Download Amino Acids

Amino Acids
Introduction
Amino acids are the building blocks of proteins. The sequence of amino
acids in individual proteins is encoded in the DNA of the cell. The
physical and chemical properties of the 20 different naturally occurring
amino acids dictate the shape of the protein and its interactions with its
environment. Certain short sequences of amino acids in the protein also
dictate where the protein resides in the cell. Proteins are composed of
hundreds to thousands of amino acids. As you can imagine, protein
folding is a complicated process and there are many potential shapes
due to the large number of combinations of amino acids. By
understanding the properties of the amino acids you will gain an
appreciation for the limits of protein folding and will learn how to
predict the potential higher-order structure of the protein.
All amino acids have the same backbone structure, with an amino group,
a carboxyl group, an alpha- hydrogen, and a variety of functional
groups (R) all attached to the alpha-carbon.
If all of the amino acids have the same basic structure with an amino, a
carboxyl and hydrogen fixed to the alpha-carbon, then the large
variation in the properties and structure of the amino acids must come
from the fourth group attached to the alpha carbon. This group is
referred to as the side chain of the amino acid or the R group.
The structures of the 20 common amino acids are shown on the chart
below. The simplest amino acid, glycine, is shown in the upper left. The
main-chain atoms of glycine are highlighted in yellow and its side chain
(H) is highlighted in green. All amino acids have the same main-chain
atoms, but differ in the side chains. For clarity, the alpha- proton is
omitted in the remaining drawings.
The side-chain groups of these amino acids contain many common
groups of atoms called functional groups. The majority of functional
groups, such as the hydroxyl group (–OH), are commonly polar,
allowing them to interact with water. Details of the functional groups
can be found in the functional groups interactive chart, which can be
accessed by clicking on the Learn by doing link below.
Peptide Bonds
Proteins are polymers of amino acids. The amino acids are joined
together by a condensation reaction. Each amino acid in the polymer is
referred to as a "residue." Individual amino acids are joined together by
the attachment of the nitrogen of an amino group of one amino acid to
the carbonyl carbon (C=O) of the carboxyl group of another amino acid,
to create a covalent peptide bond and yield a molecule of water, as
shown below.
The resulting peptide chain is linear with defined ends. Short polymers
(less than 50 residues or amino acids) are usually referred to as
peptides, and longer polymers as polypeptides. Several polypeptides
together can form some large proteins. Because the synthesis takes place
from the alpha-amino group of one amino acid to the carboxyl group of
another amino acid, the result is that there will always be a free amino
group on one end of the growing polymer (the N-terminus) and a free
carboxyl group on the other end (the C-terminus).
Note that after the amino acid has been incorporated into the protein,
the charges on the amino and carboxyl termini have disappeared, thus
the main-chain atoms have become polar functional groups. Since each
residue in a protein has exactly the same main-chain atoms, the
functional properties of a protein must arise from the different sidechain groups.
By convention, the sequences of peptides and proteins are written with
the N-terminus on the left and the C-terminus on the right. The name of
the N-terminal residue is always the first amino acid. The name of each
amino acid then follows. The primary sequence of a protein refers to
its amino acid sequence.