Editing Protein (section)

== Biochemistry ==

[[File:Peptide-Figure-Revised.png|thumb|upright=1.35|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). The bond itself is made of the [[CHON]] elements.]]
[[File:Mesomeric peptide bond.svg|thumb|upright=1.35|[[Resonance (chemistry)|Resonance]] structures of the [[peptide bond]] that links individual amino acids to form a protein [[polymer]]]]

{{Main|Biochemistry|Amino acid|Peptide bond}}

Most proteins consist of linear [[polymer]]s built from series of up to 20 [[Chirality (chemistry)#In biochemistry|<small>L</small>-α-]]amino acids. All [[proteinogenic amino acid]]s have a common structure where an [[alpha carbon|α-carbon]] is [[chemical bond|bonded]] to an [[amino]] group, a [[carboxyl]] group, and a variable [[side chain]]. Only [[proline]] differs from this basic structure as its side chain is cyclical, bonding to the amino group, limiting protein chain flexibility.<ref name=Nelson2005/> The side chains of the [[list of standard amino acids|standard amino acids]] have a variety of chemical structures and properties, and it is the combined effect of all amino acids that determines its three-dimensional structure and chemical reactivity.<ref name=Gutteridge2005/>

The amino acids in a polypeptide chain are linked by [[peptide bond]]s between amino and carboxyl group. An individual amino acid in a chain is called a ''residue,'' and the linked series of carbon, nitrogen, and oxygen atoms are known as the ''main chain'' or ''protein backbone.''<ref name = "Murray_2006">{{cite book | vauthors = Murray RF, Harper HW, Granner DK, Mayes PA, Rodwell VW |title=Harper's Illustrated Biochemistry |publisher=Lange Medical Books/McGraw-Hill |location=New York |year=2006 |isbn=978-0-07-146197-9}}</ref>{{rp|19}} The peptide bond has two [[resonance (chemistry)|resonance]] forms that confer some [[double-bond]] character to the backbone. The alpha carbons are roughly [[coplanar]] with the nitrogen and the carbonyl (C=O) group. The other two [[dihedral angle]]s in the peptide bond determine the local shape assumed by the protein backbone. One conseqence of the N-C(O) double bond character is that proteins are somewhat rigid.<ref name = "Murray_2006" />{{rp|31}} A polypeptide chain ends with a free amino group, known as the ''[[N-terminus]]'' or ''amino terminus,'' and a free carboxyl group, known as the ''[[C-terminus]]'' or ''carboxy terminus''.<ref name=Reusch2013MSU>{{Cite web|url=https://www2.chemistry.msu.edu/faculty/reusch/virttxtjml/protein2.htm|title=Peptides & Proteins|last=Reusch|first=William|date=5 May 2013|website=Michigan State University Department of Chemistry}}</ref> By convention, peptide sequences are written N-terminus to C-terminus, correlating with the order in which proteins are [[translation (biology)|synthesized by ribosomes]].<ref name=Reusch2013MSU/><ref>{{cite book | last = Stryer | first = Lubert | name-list-style = vanc | title = Biochemistry | edition = Fifth | publisher = [[W. H. Freeman and Company]] | year = 2002 | isbn = 0-7167-4684-0 | page = 826 }}</ref>

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 [[tertiary structure|conformation]], whereas ''peptide'' is generally reserved for a short amino acid oligomers often lacking a stable 3D structure. But the boundary between the two is not well defined and usually lies near 20–30 residues.<ref name=Lodish2004/>

Proteins can interact with many types of molecules and ions, including [[protein–protein interaction|with other proteins]], [[Protein–lipid interaction|with lipids]], [[Protein–carbohydrate interaction|with carbohydrates]], and [[Protein–DNA interaction|with DNA]].<ref>{{cite journal | vauthors = Ardejani MS, Powers ET, Kelly JW | title = Using Cooperatively Folded Peptides To Measure Interaction Energies and Conformational Propensities | journal = Accounts of Chemical Research | volume = 50 | issue = 8 | pages = 1875–1882 | date = August 2017 | pmid = 28723063 | pmc = 5584629 | doi = 10.1021/acs.accounts.7b00195 }}</ref><ref name = "Brandon_1999">{{cite book |vauthors=Branden C, Tooze J |title=Introduction to Protein Structure |publisher=Garland Pub |location=New York |year=1999 |isbn=978-0-8153-2305-1}}</ref><ref name = "Van_Holde_1996">{{cite book |vauthors=Van Holde KE, Mathews CK |title=Biochemistry |publisher=Benjamin/Cummings |location=Menlo Park, California |year=1996 |isbn=978-0-8053-3931-4 |url=https://archive.org/details/biochemistry00math }}</ref>

=== Abundance in cells ===

A typical [[bacteria]]l cell, e.g. ''[[Escherichia coli|E. coli]]'' and ''[[Staphylococcus aureus]]'', is estimated to contain about 2 million proteins. Smaller bacteria, such as ''[[Mycoplasma]]'' or ''[[Spirochaete|spirochetes]]'' contain fewer molecules, on the order of 50,000 to 1 million. By contrast, [[Eukaryote|eukaryotic]] cells are larger and thus contain much more protein. For instance, [[Saccharomyces cerevisiae|yeast]] cells have been estimated to contain about 50 million proteins and [[human]] cells on the order of 1 to 3 billion.<ref>{{cite journal | vauthors = Milo R | title = What is the total number of protein molecules per cell volume? A call to rethink some published values | journal = BioEssays | volume = 35 | issue = 12 | pages = 1050–1055 | date = December 2013 | pmid = 24114984 | pmc = 3910158 | doi = 10.1002/bies.201300066 }}</ref> The concentration of individual protein copies ranges from a few molecules per cell up to 20 million.<ref name="pmid22068332">{{cite journal | vauthors = Beck M, Schmidt A, Malmstroem J, Claassen M, Ori A, Szymborska A, Herzog F, Rinner O, Ellenberg J, Aebersold R | title = The quantitative proteome of a human cell line | journal = Molecular Systems Biology | volume = 7 | pages = 549 | date = November 2011 | pmid = 22068332 | pmc = 3261713 | doi = 10.1038/msb.2011.82 }}</ref> 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.<ref>{{cite journal | vauthors = Wu L, Candille SI, Choi Y, Xie D, Jiang L, Li-Pook-Than J, Tang H, Snyder M | title = Variation and genetic control of protein abundance in humans | journal = Nature | volume = 499 | issue = 7456 | pages = 79–82 | date = July 2013 | pmid = 23676674 | pmc = 3789121 | doi = 10.1038/nature12223 | bibcode = 2013Natur.499...79W }}</ref>  The most abundant protein in nature is thought to be [[RuBisCO]], an enzyme that catalyzes the incorporation of [[carbon dioxide]] into organic matter in [[photosynthesis]].  Plants can consist of as much as 1% by weight of this enzyme.<ref>{{cite journal |doi=10.1016/0968-0004(79)90212-3 |title=The most abundant protein in the world |date=1979 |last1=Ellis |first1=R.John |journal=Trends in Biochemical Sciences |volume=4 |issue=11 |pages=241–244 }}</ref>