Proteins (/'pro??ti?nz/ or /'pro?ti.?

nz/) are large biological molecules, or mac

romolecules, consisting of one or more long chains of amino acid residues. Prote
ins perform a vast array of functions within living organisms, including catalyz
ing metabolic reactions, replicating DNA, responding to stimuli, and transportin
g molecules from one location to another. Proteins differ from one another prima
rily in their sequence of amino acids, which is dictated by the nucleotide seque
nce of their genes, and which usually results in folding of the protein into a s
pecific three-dimensional structure that determines its activity.
A linear chain of amino acid residues is called a polypeptide. A protein contain
s at least one long polypeptide. Short polypeptides, containing less than about
20-30 residues, are rarely considered to be proteins and are commonly called pep
tides, or sometimes oligopeptides. The individual amino acid residues are bonded
together by peptide bonds and adjacent amino acid residues. The sequence of ami
no acid residues in a protein is defined by the sequence of a gene, which is enc
oded in the genetic code. In general, the genetic code specifies 20 standard ami
no acids; however, in certain organisms the genetic code can include selenocyste
ine and in certain archaea pyrrolysine. Shortly after or even during synthesis, the
residues in a protein are often chemically modified by posttranslational modific
ation, which alters the physical and chemical properties, folding, stability, ac
tivity, and ultimately, the function of the proteins. Sometimes proteins have no
n-peptide groups attached, which can be called prosthetic groups or cofactors. P
roteins can also work together to achieve a particular function, and they often
associate to form stable protein complexes.
Once formed, proteins only exist for a certain period of time and are then degra
ded and recycled by the cell's machinery through the process of protein turnover
. A protein's lifespan is measured in terms of its half-life and covers a wide r
ange. They can exist for minutes or years with an average lifespan of 1 2 days in
mammalian cells. Abnormal and or misfolded proteins are degraded more rapidly ei
ther due to being targeted for destruction or due to being unstable.
Biochemistry
Main articles: Biochemistry, Amino acid and peptide bond
Chemical structure of the peptide bond (bottom) and the three-dimensional struct
ure of a peptide bond between an alanine and an adjacent amino acid (top/inset)
Resonance structures of the peptide bond that links individual amino acids to fo
rm a protein polymer
Most proteins consist of linear polymers built from series of up to 20 different
L-a-amino acids. All proteinogenic amino acids possess common structural featur
es, including an a-carbon to which an amino group, a carboxyl group, and a varia
ble side chain are bonded. Only proline differs from this basic structure as it
contains an unusual ring to the N-end amine group, which forces the CO NH amide mo
iety into a fixed conformation.[1] The side chains of the standard amino acids,
detailed in the list of standard amino acids, have a great variety of chemical s
tructures and properties; it is the combined effect of all of the amino acid sid
e chains in a protein that ultimately determines its three-dimensional structure
and its chemical reactivity.[2] The amino acids in a polypeptide chain are link
ed by peptide bonds. Once linked in the protein chain, an individual amino acid
is called a residue, and the linked series of carbon, nitrogen, and oxygen atoms
are known as the main chain or protein backbone.[3]
The peptide bond has two resonance forms that contribute some double-bond charac
ter and inhibit rotation around its axis, so that the alpha carbons are roughly
coplanar. The other two dihedral angles in the peptide bond determine the local
shape assumed by the protein backbone.[4] The end of the protein with a free car
boxyl group is known as the C-terminus or carboxy terminus, whereas the end with
a free amino group is known as the N-terminus or amino terminus. The words prot
ein, polypeptide, and peptide are a little ambiguous and can overlap in meaning.

Protein is generally used to refer to the complete biological molecule in a sta

ble conformation, whereas peptide is generally reserved for a short amino acid o
ligomers often lacking a stable three-dimensional structure. However, the bounda
ry between the two is not well defined and usually lies near 20 30 residues.[5] Po
lypeptide can refer to any single linear chain of amino acids, usually regardles
s of length, but often implies an absence of a defined conformation.
Biosynthesis
Main article: Protein biosynthesis
A ribosome produces a protein using mRNA as template.
The DNA sequence of a gene encodes the amino acid sequence of a protein.
Proteins are assembled from amino acids using information encoded in genes. Each
protein has its own unique amino acid sequence that is specified by the nucleot
ide sequence of the gene encoding this protein. The genetic code is a set of thr
ee-nucleotide sets called codons and each three-nucleotide combination designate
s an amino acid, for example AUG (adenine-uracil-guanine) is the code for methio
nine. Because DNA contains four nucleotides, the total number of possible codons
is 64; hence, there is some redundancy in the genetic code, with some amino aci
ds specified by more than one codon.[6] Genes encoded in DNA are first transcrib
ed into pre-messenger RNA (mRNA) by proteins such as RNA polymerase. Most organi
sms then process the pre-mRNA (also known as a primary transcript) using various
forms of Post-transcriptional modification to form the mature mRNA, which is th
en used as a template for protein synthesis by the ribosome. In prokaryotes the
mRNA may either be used as soon as it is produced, or be bound by a ribosome aft
er having moved away from the nucleoid. In contrast, eukaryotes make mRNA in the
cell nucleus and then translocate it across the nuclear membrane into the cytop
lasm, where protein synthesis then takes place. The rate of protein synthesis is
higher in prokaryotes than eukaryotes and can reach up to 20 amino acids per se
cond.[7]
The process of synthesizing a protein from an mRNA template is known as translat
ion. The mRNA is loaded onto the ribosome and is read three nucleotides at a tim
e by matching each codon to its base pairing anticodon located on a transfer RNA
molecule, which carries the amino acid corresponding to the codon it recognizes
. The enzyme aminoacyl tRNA synthetase "charges" the tRNA molecules with the cor
rect amino acids. The growing polypeptide is often termed the nascent chain. Pro
teins are always biosynthesized from N-terminus to C-terminus.[6]
The size of a synthesized protein can be measured by the number of amino acids i
t contains and by its total molecular mass, which is normally reported in units
of daltons (synonymous with atomic mass units), or the derivative unit kilodalto
n (kDa). Yeast proteins are on average 466 amino acids long and 53 kDa in mass.[
5] The largest known proteins are the titins, a component of the muscle sarcomer
e, with a molecular mass of almost 3,000 kDa and a total length of almost 27,000
amino acids.[8]