Organic Chemistry
Chem 230
Chapter 28
Amino acids and Proteins
Introduction
Each amino acid has an amino group (NH2) bonded
to the α carbon of a carboxy group (COOH), and so
they are called α-amino acid.
The side group (chain) “R” that makes each amino
acid unique.
The sequence of amino acids in each peptide or
protein determines its unique shape and function.
All proteins are polyamides formed by joining amino
acids together.
There are 20 amino acids occur naturally in proteins differ
in the identity of the R group bonded to the α carbon. R
group is called the side chain of amino acid.
Amino acids with an additional carboxy group in the side
chain are called acidic amino acids.
Those with an additional basic N atom in the side chain
are called basic amino acids.
All others are neutral amino acids.
Acid-Base Behavior
An amino acid has both an acidic and a basic functional group, so
proton transfer forms a salt called a zwitterion.
Amino acids do not exist to any appreciable extent as uncharged
neutral compounds.
They exist as salts, giving them high melting points and making
them water soluble.
Amino acids exist in different charged forms, depending on the PH
of the aqueous solution in which they are dissolved.
For neutral amino acids, the overall charge is +1, 0, -1. Only at PH =
6 does the zwitterion form exist.
Peptides
When amino acids are joined together by amide bonds, they form
larger molecules called peptides and proteins.
A dipeptide has 2 amino acids joined together by one amide bond.
A tripeptide has 3 amino acids joined together by two amide bonds.
Peptide (amide) bond
Proteins
Polypeptides and proteins both have many amino acids joined
together in long linear chains, but the term protein is usually
reserved for polymers of more than 40 amino acids.
Protein Shapes
• Hydrophilic side groups are attracted to water.
• Hydrophobic side groups repel water.
• Coiled and twisted chains help to provide stability.
Protein Structure
The Primary Structure of proteins is the particular sequence of
amino acids that is joined by peptide bonds.
Rotation around the amide C–N bond is restricted because of
electron delocalization. In each peptide bond, the N–H and C=O
bonds are directed 180°from each other.
Rotation about the other σ bonds in the protein backbone is not. As
a result, the peptide chain can twist and bend into a variety of
different arrangements.
The three-dimensional conformations of localized regions of a
protein are called its Secondary Structure. These regions arise due
to hydrogen bonding between the N–H proton of one amide and the
C=O oxygen of another. Two arrangements that are particularly
stable are called the α-helix and the β-pleated sheet.
α-Helix forms when a peptide chain twists into a right-handed or
clockwise spiral.
β-pleated sheet forms when two or more peptide chains, called
strands, line up side-by-side.
The three-dimensional shape adopted by the entire peptide chain is
called its tertiary structure.
The shape adopted when two or more folded polypeptide chains
aggregate into one protein complex is called the quaternary
structure of the protein.
Protein Digestion
Stomach acid and enzymes facilitate the digestion
of protein.
It is first denatured, then broken down to
polypeptides.
The small intestine continues to break down protein
into smaller peptides and amino acids so it can be
absorbed.
Protein Functions
Regulators of Fluid Balance
• Plasma proteins attract water.
• Maintain the volume of body fluids to prevent edema which is
excessive fluid.
• Maintain the composition of body fluids.
Transporters
• Carry lipids, vitamins, minerals and oxygen in the body
• Act as pumps in cell membranes, transferring compounds from
one side of the cell membrane to the other.
Antibodies
• Fight antigens, such as bacteria and viruses, that invade
the body.
• Provide immunity to fight an antigen more quickly.
Other Roles
• Source of energy and glucose if needed.
• Blood clotting by producing fibrin which forms a solid clot.