Further Reading

1. Lehninger Biochemistry, Chapter 3, pp. 75-86, 102-106
2. Matthews and van Holde (MvH) Biochemistry, Chapter 5, pp. 126-142
3. Branden and Tooze (BT) Introduction to Protein Structure, Chapter 1.
4. Aebersold R, Mann M. (2003) Mass spectrometry-based proteomics. Nature. 422:198-207 [Entrez]

Topics

• Names, abbreviations, general structure of amino acids
• Amino Acid chemical classes (polar, hyrdophobic, acidic, basic, aromatic, S-containing)
• Amino Acid structural classes/affinity
• amino acid evolutionary classes
• pK - Henderson-Hasselbach equation
• structure of peptide bond
• Proteomics - Mass Spec protein sequencing

Names, abbreviations, general structure

An excellent introduction to the structures and properties of amino acids can be found from the image library of biological macromolecules at http://www.imb-jena.de/IMAGE_AA.html.

An introduction to the structure of amino acids using the CHIME plugin for Netscape is available from Carnegie-Mellon http://www.bio.cmu.edu/Courses/BiochemMols/AAViewer/AAVFrameset.htm

In addition, the 3-D structures of 20 amino acids are provided by the Library of 3-D Molecular Structues. They can be visualized in an alphabetic order at http://www.nyu.edu:80/pages/mathmol/library/life/life1.html. Some of the structures (such as Glu, His and Thr), however, are different from those illustrated by the image library. See if you can figure out which structures are energetically more favorable. The structue of Asp shown by the library of 3-D Molecular Structures is, for example, energetically unfavorable; can you figure out why?

Amino-acid Chemical/Structural/Evolutionarly classes

A good discussion of homology modeling at http://swift.cmbi.kun.nl/swift/future/aainfo/ provides a lot of information about the chemical structures and chemical/structural classes of amino-acids.

A solvent accessibility table is available from: http://swift.cmbi.kun.nl/swift/future/aainfo/access.htm

Henderson-Hasselbach equation

A website prepared by E. K. O'Neil and C. M. Grisham of UVA contains the titration behavior of individual amino acid. You can visit the website at http://cti.itc.Virginia.EDU/~cmg/.

Review questions

1. List the 20 amino acids, with their 1-letter and 3-letter abbreviations.
2. What are some of the most common amino-acids? Least common?
3. Which amino acids contain hydroxyl groups that can be phosphorylated? (Why is this important?)
4. Which amino-acids contain aromatic rings?
5. Which amino-acids are more likely to be on the outside of proteins? On the inside? Why?
6. Which amino-acid is likely to change its charge state with pH changes within the physiological range (pH 6.5 8.0)? Why?
7. Outline the steps required for MS/MS protein identification
8. Which MS/MS protein sequencing techniques require a comprehensive protein sequence database?

Questions from previous exams

1. 1. Pick an acidic or basic amino-acid. (a) name the amino-acid; (b) draw the charge-structure of the amino-acid for each of the charge-states that it can assume (the actual covalent structure need not be correct, focus on the ionizable groups); (c) suggest an approximate pK for each of the ionizable groups. (d) Indicate the most abundant charge-state at pH 7.0.
2. The carboxyl group of amino acid alanine has a pKa value of 2.4 . In order to have 99% of the alanine in its COO form, what must the numerical relation be between the pH of the solution and the pKa of the carboxyl group of alanine.
3. Pick 5 amino acids including some that are more common and some that are less common. Construct a "PAM" amino-acid similarity matrix using those 5 amino acids, using +5 or +3 for identities, +1 for "conserved" amino acids (amino acids with similar properties), and -2 or -5 for non-conservative amino acids.