BIOCHEM 301

GLOSSARY OF PROTEIN STRUCTURE TERMS

Alpha helixone of the two common secondary structural elements found in proteins,
in which a section of protein backbone adopts a helical conformation.

Amino-terminus or N-terminusthe end of the protein that has a free amino group.
Note that amino-terminal or N-terminal is an adjective, not a noun; the noun form
properly ends in us.

Apoan adjective meaning that a protein is lacking some prosthetic group that it would
normally have.

Backbonethe alpha carbons, peptide bond carbonyl groups, and peptide bond amide
nitrogen groups of a protein.

Beta sheetone of the two common secondary structural elements found in proteins, in
which multiple sections of protein backbone are arranged side-by-side.

Carboxy-terminus or C-terminusthe end of the protein that has a free carboxylic acid
group. Note that carboxy-terminal or C-terminal is an adjective, not a noun; the
noun form properly ends in us.

Chaina single polypeptide molecule, consisting of amino acids covalently linked by
peptide bonds. A large protein may be built with more than one chain.

Complexas a noun, an assembly of multiple independently folding protein subunits
joined by noncovalent interactions (or in a few cases, disulfides). The subunits may be
part of the same chain, or part of multiple chains, and some or all of the subunits may be
identical to one another or different from one another.

Domaina continuous section of a polypeptide chain which folds into a stable three-
dimensional structure. A single chain may have more than one domain. A domain is the
smallest unit of structure that can fold and remain stable independently; a chain with
multiple domains can be cut at each domain boundary, and each domain should remain
independently stable. Some domain folds are so common as to have names, e.g. the WW
domain or the immunoglobulin domain.

Foldas a noun, a particular arrangement of secondary structural elements which
constitutes the tertiary structure of a protein. The word fold is often used to refer to a
pattern of tertiary structure that occurs in many different proteins (or even whole families
of proteins). A fold is distinguished from a motif in that a fold is a structural
pattern that occurs at the level of a whole protein, a whole domain, or a whole subunit,
while a motif is a portion of a larger structure that would be too small and too
incomplete to be stable if it were cut free of the rest of the protein. As a verb, the process
whereby a protein assumes its three-dimensional structure.

Holoan adjective meaning that a protein has all of the prosthetic groups that it would
normally have.

Main chaina synonym for the backbone.

Motifan arrangement of a small number of secondary structural elements that is
regularly found in a variety of different proteins as a part of those proteins tertiary
structure, but which is too small and incomplete to constitute a complete folda motif
on its own would not be stable. Some motifs tend to have the same functional role in
most of the proteins in which they appear.

Peptidea molecule built by linking the amino and carboxylic acid groups of amino
acids to form a chain, distinguished from proteins by being too short to adopt a single
folded conformation. There is no agreed definition on where to draw the line between
peptides and proteins, in terms of the number of residues, but most biochemists would it
in the range of 20-30 amino acids.

Peptide bonda term for the amide linkage between two amino acid residues

Primary (1) structurethe sequence of a protein.

Prosthetic groupa group within a protein that is not made of amino acids. Includes
various small organic and inorganic molecules, as well as metal ions.

Proteina molecule built by linking the amino and carboxylic acid groups of amino
acids to form a chain, conventionally distinguished from peptides by being long enough
to adopt a single folded conformation (although some proteins with hundreds of residues
have been discovered that only adopt a specific conformation under certain
circumstances; these are considered proteins). There is no agreed definition on where to
draw the line between peptides and proteins, in terms of the number of residues, but most
biochemists would it in the range of 20-30 amino acids.

Quaternary (4) structurethe phenomenon whereby multiple independently folding
protein subunits, which may or may not be part of the same chain, come together to form
a larger complex held together by noncovalent interactions (or in some cases, disulfides).
The term quaternary structure can also mean the particular three-dimensional
arrangement of subunits in a complex or the stoichiometry of subunits of various types
found in a complex.

Residuea group of atoms in a protein or peptide corresponding to what was originally
an individual free amino acid, but which is now covalently linked to other amino acid
residues to form the much longer macromolecule.

Rotamerone of the energetically preferred conformations for a molecule or part of the
molecule, taking into account steric hindrance as well as attractive and repulsive forces.
The gauche and anti conformations of an alkane are examples of rotamers. With
proteins, the term is applied most commonly to sidechains.

Secondary (2) structurethe phenomenon whereby proteins fold into collections of
alpha helices and beta sheets, the secondary structural elements, which can then be
combined to build higher-order three-dimensional structures. An individual secondary
structural element is held together by hydrogen bonds between backbone atoms. The
term secondary structure can also mean the collection of all the secondary structural
elements found in a particular protein.

Sidechain or Side chainthe R group of an amino acid residue, so called because it is a
chain of atoms that branches off to the side from the backbone.

Subunitan independently folding component of a protein complex. A subunit may be
one domain out of several on a chain, or it may be a completely independent chain.

Tertiary (3) structurethe phenomenon of proteins or single subunits from
multisubunit proteins adopting a three-dimensional structure formed by arranging the
protein or subunits various secondary structural elements and the strands into a
particular shape. Tertiary structure is mostly held together by hydrophobic interactions
and hydrogen bonds; some proteins also incorporate one or more salt bridges or disulfide
bonds in order to provide greater stability for their tertiary structure. The term tertiary
structure can also mean the particular arrangement of secondary structural elements
and connecting loops found in a specific protein.