CH 3 Amino Acids and peptides

carboxyl, amino, side chain (R group), Hydrogen

name the groups on an amino acid

chiral

4 different groups and nonsuperimposable images

-Ex) like hands

achiral

doesn’t have 4 different groups, molecules can be superimposed

Ex) Glycine is the only achiral amino acid

stereoisomers

• molecules that differ from each other only in their configuration (3-dimensional shape), also called optical isomer

• configuration can determine characteristic and funciton

L, D

For amino acids, alpha-C has 4 different groups giving rise to 2 nonsuperimposable images of one another written as ___ and ___

L

what stereoisomers form do amino acids exist as

uncommon amino acids

derived from common amino acids and are produced by modification of parent amino acid after the protein is synthesized by the organism (post translational modification)

It extends the range of functions of the protein by attaching it to other biochemical functional groups

• Ex) proline and hydroxyproline in protein folding (added -OH group)

molecule is protonated

when pH<pka

molecule is deprotonated

when pH>pka

charged, negatively, positively

carboxyl group and amino group of the general structure are ____ at neutral pH—the carboxylate portion _____ and the amino group _____.

R groups with no charges

what amino acids exist as zwitterions in pH 7 with no net charge

because:

• the pKa value of the amine group is around 9-10 and at pH 7 since pH<pka it will remain protonated NH3+

• the pKa value of the carboxyl group is around 2 and at pH 7 since pH>pKa it would have deprotonated leaving a negative charge

• the ranges of deprotonation don’t coincide so it’s possible to have both uncharged at the same time

why do neutral amino acids (pH 7) do not exist in the form NH2-CHR-COOH

diprotic, carboxyl (COO-) , amine (NH3+

most amino acids are ___ meaning they only have two titratable groups which are the ____ and ___

only has the 2 titratable groups because the side chain -OH doesn’t titrate under normal biochemical conditions. -OH pKa: 13-15 and pH never really gets above 14

why doesn’t a molecule like Serine with a polar -OH group participate in titration

isoelectric pH

the pH at which a molecule has no net charge; also known as the isoelectric point

• PI= (pKa1+pKa2)/ 2

functional group that was deprotonated at isoelectric point

what is pKa1

functional point that remains protonated at isoelectric point

what is pKa2

1, 0

when titrating triprotic bases or acids you want to take the pKa values that are protonated and deprotonated between ±__ and ___ net charge

between a-carboxyl group of one amino acid and a-amine group of another

*water is eliminated in the process

Where are amino acids covalently linked?

residues

• portions of monomer units included in polymers after splitting out water between amino acids in protein

• Once an amino acid forms a peptide bond, it is no longer a “free amino acid” — it becomes a residue.

peptide bond

an amide bond between amino acids in a protein

peptides

molecules formed by linking 2 or more amino acids by peptide bonds

polypeptide chain

backbone of a protein it is formed by linking amino acids by peptide bonds (can fold into proteins)

resonance structures

structural formulas that differ from each other only in position of electrons

stability from resonance can give it a partial double bond character

Why are the peptide bonds more stable than normal single covalent bonds

Phenylalanine, Valine, Threonine, Tryptophan, Methionine, Leucine, Isoleucine, Lysine, and Histidine

What are the 9 essential amino acids

most are supplemental in diet so the chains of production our ancestors may have had no longer became necessary

Why don’t we make all the essential amino acids ourselves

Beta carbon amino acids have their amino group bound to the beta carbon rather than the alpha carbon

What’s the difference between alpha and beta carbon amino acids?

Draw the reaction between two AAs to make a peptide bond

1.80-2.46

What’s the pKa range of the alpha carbon carboxyl group of amino acids

8.72- 10.70

what’s the pKa range of the alpha carbon amino group on AAs

R configuration

priority sequence proceeds clockwise around chiral center

S configuration

priority sequence proceeds counterclockwise around chirality center