BCH 4053 Exam I Review Spring 2017

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1 BCH 4053 SI - Spring 2017 Reed BCH 4053 Exam I Review Spring 2017 Chapter 1 1. Calculate G for the reaction A + A P + Q. Assume the following equilibrium concentrations: [A] = 20mM, [Q] = [P] = 40fM. Assume physiological conditions. A J/mol B kJ/mol C J/mol D kj/mol E kj/mol 2. Consider the data below. Use this information to calculate the enthalpy of the system. At room temperature, a reaction exhibits an equilibrium constant of 3.6 and at physiological temperature the same reaction exhibits an equilibrium constant of A kj/mol B kj/mol C kj/mol D kj/mol E. None of the above 3. Consider the reaction where A 2B, at equilibrium the concentration of A is 15 mm, and the concentration of B is 27 mm. Use this information to calculate the value of G at 25 C. A kj/mol B kj/mol C kj/mol D kj/mol E. None of the above 4. Which of the following provided evidence for endosymbiosis? A. Mitochondria B. Chloroplasts C. Ribosomes D. A and B E. A, B and C 5. Which of the following was done by Miller and Urey? A. Created an environment that allowed RNA to catalyze reactions, these RNA enzymes were later coined ribozymes B. Used crystal diffraction patterns produced by Rosalind Franklin to show that DNA was a double helix. C. Subjected simple inorganic molecules to heat and electricity to produce organic compounds, including amino acids D. Developed a system of equations that could be used to calculate the ratio of acid and base in a buffer solution based only on the ph and pk a of the acid E. None of the above is correct The questions in this review packet are just my best guesses for what you may or may not see on your exam. Please do not use this as your only source of studying. You should have read and outlined the required chapters in the book and done ALL the book questions. Also: you should have started studying the first day of class, only studying the night before an exam will likely not serve you well. Best of Luck.

2 BCH 4053 SI - Spring 2017 Reed Chapter 2 6. Erythromycin is an antibiotic commonly used to treat certain infections caused by bacteria, such as Bronchitis; Diphtheria; Legionnaires disease; and Pertussis. It has an empirical formula of C 37H 67NO 13, a molecular weight of approximately 734 amu and a density of 1.21 g/ml. The structure of Erythromycin is shown below. Determine the number of hydrogen bond donors and acceptors the molecule can form. Assume an acceptor is counted as just the atom and not the number of lone pairs. A. Donors: 14 Acceptors: 5 B. Donors: 6 Acceptors: 13 C. Donors: 5 Acceptors: 14 D. Donors: 13 Acceptors: 6 E. Donors: 5 Acceptors: Streptomycin is an antibiotic drug that was the first remedy for Tuberculosis. It belongs to a class of aminoglycosides and was discovered in October of 1943 by Albert Schatz. The structure of Streptomycin is shown below. How many hydrogen bonds can streptomycin donate or accept from surrounding water molecules in an aqueous environment? A. Donors: 16 a. Acceptors: 17 B. Donors: 17 a. Acceptors: 17 C. Donors: 17 a. Acceptors:18 D. Donors: 18 a. Acceptors: 18 E. Donors: 17 a. Acceptors: 17

3 BCH 4053 SI - Spring 2017 Reed 8. Determine the chirality of each stereo center in the molecule shown. A. 1R, 2R B. 1R, 2S C. 1S, 2S D. 1S, 2R E. The molecule is achiral 9. A solution contains 24 mg of sodium succinate (MW= g/mol) and 32 mg of succinic acid (MW=118.09). The K a of succinic acid is 6.31x10-5. Use this information to calculate the ph of a 25 ml solution. A B C D E. None of the above is correct 10. What is the ratio of hydrogen phosphate to phosphate in a solution of if the pka s of phosphoric acid are 2.148, 7.198, and A B C D E What is the maximum number of hydrogen bonds the polypeptide RVHE can donate to surrounding water molecules, in aqueous solution? Assume physiological ph. A. 8 B. 9 C. 10 D. 11 E. 12 Chapter The site of enzyme modification by phosphorylation is the amino acid: A. Arginine B. Leucine C. Phenylalanine D. Serine E. Glycine

4 BCH 4053 SI - Spring 2017 Reed 13. Calculate the isoelectric point for the polypeptide AVHREHPCSQ. A B C D E The polypeptide VFHAILHQER was mixed in a solution buffered to a ph of 4.5. What is the charge of the polypeptide at this ph? A. +1 B. +2 C. +3 D. +4 E. Unable to be determined with the information given. 15. Provide a name for the structure shown. A. 1-methylproline B. 2-methylproline C. 3-methylproline D. 4-methylproline E. 5-methyproline 16. Provide a name for the structure shown. A. 4-hydroxytryptophan B. 7-tryptopanol C. 4-tryptophanol D. 7-hydroxytryptophan E. 3-hydroxytryptophan Chapter Which of the following amino acids would be last to elute at ph 8.0 from an anion-exchange column? A. Lysine B. Alanine C. Glutamic acid D. Asparagine E. Glycine

