AMINO ACIDS, POLYPEPTIDES, AND PROTEINS

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1 29 09/28/2013 8:30:17 Page 427 APTER 29 AMIN AIDS, PLYPEPTIDES, AND PRTEINS SLUTINS T REVIEW QUESTINS 1. The designation a (alpha) means that the amine group in common amino acids is connected to the carbon immediately adjacent to the carboxylic acid. The designation, L, means that the common amino acids all have a specific configuration around the a-carbon. The amine group is on the left when the amino acids are written in a standard Fischer projection formula N ( 2 ) 4 3 N 2 N 2 I, isoleucine K, lysine 3. The amino acid, lysine (K), has a p of 9.7 at its isoelectric point. This p fits into the range of 7.8 to 10.8 found for basic amino acids. 4. The zwitterion form of isoleucine (I) follows: N 3 This is a zwitterion because the compound is ionized but the charges cancel so that the overall charge is zero at its isoelectric point. 5. Amino acids are amphoteric because the carboxyl group can react with a base to form a salt, or the amine group can react with an acid to form a salt. They are optically active because the alpha carbon is chiral, except for glycine. They commonly have the L configuration at carbon two, as in L-serine. 6. At its isoelectric point, a protein molecule must have an equal number of positive and negative charges. 7. (a) Primary structure. The number, kind, and sequence of amino acid units comprising the polypeptide chain making up a molecule. (b) Secondary structure. Regular three-dimensional structure held together by the hydrogen bonding between the oxygen of groups and the hydrogen of the N groups in the polypeptide chains. (c) Tertiary structure. The distinctive and characteristic three-dimensional conformation or shape of a protein molecule. (d) Quaternary structure. The three-dimensional shape formed by an aggregate of protein subunits found in some complex proteins. 8. The sulfur-containing amino acid, cysteine, has the special role in protein structure of creating disulfide bonding between polypeptide chains which helps control the shape of the molecule

2 29 09/28/2013 8:30:17 Page hapter ollagen is a good structural protein because its three-dimensional structure is held together strongly. Three protein strands are coiled in left-handed helices and then wrapped together in a right-handed helix. This cable construction resists stretching. 10. Ferritin is a good iron storage protein because its three-dimensional structure provides a sack for holding iron atoms. This protein is made up of many subunits that together form a hollow sphere (a quaternary structure) within which the iron is stored. 11. ydrolysis breaks the peptide bonds, thus disrupting the primary structure of the protein. Denaturation involves alteration or disruption of the secondary, tertiary, or quaternary but not of the primary structure of proteins. 12. Amino acids containing a benzene ring give a positive xanthoproteic test (formation of yellow-colored reaction products). Among the common amino acids, these would include phenylalanine, tryptophan, and tyrosine. 13. The visible evidence observed in the: (a) Xanthoproteic test gives a yellow-colored reaction product when a protein containing a benzene ring is reacted with concentrated nitric acid. (b) Biuret test gives a violet color when dilute us 4 is added to an alkaline solution of a peptide or a protein. (c) Ninhydrin test gives a blue solution with all amino acids except proline and hydroxyproline, both of which produce a yellow solution when ninhydrin is added to an amino acid. (d) In the Lowry Assay test a dark violet-blue color is produced when a protein contains tyrosine and tryptophan amino acids. (e) In the Bradford Assay test a deep blue color develops when a protein binds to the dye oomassie Brilliant Blue. 14. Protein column chromatography uses a column packed with polymer beads (solid phase) through which a protein solution (liquid phase) is passed. Proteins separate based on differences in how they react with the solid phase. The proteins move through the column at different rates and can be collected separately. 15. (a) Thin layer chromatography is a way of separating substances based on a differential distribution between two phases, the liquid phase and the solid phase. (b) A strip (or sheet) is prepared with a thin coating (layer) of dried alumina or other adsorbent. A tiny spot of solution containing a mixture of amino acids is placed near the bottom of the strip. After the spot dries, the bottom edge of the strip is placed in a suitable solvent. The solvent ascends in the strip, carrying the different amino acids upwards at different rates. When the solvent front nears the top, the strip is removed from the solvent and dried. (c) Ninhydrin is the reagent used to locate the different amino acids on the strip. 16. In ordinary electrophoresis the rate of movement of a protein depends on its charge and size. In SDS electrophoresis a detergent, sodium dodecyl sulfate, is added to the protein solution, which masks the differences in protein charges, leaving the separation primarily due to the size of the various proteins. 17. Simple proteins contain only amino acids in their structure. onjugated proteins contain another substance in their structure

