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Problem set 1

Problem set 1 - BIMM100 Problem set#1 Answers...

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Unformatted text preview: BIMM100 Problem set #1 8/5/11 Answers will not be posted online. Please consult your TAs during section for help solving these problems. 1. You are told that a sample of DNA contains 15% cytosine (C). What is the composition of each of the other bases? If the composition of C is 22%, what would happen to the Tm of the DNA? Why? 2. Identify the following bases. Which are purines, and which are pyrimidines? Where do their sugar residues attach? Which of these bases can be deaminated to make uracil? Does this tell us anything about why DNA is used (versus RNA) as a long ­term information molecule in the genome? 3. What is the function of topoisomerase I and topoisomerase II? How are they similar? How are they different? 4. How many genes are in the trp operon? How many transcripts are produced from this operon? How many proteins are translated from this operon? 5. What is the difference between an operon and a gene? 6. mRNA is synthesized from ____ to ____. 7. Briefly explain two differences between DNA and RNA molecules. 8. How are nucleotides joined together in a polymer of DNA? 9. What is the difference between a nucleoside and a nucleotide? 10. True or false: adenosine triphosphate is a nucleotide. 11. What are three modifications made to eukaryotic mRNA after being transcribed. Where does transcription occur? Where does processing occur? 12. What are the distinguishing features of a 5’ methylated cap from a processed yeast mRNA? 13. True or false: the phosphate backbone of DNA is hydrophobic. 14. What is the Tm of the following sequence CCA AAG TTA GCC ACC? 15. What is wobble base pairing? Why is it important? What base is the wobble position in mRNA? In tRNA? Does Watson ­Crick base pairing occur at the wobble position? 16. What enzyme “charges” tRNA molecules with amino acids? What is this bond called (between the tRNA and amino acid)? Where does the amino acid get attached to the tRNA? 17. True or false: tRNA molecules can bind to more than one codon. 18. Draw a replication fork and label the leading and lagging strands, Okazaki fragments, and the polarity of each of the strands. Which enzymes are involved in this process? What is primase? 19. During DNA replication, why is DNA polymerase δ used instead of DNA polymerase α? 20. What are “non ­templated” events? Give two examples. 21. You are given the sequence of an mRNA that is 4.5kb in length. How many reading frames does it have? How can you determine the sequence of the protein that will be translated from this mRNA? 22. What is the difference between Met ­tRNAiMet and Met ­tRNAMet? 23. RNA polymerase transcribes a region of DNA, generating an mRNA transcript that reads CCU AUU CUA UUG. What is the sequence of the non ­template strand of DNA used to generate this transcript? What is the sequence of the template strand? Where does transcription occur in the cell? 24. You determine that an mRNA sequence in a protein you have been studying in the laboratory (the wt codon, UGA has been mutated to UGG). Explain why this may be an issue for your studies. What if the opposite were true (UGG was mutated to UGA). Would it still be a problem? Why or why not? 25. True or false: Non ­homologous end joining is primarily used to protect the genome against double stranded DNA breaks. 26. Fill in the following chart: Where does it Use GTP? What does it Step in bind? do? translation? eIF1 eIF2 eIF3 eIF4 eIF5 eIF6 EF1 EF2 eRF1 eRF3 27. Order these enzymes (in order of their necessity during the process) in lagging strand synthesis: DNA polymerase, RNA polymerase, RNase, ligase, helicase. 28. Which DNA repair happens before replication? Focus on classic experiments: These are the things you should think about when reading/analyzing the classic experiments. 1. Defining the question. Why was this experiment performed? What was the question that the authors/researchers were trying to answer? 2. Designing of the experiment. What was examined in the experiment? a. What are the variables in the experiment? b. What are the controls? Essential ­ shows that the results were due to the result of the experimental treatment or variables! i. Experimental controls ­ did the experiment work? ii. Positive control ­ what data would look like if the treatment had the desired effect iii. Negative control ­ what data would look like without treatment c. Sample numbers ­ reproducibility is good! How many times were these data repeated? Keeping these things in mind (for all the experiments you read and design)… 1. What was the question that Meselson and Shahl were trying to answer? 2. What were the experimental variables in this experiment? 3. How did they perform this experiment? 4. What are some possible controls for this experiment? 5. Can you think of a way to design an experiment to obtain similar results? Hint: you don’t have to use 1950’s technology to answer this question. ...
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