Draft:Proteins

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This is a computer representation of the crystal structure of the asymmetric GroEL-GroES-(ADP)7 chaperonin complex. Credit: Thomas Splettstoesser.

A protein is one or more polypeptides held together by peptide bonds.

Theoretical proteins

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Here's a theoretical definition:

Def. any naturally occurring complex combinations of amino acids that contain at least the elements: carbon (C), hydrogen (H), nitrogen (N), and oxygen (O) are called proteins.

Def. any "of numerous large, complex naturally-produced molecules composed of one or more long chains of amino acids, in which the amino acid groups are held together by peptide bonds"[1] is called a protein.

Def. a "large, complex molecule composed of one or more long chains of amino acids, in which each chain is held together by peptide bonds"[2] is called a protein.

Def. a "large, complex molecule composed of long chains of amino acids linked by a peptide bond"[3] is called a protein.

Def. "any of numerous naturally occurring extremely complex combinations of amino acids that contain the elements carbon, hydrogen, nitrogen, oxygen, usually sulfur, occasionally phosphorus, iron, or other elements, are essential constituents of all living cells, and are synthesized from raw materials by plants but assimilated as separate amino acids by animals"[4] is called a protein.

Biochemistry

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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.[5] 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.[6]

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.[7][8]

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.[7]

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 20–30 residues.[9]

Proteins can interact with many types of molecules, including with other proteins, with lipids, with carboyhydrates, and with DNA.[10][11][12][13]

Amino acids

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Main article: Amino acids

Def. "[a]ny organic compound containing both an amino and a carboxylic acid functional group"[14] is called an amino acid.

Def. any amino acid "having the amino, and carboxylic acid groups on the same carbon atom"[14] is called an α-amino acid.

Def. "[a] functional group formally derived from ammonia by replacing one, two or three hydrogen atoms"[15] is called an amine, or amino group.

Def. "[a] univalent functional group consisting of a carbonyl [-CO] and a hydroxyl [·OH] functional group"[16] is called a carboxyl, or carboxylic acid group.

Notation: let the symbol COOH represent the carboxylic acid group.

Def. "amino acids that are precursors to proteins, and are produced by cellular machinery coded for in the genetic code[17] of any organism"[18] are called proteinogenic amino acids.

"The proteinogenic amino acids have been found to be related to the set of amino acids that can be recognized by ribozyme auto-aminoacylation systems.[19]"[18]

Peptides

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Main articles: Chemicals/Bio-organics/Peptides and Peptides
Shown in the diagram is a ball and stick model (above) with the chemical formula (below) of a peptide bond between alanine and an adjacent amino acid. Credit: Chemistry-grad-student.
A tetrapeptide with the N-terminus in green and the C-terminus in blue. Credit: Jü.

Def. a "covalent bond [amide bond][20] formed between the amino and carboxyl functional groups of separate amino acids"[21] is called a peptide bond.

Def. "various numbers of amino acids in which the amine of one is reacted with the carboxylic acid of the next to form an amide bond"[22] is called a peptide.

Def. "two amino acids joined by a peptide bond"[23] is called a dipeptide.

Def. "three amino acids joined by peptide bonds"[24] is called a tripeptide.

Def. four amino acids joined by peptide bonds is called a tetrapeptide.

Def. five amino acids joined by peptide bonds is called a pentapeptide.

Def. a "peptide containing a relatively small number of amino acids"[25] is called an oligopeptide.

Def. "[a]ny polymer of (same or different) amino acids joined via peptide bonds"[26] is called a polypeptide.

In the diagram at top right, the remainder of the carboxyl group (C = O) has been bonded to the the remainder of the amino group (NH) of an adjacent amino acid by a peptide bond. The remainder of the carbonyl group and amino group has been formed into H2O ← OH (from -C=O·OH) + H (from ).

The second from the top diagram shows the amino group end (or N-terminus) in green and the carboxyl group end (or C-terminus) in blue of a tetrapeptide ([Valine] Val-[Glycine] Gly-[Serine] Ser-[Alanine] Ala).

"The convention for writing peptide sequences is to put the N-terminus on the left and write the sequence from N- to C-terminus."[27]

Preproteins

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Main articles: Chemicals/Bio-organics/Preproteins and Preproteins

Def. any protein or polypeptide containing a signal sequence that specifies its insertion into or through membranes is called a preprotein.

