. TFIIE joins the growing complex and recruits TFIIH. e. The template strand of the transcription bubble engages with the RNA polymerase II active site and RNA synthesis begins. 4. (3 pts) The transcriptional regulatory region of Gene X is shown below. Which of the following mutant(s) are likely to be transcribed at normal levels? 5. (2 pts) Which of the following are transcribed by RNA polymerase II? (Circle the correct option) (a.) mRNA (b.) miRNA c. 5S rRNA d. 5.8S rRNA e. tRNA 6. (3 points) In prokaryotes, the expression of the operon containing genes for lactose metabolism is controlled by an activator and a repressor. Considering the possible food sources available to the bacteria, why are both an activator and a repressor necessary? An inducible system is a catabolic pathway in which the production of a specific enzyme in response to the presence of substrate; if lactose is present, the pathway turns on. It is usually off but can be turned on. E. Coli break down lactose into other sugars through an inducible system. Repression of the proteins that metabolize lactose insures that the bacteria will only invest energy in the production of proteins that metabolize lactose when lactose is present, allowing the cell to save energy and be more efficient. The activator is necessary to active the production of proteins that metabolize lactose so that the bacteria can take advantage of lactose when present. 7. (2 pts) Why is it easier to denature DNA than proteins? Is this a trick question? First of all DNA denatures at a higher temperature then protiens. So in that sense DNA is harder to denature then proteins. DNA is denatured when the numerous hydrogen bonds are broken which takes a lot of energy. The covalently bonded phosphate sugar backbone is even harder to break. The primary structure of proteins may be strong, but the quaternary or tertiary structure are held together by weak hydrophobic interactions. In another since, and what I think you are trying to get at, is that it is easier to unzip the linear DNA then it is to unwind the messy quaternary, tertiary, and secondary structure of protein. Protein is much more messy while DNA is linear and structured to be unzipped. 8. (6 pts) Fill in the blanks: Transcription is the process by which RNA polymerase makes a pre-mRNA copy from DNA. Translation is the process by which the ribosome makes a protein/amino acid copy from mRNA.