BIO2107-PROB_SET1 2021_

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University of Southern Queensland *

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2107

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Biology

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Jan 9, 2024

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BIO2107 Cell & Molecular Biology 1 Problem Set #1 BIO2107 - CELL& MOLECULAR BIOLOGY I PROBLEM SET ONE (13%) Due via the course Study Desk 19/3/21 Name:_________________________________ Total /50 1. Outline the structure of the genome of SARS CoV-2 (COVID 19 virus). What are the main diagnostics methods for this virus? /4 marks 2. What is Chargaff’s rule in relation to the structure of DNA? How did Chargaff’s research indicate that DNA could be a potential information bearing molecule? /2 marks 3 . Nucleotides play roles in cells other than carrying genetic information. Name two of these other roles. /2 marks 4. In the DNA of certain bacterial cells, 37% of the nucleotides contain cytosine. What are the percentages of the other nucleotides? /3 marks 37% Guanine 13% adenine 13% thymine 5. Given two dsDNA molecules, the overall composition of which is represented by the segments shown below, determine which molecule would have the highest melting temperature and explain why this is the case. /3 marks Molecule A : TTCAGAGAACTT AAGTCTCTTGAA Molecule B: CCTGAGAGGTCC GGACTCTCCAGG Molecule _ has the highest melting temperature. Reason: 6. Consider the enzyme ApaL1 cutting a DNA molecule of 40% GC /4 marks a) What sequence does this enzyme recognise? b) What proportion of this DNA is made up of thymine bases? 30% c) How often would ApaL1 cut this molecule (in bp)? - 1 -

BIO2107 Cell & Molecular Biology 1 Problem Set #1 d) If this DNA molecule was 35,000 bp in length, how many fragments would be produced on average? 7. A plasmid (pUSQ2) is cut with a series of four restriction enzymes (A, B, C and D: each with different restriction sites) and this produces the following bands after submarine gel electrophoresis: 6 marks Enzyme(s) Bands observed (bp) A 1000, 2000 B 3000 C 3000 D 3000 A + B 500*, 2000 A + C 400, 600, 2000 A + D 300, 700, 2000 A + C + D 100, 300, 600, 2000 ( note: * indicates very intense/bright bands) On the diagram below, construct a circular plasmid map of the plasmid consistent with the above data, showing: (i) The location of each enzyme cut site (ii) The distances between the cut sites The single enzyme “B” cut site has been marked for you on the map at position “0” and marks have been placed at 500bp intervals around the 3000bp map to assist you. - 2 -

BIO2107 Cell & Molecular Biology 1 Problem Set #1 8. You wish to localise a highly expressed mRNA species in a Drosophila embryo so that it is visible under the brightfield light microscope. Outline the steps you would follow to achieve this. /6 marks 9. What is the most suitable annealing temperature for the PCR primer set below? Give reasons for your answer /3 marks TCCGTAGGTGAACCTGCGG TCCTCCGCTTATTGATATGC 10. The duration of the DNA synthetic period (S phase) in a certain chicken cell is 12 hours, not very different from the 10 hours characteristic of human cells. Replication in both cells occurs at about 100bp/sec/fork. The chicken cell you are studying comes from an organism with 3.5 x 10 10 bp of DNA per genome. What is the minimum number of bidirectional forks required to replicate the chicken genome during the DNA synthetic period? Show your working /4 marks 11. What is 8-oxoguanine? Outline the mechanisms that cause it to be removed from and replaced in eukaryotic DNA. /6 marks 12. Outline the function of the following molecules during DNA replication in eukaryotes /3 marks PCNA protein Pol α protein RFC protein - 3 -