Def. any preprotein of a proprotein is called a preproprotein.

Proproteins

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Main articles: Chemicals/Bio-organics/Proproteins and Proproteins

Def. "[a]ny protein that is cleaved by a convertase to form a smaller protein or biologically-active polypeptide"[28] is called a proprotein.

Proteoses

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Main articles: Chemicals/Bio-organics/Proteoses and Proteoses

Def. a "mixture of peptides produced by the hydrolysis of proteins"[29] is called a proteose.

Peptones

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Main articles: Chemicals/Bio-organics/Peptones and Peptones

Def. any "water-soluble product, a mixture of polypeptides and amino acids formed by the partial hydrolysis of protein"[30] is called a peptone.

Albumins

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Main articles: Chemicals/Bio-organics/Albumins and Albumins
Cartoon representation is of the molecular structure of serum albumin. Credit: Jawahar Swaminathan and MSD staff at the European Bioinformatics Institute.

Def. a "class of monomeric proteins that are soluble in water, and are coagulated by heat; they occur in egg white, milk etc; they function as carrier protein for steroids, fatty acids, and thyroid hormones and play a role in stabilizing extracellular fluid volume"[31] is called albumins.

Globulins

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Main articles: Chemicals/Bio-organics/Globulins and Globulins
Crystal structure is of pumpkin seed globulin with molecular surface. Credit: MarinaVladivostok.

Def. any "of a group of simple proteins, soluble in water only in the presence of salts, that are coagulated by heat; one of the two parts of hæmoglobin"[32] is called a globulin.

Prolamins

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Main articles: Chemicals/Bio-organics/Prolamins and Prolamins

Def. any "of a group of plant storage proteins, that have a high proline content, found in cereals"[33] is called a prolamin.

Histones

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Main articles: Chemicals/Bio-organics/Histones and Histones
Structure is of the H2AFJ histone. Credit: Emw.

Def. any "of various simple water soluble proteins that are rich in the basic amino acids lysine and arginine and are complexed with DNA in the nucleosomes of eukaryotic chromatin"[34] is called a histone.

Protamines

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Main articles: Chemicals/Bio-organics/Protamines and Protamines

Def. "any of a class of proteins, rich in arginine, found in the sperm of fish; used medicinally to control the action of insulin"[35] is called a protamine.

Conjugated proteins

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Main articles: Chemicals/Bio-organics/Conjugated proteins and Conjugated proteins
This is a model of hemoglobin. Credit: Роман Беккер.

Def. any "protein that consists of both a polypeptide and a prosthetic group such as a lipid (in lipoproteins), sugar (in glycoproteins) or porphyrins and metals (in hemoglobin etc)"[36] is called a conjugated protein.

Cytochromes

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Main articles: Chemicals/Bio-organics/Cytochromes and Cytochromes
This is a model for the structure of horse heart cytochrome c. Credit: Klaus Hoffmeier.

Def. any "of various related hemoproteins found in the cells of most organisms, which are an important part of cell respiration"[37] is called a cytochrome.

Flavoproteins

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Main articles: Chemicals/Bio-organics/Flavoproteins and Flavoproteins
Cartoon representation is of the molecular structure of protein 4'-phosphopantothenoylcysteine decarboxylase. Credit: Jawahar Swaminathan and MSD staff at the European Bioinformatics Institute.

Def. "any of a group of enzymes, containing flavin, that act as dehydrogenases"[38] is called a flavoprotein.

Glycoproteins

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Main articles: Chemicals/Bio-organics/Glycoproteins and Glycoproteins
This is a computer model of the glycoprotein miraculin. Credit: Jmol development team.

Def. a "protein with covalently bonded carbohydrates"[39] is called a glycoprotein.

Hemeproteins

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Main articles: Chemicals/Bio-organics/Hemeproteins and Hemeproteins

Def. any "conjugated protein containing heme as the prosthetic group"[40] is called a hemeprotein.

Lipoproteins

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Main articles: Chemicals/Bio-organics/Lipoproteins and Lipoproteins
This is a model of the chylomicron structure. Credit: Xvazquez.
Illustration is from Anatomy & Physiology, Connexions Web site. Credit: OpenStax College.

