Amino Acids
The fundamental structure of an
amino acid. An amino group, a
carboxyl group, and a branch (R)
that may vary in structure.
carboxyl
O
amino
H2 N
OH
O
At physiological pH (near 7) the
carboxyl group loses a proton and
the amino group gains a proton
forming a zwitterion.
H3 N
+
O
R
R
Some representative amino acids and one unusual amino acid.
Amino acids are categorized by the nature of their side chain as acidic (carboxyl group), basic
(amino group), nonpolar neutral (hydrocarbon), or polar neutral (heteroatom). The catagory for each
of the amino acids below is shown in parentheses.
O
O
O
H3 N
O
+
O
H3 N
H3 N
+
H3 N
+
+
O
O
O
H
Glycine
(Nonpolar)
Alanine
(Nonpolar)
O
H3 N
Phenylalanine
(Nonpolar)
Lysine
(Basic)
NH2
O
+
O
H3 N
+
O
O
OH
Aspartic Acid
(Acidic)
H
N
O
O
SH
Cysteine
(Polar)
Proline is unique among the amino
acids because its "branch" and amino
group are linked forming a ring.
The presence of proline in a peptide
usually creates a bend in the chain.
Proline
(Nonpolar)
Portion of a Peptide Chain
Amino acids —> peptides —> polypeptides — > proteins
Amino acids are linked by condensation reactions to form peptides
and proteins. The carboxyl group of one amino acid links to the
amino group of another amino acid to form a neutral amide. This
link is called a peptide bond.
These peptides have two different ends. The amino end (N-terminus)
is normal ly written on the left with the carboxyl end (C-terminus) on
the right.
Peptide Bond
H
O
N
R
H
N
N
R
O
H
O
R
H
N
N
R
O
H
O
N-terminus
N
R
Portion of Pleated Sheet
Protein Structure:
The structure of a protein is crutial to its proper function. Its active or
normal structure is called its native state and can be described on four
levels.
Primary - the amino acid sequence (Ala-Gly-Phe-Cys-...)
Secondary - the arrangement of small groups of amino acids
(β-pleated sheet; α-helix)
Tertiary - the shape of the entire peptide chain
(fibrous; globular)
Quaternary - the grouping of multiple peptide chains
H
O
N
R
H
R
H
O
N
N
N
H
O
R
H
O
R
H
O
H
R
O
H
R
O
N
N
H
O
N
N
R
R
H
C-terminus
N
N
O
H
R
H
N
N
O
H
R