Amino Acid - Organic Chemistry of Biological Molecules - Solved Exam, Exams of Organic Chemistry

Download Amino Acid - Organic Chemistry of Biological Molecules - Solved Exam and more Exams Organic Chemistry in PDF only on Docsity! AA.1 Practice Problems on Amino Acids and Peptides 1. Which one of the following is a standard amino acid found in proteins? 2. Which one of the following amino acids is least likely to be naturally occurring? O2C NH3 HSH2C H CO2 CH2SH NH3H CH2CH2SCH3 H CO2 NH3 CO2H3N CH2CH2SCH3H CH2SH HH3N CO2 A B C D E 3. Amino acids are amphoteric. Which statement best describes the definition of the term amphoteric? A) Amino acids exist as a zwitterion in the solid state B) Amino acids possess both acidic and basic functional groups C) An aqueous solution of an amino acid will conduct electricity D) Amino acids are soluble in water E) Amino acids are colourless NH2 CH2 CH2 COOH CH3 CH SO3H NH2 Ph CH2 CH COOH (CH3)2N N COOH CH2OH CH H2N COOH a) c) e) b) d) AA.2 4. Ninhydrin reacts with most -amino acids to produce a purple compound. Which structure is not reasonably involved in the formation of the compound? O O N CO2 R OH O N R O O N O O N O O NH2 OH O NH2 E A B C D 5. All but one of the natural amino acids react with ninhydrin (I) to give a purple pigment (II). Which one of the five listed will not react with ninhydrin to give II? Asp Cys Met Pro Leu 6. In order to work out the structure of a protein, a necessary first step is to analyze for the amounts of each amino acid contained in it. The amino acid analyzer developed for this purpose involves which one of the following? A) A set of twenty specific enzymes, one to react with each amino acid, producing a characteristic color reaction. B) Separating the amino acids by paper chromatography and then converting the spots to colored derivatives. C) Converting the amino acids to colored derivatives and then separating them by column chromatography. D) Converting the amino acids to colored derivatives and then separating them by paper chromatography. E) Separating the amino acids by column chromatography and then doing a color reaction to measure the amount of each. O O O O O N O O I II AA.5 12. Which form of arginine is most likely to exist at pH = 1? H3N CH C CH2 OH O H2C CH2 H2N C H2N NH3 H3N CH C CH2 O O H2C CH2 HN C H2N NH2 H2N CH C CH2 O O H2C CH2 HN C H2N NH2 H3N CH C CH2 OH O H2C CH2 HN C H2N NH2 H2N CH C CH2 O O H2C CH2 HN C H2N NH A B C D E 13. Which one of the following statements best describes how the C-terminal amino acid of an oligopeptide is identified? A) The oligopeptide is degraded by acid hydrolysis and amino acids are identified by TLC B) The oligopeptide is treated with carboxypeptidase and, after reaction has occurred, the peptide is analyzed to see which residue has been removed C) The C-terminal amino acid may be derivatized with Sanger's reagent and identified after oligopeptide hydrolysis by chromatography D) Carboxypeptidase is used to degrade the peptide, the first amino acid to be released is identified by running amino acid analyses at regular time intervals E) None of the above 14. A pentapeptide was found to have the composition Ala Arg Gly Pro Trp. Reaction of the pentapeptide with Sanger’s reagent, followed by hydrolysis, gave the DNP derivative of proline. Treatment of the pentapeptide with carboxypeptidase initially produced alanine. Treatment of the pentapeptide with trypsin gave a tetrapeptide which, when treated with chymotrypsin, produced a tripeptide. Which one of the following is the sequence of the pentapeptide? (note: trypsin cleaves after basic amino acids) A) Pro Gly Arg Trp Ala B) Pro Arg Gly Trp Ala C) Pro Trp Arg Gly Ala D) Pro Gly Trp Arg Ala E) Pro Trp Gly Arg Ala AA.6 15. Dithiothreitol reacts with disulfide bridges in proteins in the same way as 2- mercaptoethanol or thioacetic acid do. When an excess of dithiothreitol is used, what the are the most likely products of this reaction? SH SH HO HO Dithiothreitol N-term.-peptide -S-S-peptide -C-term.+ ? SS HO OH HS HS OH O S S HO HO S S HO HO S SH HO HO + S-peptide-C-term + + + HS S OH OH SN-term-peptide- S S OH OH N-term.-peptide-SH + HS-peptide-C-term. N-term.-peptide-SH + HS-peptide-C-term. S-peptide-C-term.SN-term.-peptide- S-peptide-C-term. SH SH HO OSN-term.-peptide- A B C D E 16. Which one of the following hydrogen bonds (shown as dotted bonds) best represents the type of hydrogen bond that keep the -helix and the -sheet from falling apart? A) O-H·····O=C B) O-H·····NH=C C) N-H·····NH=C D) N-H·····O=C E) N·····H-N=C AA.7 17. Oxytocin, a hormone peptide of nine amino acids, is widely used in obstetrics to induce uterine contractions. There is an intramolecular disulfide bond which must be reduced before sequencing. Reduced oxytocin has the composition Asn Cys2 Gln Gly Ile Leu Pro Tyr Partial hydrolysis of reduced oxytocin led to the following fragments Asn-Cys Cys-Tyr Tyr-Ile-Gln Cys-Pro-Leu Ile-Gln Leu-Gly Gln-Asn-Cys Reaction of reduced oxytocin with carboxypeptidase showed glycine as the first liberated amino acid. Which one of the following is the sequence of oxytocin? A) Asn Cys Tyr Ile Gln Cys Pro Leu Gly B) Gln Asn Cys Tyr