#03 Biochemistry Amino Acids Lecture for BB 450/550 Fall 2011

A lecture by Kevin Ahern to BB 450/550 at Oregon State University.

A lecture by Kevin Ahern of Oregon State University to his BB 450/550 class.

See the full course at http://oregonstate.edu/instruction/bb450/

This course can be taken for credit (wherever you live) via OSU's ecampus. For details, see http://ecampus.oregonstate.edu/soc/ecatalog/ecourselist.htm?termcode=all&...

Download Metabolic Melodies at
http://www.davincipress.com/metabmelodies.html

Related courses include
BB 350 - http://oregonstate.edu/instruction/bb350/
BB 451 - http://oregonstate.edu/instruction/bb451/
BB 100 - http://oregonstate.edu/instruction/bb100/

Topics covered include amino acid structure/function, pH, pKa, pI, charge, ions, ionization, buffers, buffering capacity, proteins, shape, and zwitterions.


1. Molecules can have more than one buffering region. Alanine, for example has two pKas, one for the carboxyl group and one for the amine group.

2. A buffer system will be at maximum capacity when the concentration of the undissociated acid (HA) equals that of the salt (A-)- (Acid = Salt).

3. Amine systems (also in amino acids) have two forms:
NH3+ and NH2. Note that the NH3+ is the acid and NH2 is the salt in my nomenclature. Carboxyl systems have two forms too. COOH has no charge and when it loses its proton, COO- has a negative one charge.

4. The Henderson Hasselbalch equation tells us we can predict the ratio of salt to acid as a function of pH if we know the pKa. Consequently, we can predict the charge on amino acids in a protein as the pH changes.

5. The value of the Henderson Hasselbalch equation is that by knowing the pH and the pKa of a molecule, the approximate charge of it in solution can be determined.

6. Protein structure dictates protein function. The structure of a protein is a function of the sequence of amino acids comprising it.

7. Amino acids are the monomeric (building block) units of proteins. They are covalently joined together in peptide bonds to make proteins (polypeptides).

8. There are 20 amino acids commonly found in proteins and of these 20, 19 have a chiral center and thus can exist in two stereoisomeric forms. The only one that doesn't have a chiral center is glycine. Almost all biologically made amino acids are in the same stereoisomeric form - the 'L' form.

9. Amino acids are grouped into several structural categories based on the composition of their R groups - we will use the designations of your book, as I described in the outline.

10. I mentioned briefly some of the properties of individual amino acids in the lecture. You should know those general properties (such as hydrophobic, hydrophilic, sulfhydryl, and ionizing side chains.)

11. A titration plot for a simple amino acid (no R groups that can lose protons) has two flattened regions - each one occurring at the respective pKa.

12. A zwitterion is a molecule whose net charge is zero.

13. The pI of a molecule is the point at which its charge is exactly zero. The assumptions above about protons on/off cannot be used to find the pI. It must be calculated. The pI of a molecule is the average of the pKa values around the point on the titration curve where the charge is zero

14. The sequence of amino acids in a protein is ultimately responsible for all of the properties a protein has. The sequence of amino acids of a protein is referred to as its primary structure.

15. Bonds holding amino acids together in a protein are called peptide bonds and they occur between the alpha amino group of one amino acid and the alpha carboxyl group of the next one.

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[mechwarriorbob]

Good Video. Amazing how biochem works.