Def. any "of a large group of complexes of protein and lipid with many biochemical functions"[41] is called a lipoprotein.

Metalloproteins

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Main articles: Chemicals/Bio-organics/Metalloproteins and Metalloproteins
The structure of hemoglobin contains the heme cofactor with iron, shown in green. Credit: Richard Wheeler.

Def. "a protein, such as haemoglobin or chlorophyll, that contains a metal atom as a cofactor"[42] is called a metalloprotein.

Opsins

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Main articles: Chemicals/Bio-organics/Opsins and Opsins
This is a model of the 3D structure of bovine rhodopsin. Credit: Roland Deschain.

Def. any "of a group of light-sensitive proteins in the retina"[43] is called an opsin.

Phosphoproteins

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Main articles: Chemicals/Bio-organics/Phosphoproteins and Phosphoproteins

Def. "any protein containing bound phosphate"[44]is called a phosphoprotein.

Phytochromes

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Main articles: Chemicals/Bio-organics/Phytochromes and Phytochromes
This is a screenshot of a model of phytochrome. Credit: Jmol Development Team.

Def. any "of a class of pigments that control most photomorphogenic responses in higher plants"[45] is called a phytochrome.

Scleroproteins

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Main articles: Chemicals/Bio-organics/Scleroproteins and Scleroproteins
Fancy cartoon model is of the collagen triple helix. Credit: Vossman.

Def. any "of many fibrous proteins found in connective tissue etc"[46] is called a scleroprotein.

Hypotheses

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Main article: Hypotheses
  1. Amino acids in addition to the critical 22 are also coded genetically.

