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Chem 40.

1 Problem Set II

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I. Modified True or False. Write TRUE if the statement is true. Otherwise, change the underlined word(s) to make the statement true 1. SDS distrupts the covalent interaction of histones and phosphate backbone of DNA. 2. In the isolation of DNA, SDS binds to the DNA, giving it an anionic character. 3. Pectinic acid will form gel in the presence of divalent cations. 4. The principal monosaccharide unit of pectin is D-galacturonate. 5. A solution containing pancreatin + bile salt + oil will consume more NaOH during titration than a solution containing pancreatin + CaCl2 + oil. 6. The action of neutral pepsin on egg white is more efficient if added with soda ash rather than with vinegar. 7. The two main products of saponification of triglycerides are alcohol and carboxylic acid. 8. A higher 280/260 absorbance ratio indicates a more purified DNA extract. 9. In the pectin experiment, a ripe fruit requires a lower V1 that that of an unripe fruit. 10. 1% NaOH inactivates nucleases during alkaline RNA extraction. 11. Nucleic acids are stable at pH 4-6. 12. Migration of nucleic acid in agarose gel electrophoresis is affected by the size and shape of DNA. 13. Na2S2O3 was used to liberate I2 from the unreacted Hanus reagent.

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II. Cause and Effect Determine the effect (increase, decrease or no effect) of the stated condition on the parameter indicated in the parentheses. Briefly justify your answer by using not more than 3 lines of your bluebook. Make sure to leave a space after every number. 1. The EtOH used in RNA extraction was not acidified. (percent yield of DNA) 2. Tris-Borate-EDTA was used as the buffer in the AGE experiment. (migration of DNA) 3. Water instead of Ficoll solution was added in the loading buffer. (resolution of bands) 4. The sample and the blank were refluxed for only 30 minutes. (VHCl used both for the sample and the blank) 5. The oil sample was reacted with KOH at room temperature for 1 hour. (Calculated MW) 6. 0.5 g of oil sample was used instead of 1.0 g. (SN) 7.The gastric juice was contaminated with excess lactic acid (VNaOH to reach topfers endpoint) 8. 0.02 N NaOH was used in the second titration instead of 0.01 N NaOH (Calculated % Methoxy) 9. Heating was not performed during the isolation of RNA from yeast. (% Recovery of RNA)

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1. PECTIN. A pectin sample, isolated from a certain citrus peel, was dissolved in ethanol and CO2-free water. Phenol red reagent was added to the solution and then immediately titrated with 0.10 N NaOH requiring 3.5 mL. 12.00 mL of 0.25 N NaOH was added to the titrated solution and incubated for 30 mins. After which, an equal amount of 0.25 N HCl was added and titration is resumed using 48 mL of 0.010 N NaOH back to its original color. a) Calculate the % methoxy content of the sample. b) Is the sample highly esterified? c) What are the proper conditions for the gelatination of this sample to occur? d) If it was determined that the pectin sample contains 20 units of galacturonic acid, what is the estimated molecular weight of the sample?

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2. SAPONIFICATION NUMBER. A 15-g oil sample with a molecular weight of 4000g/ mol was saponified using alcoholic KOH. 60 mL of 0.765M standardized HCl was used to titrate the saponified sample. a) Calculate the number of moles of reacted KOH in the titration step. b) Calculate the SN of the oil.

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3. IODINE NUMBER. Tingks wants to identify which of the two unlabeled oils is healthier to use for the vegetable salad. He sampled 10 g of each oil and prepared each for titration with 0.15 N Na2S2O3. When the oil solution turned pale yellow, 10 mL of 1 % starch solution was added to each oil and then titrated again with 0.15 Na2S2O3. He obtained the following data:

! Which oil should Tingks used? Support your explanation with calculations. !

Sample Oil A Oil B Blank

Titrant Volume (mL) 12.3 15.8 32.1

4. DIGESTION. a) Deduce the sequence of the original peptide using the following observations.

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The peptide was not hydrolyzed by carboxypeptidases.! A sample was treated with trypsin, and sequencing yielded LFNESR, VIWTLMIK and LYMVR.! Another sample was treated with chymotrypsin and sequencing yielded TLMIKLY, MVRLF and NESRVIW. !

b) What are the fragments formed after treatment with pepsin? Pepsin + !mercaptoethanol? Glu-Gln-Phe-Cys-Cys-Try-Ala-Ser-Val-Cys-Phe-Ser-Leu-Pro I Gln-His-Try-Leu-Cys-Gly-Lys-Cys-Phe-His-Leu-Val-Try-Ala

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5. AGE. Gian bought his favorite chocolate and left it on his table. When he returned, he found it half eaten. To find the culprit, he analyzed the DNA fragment found in the chocolate wrapper. The age profile is shown below.

a. Who ate Gians chocolate?! b. If the equation of the line obtained from the plot of log MW vs distance migrated by the DNA marker was y= -3.704 x 10-3x + 2.365. Find the MW of the 3rd smallest DNA fragment of the culprit !