H H N - C - C 2 R. Three possible forms (not counting R group) depending on ph

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1 Amino acids - 0 common amino acids there are others found naturally but much less frequently - Common structure for amino acid - C, -N, and functional groups all attached to the alpha carbon N - C - C Three possible forms (not counting group) depending on p N - C - C N - C - C N - C - C p 1.0 p 7.0 p 11.0 pka of the α amino and α carboxy differ based on group and microenvironment. See table 4-1 pp Amino acids are zwitterions - a molecule with both a pos and neg charge - All naturally occurring amino acids are optically active isomers, except glycine. L amino acids -All amino acids can be based on one of three basic groups, non-polar, uncharged polar and charged polar (table 4-1). - -groups determine the functionality of the amino acids. Classified based on hydrophobicity, reactivity, acidic and basic nature, relative size of the side groups Amino Acid Characterization - Glycine, alanine, valine, leucine and isoleucine: Aliphatic and inert. These are very hydrophobic amino acids with various sized side groups. Leucine and isoleucine are bulky and can cause steric hindrance. These amino acids have a large effect on the structure of proteins - Proline is the only aa where the alpha amino group is tied up in a ring structure. This amino acid is only slightly hydrophobic. The ring structure decreases the flexibility of the peptide backbone. - Phenylalanine, tyrosine and tryptophan, All are aromatic rings. Pi bonds / e- clouds create a very hydrophobic aa. Phe is very low in relative concentrations. Trp and Tyr absorb at 80 nm. While the peptide backbone will absorb at 60 nm. Tyrosine is very reactive and is often phosphorylated at the. Phenyl and indol rings. 1

2 - Methionine and Cysteine - hydrophobic amino acids contain sulfur. The cysteine is very reactive and involved in the structure of the protein. Involved in disulfide bonds when oxidized. - Asparate, glutamate asparagine and glutamine. All are hydrophilic and the side groups are involved in bonding. - Lysine, arginine and histadine - These are basic and hydrophilic amino acids. Both the guanidino group of arginine and the imidazole ring of histadine contain resonance forms. The histadine is the only amino acid with a side group pka in the physiological p range. It is often found in sites of catalysis (very reactive). is also is a good chelator of divalent transition metals Zn. - Serine and threonine - only slightly hydrophilic. The is only ionizable under very basic conditions. The groups are very reactive and are phosphorylated similar to tyrosine. ere (see pages 89 and 90) are some amino acids that are found in proteins, but are comparatively rare. They are not synthesized by ribosomal processes; most typically arise from posttranslational modifications to the protein, which are catalyzed by specific enzymes. Common post-translational modifications include hydroxylation, methylation, acetylation, and phosphorylation. You are not responsible for knowing these amino acids, however, if asked you should be able to recognize that they are not one of the common 0. Isoelectric point (pi) When the amino acid is has a 0 net charge it is considered the isoelectric point. For amino acids with side groups that contain an ionizable moiety it is the average of the two pka that are charged when the net charge is zero.

3 - If the side group is not ionizable, then the pi is the average of the C and N groups pka - Calculations of pi for a compound with more than two dissociable groups carries more possibility for error - First write out all possible ionic structures for a compound in order that they occur starting with the most basic to the most acidic - Next, identify the isoionic, zwiterionic or neutral representation - The pi is the p at the midpoint between the pk values on either side of the isoionic species - What about peptides or proteins? The classification of the 0 amino acids is based on the side chains. - You should know for each of the amino acids -The name and letter designation - Based on the side chain ( group) if the amino acid is aliphatic, aromatic, sulfur containing, hydroxyl, basic, acidic, or an amide derivative -The charge at high neutral and low p - chemical reactivity - if the amino acid is hydrophobic or hydrophilic, acidic or basic, polar, uncharged but polar and charged polar - relative size Peptides & Primary Structure Protein Functions Enzymes -Catalyze a thermodynamically favorable reaction Storage/transport - binding proteins fatty acids w/albumin no catalytic activity but do form chemical bonds with ligands Structure - Several levels cytoskeleton, collagen, bone... eceptors Growth factors Amino Acid / protein modification - acetylation - hydroxylation - phosphorylation - carboxylation - lipid esterification

4 Peptides When amino acids are linked together it is through the formation of a peptide bond. The formation of a peptide bond occurs by the loss of a water or dehydration of water from the a carboxyl and of one amino acid and the a amino of another amino acid N C C N C C N C C- - Each amino acid is called a residue - Addition of acid or base hydrolyzes the peptide bond and adds water back across the peptide bond. - The amino (N) terminal is written on the left and the carboxyl (C) terminal is on the right. - The actual sequence of amino acids is considered the primary structure. No other factor is considered in this level of structure. Most DNA mutations have there effect at the primary level. - For proper folding and native state (enzymatic activity) approximately 40 amino acids need to be aligned Peptide bond x of bond formation costs energy (ATP) but degradation of proteins is thermodynamically favorable. (entropy) C-N bond shorter than normal and more like double bond This results in rigid planar, non-rotating links between aa Size of peptides and proteins are described in Daltons 1 atomic unit = 1 dalton ; MW = Dalton / kd Many peptides have important biological activities Insulin - Short peptide produced as a pre-pro-peptide. The initial peptide is much longer and is modified twice, each time a set of peptide bonds are hydrolyzed. The final shortened version is active. There are two subunits, held together by a disulfide bond. xytocin and Vasopressin Start as long precursors in hypothalamus- whose final form is 9 aa differ by residues 4

5 oxytocin - uterine contraction during childbirth and milk production during lactation vasopressin - alters blood pressure by forcing kidney to retain water, increasing the volume of blood Met-enkephalin (opioid peptides) Naturally produced peptides, bind to receptors, and reduce pain cause pleasure. Morphine like Substance P pposite effect from opioids. Stimulates perception of pain (protective mechanism) 5

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