Proteins

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

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.

Amino acids

Def. "[a]ny organic compound containing both an amino and a carboxylic acid functional group"[1] is called an amino acid.

Def. any amino acid "having the amino, and carboxylic acid groups on the same carbon atom"[1] is called an α-amino acid.

Def. "[a] functional group formally derived from ammonia by replacing one, two or three hydrogen atoms"[2] is called an amine, or amino group.

Def. "[a] univalent functional group consisting of a carbonyl [-CO] and a hydroxyl [·OH] functional group"[3] 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[4] of any organism"[5] 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.[6]"[5]

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]n amide bond formed between the amino and carboxyl functional groups of separate amino acids"[7] 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"[8] is called a peptide.

Def. "two amino acids joined by a peptide bond"[9] is called a dipeptide.

Def. "three amino acids joined by peptide bonds"[10] 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"[11] is called an oligopeptide.

Def. "[a]ny polymer of (same or different) amino acids joined via peptide bonds"[12] 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 NH2-).

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."[13]

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

Def. "[a]ny protein that is cleaved by a convertase to form a smaller protein or biologically-active polypeptide"[14] is called a proprotein.

Proteoses

Def. a "mixture of peptides produced by the hydrolysis of proteins"[15] is called a proteose.

Peptones

Def. any "water-soluble product, a mixture of polypeptides and amino acids formed by the partial hydrolysis of protein"[16] is called a peptone.

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"[17] is called albumins.

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"[18] is called a globulin.

Prolamins

Def. any "of a group of plant storage proteins, that have a high proline content, found in cereals"[19] is called a prolamin.

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"[20] is called a histone.

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"[21] is called a protamine.

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)"[22] is called a conjugated protein.

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"[23] is called a cytochrome.

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"[24] is called a flavoprotein.

Glycoproteins

This is a computer model of the glycoprotein miraculin. Credit: Jmol development team.

Def. a "protein with covalently bonded carbohydrates"[25] is called a glycoprotein.

Hemeproteins

Def. any "conjugated protein containing heme as the prosthetic group"[26] is called a hemeprotein.

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"[27] is called a lipoprotein.

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"[28] is called a metalloprotein.

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"[29] is called an opsin.

Phosphoproteins

Def. "any protein containing bound phosphate"[30]is called a phosphoprotein.

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"[31] is called a phytochrome.

Scleroproteins

Fancy cartoon model is of the collagen triple helix. Credit: Vossman.

Def. any "of many fibrous proteins found in connective tissue etc"[32] is called a scleroprotein.

Research

Hypothesis:

  1. Amino acids in addition to the critical 22 are also coded genetically.

Control groups

This is an image of a Lewis rat. Credit: Charles River Laboratories.

The findings demonstrate a statistically systematic change from the status quo or the control group.

“In the design of experiments, treatments [or special properties or characteristics] are applied to [or observed in] experimental units in the treatment group(s).[33] In comparative experiments, members of the complementary group, the control group, receive either no treatment or a standard treatment.[34]"[35]

Proof of concept

Def. a “short and/or incomplete realization of a certain method or idea to demonstrate its feasibility"[36] is called a proof of concept.

Def. evidence that demonstrates that a concept is possible is called proof of concept.

The proof-of-concept structure consists of

  1. background,
  2. procedures,
  3. findings, and
  4. interpretation.[37]

See also

  • Biochemistry/Proteins
  • Biosynthesis of a human protein
  • Biosynthesis of amino acids
  • Factor
  • Folding
  • Food
  • Post translational modification
  • Principles of biosynthesis

