Organic Chemistry - Problem Drill 23: Amino Acids, Peptides, and Proteins

Transcription

1 rganic Chemistry - Problem Drill 23: Amino Acids, Peptides, and Proteins No. 1 of Which amino acid does not contain a chiral center? (A) Serine (B) Proline (C) Alanine (D) Phenylalanine (E) Glycine Serine does have a chiral α-carbon. Go back and review the different amino acids to find the one that is achiral. Proline does have a chiral α-carbon. Go back and review the different amino acids to find the one that is achiral. Alanine does have a chiral α-carbon. Go back and review the different amino acids to find the one that is achiral. Phenylalanine does have a chiral α-carbon. Go back and review the different amino acids to find the one that is achiral. E. Correct! Glycine does not have a chiral α-carbon. Its α-carbon has two hydrogens bonded to it. (1) Recall the structures of the amino acids. Alpha-amino acids all have the same general structure (where R is the individual side chains): H 2 N R * H H The carbon marked with a star is the α-carbon. In 19 of the 20 α-amino acids, the α-carbon is bonded to four different groups making it a stereocenter. For one amino acid, however, R is a hydrogen making its α-carbon achiral. The achiral amino acid is glycine. (2) Read each choice and choose the correct answer. Therefore, the correct answer is (E).

2 No. 2 of Which amino acid has the one letter code of K? (A) Lysine (B) Phenylalanine (C) Valine (D) Threonine (E) Serine A. Correct! Lysine was given the one letter code of K. Phenylalanine has the one letter code of F. Go back and review the codes given to the amino acids. Valine has the one letter code of V. Go back and review the codes given to the amino acids. Threonine has the one letter code of T. Go back and review the codes given to the amino acids. Serine has the one letter code of S. Go back and review the codes given to the amino acids. (1) Recall the letter codes for amino acids. There are two systems of letter codes for amino acids. ne system uses three letter abbreviations for each amino acid and the other uses just one letter abbreviations. The question asked about the one letter code of K. As with the structures of the amino acids, the three letter code system and the one letter code systems have to be memorized. You are likely to be asked about either system so you should be familiar with both. The one letter code of K corresponds to the amino acid lysine. Therefore, the correct answer is (A).

3 No. 3 of What is the name of the amino acid below? H H 2 N C C H CH 2 CH 2 CH 2 NH C NH NH 2 (A) Asparagine (B) Histidine (C) Arginine (D) Lysine (E) Phenylalanine Asparagine contains an amide in its side chain. Go back and review the structure of the amino acids. Histidine has an imidazole ring in its side chain. Go back and review the structure of the amino acids. C. Correct! Arginine has a guanidino group in its side chain making it one of the basic amino acids. Lysine has an amino group in its side chain. Go back and review the structure of the amino acids. Phenylalanine has a benzyl group in its side chain. Go back and review the structure of the amino acids. (1) Recall the different amino acid structures. The amino acid shown is arginine. It is the only amino acid with a guanidino group in its side chain. There are a number of things regarding amino acids you should know prior to taking an exam on them. You need to know the structure of all 20 amino acids, what category the side chain is a part of (aliphatic, acidic, basic, etc.), the three letter abbreviation for each amino acid and the one letter abbreviation for each amino acid. Putting this information of flash cards is usually very helpful to students. Therefore, the correct answer is (C).

4 No. 4 of Which statement about amino acids is incorrect? (A) All amino acids incorporated into proteins are in the D-form. (B) There are twenty α-amino acids. (C) In a neutral solution, amino acids are zwitterionic, with a positive charge on the amino group and a negative charge on the carboxylic acid group. (D) The amino acids each have a unique side chain that varies in several ways including size, shape, hydrogen bonding capacity and affinity for water. (E) All but one of the amino acids are chiral due to their α-carbons having four different groups on them. A. Correct! All amino acids incorporated into proteins are in the L-form. (Carbohydrates used in the body are in the D-form.) There are twenty α-amino acids though humans can synthesize only about half of them. Go back and review the information on amino acids in the tutorial. The amino and carboxylic acid groups in amino acids can protonated or deprotonated respectively while in solution. This process leads to a zwitterion in neutral solution where the amino group is positively charged and the acid group is negatively charged. Go back and review the information on amino acids in the tutorial. Each of the amino acids side chains are unique and vary in many ways including size, shape, hydrogen bonding capacity, and their affinity for water. Go back and review the information on amino acids in the tutorial. nly the residue glycine is achiral due to its α-carbon having two hydrogens on it. Go back and review the information on amino acids in the tutorial. (1) Recall the infomation on amino acids in the tutorial. All amino acids incorporated into proteins are in the L form. There are twenty α-amino acids. The amino acids each have a unique side chain that varies in several ways including size, shape, hydrogen bonding capacity and affinity for water. Due to their α-carbons having four different groups on them, most amino acids are chiral. Glycine is the only amino acid that is achiral. And in a neutral aqueous solution, amino acids are zwitterionic, with a positive charge on the amino group and a negative charge on the carboxylic acid group. (2) Read each statement carefully and choose the one that incorrect. Therefore, the correct answer is (A).

