TA's Molecular Biology Exam 1 Review Sheet

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TA’s Molecular Biology Exam 1 Review Sheet 1. For each of the following figures give the most specific name for the monomer shown, identify the purines vs. pyrimidines, and identify the common names and tautomer names for each base. For the first one only, also label the carbons of the sugar, the glycosidic bond, and the phosphoester bond. 2. Take this space below to write out a mnemonic or another method to help you remember purine vs. pyrimidines, and what bases belong to each. 3. What are the names for the 3 phosphates in a nucleoside triphosphate? What are their relative positions to the carbon sugar? University of Oklahoma BIOL/MBIO 4843/5843 Dr. Vitiello

4. Which phosphate remains attached when a nucleotide is incorporated into a growing DNA molecule? 5. In the image below label the following: -Base Pair Hydrogen Bonds -Phosphodiester Covalent Bonds -Van der Waals Forces -5’ terminus of each strand -3’ terminus of each strand -Base Names University of Oklahoma BIOL/MBIO 4843/5843 Dr. Vitiello

6. In the image below highlight/label the major and minor grooves: 7. The angle of what bond dictates the major and the minor groove? What are the angles of the major and minor groove respectively? 8. Experiments have shown that many proteins often associate with the major groove instead of the minor groove, list some reasons for this. 9. List the forms of DNA that can be found in the cell, which one is the major form found in vivo? University of Oklahoma BIOL/MBIO 4843/5843 Dr. Vitiello

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10. What are the major features of B-DNA (bases per turn etc.)? 11. What are the major differences between A, B, and Z DNA? 12. When salt is added to DNA its ______________ will increase, and this is because the ______________ charge of the phosphodiester backbone will be masked by the __________ within the salt. 13. Name the local RNA structures and write a small description about them: University of Oklahoma BIOL/MBIO 4843/5843 Dr. Vitiello

14. Utilizing Chargaff’s rule, identify how many Guanines would be present in a stretch of DNA that has 15% of its sequence being Adenine. 15. Due to Chargaff’s rule, within dsDNA the amount of ____________ and _____________ should be present in a ratio of 1.0 16. What is the 2+4 rule? Why do we use the number 4 instead of 3 for the rule? 17. Circle the following sequence that has the greatest T m : University of Oklahoma BIOL/MBIO 4843/5843 Dr. Vitiello

5’-ATATGCCATA-3’ 5’-GCCATAGCCT-3’ 5’-ATAAATTTATATTATAA-3’ 5’-GCATACGAACCGAT-3’ 5’-GCGGCCGG-3’ 5’-ATAGCCCGGGGACCG-3’ 18. Define what constitutes primary, secondary, tertiary, and quaternary protein structure: a. Primary: b. Secondary: c. Tertiary: d. Quaternary: 19. A homooligomer is composed of the ________ subunits, whereas a heterooligomer is composed of ____________ subunits. 20. A (a)________________ is a functional unit of a protein; whereas a (b)_______________ is a shared structure amongst many proteins and is a part of a whole for (a). 21. Give a specific example of letter (b) in the prior question: University of Oklahoma BIOL/MBIO 4843/5843 Dr. Vitiello

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22. Name the 2 major secondary structures, and then label which one is associated with hydrophobic R groups. 23. Give an example of a protein that can freely associate with DNA and is not sequence specific. 24. Recall the 4 major amino acid residues that were affected in Kleinstiver et al. 2016, and label which amino acid class that they were each apart of. 25. What is a PAM sequence? Give an example of one below. 26. How do sgRNA and Cas9 interact with one another? What function does sgRNA provide the Cas9? University of Oklahoma BIOL/MBIO 4843/5843 Dr. Vitiello

27. What are the 2 main repair mechanisms for DNA after Cas9 splices it? What are the differences between each of them? 28. Kleinstiver et al. replaced the four amino acids with __________ because it ______ (does or does not) hydrogen bond with nucleotide bases. 29. What is the structure of bacterial DNA and how many chromosomes are present? 30. True or False. All DNA inside eukaryotes is linear. 31. True or False. The more DNA in a cell, the more complex the organism. 32. _______ is when one strand crosses over another strand whereas ______ is when the helix crosses over itself. A ________ fold creates a left-handed helix. University of Oklahoma BIOL/MBIO 4843/5843 Dr. Vitiello

33. A strand of DNA has a linking number of 36 when relaxed. In its current state, it has a Tw = 34 and a Wr = -2. What is the value of ΔL K? 34. True or False. A positive ΔL K indicates that the DNA is overwound. 35. After running a gel electrophoresis, how far would supercoiled DNA travel compared to relaxed DNA? 36. Topoisomerases have 3 main functions. What are they? 37. Unlike type ____ topoisomerase, type ____ topoisomerase utilizes ATP hydrolysis to nick both strands of DNA. Their mechanisms are still relatively similar. 38. The amino acid __________ attacks the phosphodiester bond of DNA and forms a _________________ linkage. It can do this because of the presence of a _______ on its side chain. 39. Each chromosome is made up of two chromatids held together by ________ proteins at the ________________. It is made up of repetitive DNA that has been tightly packed into heterochromatin; this is like DNA of the ____________, which are found at the ends of the chromatids. University of Oklahoma BIOL/MBIO 4843/5843 Dr. Vitiello

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40. At what order of structure does the DNA resemble beads on a string? What proteins form the “beads” and what protein brings them together to initiate the next order of structure? 41. How many histone proteins are found in a single nucleosome? Are they a homooligomer or a heterooligomer? 42. The amino acids _________ and _________ are found in abundance on the histone tails. This is because their ___________ charge interacts with the DNA backbone. 43. The _______________ motif is present in each subunit and serves multiple roles, including holding histone dimers together. It is made up of ____ helices and ____ loops. 44. Which amino acid on what subunit is commonly acetylated and deacetylated? How does acetylation affect transcription. 45. Where does DNA methylation occur? How does this affect transcription? 46. The _____________________ is responsible for loop propagation of the DNA around the histone core. Similarly, _____________ creates a bulge in the DNA that propagates around the histone core. University of Oklahoma BIOL/MBIO 4843/5843 Dr. Vitiello

47. Which histone subunit variant keeps the chromatin transcriptionally active? Which subunit variant is utilized for DNA repair and how does it recruit the repair enzymes? 48. How is transcription affected by the presence of trimethylation in the Chutake et al. paper? 49. Friedrich’s Ataxia causes a reduced occupancy of CTCF. This binding factor acts as a(n) _________ that prevents the spread of ___________________. 50. True or False. Individuals with FRDA have a lower-than-normal presence of GAA repeats in the FXN gene, resulting in transcriptional deficiency. 51. One method to determine RNA secondary structure is by using a primer extension assay. This assay utilizes adducts, denaturation, and reverse transcription. Please detail how it works below. University of Oklahoma BIOL/MBIO 4843/5843 Dr. Vitiello

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