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Most microorganisms and plants can biosynthesize all 20 standard amino acids, while animals (including humans) must obtain some of the amino acids from the diet. [44] The amino acids that an organism cannot synthesize on its own are referred to as essential amino acids. Key enzymes that synthesize certain amino acids are not present in animals—such as aspartokinase, which catalyses the first step in the synthesis of lysine, methionine, and threonine from aspartate. If amino acids are present in the environment, microorganisms can conserve energy by taking up the amino acids from their surroundings and downregulating their biosynthetic pathways. Nelson DL, Cox MM (2005). Lehninger's Principles of Biochemistry (4thed.). New York, New York: W. H. Freeman and Company.

Proteins were first described by the Dutch chemist Gerardus Johannes Mulder and named by the Swedish chemist Jöns Jacob Berzelius in 1838. [2] [3] Mulder carried out elemental analysis of common proteins and found that nearly all proteins had the same empirical formula, C 400H 620N 100O 120P 1S 1. [4] He came to the erroneous conclusion that they might be composed of a single type of (very large) molecule. The term "protein" to describe these molecules was proposed by Mulder's associate Berzelius; protein is derived from the Greek word πρώτειος ( proteios), meaning "primary", [5] "in the lead", or "standing in front", [6] + -in. Mulder went on to identify the products of protein degradation such as the amino acid leucine for which he found a (nearly correct) molecular weight of 131 Da. [4] Prior to "protein", other names were used, like "albumins" or "albuminous materials" ( Eiweisskörper, in German). [7] Mulder GJ (1838). "Sur la composition de quelques substances animales". Bulletin des Sciences Physiques et Naturelles en Néerlande: 104. Yuste R (December 2005). "Fluorescence microscopy today". Nature Methods. 2 (12): 902–4. doi: 10.1038/nmeth1205-902. PMID 16299474. S2CID 205418407. Samarin S, Nusrat A (January 2009). "Regulation of epithelial apical junctional complex by Rho family GTPases". Frontiers in Bioscience. 14 (14): 1129–42. doi: 10.2741/3298. PMID 19273120.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 metabolic use. Brosnan JT (June 2003). "Interorgan amino acid transport and its regulation". The Journal of Nutrition. 133 (6 Suppl 1): 2068S–72S. doi: 10.1093/jn/133.6.2068S. PMID 12771367. Linus Pauling is credited with the successful prediction of regular protein secondary structures based on hydrogen bonding, an idea first put forth by William Astbury in 1933. [12] Later work by Walter Kauzmann on denaturation, [13] [14] based partly on previous studies by Kaj Linderstrøm-Lang, [15] contributed an understanding of protein folding and structure mediated by hydrophobic interactions. Schwarzer D, Cole PA (December 2005). "Protein semisynthesis and expressed protein ligation: chasing a protein's tail". Current Opinion in Chemical Biology. 9 (6): 561–69. doi: 10.1016/j.cbpa.2005.09.018. PMID 16226484.

Finally, the gold-standard method of cellular localization is immunoelectron microscopy. This technique also uses an antibody to the protein of interest, along with classical electron microscopy techniques. The sample is prepared for normal electron microscopic examination, and then treated with an antibody to the protein of interest that is conjugated to an extremely electro-dense material, usually gold. This allows for the localization of both ultrastructural details as well as the protein of interest. [63]

Amino acids

Bairoch A (January 2000). "The ENZYME database in 2000" (PDF). Nucleic Acids Research. 28 (1): 304–05. doi: 10.1093/nar/28.1.304. PMC 102465. PMID 10592255. Archived from the original (PDF) on June 1, 2011. Zhang C, Kim SH (February 2003). "Overview of structural genomics: from structure to function". Current Opinion in Chemical Biology. 7 (1): 28–32. doi: 10.1016/S1367-5931(02)00015-7. PMID 12547423. Archived from the original on 2018-11-19 . Retrieved 2019-06-29.

Hoffmann M, Wanko M, Strodel P, König PH, Frauenheim T, Schulten K, Thiel W, Tajkhorshid E, Elstner M (August 2006). "Color tuning in rhodopsins: the mechanism for the spectral shift between bacteriorhodopsin and sensory rhodopsin II". Journal of the American Chemical Society. 128 (33): 10808–18. doi: 10.1021/ja062082i. PMID 16910676. Dobson CM (2000). "The nature and significance of protein folding". In Pain RH (ed.). Mechanisms of Protein Folding. Oxford, Oxfordshire: Oxford University Press. pp.1–28. ISBN 978-0-19-963789-8.Standley DM, Kinjo AR, Kinoshita K, Nakamura H (July 2008). "Protein structure databases with new web services for structural biology and biomedical research". Briefings in Bioinformatics. 9 (4): 276–85. doi: 10.1093/bib/bbn015. PMID 18430752. Gonen T, Cheng Y, Sliz P, Hiroaki Y, Fujiyoshi Y, Harrison SC, Walz T (December 2005). "Lipid-protein interactions in double-layered two-dimensional AQP0 crystals". Nature. 438 (7068): 633–38. Bibcode: 2005Natur.438..633G. doi: 10.1038/nature04321. PMC 1350984. PMID 16319884. Wu L, Candille SI, Choi Y, Xie D, Jiang L, Li-Pook-Than J, Tang H, Snyder M (July 2013). "Variation and genetic control of protein abundance in humans". Nature. 499 (7456): 79–82. Bibcode: 2013Natur.499...79W. doi: 10.1038/nature12223. PMC 3789121. PMID 23676674. Transmembrane proteins can also serve as ligand transport proteins that alter the permeability of the cell membrane to small molecules and ions. The membrane alone has a hydrophobic core through which polar or charged molecules cannot diffuse. Membrane proteins contain internal channels that allow such molecules to enter and exit the cell. Many ion channel proteins are specialized to select for only a particular ion; for example, potassium and sodium channels often discriminate for only one of the two ions. [30] :232–34 Structural proteins