5 No. 5 of How many peptide bonds are in the peptide chain below? H 2 N CH C CH 3 N H CH C CH 2 H N H CH C H CH H CH 3 (A) 1 (B) 2 (C) 3 (D) 4 (E) 5 There is more than one peptide bond in this tripeptide. Go back and review the structure and formation of peptide bonds. B. Correct! There are three amino acids in this tripeptide that are bonded together with peptide bonds (amide linkages). There are two peptide bonds in the structure. Remember, the number of peptide bonds is always one less than the number of amino acids in the chain. There are less than 3 peptide bonds in this tripeptide. Go back and review the structure and formation of peptide bonds. There are less than 4 peptide bonds in this tripeptide. Go back and review the structure and formation of peptide bonds. There are less than 5 peptide bonds in this tripeptide. Go back and review the structure and formation of peptide bonds. (1) Determine the number of peptide bonds in the molecule. You can approach this problem two ways. In the first, you can count the number of amino acid residues that are present in the peptide. There are three amino acids. You learned in the tutorial that the number of peptide bonds is one less than the number of amino acid residues present so that must mean there are 2 peptide bonds in this molecule. In the second approach, you can count the number of amide bonds in the molecule because all a peptide bond is, is a bond between a carbonyl group and an amine. We have seen this before when studying the functional group of amides. Therefore, the correct answer is (B).

6 No. 6 of What is the name of the process below? H H 2 N CH C H + H 2 N CH C H H 2 N CH C N CH C H + H 2 CH 2 CH 3 CH 2 CH 3 SH SH (A) reductive amination (B) hydrolysis (C) amidation (D) amino acid synthesis (E) oxidative addition Reductive amination is the process of taking a carbonyl compound and transforming it to an amine. Go back and review the reactions of peptides. Hydrolysis is the process of adding water to an amide to reform the carboxylic acid and the amine. Hydrolysis is the reverse process of the one shown. Go back and review the reactions of peptides. C. Correct! Amidation is the process of substituting an amine onto a carboxylic acid to form an amide. Amino acid synthesis is the making of amino acids. Here the amino acids are being joined together in a different process. Go back and review the reactions of peptides. xidative addition is a reaction known in organometallic chemistry and has no bearing on peptide synthesis. Go back and review the reactions of peptides. (1) Look at the equation and determine the process that is occurring. In the above equation, a new peptide bond is being formed between the acid group of one amino acid and the amine group of the second amino acid. (2) Recall the types of reactions listed as choices. Reductive amination is the process of taking a carbonyl compound, like a ketone, forming the imine and then reducing the imine to give an amine as the final product. We learned this synthesis of amines in the amine tutorial. Hydrolysis is the process of deconstructing a molecule usually by its reaction with water. Hydrolysis of a peptide occurs when the peptide bonds are broken to give an acid and amine as the final products. Amino acid synthesis involves constructing amino acids. xidative addition is a reaction known in organometallic chemistry and has no bearing on peptide synthesis. Amination is the process of substituting an amine onto a carboxylic acid to form an amide. That is the process occurring in this reaction. Therefore, the correct answer is (C).

7 No. 7 of How many amino acids are in an oligopeptide? (A) 1-10 (B) (C) (D) more than 30 (E) All of the above. Peptide chains that consist of 1-10 amino acids are often named using numerical prefixes followed by the word peptide. Example: A chain of 3 amino acids is called a tripeptide. B. Correct! ligopeptides (oligo is from the Greek for little/few) consist of amino acids. Most peptide chains that consist of 20 or more amino acids are often called polypeptides. Go back and review the classification of peptides. Most peptide chains that consist of 20 or more amino acids are often called polypeptides. Go back and review the classification of peptides. By definition, oligopeptides consist of a finite number of amino acid residues. Go back and review the classification of peptides. (1) Recall the definition of oligopeptide. An oligopeptide is a peptide consisting of between amino acids. (2) Read each choice and choose the correct one. Therefore, the correct answer is (B).