See also

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References

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  1. ↑ H Padleckas (20 February 2011). "protein". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 1 September 2019. {{cite web}}: |author= has generic name (help)
  2. ↑ Mr gronk (7 December 2008). "protein". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 1 September 2019. {{cite web}}: |author= has generic name (help)
  3. ↑ Jag123 (10 March 2005). "protein". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 1 September 2019. {{cite web}}: |author= has generic name (help)
  4. ↑ Philip B. Gove, ed. (1963). "Webster's Seventh New Collegiate Dictionary". Springfield, Massachusetts: G. & C. Merriam Company. p. 1221. Retrieved 2011-08-26.
  5. ↑ Lehninger's Principles of Biochemistry (4th ed.). New York, New York: W. H. Freeman and Company. 2005. 
  6. ↑ "Understanding nature's catalytic toolkit". Trends in Biochemical Sciences 30 (11): 622–29. November 2005. doi:10.1016/j.tibs.2005.09.006. PMID 16214343. 
  7. ↑ 7.0 7.1 Harper's Illustrated Biochemistry. New York: Lange Medical Books/McGraw-Hill. 2006. ISBN 978-0-07-146197-9. 
  8. ↑ Biochemistry. Menlo Park, California: Benjamin/Cummings Pub. Co., Inc. 1996. ISBN 978-0-8053-3931-4. 
  9. ↑ Molecular Cell Biology (5th ed.). New York, New York: WH Freeman and Company. 2004. 
  10. ↑ Ardejani, Maziar S.; Powers, Evan T.; Kelly, Jeffery W. (2017). "Using Cooperatively Folded Peptides To Measure Interaction Energies and Conformational Propensities". Accounts of Chemical Research 50 (8): 1875–82. doi:10.1021/acs.accounts.7b00195. ISSN 0001-4842. PMID 28723063. PMC 5584629. //www.ncbi.nlm.nih.gov/pmc/articles/PMC5584629/. 
  11. ↑ Introduction to Protein Structure. New York: Garland Pub. 1999. ISBN 978-0-8153-2305-1. 
  12. ↑ Harper's Illustrated Biochemistry. New York: Lange Medical Books/McGraw-Hill. 2006. ISBN 978-0-07-146197-9. 
  13. ↑ Biochemistry. Menlo Park, California: Benjamin/Cummings Pub. Co., Inc. 1996. ISBN 978-0-8053-3931-4. 
  14. ↑ 14.0 14.1 "amino acid, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. August 29, 2012. Retrieved 2012-10-03.
  15. ↑ "amine, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. November 18, 2013. Retrieved 2013-11-29.
  16. ↑ "carboxyl, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. August 29, 2012. Retrieved 2012-10-03.
  17. ↑ Ambrogelly A, Palioura S, Söll D (January 2007). "Natural expansion of the genetic code". Nat Chem Biol 3 (1): 29–35. doi:10.1038/nchembio847. PMID 17173027. http://www.nature.com/nchembio/journal/v3/n1/abs/nchembio847.html. 
  18. ↑ 18.0 18.1 "Proteinogenic amino acid, In: Wikipedia". San Francisco, California: Wikimedia Foundation, Inc. September 3, 2012. Retrieved 2012-10-03.
  19. ↑ Erives A (2011). "A Model of Proto-Anti-Codon RNA Enzymes Requiring L-Amino Acid Homochirality". J Molecular Evolution 73: 10-22. doi:10.1007/s00239-011-9453-4. PMID 21779963. 
  20. ↑ SemperBlotto (16 September 2005). "peptide bond". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 2012-10-01. {{cite web}}: |author= has generic name (help)
  21. ↑ Jag123 (10 March 2005). "peptide bond". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 2012-10-01. {{cite web}}: |author= has generic name (help)
  22. ↑ SemperBlotto (16 September 2005). "peptide". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 2012-10-01. {{cite web}}: |author= has generic name (help)
  23. ↑ SemperBlotto (16 September 2005). "dipeptide". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 2012-10-01. {{cite web}}: |author= has generic name (help)
  24. ↑ Kappa~enwiktionary (12 June 2006). "tripeptide". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 2012-10-01. {{cite web}}: |author= has generic name (help)
  25. ↑ SemperBlotto (9 December 2007). "oligopeptide". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 2012-10-01. {{cite web}}: |author= has generic name (help)
  26. ↑ SemperBlotto (14 July 2008). "polypeptide". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 2012-10-01. {{cite web}}: |author= has generic name (help)
  27. ↑ "N-terminus". San Francisco, California: Wikimedia Foundation, Inc. April 26, 2012. Retrieved 2012-10-03.
  28. ↑ "proprotein, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. August 14, 2008. Retrieved 2012-10-03.
  29. ↑ "proteose, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. June 18, 2013. Retrieved 2013-11-29.
  30. ↑ "peptone, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. November 10, 2013. Retrieved 2013-11-29.
  31. ↑ "albumin, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. October 18, 2013. Retrieved 2013-11-29.
  32. ↑ "title, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. October 8, 2013. Retrieved 2013-11-29.
  33. ↑ "prolamin, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. June 18, 2013. Retrieved 2013-11-29.
  34. ↑ "histone, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. October 7, 2013. Retrieved 2013-11-29.
  35. ↑ "protamine, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. June 18, 2013. Retrieved 2013-11-29.
  36. ↑ "conjugated protein, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. June 18, 2013. Retrieved 2013-11-29.
  37. ↑ Widsith and SemperBlotto (25 May 2010). "cytochrome, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 2015-07-10. {{cite web}}: |author= has generic name (help)
  38. ↑ SemperBlotto (23 April 2006). "flavoprotein, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 2015-07-10. {{cite web}}: |author= has generic name (help)
  39. ↑ Jag123 and SemperBlotto (9 March 2005). "glycoprotein, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 2015-07-09. {{cite web}}: |author= has generic name (help)
  40. ↑ SemperBlotto (18 April 2008). "hemeprotein, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 2015-07-10. {{cite web}}: |author= has generic name (help)
  41. ↑ SemperBlotto (29 June 2005). "lipoprotein, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 2015-07-09. {{cite web}}: |author= has generic name (help)
  42. ↑ SemperBlotto (3 November 2005). "metalloprotein, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 2015-07-10. {{cite web}}: |author= has generic name (help)
  43. ↑ SemperBlotto (20 February 2007). "opsin, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 2015-07-10. {{cite web}}: |author= has generic name (help)
  44. ↑ SemperBlotto (22 November 2006). "phosphoprotein, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 2015-07-10. {{cite web}}: |author= has generic name (help)
  45. ↑ SemperBlotto (11 April 2008). "phytochrome, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 2015-07-10. {{cite web}}: |author= has generic name (help)
  46. ↑ "scleroprotein, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. June 18, 2013. Retrieved 2013-11-29.
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