BCHM 461_0101 Name______________________________________ 1March 7 2017Dr. Paul PaukstelisExam 1Exams written in pencil or erasable ink will NOT be re-graded under any circumstances.The University of Maryland Honor PledgeThe Honor Pledge is a statement that University of Maryland students are required to agree to onall examinations.The Pledge reads:I pledge on my honor that I have not given or received any unauthorized assistance on this examination.After you have completed this examination, sign your name to acknowledge that you agree to thispledge.BCHM 461_0101 Name______________________________________ 2March 7 2017Dr. Paul PaukstelisExam 1(100 points)1) (20 points ) Bioenergetics and Nucleic Acidsa. For both GMP and dGMP, the standard free energy change (DG'o) for the conversion from Pucker A to Pucker B (shown below) is a very small (though non-zero) value. In just one or two sentences explain what this would mean (generally) about the distribution of these different sugar puckers in an equilibrated solution and why.b. In the box provided, identify the sugar puckers using the appropriate naming scheme. In-plane atoms are shown by the line running (roughly) through their centers!c. When the DG'o for the same pucker conversion is determined for GMP and dGMP, now as part ofa nucleotide chain that forms an RNA or DNA duplex, the value is negative for dGMP, but muchmore positive for GMP. In two or three sentences, describe a likely reason for this in the context ofthe duplex structures.BCHM 461_0101 Name______________________________________ 3March 7 2017Dr. Paul Paukstelis2)(30 points) Acid-Base Chemistry and Amino Acidsa. Homocysteine (shown below in its non-ionized form) is an amino acid similar to cysteine. ThepKa's for the L-homocysteine functional groups are similar, but distinct from those of L-cysteine. Thechart below shows a comparison. Provide analysis for WHY these are different. You may draw orreference the image if that assists you, but make sure your answer is specific.pK1 (COOH) pK2 (NH3+) pKRL-cysteine 1.96 10.28 8.18L-homocysteine 2.3 9.0 10.0b. You are working with a peptide of the sequence: TAGYERIT1. Using the method we used in class, estimate the isoelectric point of this peptide2. When a titration of this peptide is performed, it turns out that the measured isoelectric point is 7.2.Based on this:a. Overall, will the peptide carry a positive or negative charge at neutral pH? Explain your answer ingeneral terms.BCHM 461_0101 Name______________________________________ 4March 7 2017Dr. Paul Paukstelisb. Describe two reasons why pI estimates are often times much different than the experimentalvalues. Your answer can be general, but you can use the above peptide to highlight your point.c. This photo was posted on the March for Science (April 22nd on the Mall; see you there) facebookgroup a couple of days ago. Identify three things that are wrong with this drawing and justify eachof them with one sentence in the space provided. Two are easy, one is harder (stereochemistry isnot one of them) and and single residue can only count for one thing.Thing 1:Thing 2:Thing 3:BCHM 461_0101 Name______________________________________ 5March 7 2017Dr. Paul Paukstelis3) (25 points) ProteinsBelow is a sequence alignment of two related proteins. “Regions” are defined by the boxes of aminoacids and labeled. The alignment is duplicated on the scratch page for you to work on.a. Which region has the highest similarity and what is it (as a percent or fraction)?b. Which region has the highest identity and what is it (as a percent or fraction)?c. Which region has the lowest similarity and what is it (as a percent or fraction)?d. If Protein 1 were cleaved with chymotrypsin, what is the maximum number of fragments that wouldbe present after complete cleavage?e. Of the peptide fragments generated from the chymotrypsin treatment, which two (write theirsequences out) would likely have the strongest interactions, based solely on the amino acidproperties of those peptides? Justify your answer in one or two sentences.BCHM 461_0101 Name______________________________________ 6March 7 2017Dr. Paul Paukstelis4) (25 points) Thinking questionYou are given solutions of the following macromolecules:Mol. 1 = GUGUCGAUCGAAG, epeak = 170.3 mM-1 cm-1Mol. 2 = GAUCGAAUUUCGAUC, epeak = 191.1 mM-1 cm-1Mol. 3 = AFWLWGGFWP, epeak = 17070 M-1 cm-1Mol. 4 = KTSAQCNAR, epeak = 110 M-1 cm-1All four macromolecules are at equal concentrations and their absorbances are measured in aspectrophotometer. All samples are in a salt solution buffer at pH 7.0 and measured at 4 °C. “Peak”refers to the wavelength with maximum absorbance.A) For the UV absorbance spectra below, assign which molecule is associated with that spectra inthe box, and provide two reasons why you chose that molecule.BCHM 461_0101 Name______________________________________ 7March 7 2017Dr. Paul PaukstelisB) What is the concentration of Mol. 4 (in micromolar) as it is shown above? Show your work.Score:#1_______/20#2_______/30#3_______/25#4_______/25Total: /100BCHM 461_0101 Name______________________________________ 8March 7 2017Dr. Paul PaukstelisTHIS IS A SCRATCH PAGE. DO NOT INCLUDE OR REFERENCE ANSWERS TO THIS PAGE. THEVERY FIRST THING I AM GOING TO DO IS TEAR THIS PAGE OFF AND THROW IT IN ARECYCLING