3-7 CHAPTER 3 REVIEW WKST 1. The study of amino acids will help biochemists to further understand the _______________ and _______________ of proteins. 2. Identify three scientific challenges that may be solved by studying proteins. 3. Identify seven biological functions of proteins. 4. Draw a wedge-and-dash structure for L-isoleucine as it would look in the physiological pH range. Name it using the IUPAC system of nomenclature. Label the carbons using the Greek alphabet system. 5. In 19 of the 20 amino acids, the ___-carbon is chiral. What does it mean to be chiral? Draw the only amino acid that is an exception to this. 6. Why can two stereoisomers not be easily converted from one to the other? 7. Draw the two enantiomers of valine. Identify the one that is biologically favored. This is proof that all species on Earth are descended from a common _______________. What would a mixture of these two enantiomers be called? The predominance of the biologically favored enantiomer is due to the evolution of _______________ pathways that produce that enantiomer instead of the other. 8. The property that helps to determine how proteins fold is called _______________ hydrophobic side chains will be clustered in the _______________ of a protein where hydrophilic are usually found on the _______________. 9. The properties of the side chains greatly influence the _______________ of a protein. 10. Draw a Fischer projection of 2-aminopropanoic acid in its L- form and in its biologically favored form, and identify it by its common name. Replace a hydrogen on the carbon with an isopropyl group and identify it by its common name. 11. Which four aliphatic amino acids play important roles in the 3D structures of proteins because they cluster away from water? 12. Draw and identify the amino acid that has a heterocyclic ring and restricts the _______________ of polypeptides, which can sometimes cause abrupt changes in the _______________ of a peptide chain. 13. Draw the amino acid that is the most hydrophobic of the aromatics, and the two that absorb UV light at 280 nm, which is used in _______________ to estimate the concentration of proteins in solution. 14. Draw the amino acid that is almost always first in a polypeptide chain, and the amino acid that forms disulfide bridges between side chains, _______________ the structures of some proteins by cross-linking their residues. 15. Draw the amino acids that have R groups that can weakly ionize like primary and secondary alcohols. 16. Draw the amino acid that has an imidazole ring, the one that is a diamino acid, and the most basic of the 20 amino acids because its _______________ ion side chain is protonated under all normal cellular conditions. 17. Draw the smallest of the two dicarboxylic acids, the amino acid that is familiar as its monosodium salt, and the two amino acids that are highly polar and found at the surface of proteins. 18. How can amino acids other than the 20 common ones form? Some of them are chemically modified to produce biologically important _______________, and this can happen _______________ they’ve been incorporated into polypeptides. The 21st and 22nd amino acids (_______________ and _______________) are derivatives of what two common amino acids? 19. The physical properties of amino acids are influenced by the ionic states of what two (or three) parts of amino acids? These ionic states influence the __-__ structures of proteins, and can help understand the mechanisms of _______________. 20. Draw a titration curve for cysteine with OH– equivalents given that it’s carboxyl group pKa = 1.9, its side chain pKa = 8.4 and its amino group pKa = 10.7. Draw the structure at each stage of ionization, and label them as cation, zwitterion and anion. 21. Refer to table 3.2 on page 64 to calculate the isoelectric points for the following amino acids. Also determine the pH ranges in which each amino acid could be an effective buffer. a. Thr b. Val c. Asn 22. The primary structure of a protein can be described as the linear _______________ of amino acid residues in a polypeptide chain. 23. Why are the reactions that form peptide bonds not thermodynamically favored in cells? What helps to overcome this barrier? 24. Write an equation for the formation of a dipeptide from Met and Thr, name the product, identify the N-terminus and the C-terminus, and explain why residues are numbered from the N- to the C-terminus. 25. Why is most of the ionic character of a polypeptide from its side chain? What properties does this affect? 26. (# 15, pg 82) Several common amino acids are modified to produce biologically important amines like Serotonin shown on the right, which is an important neurotransmitter synthesized in the brain. Low levels of serotonin in the brain have been linked to depression, aggression, and hyperactivity. From what amino acid is serotonin derived? 27. Draw the structure of the sequences of amino acids given. a. Cytochrome c from alligator (amino acids 41-50) GQAPGFSYTE b. Cytochrome c from bullfrog (amino acids 31-40) NLYGLIGRKT 28. Some concerns with purifying proteins include _______________ it from all other cell components and other similar proteins, finding a suitable _______________ for the desired protein, keeping the protein biologically _______________, and doing it between _____ and _____ to avoid degradation and denaturation. 29. Protein purification uses the differences in _______________, _____ __________, __________ and _______________ _______________. 30. Protein purification includes… a. preparing a _______________ of proteins through dissolving cells into a _______________, allowing the cell to _______________ and cause proteins to _______________... b. separating the mixture of proteins with _______________ _______________ as the _______________ agent, and then using _______________ to isolate the fraction containing the desired protein… c. separating using _______________ by washing the fraction through an _______________ material (matrix) using a specific solvent, dividing the mixture into _______________ fractions, which must be _______________. 31. Proteins can be further separated using _______________, which separates proteins on their migration in an _______________ field. _______________ _____ electrophoresis (PAGE) uses a basic gel matrix with an electric field passed through it to _______________ the migration of large molecules, thus fractionating the protein mixture based on both _______________ and _______________. The fractions of proteins can be visualized by _______________. _______________ _______________ _______________ (SDS) is sometimes added to overwhelm the native charge on proteins so they are separated based only on _______________. This helps to assess the _______________ and the _______________ weight of the protein. The “bands” of proteins can be cut out of the _____ and isolated for _______________ analysis, preparation of _______________, or other purposes. 32. The technique known as __________ _______________ determines the __________ of a molecule by measuring the __________ it takes for a charged gas phase molecule to travel from the _______________ point to the _______________. The time depends on the __________ and __________ of the molecule, and the technique was not applicable to biochemists until _______________ MS was developed which disperses charged _______________ molecules into a _______________ stream of particles. MS can determine the mass of a protein from _______________ quantities isolated from SDSPAGE gel, and the correct mass can be determined with an accuracy of less than the mass of a single _______________! 33. Once a protein is isolated, its amino acid composition is determined by cleaving the peptide bonds by acid _______________ using 6 M _____, as exemplified below. Complete the equation where R1 = Met, R2 = Thr and R3 = Asn. 34. Write a mechanism for the use of PITC at pH = 9.0 on Ala to generate ____________________-amino acid derivatives, in this case PTC-Ala. What technique will separate a PTC-amino acid mixture? What setback may occur using acid hydrolysis? 35. Show how the Edman reagent can remove Gly from Gly-Val-Glu. 36. Show how 2-mercaptoethanol cleaves a generic disulfide bridge and how iodoacetate prevents the re-formation of the disulfide bond. 37. Edman degradation can approach _____ yield under carefully controlled conditions. Treatment of proteins with cyanogen bromide, trypsin, S. aureus V8 protease and chymotrypsin will _______________ proteins that have too many residues to be completely sequenced by Edman degradation. 38. Who was the first to determine the complete sequence of a protein, what protein did he use, when did he accomplish this, and what did he earn? Why did he earn two of what he earned?