Lecture 4 -- Amino Acids Proteins are polymers of amino acids o Amino acids are often both basic and
d acidic at the same time as monomers o Complicated titration curves Proteins are built up by amino acids that are linked by peptide bonds into a polypeptide chain o The central carbon is the alpha carbon. Its a chiral sp3 center and gives amino acids (and therefore proteins) their chirality. Stereoisomerism o Stereoisomers have the same bonds but ehibit different spatial arrangements of the atoms. There are two conventions for naming mirror images. Optical Activity (D or L) based on the rotation of polarized light o Dextrorotory (D) or Levorotory (L) Absolute configuration o Putting the H at the back and then ranking them from heaviest to lightest in a circle. L and D ddo not depend on S and R. Consider the electric field component of light o First we select one component, pass it through the sample, and measure the rotation. o Samples that rotate light have optical activity. Proteins are spelled starting from amino terminus so that the diagram on the left above is particularly convenient for remembering stereochemistry. Why the symmetry was brokeni.e. one form was chosen, remains a source of debate. o Having molecules with a particular symmetry makes the chemistry of life specific. Stereo specificity is an important element of essentially all biomolecular properties. Amidation forms the peptide bond. Resonance gives the partial double bond character to the peptide plane keeping it flat. For a given composition, how many possible sequences are there? o N=2: Ala-G;y or Gly-Ala so S=2 o N=3: Ala-Gly-Val Ala-Val-Gly Gly-Val-Ala Gly-Ala-Val Val-Gly-Ala Val-Ala-Gly S=6 or 3! o In general, there are N! possible sequences all having the same composition. i.e. if I have 20 amino acids and I make a polymer 100 long, then I have 20100 = 10130 possibilities. Chemistries of Amino Acids are diverse o Sulfur in amino acids presents opportunities SH is easier to oxidize than OH o We make disulfide bonds that cross link intra and inter-molecularly S-SDisulfieds are made when cysteine reacts with itself.
This reaction can be used to cross link proteins. Example would be hair. Hair protein has many cysteines o Natural cysteins linkages in hair give the material its shape. Reduction causes a loss of linkages. Mechanical force (rollers) realigns the polymers and can be reoxidized to hold that shape. Four distinct mechanisms (Scheraga) **find them in the book** Structure of Rnase A has 4 disulfide bonds. The different amino acids also can have many different protonation states depending on their environment o Like dissolves like Consider the states of a simple organic acid The polarity of the solvent can either stabilize or destabilize a form o Water is polar so polar things, like ions, dissolve in it. o The free energy penalty for ion formation is offset by the solvation free energy gain i.e. water likes ions. o In a nonpolar solvent, there is no real gain in solvation energy fo the ions. o No DRIVING FORCE The interior of proteins is often a mix of nonpolar and polar moieties. Look at the side chains of the amino acids. o When an acid or base is buried determining the pKa and therefore the protonation state is difficult. See the titration graphs for strong acid/strong baseetc. Chapter 5 and do problems 4.6 and 4.9