Ile Cys Pro Leu Gly C) Cys Pro Gln Asn Cys Tyr Ile Leu Gly D) Cys Tyr Ile Gln Asn Cys Pro Leu Gly E) Gln Asn Cys Tyr Ile Cys Pro Leu Gly AA.9 21. An oligopeptide was analyzed. Given the data below, what is its sequence? AA analysis revealed the composition Asp Asn Glu2 Gly Lys Met2 Phe Pro2 Carboxypeptidase digestion gave the results shown in this plot Gly Asp Met Asn Sanger N-terminal analysis afforded the DNP derivative of glutamic acid Treatment of the peptide with cyanogen bromide gave three fragments. Sanger N-terminal analysis of these three fragments gave the DNP derivatives of Glu, Pro, and Asp. Cleavage of the oligopeptide with trypsin gave two fragments. Sanger analysis of these two fragments both gave the DNP derivative of Glu Cleavage of the oligopeptide with chymotrypsin gave two fragments. Sanger analysis of these two fragments gave DNP derivatives of Glu and Lys. A) Glu Pro Met Pro Gly Lys Phe Met Asp Asn Glu B) Glu Met Pro Pro Phe Lys Gly Asp Met Asn Glu C) Gly Asp Met Asn Glu Pro Pro Met Phe Lys Glu D) Glu Met Pro Pro Phe Lys Glu Asn Met Asp Gly E) Glu Pro Met Pro Lys Phe Glu Asn Met Asp Gly AA.10 22. The compound shown on the right is the phenylthiohydantoin derivative of which amino acid? A) Alanine B) Phenylalanine C) Cysteine D) Proline E) Cannot tell, because every amino acid forms the same compound 23. Which statement about the group marked by { in the structure shown is most correct? A) It makes the amino acid coloured and easier to detect B) It acts as an activating group, making peptide bond formation easier C) It acts as a protecting group, keeping the NH2 of the amino acid from reacting as a nucleophile D) It acts to protect the amino acid against destruction in acid E) It provides a thermodynamic driving force for peptide bond formation, by releasing CO2 24. In Merrifield's method for protein synthesis, the polymer is used… A) To keep the growing peptide soluble B) To provide a suitable "solvent" for the reactions C) To prevent undesired side reactions by limiting access by reagents to the peptide chain D) To make the growing peptide insoluble but accessible E) To provide essential catalytic groups SCH3 CH2 CH2 CH COOHNH CO O C CH3H3C CH3 HN N S O AA.11 25. Which one of the following compounds will NOT cleave on mild treatment with CF3COOH? 26. Which statement about the Merrifield synthesis of proteins is incorrect? A) The method relies on synthesizing the polypeptide as an insoluble polymer bound chain, which can be separated from any solvents or reactants by filtration B) The method is conveniently automated, with bottles of all 20 protected amino acids and the various solvents and reagents connected to a reaction vessel through computer controlled valves C) Adding another residue involves the use of DCC to form an amide bond between the terminal COOH of the growing chain and an amino acid with the COOH protected. D) It is possible to use excess amounts of reagents to push reactions to completion, because the excess can be removed by filtration. E) The final product peptide can be removed from the polymer by treating with strong acid, typically HBr. R NH C O O C CH3 CH3 CH3 R NH C O O C CH3 CH3 R NH C O O C CH3 CH3 OCH3 R NH C O O C CH3 CH2 OCH3CH2CH2CH2 O OCNHR a) b) c) d) e) AA.14 33. Given the average strength of a hydrogen bond is 5 kcal/mol, what is the overall free energy change ( G) of the following reaction? + OH2 HOHO OH H3C4 HOH OH2 + O OH O HO O HO CH3 O OH H3C OH2 H2O O OHO HO HOH HOH 2 +10 10 0 +5 5 (kcal/mol) 34. Biological molecules often have phosphate or pyrophosphate monoester groups. Which one of the following statements regarding this is least correct? A) The phosphate or pyrophosphate provides a handle for electrostatic binding of the molecule by an enzyme B) Phosphates or pyrophosphates will accept hydrogen bonds, helping give specific binding to enzymes C) In the presence of an enzyme, phosphate and pyrophosphate are good leaving groups at physiological pH D) The introduction of phosphates or pyrophosphates does not require energy E) Phosphates or pyrophosphates are hydrophilic and can make organic molecules water soluble 35. What types of interactions are likely involved in the initial binding of a substrate to an enzyme? Circle all that apply. Hydrophobic interactions Hydrogen bonding Covalent bonding Electrostatic interactions AA.15 36. Which one of the following compounds would you expect to undergo the most rapid acid catalyzed lactonization? 37. Which one of the following reactions gives a poor yield of the product shown when a condensation reagent, such as DCC, is added to the reactant(s)?? HOHO O O O HOHO O OHO O OHO OH O NH O N 2 CO2H OH O O E HO O H2N H2N O + + O H N NH2O A B C D A B C D E OH COOH OH COOH OH COOH HO COOH OH COOH AA.16 38. The active site of an enzyme is shown on the right. The binding of which of substrates A – E would result in the most positive G of reaction? A) SH CH3 O NH2 B) NH3 OH C) NH3 OH D) OH E) NH3 NH3 39. Which one of the peptide bonds in the molecule shown would be hydrolyzed the fastest with chymotrypsin? A B C D E (CH2)4 NH NH O COOH CH2 NH O NH2 (CH2)4 NH OCH2 NH OCH3 NH O CH2NH NH2H2N O NH CH2 O H N COO OH