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Proteins (/protinz/ or /proti.
nz/) are large biomolecules, or macromolecules, consisting of one

or more long chains of amino acid residues. Proteins perform a vast array of functions
within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli,
and transporting molecules from one location to another. Proteins differ from one another primarily in
their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and
which usually results in protein folding into a specific three-dimensional structure that determines its
activity.
A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long
polypeptide. Short polypeptides, containing less than 2030 residues, are rarely considered to be
proteins and are commonly called peptides, or sometimes oligopeptides. The individual amino acid
residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of
amino acid residues in a protein is defined by the sequence of a gene, which is encoded in
the genetic code. In general, the genetic code specifies 20 standard amino acids; however, in certain
organisms the genetic code can include selenocysteine andin certain archaeapyrrolysine.
Shortly after or even during synthesis, the residues in a protein are often chemically modified
by post-translational modification, which alters the physical and chemical properties, folding, stability,
activity, and ultimately, the function of the proteins. Sometimes proteins have non-peptide groups
attached, which can be called prosthetic groups or cofactors. Proteins 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 degraded 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 range. They can exist for minutes or years with an average
lifespan of 12 days in mammalian cells. Abnormal or misfolded proteins are degraded more rapidly
either due to being targeted for destruction or due to being unstable.
Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are
essential parts of organisms and participate in virtually every process within cells. Many proteins
are enzymes that catalyse biochemical reactions and are vital to metabolism. Proteins also have
structural or mechanical functions, such as actin and myosin in muscle and the proteins in
the cytoskeleton, which form a system of scaffolding that maintains cell shape. Other proteins are
important in cell signaling, immune responses, cell adhesion, and the cell cycle. In animals, proteins
are needed in the diet to provide the essential amino acids that cannot
be synthesized. Digestion breaks the proteins down for use in the metabolism.
Proteins may be purified from other cellular components using a variety of techniques such
as ultracentrifugation, precipitation, electrophoresis, and chromatography; the advent of genetic
engineering has made possible a number of methods to facilitate purification. Methods commonly
used to study protein structure and function include immunohistochemistry, site-directed
mutagenesis, X-ray crystallography, nuclear magnetic resonance and mass spectrometry.
Contents
[hide]
1Biochemistry
o 1.1Abundance in cells
2Synthesis
o 2.1Biosynthesis
o 2.2Chemical synthesis
3Structure
o 3.1Structure determination
4Cellular functions
o 4.1Enzymes
o 4.2Cell signaling and ligand binding
o 4.3Structural proteins
5Methods of study
o 5.1Protein purification
o 5.2Cellular localization
o 5.3Proteomics
o 5.4Bioinformatics
5.4.1Structure prediction and simulation
5.4.2Protein disorder and unstructure prediction
6Nutrition
7History and etymology
8See also
9References
10Textbooks
11External links
o 11.1Databases and projects
o 11.2Tutorials and educational websites
Biochemistry
Chemical structure of the peptide bond (bottom) and the three-dimensional structure 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 form a protein polymer
Main articles: Biochemistry, Amino acid, and Peptide bond

Most proteins consist of linear polymers built from series of up to 20 different L--amino acids.
All proteinogenic amino acids possess common structural features, including an -carbon to which
an amino group, a carboxyl group, and a variable 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 moiety 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 structures and properties; it is
the combined effect of all of the amino acid side chains in a protein that ultimately determines its
three-dimensional structure and its chemical reactivity.[2] The amino acids in a polypeptide chain are
linked 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 character 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
with a free amino group is known as the N-terminus or amino terminus, whereas the end of the
protein with a free carboxyl group is known as the C-terminus or carboxy terminus (the sequence of
the protein is written from N-terminus to C-terminus, from left to right).
The words protein, 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
stable conformation, whereas peptide is generally reserved for a short amino acid oligomers often
lacking a stable three-dimensional structure. However, the boundary between the two is not well
defined and usually lies near 2030 residues.[5] Polypeptide can refer to any single linear chain of
amino acids, usually regardless of length, but often implies an absence of a defined conformation.
Abundance in cells
It has been estimated that average-sized bacteria contain about 2 million proteins per cell (e.g. E.
coli and Staphylococcus aureus). Smaller bacteria, such as Mycoplasma or spirochetes contain
fewer molecules, namely on the order of 50,000 to 1 million. By contrast, eukaryotic cells are larger
and thus contain much more protein. For instance, yeast cells were estimated to contain about 50
million proteins and human cells on the order of 1 to 3 billion.[6]The concentration of individual protein
copies ranges from a few molecules per cell up to 20 million.[7] Not all genes coding proteins are
expressed in most cells and their number depends on for example cell type and external stimuli. For
instance, of the 20,000 or so proteins encoded by the human genome, only 6,000 are detected
in lymphoblastoid cells.[8] Moreover, the number of proteins the genome encodes correlates well with
the organism complexity. Eukaryotes, bacteria, Archaea and viruses have on average 15145, 3200,
2358 and 42 proteins respectively coded in their genomes.[9]
Synthesis
Biosynthesis
A ribosome produces a protein using mRNA as template

The DNA sequence of a gene encodes the amino acid sequence of a protein
Main article: Protein biosynthesis

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 nucleotidesequence of the gene encoding
this protein. The genetic code is a set of three-nucleotide sets called codons and each three-
nucleotide combination designates an amino acid, for example AUG (adenine-uracil-guanine) is the
code for methionine. 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 acids specified by more
than one codon.[10] Genes encoded in DNA are first transcribed into pre-messenger RNA (mRNA) by
proteins such as RNA polymerase. Most organisms 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 then 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 after 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 cytoplasm, 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 second.[11]
The process of synthesizing a protein from an mRNA template is known as translation. The mRNA is
loaded onto the ribosome and is read three nucleotides at a time 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 correct amino acids. The growing polypeptide is often termed the nascent chain. Proteins
are always biosynthesized from N-terminus to C-terminus.[10]
The size of a synthesized protein can be measured by the number of amino acids it contains and by
its total molecular mass, which is normally reported in units of daltons (synonymous with atomic
mass units), or the derivative unit kilodalton (kDa). The average size of protein increases from
Archaea, Bacteria to Eukaryote (283, 311, 438 residues and 31, 34, 49 kDa respecitvely) due bigger
number of protein domains constituting proteins in higher organisms.[9] For instance, 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 sarcomere, with a molecular mass of almost 3,000 kDa and a
total length of almost 27,000 amino acids.[12]
Chemical synthesis
Short proteins can also be synthesized chemically by a family of methods known as peptide
synthesis, which rely on

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Proteins (/protinz/ or /proti.

nz/) are large biomolecules, or macromolecules, consisting of one

Main articles: Biochemistry, Amino acid, and Peptide bond

A ribosome produces a protein using mRNA as template

Main article: Protein biosynthesis

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