Study Guide - Chapter 5
1. Write the correct projection diagrams and use these diagram to show the difference between D and
L alanine and D and L glyceraldehyde
2. Know the names of the 20 standard amino acids, their structures, their three letter abbreviations,
their 1 letter abbreviations, and if the have an ionizabel side chain, the pKa of the side chain, and the
charge on that side chain if pH<pKa and if pH > pKa
3. Group the amino acids in polar, nonpolar, aromatic, basic or acidic side chains.
4. What amino acids have an absorb ultraviolet light?
5. In lab we showed that the ultra violet absorbance of the protein undergoing dialysis was roughly the
same before and after dialysis. I stated that this was evidence that the protein had not left the dialysis
tubing during the experiment. Explain the tie between absorbance of UV light and protein
concentration.
6. There are some non-standard amino acids. Where do these come from? Freaks of nature? Bad
dreams of some organic chemist? Nasty examples thought up by the instructor? Of something else?
7. Given what you know about amino acid pKa’s, be able to draw a rough titration curve of any amino
acid and describe the net charge on the amino acid at any place on the titration curve. In particular,
where is the pI of the amino acid.
8. Given what you know about amino acid pKa’s, be able to draw a rough titration curve of a simple
peptide containing about three amino acids and describe the net charge on the peptide at any place on
the titration curve. In particular, where is the pI of the peptide.
9. What is a peptide, a protein, an oligopeptide, a polypeptide? What is meant by the amino- terminus
or the carboxyl-terminus of a peptide?
10. What are conjugated proteins, prosthetic groups, lipoproteins, glycoproteins, metaloproteins?
11. What is meant by primary structure, secondary structure, tertiary structure and quaternary structure
in a protein.
12 Describe the three major chromatographic methods used to separate proteins. Given a mixture of
proteins or peptides with various molecular properties, propose a separation method and justify your
method.
13. What is electrophoresis? Discuss the various electrophoresis methods discussed in the text.
14. What is the difference between the activity of an enzyme and the specific activity of an enzyme?
15. How do you determine the amino acid composition of a protein?
16. How do you determine the molecular weight of a protein?
17. How do you determine the N-terminal amino acid of a peptide?
18. Describe, in as much detail as possible (including chemical reactions and names or structures of
reagents) how one can determine the sequence of a small peptide.
19. Why can’t the above process be used to determine the entire sequence of a protein?
20. Since the sequencing process given in #18 can’t do a complete protein, how do we do it then?
21. Given a peptide, predict the cleavage pattern that would be found using any of the methods given in
table 5-7.
22. Given the complete cleavage pattern found using one or more of the methods given in table 5-7
recreate a protein’s sequence.
23. How do yo locate disulfide bonds in a protein’s covalent structure?
24. What is the proteome? How can it be useful? What information can be found by comparing the
sequence of proteins?
25. How can a peptide be synthesized?