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2 120:201:B3 Foundations of Biology CMB PRACTICE QUESTIONS FOR EXAM N 3 Summer 2015, Session I/Prof. Cervantes 1. For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below. Not all words or phrases will be used; use each word or phrase only once. The instructions specified by the DNA will ultimately specify the sequence of proteins. This process involves DNA, made up of different nucleotides, which gets into RNA, which is then into proteins, made up of different amino acids. In eukaryotic cells, DNA gets made into RNA in the, while proteins are produced from RNA in the. The segment of DNA called a is the portion that is copied into RNA; this process is catalyzed by RNA. 4 gene proteasome 20 Golgi replisome 109 kinase sugar-phosphate 128 nuclear pore transcribed cytoplasm nucleus transferase exported polymerase translated 2. The distinct characteristics of different cell types in a multicellular organism result mainly from the differential regulation of the A) replication of specific genes. B) transcription of genes transcribed by RNA polymerase II. C) transcription of housekeeping genes. D) packing of DNA into nucleosomes in some cells and not others. 3. Which of the choices represents the correct way to repair the mismatch shown in the figure below? A) B) C) D) E) 4. Which of the following processes is not used by eukaryotic cells to regulate the amount of a protein in the cell? A) Chromatin remodeling may prevent a locus from being genetically expressed. B) Genes can be transcribed into mrna with different efficiencies. C) Many ribosomes can bind to a single mrna molecule. D) Proteins can be tagged with ubiquitin, marking them for degradation. E) Nuclear pore complexes can regulate the speed at which newly synthesized proteins are exported from the nucleus into the cytoplasm.

3 120:201 Foundations CMB/Summer 2015 Practice Questions for Exam 3/Part 2 Page 2 of 6 5. RNA in cells differs from DNA in that. A) it contains the base uracil, which pairs with cytosine. B) it is single-stranded and cannot form base pairs. C) it is single-stranded and can fold up into a variety of structures. D) the sugar ribose contains fewer oxygen atoms than does deoxyribose. 6. Transcription is similar to DNA replication in that. A) an RNA transcript is synthesized discontinuously and the pieces are then joined together. B) it uses the same enzyme as that used to synthesize RNA primers during DNA replication. C) the newly synthesized RNA remains paired to the template DNA. D) nucleotide polymerization occurs only in the 5 -to-3 direction. 7. Match the following structures with their names. 8. Unlike DNA, which typically forms a helical structure, different molecules of RNA can fold into a variety of three-dimensional shapes. This is largely because. A) RNA contains uracil and uses ribose as the sugar. B) RNA bases cannot form hydrogen bonds with each other. C) RNA nucleotides use a different chemical linkage between nucleotides compared to DNA. D) RNA is single-stranded. 9. Which one of the following is the main reason that a typical eukaryotic gene is able to respond to a far greater variety of regulatory signals than a typical prokaryotic gene or operon? A) Eukaryotes have three types of RNA polymerase.? B) Eukaryotic RNA polymerases require general transcription factors. C) The transcription of a eukaryotic gene can be influenced by proteins that bind far from the promoter. D) Prokaryotic genes are packaged into nucleosomes. 10. Match the following types of RNA with the main polymerase that transcribes them.

4 120:201 Foundations CMB/Summer 2015 Practice Questions for Exam 3/Part 2 Page 3 of The following segment of DNA is from a transcribed region of a chromosome. You know that RNA polymerase moves from left to right along this piece of DNA, that the promoter for this gene is to the left of the DNA shown, and that this entire region of DNA is made into RNA. 5 -GGCATGGCAATATTGTAGTA-3 3 -CCGTACCGTTATAACATCAT-5 Given this information, a student claims that the RNA produced from this DNA is: Give two reasons why this answer is incorrect. 3 -GGCATGGCAATATTGTAGTA You have a segment of DNA that contains the following sequence: 5 -GGACTAGACAATAGGGACCTAGAGATTCCGAAA-3 3 -CCTGATCTGTTATCCCTGGATCTCTAAGGCTTT-5 You know that the RNA transcribed from this segment contains the following sequence: 5 -GGACUAGACAAUAGGGACCUAGAGAUUCCGAAA 3 Which of the following choices best describes how transcription occurs? A) the top strand is the template strand; RNA polymerase moves along this strand from 5 -to-3 B) the top strand is the template strand; RNA polymerase moves along this strand from 3 -to-5 C) the bottom strand is the template strand; RNA polymerase moves along this strand from 5 -to-3 D) the bottom strand is the template strand; RNA polymerase moves along this strand from 3 -to Imagine that an RNA polymerase is transcribing a segment of DNA that contains the following sequence: 5 -AGTCTAGGCACTGA-3 3 -TCAGATCCGTGACT-5 A) If the polymerase is transcribing from this segment of DNA from left to right, which strand (top or bottom) is the template? B) What will be the sequence of that RNA (be sure to label the 5 and 3 ends of your RNA molecule)? 14. The sigma subunit of bacterial RNA polymerase. A) contains the catalytic activity of the polymerase. B) remains part of the polymerase throughout transcription. C) recognizes promoter sites in the DNA. D) recognizes transcription termination sites in the DNA. 15. There are several reasons why the primase used to make the RNA primer for DNA replication is not suitable for gene transcription. Which of the statements below is not one of those reasons? A) Primase initiates RNA synthesis on a single-stranded DNA template. B) Primase can initiate RNA synthesis without the need for a base-paired primer. C) Primase synthesizes only RNAs of about 5 20 nucleotides in length. D) The RNA synthesized by primase remains base-paired to the DNA template. 16. Which of the following does not occur before a eukaryotic mrna is exported from the nucleus? A) The ribosome binds to the mrna. B) The mrna is polyadenylated at its 3 end. C) 7-methylguanosine is added in a 5 -to-5 linkage to the mrna. D) RNA polymerase dissociates.

