Chapter 2 Review Questions 1. What type of monomer is polymerized to form DNA? What type of monomer is polymerized to form RNA? 2. What are the three components are necessary to form a nucleotide? What must be left off to form a nucleoside? 3. Below are the pictures of a nucleotide. Please name the nucleotide and state which sugar and nitrogenous base is present within the nucleotide. Please label the carbons of this sugar. Which carbon is the phosphate group bound to? Which carbon is the nitrogenous base bound to? 4. Please state the nitrogenous bases common to DNA. Which are purines and which are pyrimidines? 5. Please state the nitrogenous bases common to RNA. Which are purines and which are pyrimadines? 6. Please state Chargaff’s rules. Please explain in detail why these rules apply? 7. Is it necessary G:C content stay the same between species? Please explain your answer. 8. Please explain the difference between deoxyribose and ribose specifically. Also, please discuss how this effects each structure and chemistry. 9. Please give the appropriate name for the nucleotide/nucleoside based off each of the descriptions below. a. Contains deoxyribose and guanine b. Contains deoxyribose, adenine and two phosphates c. Contains ribose, uracil and three phosphates d. Contains ribose, cytosine and one phosphate e. Contains deoxyribose and thymine 10. For the nucleotide below, please appropriately label the phosphates, and number the carbons in the pentose sugar. 12. What type of reaction allows for the joining of two nucleotides to allow for elongation of a DNA strand? Please state the reason for the name of the reaction that allows for the joining of two nucleotides. What type of bond is formed in this reaction. Please discuss which groups are involved in the reaction and which carbons they are bound to on the pentose sugar. 11. Does a single DNA strand have a specific polarity? Please explain your answer in detail. 12. Please take the sequence of the DNA strand below (not written in proper conventions), and write the sequence of its complement. When you write the sequence, you must use the proper conventions. 5’ ACCTCGTTGGTATTCTTATCA 3’ 13. Please state the two forces that are necessary to allow for the structural integrity of a double stranded molecule of DNA. Please describe each force. 14. How many hydrogen bonds are present between an A-T base pair 15. How many hydrogen bonds are present between a G-C base pair? 16. Which base pair is stronger? Please explain why. 17. What is meant by Watson-Crick base pairing? Please name a non-WatsonCrick base pair that may be found in DNA. 18. When looking at the exterior of a DNA molecule, name two different features you may see. Please describe them for the B-type DNA double helix. 19. Please state three different forms that the DNA double helix can take. Please describe each, and state which conditions are necessary for each to form? 20. Which forms of DNA double helices are physiologically relevant. Please explain your answer. 21. Please state one method by which you could denature double stranded DNA? How does this method denature the DNA? Please explain how it is possible to renature the DNA. 22. Are denaturation and renaturation of DNA biologically relevant processes (i.e. are they important in living systems)? Please explain your answer in detail including examples if necessary. 23. You are studying the DNA binding protein GLI in humans. GLI normally binds the DNA sequence 5’ ACGCTACGA 3’ in the IL-1 (interleukin-1) gene. You come across a skin cancer patient in which you find that GLI no longer binds the IL-1. Upon further study, you find that the binding sequence has been changed and is now 5’ ACGCCACTA 3’. Please write the complementary DNA sequences for the normal and changed binding sites. Also, please explain where within the geometry of the DNA GLI would bind and explain in DETAIL why GLI can no longer bind to the changed sequence. 24. For the following DNA molecules, please write out the complementary sequence and then determine the melting point for the double stranded DNA molecule. a. 5’ GCGCCCGGATCG 3’ b. 5’ ATGCTAGCTGAACCTGA 3’ c. 5’ CTGGGACAATATACGTATTACT 3’ 25. Can a double stranded DNA molecule be manipulated in a way that such that the two strands become two separate single strands? If so, can the two single strands reconstitute a double stranded DNA molecule. Please explain your answer in detail. 26. Are non-canonical base pairs stronger or weaker than canonical base pairs in RNA? Why? If non-canonical base pairing is weaker, please state how this is compensated for? 27. What type of secondary structure does RNA adopt? Please describe this structure in detail. 28. Explain the structure of the double stranded RNA double helix? How does the structure of this helix differ from the typical DNA structure? If a protein were to bind, where on this helix will a protein most likely bind? Why is it most likely that a protein would bind at that spot?