Bioc385-Spr2016-Homework2-KEY

Bioc385-Spr2016-Homework2-KEY - Bioc 385 Spring 2016 Dr...

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Unformatted text preview: Bioc 385 – Spring 2016 Dr. Miesfeld Homework 2 1. Choose the ONE answer below that correctly identifies the nucleic acid base, nucleic acid bases, or absence of nucleic acid base, in the chemical structures shown, i.e, there may be 0, 1, 2, or 3 bases. The atom colors are blue=nitrogen, red=oxygen, carbon=light green, phosphate=dark green. a) adenine, cytosine, uracil b) uracil c) guanine, adenine d) adenine, uracil e) adenine f) these structures do not contain nucleic acid bases g) guanine, uracil, thymine h) adenine, cytosine 1 Bioc 385 – Spring 2016 Dr. Miesfeld 2. Why does RNA contain uracil and DNA contain thymine? Choose the ONE best answer to this question. Uracil specifies RNA polymerization, and therefore, if uracil is inserted into DNA, then RNA polymerization will occur on DNA strands. RNA transcription base pairs U-­T in the RNA with DNA, whereas this process base pairs A-­T in the RNA with DNA. Therefore, if uracil were present in DNA, then U-­A and A-­U could not be distinguished. Loss of NH3 from cytosine generates uracil, which base pairs with thymine and cause damage in DNA. If deamination of thymine generated guanine, then this would not be a problem. Spontaneous cytosine deamination generates uracil, which base pairs with adenine during replication, and thereby converts a C-­G base pair to a T-­A base pair. Spontaneous cytosine deamination generates uracil, which base pairs with adenine during replication, and thereby converts a G-­C base pair to a A-­T base pair. None of these statements are correct. Ultraviolet light cause thymine dimers to accumulate in DNA, therefore if uracil were present in DNA, then these uracil dimers would not be recognized by nucleotide excision repair. DNA damage can alter the nucleotide bases and cause mutations that cannot be repaired if the base is uracil since repair enzymes recognize thymine in DNA, not uracil. 3. Select the TRUE statements below correctly describing the biochemistry of DNA replication. Choose the two BEST answers. SSB and helicase are two of the proteins in involved in replication fork looping, SSB is responsible for unwinding the DNA in front of the fork and helicase is responsible for winding it back up again later. DNA Pol I, DNA Pol II, and DNA Pol III are all DNA polymerases involved in replication of human DNA, however, DNA Pol II is also required for nick translation in the DNA repair process. The process of DNA replication involves the synthesis of one faithful copy of each template DNA strand such that the product is a hybrid molecule of template and nascent strands. Okazaki fragments are the left over pieces of RNA that fall of the DNA when the helicase unwinds the double helix, these Okazaki fragments show up as small nucleic acids in sucrose density gradients. Since the direction of DNA polymerization is 5' to 3', one strand of the DNA replication fork is synthesized continuously and the other strand is synthesized in segments, which must be ligated together. The replication fork contains both a leading and lagging strand, with the leading strand synthesized 5' to 3' and the lagging strand synthesized 3' to 5'. RNA primers are used to initiate DNA synthesis at replication origins, however these are removed by DNA ligase and replaced with ddNTPs to repair the strand. 2 Bioc 385 – Spring 2016 Dr. Miesfeld 4. The circular E. coli chromosome contains 4,639,221 bp. a) If the rate of replication is 1,000 bp/s at 37 C, how long would it take to replicate the E. coli chromosome if two replication forks proceeded in opposite directions from the same single point? b) Assume Okazaki fragments in bacteria are 1000 bases in length. In the replication of the E. coli chromosome, about how many Okazaki fragments would be formed? a) Approximately 4 minutes a) Approximately 40 minutes a) Approximately 77 minutes a) Approximately 4600 minutes b) approximately 2500 b) approximately 4500 c) approximately 10,000 5. Based on the sequence of the double stranded DNA shown above, which sequence below corresponds to the mRNA transcript? Choose the ONE best answer. 5'-­UUUGCGAUAUCGC-­3' 5'-­CGCTATAGCGTTT-­3' 3'-­CGCUAUAGCGUUU-­5' 5'-­GCGAUAUCGCAAA-­3' 5'-­CGCUAUAGCGUUU-­3' 5'-­AAAGCGAUAUCGC-­3' None of these sequences are correct. 