Dr. Terry L. Helser, Professor of Chemistry
227 Physical Sciences Building, Oneonta, NY 13820-4015
Phone: (607)436-3518 or Email to:
Study Guide - Biochemistry, The Molecular Basis of Life, 4th Ed., 2009, T. & J.R. McKee (Oxford Univ. Press)
Chapter 5: Amino Acids and Peptides

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How are amino acids, peptides, polypeptides and proteins related?

What do all alpha amino acids have in common? How do they differ?

Know the 3 letter abbreviations for the 20 "gencoded" amino acids (Table 5.1).

Which of the amino acids have neutral, aliphatic (nonpolar) side chains? Which are nonpolar, aromatic? Which is not an amino acid, but an imino acid (a secondary amine)?

Which are neutral, polar? ...ionic, acidic? ...ionic, basic? ...which are sulfur containing?

How does aspartate differ from aspartic acid? Which form is present at pH 7? Does glutamate differ from glutamic acid? Which amino acid side chains are anions and which cations at pH 7? Charges?

Define hydrophilic, hydrophobic, amphoteric and zwitterion .

Which of the five simplifying principles given in class is illustrated by the biological roles listed as 1.-3. on pp. 114-115?

Which amino acid is not optically active (not chiral)? Are all others L or D?

What is the pI and how is it calculated? What properties are associated with it?

What is the more general, organic name for a peptide bond? Be able to diagram and describe the resonance properties and trans, planar nature of the structure.

Which amino acid(s) forms disulfide bridges? What is their importance?

How would you write the complete name for the Leu enkephalin structure? (page 74)

List and give examples of the major functions of proteins.

Define primary (1°), secondary (2°), tertiary (3°) and quaternary (4°) structures in proteins.

What are the two major types of 2° structures? Which has parallel and antiparallel forms, and what are they? Of what 2° structure is collagen made? What are supersecondary structures?

What is meant by the terms native conformation and denaturation ? What conditions and reagents cause a protein to denature? Why, in each case?

Biochemical Methods chapter 5.4, p. 122f: How is amino acid composition of a peptide determined? Why is this important?

How is the primary structure of a peptide determined? How are N-terminal and C-terminal amino acids determined? What technique has been automated in the "sequenator"? Which reagents specifically cleave proteins into peptides, and what amino acid will be on the C-end of each fragment? How are fragments aligned to give the full sequence?

What techniques are used to determine 3° and 4° structures? Give an example of each.

End of chapter review questions 1.-5. 7. 10.-14. 16. 20. 21. 28. 29. 30. 37. 41. 47. 50.

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