Chapter 4 Amino Acids

Amino acids -20 common amino acids there are others found naturally but much less frequently Common structure for amino acid COOH, -NH 2, H and R functional groups all attached to the alpha carbon

Ionization of amino acids Three possible forms (not counting R group) depending on pH

Amino Acids Common amino acids are known as alpha- amino acids Primary –NH2 replaces a H in the alpha carbon atom Soul exception – proline has secondary amino group (-NH-) Amino acids readily ionize and are dipolar ions 2

Amino Acid Basics pKa of the  amino and  carboxy differ based on R group and microenvironment. See table 4-1 pp 80 (2 nd ed) pp 76-7 (3rd ed). –The average is about 2.1 for the alpha carboxyl and 9.7 for the alpha amino groups -Amino acids are zwitterions - a molecule with both a pos and neg charge -All naturally occurring amino acids are optically active isomers, except glycine. -R-groups determine the functionality of the amino acids. All amino acids can be based on one of three basic groups, non-polar, uncharged polar and charged polar (table 4-1). Also are classified based on hydrophobicity, reactivity, acidic and basic nature, relative size of the side groups

Non-Polar Amino Acids Glycine, alanine, valine, leucine and isoleucine: Aliphatic, inert. These are very hydrophobic amino acids with various sized side groups. Valine, leucine and isoleucine are branched chain and bulky and can cause steric hindrance. These amino acids have a large effect on the structure of proteins  COOH  NH 2 R-Group

Non-Polar Amino Acids 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.  COOH  NH 2 R-Group

Phenylalanine, tyrosine and tryptophan All are aromatic rings. Pi bonds / e- clouds create a very hydrophobic aa. Phenylalanine is very low in relative concentrations. Trp and Tyr absorb at 280 nm. Peptide backbone absorb at 260 nm. Tyrosine is very reactive and is often phosphorylated at the OH. These aas contain phenyl and indol rings.  COOH  NH 2 R-Group

Hydrophobic amino acids contain sulfur. The cysteine is very reactive and involved in the structure of the protein. Involved in disulfide bonds when oxidized.  COOH  NH 2 R-Group Methionine and Cysteine

Asparate, glutamate asparagine and glutamine. All are acidic, hydrophilic and the side groups are involved in H bonding.  COOH  NH 2 R-Group

Lysine, arginine and histadine These are basic 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 pH range. It is often found in sites of catalysis (very reactive). His also is a good chelator of divalent transition metals Zn +2 and NI +2.  COOH  NH 2 R-Group

Serine and threonine - Only slightly hydrophilic. - The OH is only ionizable under very basic conditions. - The OH groups are very reactive and are phosphorylated similar to tyrosine.  COOH  NH 2 R-Group

Less Common Amino Acids Here are some amino acids that are found in proteins, but are comparatively rare. They are not synthesized by ribosomal processes; most typically arise from post-translational 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 20.

More titrations When the amino acid is has a 0 net charge that 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.

Isoelectric Points 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 pH at the midpoint between the pK values on either side of the isoionic species What about peptides or proteins?

The classification of the 20 amino acids is based on the side chains. - You should know for each of the amino acids -The name and 3 letter designation - Based on the side chain (R group) if the amino acid is aliphatic, aromatic, sulfur containing, hydroxyl, basic, acidic, or an amide derivative -The charge at high neutral and low pH - 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... –Receptors –Growth factors Amino Acid / protein modification  Acetylation -  Hydroxylation -  Phosphorylation -  Carboxylation -  lipid esterification -

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 Peptides When amino acids are linked together it is through the formation of a peptide bond

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. + H 3 N CH C O NH R CH R C O NH CH COO- R

+ H 3 N CH C O NH R CH R C O NH CH COO- R Peptide bond –Rx 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; Mr=molecular weight

Many peptides have important biological activities Biologically important peptides 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.

Oxytocin and Vasopressin –Start as long precursors in hypothalamus- whose final form is 9 aa –differ by 2 residues oxytocin - uterine contraction during childbirth and milk production during lactation 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 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 »Opposite effect from opioids »Stimulates perception of pain (protective mechanism)