3 29 09/28/2013 8:30:17 Page hapter All amino acids (except one) have a chiral carbon atom. Since all proteins contain amino acids, all proteins will rotate plane polarized light. 19. Another name for a peptide-linkage is an amide bond. 20. The primary structure of a protein is not changed during denaturation. 21. The ribbon structure represents the primary structure without the side chains. The spacefilling structure represents the entire protein structure

4 29 09/28/2013 8:30:17 Page hapter 29 - SLUTINS T EXERISES 1. 2 N N 2 2 L-serine 2 D-serine The primary alcohol group causes serine to be hydrophilic and, thus, this amino acid prefers to be on the surface of proteins where it can interact with water. 2. N 2 2 N 2 2 L-phenylalanine D-phenylalanine The benzene ring causes phenylalanine to be hydrophobic and, thus, this amino acid prefers to be inside proteins and away from water. 3. Basic. The amine functional group allows the amino acid side chain to accept a proton under physiological conditions (p of about 7). Thus, this amino acid would be classed as basic and also as positively-charged. 4. Polar, uncharged. The amide functional group causes the amino acid side chain to be polar but uncharged. 5. Pro = proline + N 2 6. Gln = glutamine. N N

5 29 09/28/2013 8:30:17 Page hapter For phenylalanine: 8. For tryptophan: At a very acidic p, the dipeptide will carry two positive charges. The amine end of the dipeptide and the side chain of the arginine will be protonated. 3 2 N + N 2 N N + N

6 29 09/28/2013 8:30:18 Page hapter At a very basic p, the carboxyl end of the dipeptide will lose a proton and will carry a negative charge. 3 2 N N The two dipeptides containing serine and alanine: 2 3 N 2 N peptide bond Ser-Ala 3 2 N 2 N peptide bond Ala-Ser 14. The two dipeptides containing glycine and threonine: 3 N 2 2 N 3 N 2 N 2 Gly-Thr peptide bond peptide bond Thr-Gly 15. All the possible tripeptides containing one unit each of glycine, phenylalanine, and leucine: GFL GLF FGL FLG LGF LFG 16. All the possible tripeptides containing one unit each of tyrosine, aspartic acid, and alanine: YDA YAD DYA DAY AYD ADY 17. ydrolysis breaks the peptide bonds. ne water molecule will react with each peptide bond, a hydrogen atom attaches to the nitrogen to complete the amino group and an - group attaches to the carboxyl carbon. The tripeptide, Ala-Phe-Asp, will hydrolyze to yield the following:

7 29 09/28/2013 8:30:18 Page hapter ydrolysis breaks the peptide bonds. ne water molecule will react with each peptide bond, a hydrogen atom attaches to the nitrogen to complete the amino group and an - group attaches to the carboxyl carbon. The tripeptide, Ala-Glu-Tyr, will hydrolyze to yield the following: N N 21. Tertiary protein structure is usually held together by bonds between amino acid side chains. Serine side chains will hydrogen bond to each other: hydrogen bond 22. Tertiary protein structure is usually held together by bonds between amino acid side chains. At p ¼ 7, the lysine side chain will contain a positive charge, N þ , and the aspartic acid side chain will contain a negative charge, 2. These two side chains will be held together by an ionic bond: 2 N ionic bond 23. Elastin serves a structural function; it is an integral part of artery vessel walls. The elasticity of this protein allows arteries to flex with changes in blood pressure. Elastin is also a fibrous protein which means that it has an especially strong structure, a characteristic important to its function. 24. Epidermal growth factor (EGF) has a regulatory function. ells change their metabolism in response to EGF. This protein signals cells to grow and differentiate

