1. Contact me at kgahern@davincipress.com / Friend me on Facebook (kevin.g.ahern) 2. Download my free biochemistry book at http://biochem.science.oregonstate.edu/biochemistry-free-and-easy 3. Take my free iTunes U course at https://itunes.apple.com/us/course/biochemistry/id556410409 4. Check out my free book for pre-meds at http://biochem.science.oregonstate.edu/biochemistry-free-and-easy 5. Course video channel at http://www.youtube.com/user/oharow/videos?view=1 6. Check out all of my free workshops at http://www.youtube.com/playlist?list=PLlnFrNM93wqyTiCLZKehU1Tp8rNmnOWYB&feature;=view_all 7. Check out my Metabolic Melodies at http://www.davincipress.com/metabmelodies.html 8. My courses 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&subject;=BB 9. Course materials at http://oregonstate.edu/instruct/bb350 Highlights 1. Molecules can have more than one buffering region. Alanine has both an amine group and a carboxyl group that can gain/lose protons (hydrogen ions). It will thus have two pKas, one for the carboxyl group and one for the amine group. 2. A buffer system is at maximum capacity when the concentration of the undissociated acid (HA) equals that of the salt (A-)- (Acid = Salt). The Henderson Hasselbalch equation further reveals that when this is true, pH = pKa. 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. 3. 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. For this class, we will assume that if the pH is more than one unit below the pKa of a group, that the proton is ON it. If the pH is more than one unit above the pKa of the group, the proton is OFF it. This is only useful for estimating charge. Determination of the pI (pH at which a molecule has a charge of exactly zero) requires calculation (described later in class). Protein Structure I 1. Protein structure dictates protein function. The structure of a protein is a function of the sequence of amino acids comprising it. 2. Amino acids are the monomeric (building block) units of proteins. They are covalently joined together in peptide bonds to make proteins (polypeptides). 3. 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. The 'D' form occurs only in very rare peptides. 4. 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. You will need to know the names of the 20 amino acids of proteins, which of the groups above each one belongs to and will need to be able to predict ionization at given pH values if you are supplied pKa values. Of these amino acids, the ones we will be concerned with have R groups that can ionize. 5. Molecules that are capable of gaining/losing more than one proton, have pKa's that correspond to each functional group that can lose a proton. For example, a simple amino acid, such as alanine, has an amino group (pKa about 9.5) and a carboxyl group (pKa about 2.5). 6. 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. 7. 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. 8. 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. 9. Peptide bonds form resonance structures such that the bond itself behaves like a double bond. Double bonds cannot rotate (unlike single bonds) and thus they define a plane. Alpha carbons on either side of a peptide bond are generally arranged in a trans configuration, except when proline is involved. 10. The bonds around the alpha carbon (the carbon bonded to both an amino group and a carboxy group) can both rotate, however, because they are single bonds. One can thus describe a polypeptide as a series of planes separated by an alpha carbon, with the planes each being rotated a certain number of degrees relative to the alpha carbon. 11. Ramachandran, recognized that not all rotations of phi and psi would be theoretically feasible because steric hindrance would preclude some rotational positions.

• published: 05 Oct 2013
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