5 BCH 4053 SI - Spring 2017 Reed 18. The pk 1, 2, and 3 of the amino acid histidine are 1.8, 9.3, and 6.0, respectively. The pk 1, 2, and 3 of the amino acid arginine are 1.8, 9.0, and 12.5, respectively. You have a mixture of histidine and arginine, how would you try to separate these two amino acids? A. Anion exchange chromatography at ph 2.0 B. Anion exchange chromatography at ph 4.0 C. Cation exchange chromatography at ph 2.0 D. Cation exchange chromatography at ph 4.0 E. Cation exchange chromatography at ph Which of the following experimental set ups would be best to separate a solution of leucine, cysteine and arginine? A. Anion exchange column at ph 2.6 B. Cation exchange column at ph 3.9 C. Reverse phase hydrophobic column at ph 3.6 D. Anion exchange column at ph 10.3 E. Cation exchange column at ph The molar absorptivity constant of a particular chemical is 1.5 M -1 cm -1. What is the concentration of a solution made from this chemical that has an absorbance of a 0.72 with a cell path length of 1.1 cm? A mm B mm C mm D. 643 mm E. 436 mm 21. You have purified a new peptide hormone. To determine its amino acid sequence, you have digested it with trypsin and in another reaction you cleaved with cyanogen bromide. Cleavage with trypsin yielded the following fragments as determined by Edman degradation: Ser-Leu Asp-Val-Arg Val-Met-Glu-Lys Ser-Gln-Met-His-Lys Ile-Phe-Met-Leu-Cys-Arg Cleavage with cyanogen bromide yielded the following as determined by Edman degradation: His-Lys-Ser-Leu Asp-Val-Arg-Val-Met Glu-Lys-Ile-Phe-Met Leu-Cys-Arg-Ser-Gln-Met What is the identity of the N-terminal amino acid? A. Aspartic Acid B. Serine C. Histidine D. Glutamic Acid E. Isoleucine

6 BCH 4053 SI - Spring 2017 Reed 22. The salting in of proteins can be explained by: A. Salt counter ions reducing electrostatic attractions between protein molecules B. Proteins attracting primarily salt cations C. Proteins attracting primarily salt anions D. Releasing hydrophobic proteins from nonpolar tissue environments E. Hydration of the salt ions reducing solubility of proteins 23. For the polypeptide YALGIIQAQPDKSESELVSQIIEELIKKEK, predict the electrospray ionization mass spectrum. Assume that the molecular weight of the uncharged peptide is 3400 amu A B C D 24. For the polypeptide MATGSRTSI, how many peaks do we expect to see in the electrospray ionization mass spectrum? A. 1 B. 2 C. 3 D. 4 E. Unable to be determined with the information given.

7 Reed 25. Shown below is the ESI-MS spectrum of hen egg lysozyme. Calculate the molecular weight of the protein. Use peaks 9 and 8 A amu B amu C amu D amu E. Unable to be determined without the charge associated with each peak. 26. The characteristic absorbance at 280nm for proteins is due to A. All amino acids B. Tryptophan and Tyrosine only C. Tryptophan only D. Tyrosine, Tryptophan and Phenylalanine only Chapter Which of the following is the best description and use of NMR in biochemistry? A. Fires a stream of protons at an ionized sample of the compound resulting in a positively charged species that is then detected based off the ratio of its mass and charge. This technique is best used for determining the molecular weight of a sample, typically proteins. B. This technique is performed on samples of protein in solution, similar to how they would exist in their natural environment. Since biochemical molecules are so complex, these experiments are often run in two dimensions to help reduce clutter in the results. The experiment is based off the way nuclei feel a magnetic field and their response to the magnetic field applied.