8 No. 8 of Which statement regarding the common peptide structural motif below is incorrect? (A) This motif is representative of the α-helix, a secondary structure element in peptides. (B) The helical structure is due to hydrogen bond formation between the carbonyl and NH groups on amino acids that are three residues apart. (C) Each end of the coil will have an unbound amine group on it. (D) There is a handedness to the coil s configuration (it is chiral). (E) There are 3.6 amino acid residues per turn. This drawing is a representation of an α-helix which comprises secondary structure in peptides. Go back and review different types of protein structure. Hydrogen bond formation is responsible for the helical structure found in many peptides. The hydrogen bonds form between carbonyls and amine groups in the next turn of the coil. Go back and review the secondary structure of proteins. C. Correct! ne end of the helix will have an unbound amine group but the opposite end will have an unbound carboxylic acid group on it. An α-helix is chiral and appears to look like thread on a right handed screw. Go back and review the secondary structure of proteins. There are 3.6 residues per turn of a helix. Go back and review the secondary structure of proteins. (1) Recognize the peptide structural motif. It is an α-helix. (2) Recall the theory behind α-helices. Alpha-helices are a secondary structural element in peptides. ne end of the helix has an unbound amine group on it while the other end will have an unbound carboxylic acid group on it. The helical structure is due to the formation of hydrogen bonds between residues. Usually they occur between a carbonyl group and a NH group on amino acids that are three residues apart. There is a handedness to the coil making α-helices chiral. And lastly, there are 3.6 amino acids per turn. (3) Read each statement carefully and choose the statement that is incorrect. Therefore, the correct answer is (C).

9 No. 9 of Which level of protein structure describes the complete 3-D structure of polypeptide units of a given protein? (A) Primary structure (B) Secondary structure (C) Tertiary structure (D) Quaternary structure (E) None of the above. Primary structure is the linear order and number of amino acids present. Go back and review protein structure. Secondary structure is the regular conformational forms conferred on the protein by hydrogen bond formation between residues. Go back and review protein structure. C. Correct! Tertiary structure is the complete 3-D structure of a polypeptide. Quaternary structure describes proteins containing several distinct polypeptide chains along with nonprotein groups. Go back and review protein structure. The correct answer may be found in the above choices. Go back and review protein structure. (1) Recall the four level of protein structure. Primary structure is the linear order and number of amino acids present. Secondary structure is the regular conformational forms conferred on the protein by hydrogen bond formation between residues. Tertiary structure is the complete 3-D structure of the polypeptide units of a protein. And lastly, quaternary structure describes proteins containing several distinct polypeptide chains along with nonprotein groups. (2) Re-read the question carefully and choose the correct answer. Therefore, the correct answer is (C).

10 No. 10 of What is the name of a protein whose quaternary structure consists of four identical polypeptide chains? (A) Homotetramer (B) Heterotetramer (C) Homopentamer (D) Heterodimeric protein (E) Homogeneous A. Correct! When a protein consists of four identical polypeptide subunits, it is considered to be a homotetramer. A heterotetramer is a protein that consists of 4 subunits that are not all identical. Go back and review the quaternary structure of proteins. A protein that consists of five identical polypeptide segments is called a homopentamer. Go back and review the quaternary structure of proteins. A protein that consists of two different sets of dimers is a heterodimeric protein. Go back and review the quaternary structure of proteins. Homogeneous refers to a solution that is the same throughout. Go back and review the quaternary structure of proteins. (1) Recall the way quaternary structure is described in the tutorial. Proteins consisting of multiple polypeptide chains can be referred to in terms of the types and numbers of those chains present. Here we have four chains in the protein. The numerical prefix tetra- is placed with the suffix mer to form tetramer. Since the chains are identical, the structure is homogeneous so the prefix homo- is added to tetramer. If the chains had been different, it would have been called a heterotetramer. A homopentamer is a protein consisting of 5 polypeptide chains all of which are identical. A heterodimeric protein consists of two different dimers. Therefore the correct answer is (A).