AMINO ACID

Amino group - the —NH2 functional group

Carboxyl group- the —COOH functional group that dissociates to give the carboxylate anion,
—COO−, and a hydrogen ion

Side chain group- the portion of an amino acid that determines its identity

Stereochemistry- the branch of chemistry that deals with the three-dimensional shape of
molecules

Chiral- refers to an object that is not super imposable on its mirror image

Essential - amino acids that can’t be produced by the cell and are needed for diet

Non- essential – amino acids that can be synthesized by the cells in our body.

Proteins

- Are among the most abundant organic molecules in living systems and are way more
diverse in structure and function than other classes of macromolecules.
- A single cell can contain thousands of proteins, each with a unique function.
- All proteins are made up of one or more chains of amino acids.

Amino acid

- Are organic compound composed of nitrogen, carbon, hydrogen and oxygen along with a
variable side chain group.
- It is the building block of protein.
- They're needed for vital processes like the building of proteins and synthesis of hormones
and neurotransmitters.
- Our body need 20 different amino acids to grow and function properly. Though all 20 are
important, only 9 amino acids are classified essential and these are: Histidine, Isoleucine,
Leucine, Lysine, Phenylalanine, Threonine, Tryptophan, Valine, Methionine.
- Amino acid are represented by a single upper-case
letter or three-letter abbreviation.

L- and D-Amino Acids

- Only L-amino acids are manufactured in cells and

incorporated into proteins.
- Some D-amino acids are found in the cell walls of
bacteria, but not in bacterial proteins.
- Glycine, the simplest amino acid, has no enantiomers
because it has two hydrogen atoms attached to the central carbon atom.
 - Only when all four attachments are different can enantiomers occur.

Why is it important to specify the 3-D structure of amino acids?

- First, the three-dimensional structure of a protein is determined by its amino acid

sequence. Second, the function of a protein depends upon its three-dimensional structure.
Third, the three-dimensional structure of a protein is unique, or nearly so. Fourth, the
most important forces stabilizing the specific three-dimensional structure maintained by a
given protein are non covalent interactions. Finally, even though the structure of proteins
is complicated, several common patterns can be recognized.
- A protein's specific shape determines its function. If the three-dimensional structure of
the protein is altered because of a change in the structure of the amino acids, the protein
becomes denatured and does not perform its function as expected.

AMINO ACID ACT AS ACID AND BASE

Titration of amino acid

- The titratable groups of each of the amino acids have characteristic pKa values.
- Carboxyl group is acidic and amino group is basic
- The pKa values of a-carboxyl groups are fairly low, around 2. The pKa values of amino
groups are much higher, with values ranging from 9 to 10.5. The pKa values of side-
chain groups, including side-chain carboxyl and amino groups depend on the groups’
chemical nature.
- The classification of amino acids as acid and base depends on the pKa of the side chain
group
 Zitterion

- is the predominant species of the neutral form of the amino acid.

Example is Histadine

Isoelectric pH

- The pH at which a molecule has no net charge; also known as isoelectric point
- The 2 pKa that is needed to get the pI is the pKa before and after the net charge of zero.

pH < pKa

- There is a lot of proton in the environment of the amino acid

- It will be protonated
- H+ will be added in either carboxyl or amino group
pH> pKa

- There is a lot of OH- at the environment of the amino acid

- It will be deprotonated
- It will remove a proton on either carboxyl or amino group

pH = pKa

- Half will be protonated and the other half with be deprotonated

Given 3 pKa values

If protonated R= neutral

- Use lower 2 pKa

- pI= pKa carboxyl group + R group / 2
- Asp, Glu, Cys, Tyr

If protonated R= +

- Use upper 2 pKa

- pI= pKa amino group + R group / 2
- His, Arg, Lys

To identify if an amino acid is base or acid

- If the side chain of an amino acid has carboxyl group then it is acidic
- The amino acids that are acidic are: Aspartate and glutamate.
- If the side chain of an amino acid contains Nitrogen then it is basic
- The amino acids that are basic are: Histidine, Lysine, Arganine.