8 Reed C. A tedious process is used to produce rather fragile crystals of the protein sample. These crystals are then subjected to light allowing a diffraction pattern to be obtained. The diffraction pattern is based on how the sample scatters the light. A series of these diffraction patterns can be used to predict the 3-dimensional structure of the compound. D. This technique requires passing the sample through an instrument containing a resin that interacts with molecules based on their polarity and/or charge. As the strength and type of eluent is altered the compound will begin to leave the instrument. The fractions leaving the instrument can then be captured and analyzed by other methods. E. This technique passes high frequency light through a sample. The sample will absorb the light based on the extent of conjugation in the molecule. The remaining light is then detected and shown in the form of a graph of intensity versus wavelength. This information is often used to roughly estimate the concentration of a protein in a given sample. The residues used for this are Phenylalanine, Tyrosine and Tryptophan. 28. Which of the following is the best description and use of X-ray crystallography in biochemistry? A. Fires a stream of protons at an ionized sample of the compound resulting in a positively charged species that is then detected based off the ratio of its mass and charge. This technique is best used for determining the molecular weight of a sample, typically proteins. B. This technique is performed on samples of protein in solution, similar to how they would exist in their natural environment. Since biochemical molecules are so complex, these experiments are often run in two dimensions to help reduce clutter in the results. The experiment is based off the way nuclei feel a magnetic field and their response to the magnetic field applied. C. A tedious process is used to produce rather fragile crystals of the protein sample. These crystals are then subjected to light allowing a diffraction pattern to be obtained. The diffraction pattern is based on how the sample scatters the light. A series of these diffraction patterns can be used to predict the 3-dimensional structure of the compound. D. This technique requires passing the sample through an instrument containing a resin that interacts with molecules based on their polarity and/or charge. As the strength and type of eluent is altered the compound will begin to leave the instrument. The fractions leaving the instrument can then be captured and analyzed by other methods. E. This technique passes high frequency light through a sample. The sample will absorb the light based on the extent of conjugation in the molecule. The remaining light is then detected and shown in the form of a graph of intensity versus wavelength. This information is often used to roughly estimate the concentration of a protein in a given sample. The residues used for this are Phenylalanine, Tyrosine and Tryptophan.

9 Reed 29. Which of the following amino acids is most likely to be found in the interior of a globular protein? A. Arg B. His C. Asn D. Ala E. Asp 30. Assume that each of the sequences below repeats, which of them are possibly to be found in alpha keratin sequences? I. VERLIHD II. EDLILHY III. MPPVPF IV. WTLILFS A. I and II only B. I and IV only C. I, III, and IV only D. II and III only E. III and IV only 31. What forces stabilize protein tertiary structure? A. Disulfide bonds B. Hydrogen bonds C. Ionic interactions D. Hydrophobic interactions E. All of the above 32. While proteins are usually composed to linear chains of amino acids, branched chains of amino acids and internally covalently cross-linked chains can be found in certain proteins. Polypeptide chains are most commonly covalently linked to each other through: A. Hydrogen bonds B. Glycosidic bonds C. Peptide bonds D. Disulfide bonds E. Ester linkages 33. Which of the following tripeptides would be expected to be the most hydrophobic? A. KYG B. KYA C. GYA D. DYA E. DYG

10 Reed 34. Which of the following amino acids is most likely to disrupt an alpha helix? A. Proline B. Leucine C. Glycine D. Valine E. None of the above 35. Why are antiparallel beta sheets more stable than parallel beta sheets? A. The side chains of the polypeptide are closer in the parallel beta sheet, resulting in Van der Waals radii that encroach between side chains. B. Parallel beta sheets are conformationally similar to alpha helixes and often collapse into the energetically favorable helix. C. The hydrogen bonds of the backbone require a certain distance to achieve the lowest energy state and these hydrogen bonds are maximized in the antiparallel structure D. The conformational mobility required to achieve the parallel beta sheet is restricted to only glycine and proline residues so it doesn t often occur in biological samples. E. None of the above are true. 36. Calculate the contour length of a 20 amino acid fragment folded in an alpha helix. A. 20 Å B. 30 Å C. 40 Å D. 50 Å E. Cannot be determined with the information given 37. Estimate the number of amino acids in the structure shown below. A. 9 amino acids B. 18 amino acids C. 32 amino acids D. 98 amino acids E. 47 amino acids 38. Assume a fragment of two stranded antiparallel beta structure is 34 Å long. What is the approximate number of amino acids in this motif? A. 10 amino acids B. 15 amino acids C. 20 amino acids D. 25 amino acids E. 30 amino acids

11 Reed 39. Which of the following statements concerning the process of spontaneous folding of proteins is FALSE? A. It may be an essentially random process. B. It may be defective in some human diseases. C. It may involve a gradually decreasing range of conformational species. D. It may involve initial formation of a highly compact state. E. It may involve initial formation of a local secondary structure. 40. Which amino acid is likely involved in the cross-link shown below? A. Arginine B. Leucine C. Lysine D. Cysteine E. None of the above 41. For the unfolding reaction of Protein X, H = 210.6kJ/mol, this means that A. Unfolding is favored enthalpically B. Folding is favored enthalpically. C. The entropy is positive at all temperatures, D. The entropy is negative at all temperatures.