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BIO2107 Cell & Molecular Biology 1 Problem Set #1 13. From what organisms are the following DNA sequences likely derived? Which two species are the most closely related and give reasons for your answer? /4 marks Sample A = TGGACTGTTCGATCGTGTTGGGTAACCGGGCCCTTCTCTCGCGCTGTCTTTGTCCCTGCAACGGTTTCGC TCGACTCTCCCCCCGCCATGTGACTCCGAGTCGATGTGCGGGCCGCGTCCTCTCGGGGAGGGGGCAGGGT TGTCTCGTTGCGCGGCGGGCGTCGTTGGAGCAGGGTGGGCCAACAAACCAAAAGCACAGGGTGCCCGGCG CACCAAGGACCCGAGTTGCTGCACGGACCCTCGATCCAGTGTTCTGCGGGGGCCCGTGCGGCGTATTTGT GGAAAGGCACGACTCTCGGCAACGGATATCTCGGCCCTCGCCACGATGAAGAACGTAGCGAAATGCGATA CTTAGTGTGAATTGCAGAATCCCGTGAGTCATCCAGTCTTTGAATGCAAGTTGCGCCCGAGGCTTCGAAC GAGGGCACGTCTGCCTGGGTGTCGCACACAATCGAATCGCCCCATTTGCCTGCGTGCGGGCGGTGGAGGG GAGCTGGCTGTCCGTGTCCCTTGTGACACCGTCGGCTTAACCGGATTGGGCTCTCGTTGTCGGGCATCGG CGAGCGGTGGTTCGGTCGTCCTGGCCGATCGATACGCGACACCGTAAGTGCACGGCACGCGGGGAAGGCC CTCCTCGACTTGATCACTCGGGAGGCCTAGGCTTCGGCCGGAGTTCCTTCCGTCCACGTCACGCGACCCC AGGTCAGGCGAGAGCACCCGCTGAGTTTAAGCATATCACTAAGCGGAGGAAAAGAAA Sample B = TTTCCGTAGGTGAACCTGCGGAAGGATCATTGTCGATGCCTCACAATCAGATTGACCCGCGAACTTGTTT ATTCATCTACCGTCGGGAGGGAGGGGATGACCACGGCGCCCCGTGCGCCCGGCCTCCTCGTCCTCGCGAC AAACACAAACCCCGGCGCTTCGTGCGCCAAGGAACTCAAATCTGTTAAGTGCGACTCCCGGGGGCCCGGA GACGGTGTCCCGCGGGAGTCGTCACGACACAACATTTACATACAATGACTCTCGGCAACGGATATCTCGG CTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCG AGTCTTTGAACGCAAGTTGCGCCCGAAGCCATTAGGCCGAGGGCACGCCTGCCTGGGTGTCACACATCGT TTCCCCAACGCAAACATGTAACAATGTTGCTGCGCGGGGTGTATGCTGACCTCCCGCGAGCACCCGCCTC GTGGTTGGTTGAAATCTGGGTTCATGGCCGACTTCGCCGTGATAAAATGGTGGATGAGCCACGCTCGAGA CCAATCACGTGCGAGCCGGTCAGTTCTGGACCCATCGACGACCCTTTGCGTGCACGCACGCTCCCAACGA GACCTCAGGTCAGGCGGGGCTACCCGCTGAGTTTAA Sample C = TCGTGACCCTGACCAAAACAGACCGCGAACGCGTCACCCCTGCCCGCCGAGCGCTCGCGCGCGAGGCAAC CGAGGGCCCCGGGCCGCAACAGAACCCACGGCGCCGACGGCGTCAAGGAACACAGCGATACGCCCCGCGC CGGCCCGGTCGGCCCTGGCCGTCCGGCGGCGCGGCGCGATACCACGAGTTAAATCCACACGACTCTCGGC AACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACCTGGTGTGAATTGCAGAAT CCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAGGCCATCCGGCCGAGGGCACGCCTGCCTGG GCGTCACGCCAAAAGACGCTCCGCGCGCCCCCCCTATCCGGGAGGGCGCGGGGACGCGGTGTCTGGCCCC CCGCGCCTCGCGGCGCGGTGGGCCGAAGCTCGGGCTGCCGGCGAAGCGTGCCGGGCACAGCGCATGGTGG ACAGCTCACGCTGGCTCTAGGCCGCAGTGCACCCCGGCGCGCGGCCGGCGCGGTGGCCCCTCAGGACCCA AACGCACCGAGAGCGAACGCCTCGGACC - 4 -

BIO2107-PROB_SET1 2021_

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