Protein Structure and Function
Biologically
active proteins are polymers consisting of amino acids linked by covalent
peptide bonds. Many different conformations (three-dimensional structures) are
possible for a molecule as large as a protein. Of these many structures, one or
(at most) a few have biological activity; these are called the native conformations. Many proteins
have no obvious regular repeating structure. As a consequence, these proteins
are frequently described as having large segments of “random structure” (also
referred to as random coil). The term
random is really a misnomer, because
the same nonrepeating structure is found in the native conformation of all
molecules of a given protein, and this conformation is needed for its proper
function. Because proteins are complex, they are defined in terms of four
levels of structure.
Primary structure is the order in which the
amino acids are covalently linkedtogether. The peptide Leu-Gly-Thr-Val-Arg-Asp-His
(recall that the N-terminal amino acid is listed first) has a different primary
structure from the peptide Val-His-Asp-Leu-Gly-Arg-Thr, even though both have
the same number and kinds of amino acids. Note that the order of amino acids
can be written on one line. The primary structure is the one-dimensional first
step in specifying the three-dimensional structure of a protein. Some
biochemists define primary structure to include all covalent interactions,
including the disulfide bonds that can be formed by cysteines; however, we
shall consider the disulfide bonds to be part of the tertiary structure, which
will be considered later.
Two
three-dimensional aspects of a single polypeptide chain, called the secondary
and tertiary structure, can be considered separately. Secondarystructure is the arrangement in space of the atoms in the
peptide backbone.The α-helix and β-pleated sheet arrangements are two different
types of sec-ondary structure. Secondary structures have repetitive
interactions resulting from hydrogen bonding between the amide N-H and the
carbonyl groups of the peptide backbone. The conformations of the side chains
of the amino acids are not part of the secondary structure. In many proteins,
the folding of parts of the chain can occur independently of the folding of
other parts. Such independently folded portions of proteins are referred to as domains or super-secondary structure.
Tertiary structure includes the three-dimensional
arrangement of all theatoms in the protein, including those in the side chains
and in any prostheticgroups (groups
of atoms other than amino acids).
A
protein can consist of multiple polypeptide chains called subunits. The arrangement of subunits with respect to one another
is the quaternary structure.
Interaction between subunits is mediated by noncovalent interactions, such as
hydrogen bonds, electrostatic attractions, and hydrophobic interactions.
Proteins are made up of long chains of amino acids. The composition
and order of the amino acids are critical to the protein function.
For any native protein, there is one, or at most a few,
three-dimensional structures that function correctly.
Protein structure can be classified into primary, secondary,
tertiary, and quaternary structure.
Primary
structure is the order of the amino acids. Secondary structure is characterized
by a repetitive organization of the peptide backbone. Tertiary structure refers
to the complete three-dimensional structure of the protein. Quaternary
structure describes a protein that has multiple polypeptide chains.
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