8 29 09/28/2013 8:30:18 Page hapter (a) There are three alpha helices in trypsin. (b) The space-filling model shows trypsin to be a compact, roughly spherical molecule. Trypsin is a globular protein. 26. (a) The ribbon structure of the epidermal growth factor shows four strands of beta-pleated sheet. (b) The space-filling model shows the epidermal growth factor (EGF) to be a compact protein. EGF is a globular protein. 27. The tripeptide, Gly-Ala-Thr, will (a) react with us 4 to give a violet color. The tripeptide has the required two peptide bonds. (b) not react to give a positive xanthoproteic test because there are no benzene ring compounds in this tripeptide. (c) react with ninhydrin to give a blue solution. (ontains the required amino acids for reaction.) 28. The tripeptide, Gly-Ser-Asp, will (a) react with us 4 to give a violet color. The tripeptide has the required two peptide bonds. (b) not react to give a positive xanthoproteic test because there are no benzene ring amino acids in this tripeptide. (c) react with ninhydrin to give a blue solution. (ontains the required number of amino acids for reaction.) mol Fe 55:85 g Fe 100: g cytochrome c ¼ 1: g 1 mol cytochrome c mol Fe 0:43 g Fe mol 30. The molar mass of cytochrome c is g/mol 4 mol Fe 55:85 g Fe 100: g hemoglobin ¼ 6: g 1 mol hemoglobin mol Fe 0:33 g Fe mol The molar mass of hemoglobin is g/mol 31. The amino acid sequence of the heptapeptide is: Phe - Ala - Gly Gly - Phe - Leu Leu - Ala - Tyr Phe - Ala - Gly - Phe - Leu - Ala - Tyr 32. The amino acid sequence of the heptapeptide is: Phe - Ala - Ala Ala - Leu - Phe Phe - Gly - Tyr Phe - Ala - Ala - Leu - Phe - Gly - Tyr 33. This newly discovered protein is probably a structural-support protein. The high percentage of beta-pleated sheet means that there are many hydrogen bonds holding the protein together in a very stable structure

9 29 09/28/2013 8:30:18 Page hapter This newly discovered protein is probably not a structural-support protein because it is globular in shape and has secondary structure (beta pleated sheet) at its core. Thus, it is more likely to be a binding protein. 35. A domain is a compact piece of the overall protein structure that is relatively small (about the size of myoglobin, for example). A protein with a molar mass of about 452,000 g/mole is likely to have many domains. 36. A domain is a compact piece of protein structure of about 20,000 g/mole. The newly discovered protein with two domains is more likely to have a molar mass between 40,000 and 60,000 g/mole. 37. Alpha keratins have a high percentage of the alpha helix secondary structure. The alpha helix is like a spring in that it is stretchable, so hair is stretchable. 38. The silk protein, fibroin, has a high percentage of the secondary structure, beta-pleated sheet. The secondary structure is like a sheet of paper in that it is flexible but not stretchable. Thus, fibroin is not easily stretched. 39. The amino acid sequence of the nonapeptide is: Arg - Pro Pro - Pro Pro - Gly - Phe Phe - Ser Ser - Pro - Phe Phe - Arg Arg - Pro - Pro - Gly - Phe - Ser - Pro - Phe - Arg 40. A binding site has attractive forces and a specific shape that selectively binds a particular biochemical. 41. Most fibrous proteins provide structural support. For example, connective tissue (e.g., tendons), skin, and blood vessel walls all are strengthened by fibrous proteins. 42. Transport proteins carry chemicals from one place to another. In general, motion proteins move cells or organisms from one place to another. emoglobin is an example of a transport protein that moves oxygen from the lungs to the tissues. Myosin is an example of a motion protein that allows muscles to contract. 43. The steroisomers of threonine: N 2 2 N N 2 2 N The immunoglobulin hypervariable regions allow the body to produce millions of different immunoglobulins. Each immunoglobulin has a unique antigen binding site and two hypervariable regions with distinct amino acid sequences

10 29 09/28/2013 8:30:18 Page hapter (a) (b) (c) The net charge on lysine at p ¼ 9.0 would be positive [see the structure of lysine in part (b)]. 46. Nineteen dipeptides can be written with glycine on the N-terminal side. Another nineteen are possible with glycine on the -terminal end. Finally, one dipeptide can be written with two glycines giving a total of thirty-nine dipeptides. 47. Vasopressin will have a higher isoelectric point than oxytocin. Vasopressin has two different amino acids as compared with oxytocin, a phenylalanine instead of an isoleucine and an arginine instead of a leucine. Thus, vasopressin has one additional basic amino acid (arginine) which will cause the vasopressin isoelectric point to be higher than the oxytocin isoelectric point (a) Glutamic acid is the only one of these three amino acids with two polar bonds in its side chain. Thus, glutamic acid will be the most polar. (b) (c) (d) Dopamine does not have a chiral carbon and thus, does not exist as a pair of stereoisomers. Norepinephrine contains a primary amine while epinephrine contains a secondary amine