5 120:201 Foundations CMB/Summer 2015 Practice Questions for Exam 3/Part 2 Page 4 of Transcription in bacteria differs from transcription in a eukaryotic cell because A) RNA polymerase (along with its sigma subunit) can initiate transcription on its own. B) RNA polymerase (along with its sigma subunit) requires the general transcription factors to assemble at the promoter before polymerase can begin transcription. C) the sigma subunit must associate with the appropriate type of RNA polymerase to produce mrnas. D) RNA polymerase must be phosphorylated at its C-terminal tail for transcription to proceed. 18. Total nucleic acids are extracted from a culture of yeast cells and are then mixed with resin beads to which the polynucleotide 5 -TTTTTTTTTTTTTTTTTTTTTTTTT-3 has been covalently attached. After a short incubation, the beads are then extracted from the mixture. When you analyze the cellular nucleic acids that have stuck to the beads, which of the following is most abundant? A) DNA B) trna C) rrna D) mrna 19. Which of the following statements about RNA splicing is false? A) Introns are absolutely not found in bacterial genes. B) For a gene to function properly, every exon must be removed from the primary transcript in the same fashion on every mrna molecule produced from the same gene. C) Small RNA molecules in the nucleus perform the splicing reactions necessary for the removal of introns. D) Splicing occurs after the 5 cap has been added to the end of the primary transcript. 20. You have discovered a gene (see figure below) that is alternatively spliced to produce several forms of mrna in various cell types, three of which are shown in Figure Q7-36B. The lines connecting the exons that are included in the mrna indicate the splicing. From your experiments, you know that protein translation begins in exon 1. For all forms of the mrna, the encoded protein sequence is the same in the regions of the mrna that correspond to exons 1 and 10. Exons 2 and 3 are alternative exons used in different mrna, as are exons 7 and 8. Which of the following statements about exons 2 and 3 is the most accurate? Explain your answer. A) Exons 2 and 3 must have the same number of nucleotides. B) Exons 2 and 3 must contain an integral number of codons (that is, the number of nucleotides divided by 3 must be an integer). C) Exons 2 and 3 must contain a number of nucleotides that when divided by 3, leaves the same remainder (that is, 0, 1, or 2). D) Exons 2 and 3 must have different numbers of nucleotides. 21. Which of the following statements about the genetic code is correct? (Use the genetic code table handout.) A) All codons specify more than one amino acid. B) The genetic code is redundant.

6 120:201 Foundations CMB/Summer 2015 Practice Questions for Exam 3/Part 2 Page 5 of 6 C) All amino acids are specified by more than one codon. D) All codons specify an amino acid. 22. The piece of RNA below includes the region that codes for the binding site for the initiator trna needed in translation. 5 -GUUUCCCGUAUACAUGCGUGCCGGGGGC-3 Which amino acid will be on the trna that is the first to bind to the A site of the ribosome? A) methionine B) arginine C) cysteine D) valine 23. Which amino acid would you expect a trna with the anticodon 5 -CUU-3 to carry? A) lysine B) glutamic acid C) leucine D) phenylalanine 24. Below is a segment of RNA from the middle of an mrna. 5 UAGUCUAGGCACUGA-3 If you were told that this segment of RNA was part of the coding region of an mrna for a large protein, give the amino acid sequence for the protein that is encoded by this segment of mrna. Write your answer using the one-letter amino acid code. 25. Below is the sequence from the 3 -end of an mrna. 5 -CCGUUACCAGGCCUCAUUAUUGGUAACGGAAAAAAAAAAAAAA-3 If you were told that this sequence contains the stop codon for the protein encoded by this mrna, what is the anticodon on the trna in the P site of the ribosome when release factor binds to the A site? A) 5 -CCA-3 B) 5 -CCG-3 C) 5 -UGG-3 D) 5 -UUA One strand of a section of DNA isolated from the bacterium Escherichia coli reads: 5 -GTAGCCTACCCATAGG-3 A) Suppose that an mrna is transcribed from this DNA using the complementary strand as a template. What will be the sequence of the mrna in this region (make sure you label the 5 and 3 ends of the mrna)? B) How many different peptides could potentially be made from this sequence of RNA, assuming that translation initiates upstream of this sequence? C) What are these peptides? (Give your answer using the one-letter amino acid code.) 27. How do the following antibiotics affect translation in bacterial ribosomes? A) Chloramphenicol B) Streptomycin C) Tetracyclin D) Erythromycin

7 120:201 Foundations CMB/Summer 2015 Practice Questions for Exam 3/Part 2 Page 6 of The figure above shows the stage in translation when an incoming aminoacyl-trna has bound to the A site on the ribosome. Using the components shown in panel A as a guide, show on panels B and C what happens in the next two stages to complete the addition of the new amino acid to the growing polypeptide chain. 29. A poison added to an in vitro translation mixture containing mrna molecules with the sequence 5 -AUGAAAAAAAAAAAAUAA-3 has the following effect: the only product made is a Met-Lys dipeptide that remains attached to the ribosome. What is the most likely way in which the poison acts to inhibit protein synthesis? A) It inhibits peptidyl transferase activity. B) It inhibits movement of the small subunit relative to the large subunit. C) It inhibits release factor. D) It mimics release factor. 30. Match the labels given in the list below with the label lines in the figure above. A) ribosome-binding site B) initiator codon C) stop codon untranslated 3 region D) untranslated 5 region E) protein-coding region