DES Group 7 -- Session No.

1 Friday 31 August 2012 Group Facilitator: Scott Dougan Choose the BEST answer(s) for each question

1) Vidarabine -- an adenosine analog -- gets converted to a triphosphate by viral thymidine kinase, after which the triphosphate can serve as a substrate for viral DNA polymerase. A) Camptothecin; Adenosine B) Etoposide; Cytosine C) Vidarabine; Adenosine D) Acyclovir; Thymidine E) Azithromycin; Uracil Remember, vidarabine is just adenosine arabinoside = adenosine with an arabinoside group. 2) Why does this drug cause chain termination in viral DNA replication? The steric hindrance from the arabinoside group due to arabinosides planar configuration prevents DNA elongation by Pol III once its been incorporated. 3) In eukaryotic cells undergoing DNA replication, _____________ is used to remove the RNA primers. (circle all that apply) A) FEN-1 B) DNA Pol I C) DNA Pol II D) DNA Pol III E) RNaseH F) Primase G) DNA Helicase (DNaB) (Bonus: Which enzyme is it in prokaryotes?) DNA Pol I is the prokaryotic RNAse; it removes the RNA primer, and does this in a forward manner, i.e. in the 5`3` direction.

DNA Pol III is the main enzyme of 5`-3` DNA synthesis, but it is also involved with 3`-5` exonuclease activity, or DNA proofreading. The function of DNA Pol II is uncertain.

4) What cofactor(s) do prolyl hydroxylase and lysl hydroxylase need to function? What disease do you get if theyre missing? Vitamin C (also known as Ascorbate if they want to try and trick you); the notes also remark that molecular oxygen, ferrous iron (Fe2+) and alpha-ketoglutarate are cofactors, and the entire complex produces succinate (a TCA cycle intermediate) and CO2. 5) The hydrophilic sequences of ELASTIN are rich in lysine and alanine, while the hydrophobic sequences are rich in glycine, valine, and proline. 6) Over the past six months Harold Crick has been experiencing chronic arterial aneurysms in his circle of Willis (located in the brain) and aorta; you suspect a defect in connective tissue production. What essential metabolite might he be missing, and what enzyme is affected? Cu2+; copper (II) is an essential cofactor for lysyl oxidase, the enzyme that forms allysine from lysine. Remember that 3 allysyl side chains plus 1 unaltered lysyl side chain from the same or neighboring polypeptides form a desmosine cross-link. Desmosine is responsible for the rubbery properties of elastin. 7) The Marlboro man comes to your clinic. He presents with dyspnea and irritability (dyspnea = shortness-of-breath). You perform an arterial blood-gas measurement revealing pH 7.25, PCO2 68, and HCO3- 31 mmol/L. (Normal ranges pH 7.36-7.44, PCO2 38-42 mmHg, HCO3- 22-25 mmol/L). He is experiencing: A) Uncompensated metabolic acidosis B) Uncompensated metabolic alkalosis C) Compensated metabolic acidosis D) Compensated respiratory acidosis E) Uncompensated respiratory acidosis 8) Dr. Leonard McCoy comes into your clinic complaining of severe nausea and weakness. He presents with a history of peptic ulcer disease and has been experiencing gastric pain for the past two weeks. He has been self-medicating with large quantities of over-the-counter calcium carbonate antacids, and appears to be breathing very slowly and deeply. You perform an arterial blood-gas measurement revealing a pH of 7.46, PCO2 50, and HCO3- 35. He is experiencing: A) Uncompensated metabolic alkalosis B) Compensated metabolic alkalosis C) Compensated metabolic acidosis D) Compensated respiratory alkalosis E) Uncompensated respiratory acidosis

9) Your friend experiences a paper cut and notices her blood has a curious chocolate color. Fresh from your first semester of medical school, you accurately diagnose her as having methemoglobinemia which occurs because: Oxidation of the iron in the heme from Fe2+ to Fe3+ (ferrous to ferric iron) causes the anemia and the color change (chocolate cyanosis). The oxidation can come from some drugs (like nitroglycerin) or reactive oxygen species (free radicals), which suck away that extra e- from the Fe. 10) A patient with a congenital hexokinase deficiency would experience reduced 2,3-BPG levels which would result in a left shift on the Hb-O2 binding curve and an increased blood hemoglobin O2 affinity. Less 2,3-BPG means fewer intermolecular ionic bonds keeping the and Hb subunits clamped down to each other, which means its easier for O2 to associate with the hemoglobin. When O2 loads on Hb the Hb becomes known as oxyhemoglobin. 11) In sickle-cell anemia resulting in production of hemoglobin S (HbS), the amino acid glutamate at position 6 is replaced by the amino acid valine at position 6. All of this is occurring on the beta chain. 12) Histones are particularly rich in two amino acids. What are the names of these two? Why are they useful in making chromatin? Lysine and arginine. These are the two positively charged (cationic) amino acids; their positive charges attract the negatively-charged DNA, and allow the DNA to wrap around histones to form chromatin [chromatin = DNA + protein (histones)] 13) The octomer of the nucleosome is made up of the core histones: 2 molecules each of H2A, H2B, H3 and H4 146 bp of DNA associate.

14) The drug decitabine causes DNA hypomethylation and increased transcription.

Remember that methylation reduces transcription because the chromatin is all compact and balled up; acetylation and demethylation both open up the chromatin (make it more euchromatic); deacetylation and methylation both close down chromatin, making it more heterochromatic and more difficult to transcribe. The reason decitabine is an anti-cancer drug is that it hypomethylates DNA of the gene p15INK4b. p15INK4b is an anti-cancer gene, in that it prevents a normal cell from turning into a cancer cell by inhibiting cyclin dependent kinases. Decitabine is used in myelodysplastic syndrome and acute myeloid leukemia.