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Carnegie 03 121 – Homework Lectures 20-23 Modern Biology

Homework Lectures 20-23 Modern Biology Fall 2016DNA Replication; Mutation and Repair; Sequencing and GenomesNote: You should draw the process of DNA replication on your own for study,filling in details like strand orientations, primers, proteins involved, and leadingand lagging strand synthesis, and check against the textbook and lecturediagrams. Q1. In the process of DNA replication, the lagging strand cannot be synthesizedcontinuously because:a) Helicase cannot unwind DNA sequences that contain telomere sequence.b) Separation of the parental DNA strands proceeds upstream of and away fromthe 5’ end of the lagging strand.c) The lagging strand polymerase is too slow and the entire replication complexdissociates when the final leading strand sequences are produced.d) Transcriptional repressors block access to gene promoters. Q2. Telomerase uses RNA:a) As a primer for DNA replication at the ends of chromosomesb) As a template to add DNA to the ends of chromosomesc) As a primer for synthesis of Okazaki fragmentsd) As a riboswitch to control termination of DNA synthesis at chromosome ends Q3. A common element of the mechanisms of mismatch repair, base excisionrepair and nucleotide excision repair is:a) Use of the non-damaged strand as template for synthesis of the new versionof the damaged strand.b) Use of exonucleases to cleave the phosphodiester backbone at the site ofDNA damage c) Removal of the damaged or mismatched bases, while the phosphodiesterbackbone is reused in the repaired DNAd) Replication of the entire DNA non-damaged strand and degradation of theentire damaged DNA strand.Q4. Individuals with Xeroderma pigmentosum have mutations in one or moregenes for DNA excision repair machinery that were passed down from theirparents. Cancers that arise in these individuals are likely due toa) The presence of unrepaired double stranded breaks in their DNA.b) Mutations in additional tumor suppressor genes and proto-oncogenes thatdevelop from new DNA damage.c) Additional random mutations passed down from their parents.d) The presence of uracil bases in the genome.Q5. A restriction endonuclease can cleave DNA:a) At specific recognition sequences.b) At the site of gene mutations.c) At free 5’ and 3’ ends of the DNA.d) Anywhere allele sequences differ.Q6. Two restriction enzymes recognize the same palindromic sequence.Enzyme 1 cleaves to generate 5’ overhangs, Enzyme 2 cleaves to generate bluntends. which of the following is correct?a) Any fragment generated with E1 can be ligated to any fragment generatedwith E2.b) Any fragment generated with E2 can be ligated to any other blunt-endedfragment, even if generated with a different enzyme.c) Any fragment generated with E1 can be ligated to any other 5’overhangfragment, even if generated with a different enzyme.d) Fragments generated by E2 cannot be ligated e) b and c Q7. Which best describes why Taq polymerase is commonly used in PCRreactions?a) It is one of the easiest eukaryotic polymerases to isolateb) It is isolated from thermophilic bacteria and therefore resistant to elevatedtemperaturesc) It has the highest fidelity of DNA polymerasesd) It is the only DNA polymerase capable of recognizing DNA primersQ8. In the figure below, the 5’ and 3’ ends of the DNA template have beenlabeled. Primers hybridized to the template are shown by arrows, with thearrowhead indicating the 3’ end. Which version shows a configuration of primersthat is correct and will allow exponential amplification of target DNA? Q9. Which of these is/are features of Sanger DNA sequencing but not in vivoDNA replication in eukaryotes?a) The use of DNA primersb) The use of deoxynucleotidesc) The use of dideoxynucleotidesd) The use of Taq polymerasee) a and cQ10. Which of these differences from in vivo DNA replication is critical for thesuccess of Sanger DNA sequencing?a) The use of DNA primersb) The use of deoxynucleotidesc) The use of dideoxynucleotidesd) The use of Taq polymerasee) a and cQ11. Which best describes how genomic sequences are examined in shotgunsequencing?a) A small number of extremely long DNA sequences are obtained in each runand pieced togetherb) A huge number of short, random sequences are obtained in each run andpieced togetherc) Regions with restriction enzyme sites are often sequenced multiple times toensure the correct cleavage of the DNA.d) Some regions are represented more often because they are easier tosequence and so they are sequenced multiple times, while others may not showup at all, but computers can fill in this missing information. Q12. Which type of genomic sequence complicates alignment of DNA analyzedby shotgun sequencing?a) Tandem repeatsb) Intron-exon boundariesc) Open reading framesd) PolymorphismsQ13. In small chromosomal duplications, the duplicated genes that diverge canresult in:a) Inverted repeatsb) Gene families, such as the globin gene familyc) Activation of proto-oncogenesd) Activation of repair pathways, such as excision repair Q14. RFLPs represent:a) Alleles that bind different probesb) Alleles with different restriction sitesc) Alleles with different lengths of genesd) Alleles with different numbers of duplications

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