Biochemistry 302, Spring 2003Name ____Answer key _____Exam 2 (100 points)A. T/F (2 point each)B. Fill in the blank (2 points each line)Translation of prokaryotic mRNAs initiates with the amino acid formyl-methionine (spell it out).C. Multiple Choice (2 points each)Cleavage after the termination signal (AAUAAA) and polyadenylation of the 3( end1Biochemistry 302, Spring 2003 Name ____Answer key _____ Exam 2 (100 points) A. T/F (2 point each) 1. Deleting intervening nucleotides between the –35 and –10 E. coli consensus promoter elements would not affect RNA polymerase binding and transcriptional efficiency. __F__ 2. Transcription of all prokaryotic genes is terminated by Rho factor. __F__ 3. TATA-binding protein (TBP) is required for both basal and activated transcription of RNA polymerase II-dependent genes containing a TATA box. __T__ 4. Remodeling of nucleosomes can occur at both the initiation and elongation phases of gene transcription in eukaryotes. __T__ 5. Stabilization of nascent transcripts (synthesized by RNA polymerase II) is achieved by binding of heterogeneous nuclear ribonucleoproteins to the growing mRNA chain. __T__ 6. Exon splicing of nuclear pre-mRNAs is an entirely protein-independent process. __F__ 7. The anticodon loop of tRNAs is the site where amino acids are attached by aminoacyl-tRNA synthetases. __F__ 8. Selenocysteine is an amino acid encoded by specific stop codon in an mRNA template-dependent manner. __T__ 9. Specific DNA-binding by E. coli Trp repressor is allosterically induced by tryptophan binding to the protein. __T__ 10. Basic zipper (bZIP) proteins interact with DNA as either homo- or heterodimers. __T__ B. Fill in the blank (2 points each line) 1. The key protein in E. coli required for promoter recognition and RNA polymerase loading is called _sigma factor__. 2. DNase I footprinting is a biochemical technique useful for detecting interactions between ___protein_____ and _____ DNA______. 3. The two divalent metal ions essential for RNA polymerase II function are _____Mg2+_____ and ______Zn2+______. 4. Eukaryotic RNA polymerase III is responsible for transcribing genes encoding ____tRNA_______ and __5S rRNA (or snRNA)__.2 5. Acetylation of histones occurs on the side chain of the amino acid _____lysine_____. 6. During the elongation phase of mRNA translation, docking of aminoacylated-tRNAs to the mRNA template occurs in the small or 30S or 40S ribosomal subunit while subsequent peptide bond formation occurs in the large or 50S or 60S ribosomal subunit. 7. Translation of prokaryotic mRNAs initiates with the amino acid formyl-methionine (spell it out). 8. DNA sequencing via the Sanger method involves termination of polynucleotide chain growth using limiting concentrations of ____ddNTPs_____. (dideoxynucleotide triphosphates) C. Multiple Choice (2 points each) 1. __A__ The two enzymatic activities of TFIIH, which allow core RNA polymerase II to exit a promoter and to begin RNA chain elongation include: A. Helicase and Kinase B. Ribonuclease and Phosphatase C. All of the above D. None of the above 2. __B__ Which of the following factors would be predicted to inhibit transcription of a DNA template by the basal RNA polymerase II machinery in vitro? A. Magnesium ion B. Histone octamers C. Zinc ion D. TFIIA 3. __D__ The biochemical and functional activities of TATA-binding protein (TBP) include: A. Promoter recognition B. DNA-binding and bending C. Core RNA polymerase II recruitment D. All of the above E. None of the above 4. __A__ TFIID/TBP-associated factors (TAFs) mediate interaction between: A. Trans-activators and general transcription factor machinery B. RNA polymerase II subunits C. Poly A polymerase and spliceosome D. Termination factors and RNA polymerase II3 5. __D__ The mechanism which best describes how initiation of 5S rRNA gene transcription is inhibited in vivo: A. Methylation of TFIIIA B. Degradation of TFIIIA C. Allosteric inactivation of TFIIIA by TFIIIB D. Sequestration of TFIIIA via interaction with 5S rRNA 6. __D__ Protein synthesis in both prokaryotes and eukaryotes requires chemical energy in the form of: A. ATP B. GTP C. TTP D. Both A and B 7. __A__ Intron removal by the eukaryotic spliceosomal complex yields an intron lariat containing the following characteristic linkage: A. 2′-5′ phosphodiester bond B. 3′-3′ phosphodiester bond C. 5′-5′ phosphodiester bond 8. __C__ Catalysis mediated by self-splicing group I and group II introns differs in terms of the requirement for this factor/condition: A. Magnesium ion B. Elevated temperature and ionic strength C. Guanosine 9. __C__ A wobble base pair in codon-anticodon interaction makes possible which of the following key attributes of mRNA translation: A. Accuracy B. Specificity C. Speed 10. __E__ Aminoacyl-tRNA synthetases require the following component(s) to catalyze formation of a “charged” tRNA: A. ATP B. Magnesium ion C. tRNAAA with a free 3′ end D. Amino acid (AA) E. All of the above4 11. __A__ The Shine-Dalgarno sequence of prokaryotic transcripts and the 5′ cap of eukaryotic transcripts are analogous in that they are each responsible for: A. Initial positioning of a mRNA on the small ribosomal subunit B. Termination of mRNA translation C. Recycling of EF-Tu D. Ribosome disassembly 12. __B__ Bacterial restriction enzymes are best described as: A. Site-specific exonucleases B. Site-specific endonucleases C. Site-specific ligases D. Site-specific acetylases 13. __D__ The antibiotic puromycin interferes with protein synthesis by: A. Inducing mRNA template degradation B. Allosterically inhibiting aminoacyl-tRNA synthetases C. Blocking ribosome subunit assembly D. Promoting premature peptide chain termination 14. __A__ The chemistry of intron removal and exon splicing in nuclear pre-mRNAs involves: A. Two snRNP-mediated trans-esterification reactions B. Ribonuclease-mediated cleavage and ligation C. Intron-directed self-splicing 15. __D__ Which of the following atomic interactions has been implicated in influencing either the specificity or affinity of transcription factor-DNA binding? A. Hydrogen bonding B. Van der Waals forces C. Electrostatic contacts D. All of the above 16. __A__ Which of the following enzymatic activities is not required for RNA synthesis in eukaryotic cells? A. Primase B. Polymerase C. Helicase D. Kinase5D.