References

  1. 1 2 "amino acid, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. August 29, 2012. Retrieved 2012-10-03.
  2. ↑ "amine, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. November 18, 2013. Retrieved 2013-11-29.
  3. ↑ "carboxyl, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. August 29, 2012. Retrieved 2012-10-03.
  4. ↑ 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.
  5. 1 2 "Proteinogenic amino acid, In: Wikipedia". San Francisco, California: Wikimedia Foundation, Inc. September 3, 2012. Retrieved 2012-10-03.
  6. ↑ 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.
  7. ↑ "peptide bond, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. August 29, 2012. Retrieved 2012-10-01.
  8. ↑ "peptide, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. August 30, 2012. Retrieved 2012-10-01.
  9. ↑ "dipeptide, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. August 30, 2012. Retrieved 2012-10-01.
  10. ↑ "tripeptide, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. August 30, 2012. Retrieved 2012-10-01.
  11. ↑ "oligopeptide, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. August 30, 2012. Retrieved 2012-10-01.
  12. ↑ "polypeptide, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. August 30, 2012. Retrieved 2012-10-01.
  13. ↑ "N-terminus, In: Wikipedia". San Francisco, California: Wikimedia Foundation, Inc. April 26, 2012. Retrieved 2012-10-03.
  14. ↑ "proprotein, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. August 14, 2008. Retrieved 2012-10-03.
  15. ↑ "proteose, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. June 18, 2013. Retrieved 2013-11-29.
  16. ↑ "peptone, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. November 10, 2013. Retrieved 2013-11-29.
  17. ↑ "albumin, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. October 18, 2013. Retrieved 2013-11-29.
  18. ↑ "title, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. October 8, 2013. Retrieved 2013-11-29.
  19. ↑ "prolamin, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. June 18, 2013. Retrieved 2013-11-29.
  20. ↑ "histone, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. October 7, 2013. Retrieved 2013-11-29.
  21. ↑ "protamine, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. June 18, 2013. Retrieved 2013-11-29.
  22. ↑ "conjugated protein, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. June 18, 2013. Retrieved 2013-11-29.
  23. ↑ Widsith and SemperBlotto (25 May 2010). "cytochrome, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 2015-07-10.
  24. ↑ SemperBlotto (23 April 2006). "flavoprotein, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 2015-07-10.
  25. ↑ Jag123 and SemperBlotto (9 March 2005). "glycoprotein, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 2015-07-09.
  26. ↑ SemperBlotto (18 April 2008). "hemeprotein, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 2015-07-10.
  27. ↑ SemperBlotto (29 June 2005). "lipoprotein, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 2015-07-09.
  28. ↑ SemperBlotto (3 November 2005). "metalloprotein, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 2015-07-10.
  29. ↑ SemperBlotto (20 February 2007). "opsin, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 2015-07-10.
  30. ↑ SemperBlotto (22 November 2006). "phosphoprotein, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 2015-07-10.
  31. ↑ SemperBlotto (11 April 2008). "phytochrome, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 2015-07-10.
  32. ↑ "scleroprotein, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. June 18, 2013. Retrieved 2013-11-29.
  33. ↑ Klaus Hinkelmann, Oscar Kempthorne (2008). Design and Analysis of Experiments, Volume I: Introduction to Experimental Design (2nd ed.). Wiley. ISBN 978-0-471-72756-9. http://books.google.com/?id=T3wWj2kVYZgC&printsec=frontcover.
  34. ↑ R. A. Bailey (2008). Design of comparative experiments. Cambridge University Press. ISBN 978-0-521-68357-9. http://www.cambridge.org/uk/catalogue/catalogue.asp?isbn=9780521683579.
  35. ↑ "Treatment and control groups, In: Wikipedia". San Francisco, California: Wikimedia Foundation, Inc. May 18, 2012. Retrieved 2012-05-31.
  36. ↑ "proof of concept, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. November 10, 2012. Retrieved 2013-01-13.
  37. ↑ Ginger Lehrman and Ian B Hogue, Sarah Palmer, Cheryl Jennings, Celsa A Spina, Ann Wiegand, Alan L Landay, Robert W Coombs, Douglas D Richman, John W Mellors, John M Coffin, Ronald J Bosch, David M Margolis (August 13, 2005). "Depletion of latent HIV-1 infection in vivo: a proof-of-concept study". Lancet 366 (9485): 549-55. doi:10.1016/S0140-6736(05)67098-5. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1894952/. Retrieved 2012-05-09.

External links

This is a research project at http://en.wikiversity.org

Development status: this resource is experimental in nature.
Educational level: this is a research resource.
Resource type: this resource is an article.
Resource type: this resource contains a lecture or lecture notes.
Subject classification: this is a biochemistry resource.
Subject classification: this is a medicine resource.
This article is issued from Wikiversity - version of the Friday, February 12, 2016. The text is available under the Creative Commons Attribution/Share Alike but additional terms may apply for the media files.