5'-­GCGUAUAGCGAAA-­3' 6. What explains the observation that a single eukaryotic protein coding gene can give rise to multiple different proteins, i.e., why are there only ~25,000 human genes in the genome, but ~150,000 different proteins in the human "proteome?" Choose the TWO best correct answers. Genes can contain more than one polyadenylation site, which alters the 3' of the mRNA transcript and the inclusion/exclusion of exons. mRNA transcripts from the same gene can be differentially spliced to include/exclude exons. There are ~6 times more proteins than genes because each gene makes 6 different proteins. Serine phosphorylation of a polypeptide changes its amino acid sequence, and thereby generates multiple proteins from the same gene. Polypeptide subunits of the same protein complexes are often differentially cleaved by protease enzymes, resulting in loss of some subunits and duplication of others. Some genes are transcribed from both strands of the DNA and this generates isozymes of the same protein. 3 Bioc 385 – Spring 2016 Dr. Miesfeld 7. The processes of DNA replication and RNA transcription are similar in some respects and different in others. Select the statements below that describe BOTH DNA replication and RNA transcription. The process requires a primer. A specific region of the DNA is recognized and bound by the polymerase. The direction of enzyme movement on the template strand is 3' to 5' The process includes its own 3' to 5' exonuclease proofreading mechanism. The direction of polymerization is 5' to 3' The mechanism of reaction is attack by the 3'OH group of the pentose on the α-­phosphate of an incoming nucleoside triphosphate. 8. Nirenberg and colleagues determined a portion of the genetic code using filter binding assays that included ribosomes, trinucleotides and tRNA molecules charged with radioactively-­labeled amino acids. Choose the answer below that correctly answers the following three questions in order: 1) If the trinucleotide sequence is AAG, which amino acid will be bound to the filter paper? 2) If the position of the trinucleotide sequence that base pairs with the wobble position is changed to a U, which amino acid will be bound to the filter paper? 3) True or False: Two distinct tRNA molecules with different anticodon sequences MUST be used to bind to the codons UCA and UCG. 1) Gln, 2) Tyr, 3) False 1) Glu, 2) Phe, 3) True 1) Val, 2) His, 3) False 2) Gln, 2) Tyr, 3) True 1) Phe, 2) Leu, 3) True 1) Gln, 2) His, 3) False 1) Val, 2) Tyr, 3) False 1) Lys, 2) Asn, 3) False 1) Val, 2) His, 3) True 1) Lys, 2) Asn, 3) True 1) Phe, 2) Leu, 3) False 1) Gln, 2) His, 3) True 1) Glu, 2) Phe, 3) False 1) Val, 2) Tyr, 3) False 4 Bioc 385 – Spring 2016 Dr. Miesfeld 9. Using the DNA sequence shown above, 1) determine the sequence of the complementary DNA strand, 2) identify the six possible protein translation reading frames (3 frames possible from each DNA strand), and 3) identify the N-­ terminal sequence of the most likely protein (must start with methionine). Based on your analysis, choose the THREE correct statements about this DNA sequence. You may use online web DNA analysis tools to find open reading frames, stop codons, etc., which may be easier than analyzing by hand -­ although it is possible to answer this question using only the Genetic Code Table, a pencil, and a piece of paper. The most likely protein sequence is: MKRALTRSSGPKFHP The most likely protein sequence is: Met-­Lys-­Phe-­Gly-­Pro-­Arg-­Ala-­Pro-­Gly-­Ser-­Ala-­Leu-­His The most likely protein sequence is: Asn-­Val-­Thr-­Arg-­Tyr-­Pro-­Glu-­Leu-­Trp-­Ala-­Gln-­Ile The DNA sequence shown is the template strand for the correct mRNA specifying the most likely protein. Five of the six possible open reading frames contains a STOP codon. The most likely protein sequence is: MKFGPRAPGSALH There are two polypeptides containing the same number of amino acids, each of which encodes the N-­terminus of a protein. The DNA sequence shown is the coding strand for the correct mRNA specifying the most likely protein. 10. Choose the correct statements below. Peptide bond formation is catalyzed by the RNA component of the ribosome. Base pairing between the tRNA and the mRNA helps align the tRNA in the E site of the ribosome. In prokaryotes, the 70S ribosome binds to mRNA, IF-­3 and IF-­1 to initiate protein translation. The release factors are required for the removal of the tRNA from the E site. During the elongation cycle of protein synthesis, the tRNA molecule moves from the A site to the P site During elongation, the next amino acid is added on to the N-­terminal end of the polypeptide attached to the tRNA in the P site. 5 ...
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