Amino Acids, Peptides, and Proteins: Exercises

Ch 618B: Bauld

1. Write the structure and give the common name of the simplest -amino acid, its abbreviation (3 letter and 1 letter), and its IUPAC name. Provide also the structure of a -amino acid.

2.Draw the condensed structure of L-alanine and also its Fischer structure. Explain why it is termed L-alanine. Verify by using models that L-alanine is S-alanine in the R,S system of nomenclature.

3.Write the condensed structure of three neutral amino acids, one acidic amino acid, and one basic amino acid. What is the basis for calling these acids, respectively, neutral, acidic, or basic?

4. What is the actual structure of an -amino acid? What is the generic name for this kind of structure? By referring to the reaction between a simple amine and a simple carboxylic acid, indicate whether this structure is that expected and explain why, using a calculation based upon pKa 's. What form of a simple -amino acid is present in acidic soluttion? In alkaline solution. At neutral pH?

5. What is the isoelectric point (pI) of an -amino acid? What is the approximate pI of a neutral -amino acid? Which amino acids have pI's about 3? Be specific. Which have pI's close to 10? Be specific.

6. The pKa of the cationic form of an amino acid ( a carboxylic acid having an alpha NH3+ substituent) is quite low for a carboxylic acid (2, as compared to ca. 5 for typical carboxylic acids). Explain.

7.What is the hybridization state of N in amides? Explain any difference between this and the corresponding hybridization state in amines. Draw an orbital picture which helps to show why conjugative stabilization is greater when the N is sp2 than sp3 hybridized.

8.Draw 2 different conformations of an amide, provide the appropriate name for each, indicate which is more stable and why, and indicate whether there interconversion is relatively fast or slow (explain why).

9.Draw 2 resonance structures for an amide and explain why hydrogen bonding might be expected to be especially strong with amides, compared to other electroically neutral functionality. How many atoms are held in a coplanar relationship in an amide? Explain.

10. Write the condensed structures, using typical peptide conventions (amino terminal end group on the left), of two dipeptides which could be formed between glycine and alanine. Show both the neutral and zwitterion structures.If you were attempting to form a specific dipeptide, say gly-ala, from a mixture of glycine and alanine, how many dipeptides would you be likely to get?

11. Using a protecting group strategy, sketch a selective synthesis of gly-ala. Don't forget to remove the protecting groups at the end of the synthesis. Why is the BOC protecting group especially appropriate for protecting the amine function? Sketch a mechanism for its removal.

12. Sketch a selective synthesis of the same dipeptide, using the Merrified solid phase method. Which terminus of the dipeptide is attached to the resin first. Why are cesium salts used? How is the connection to the resin removed? Why is the Merrifield resin especially easily removed? How could this synthesis be modified to achieve the synthesis of gly-ala-phe?

13.What kind of hydrogen bonding stabilizes the - sheet structure of a protein? Which amino acids are particularly prone to forming -sheet structure? Why? Explain why the sheet is not planar, but buckled.

14.What kind of hydrogen bonding stabilizes the -helical structure?