Changes

<p>Like other biological <a title="Macromolecules" href="http://en.wikipedia.org/wiki/Macromolecules">macromolecules</a> such as <a title="Polysaccharide" href="http://en.wikipedia.org/wiki/Polysaccharide">polysaccharides</a> and <a title="Nucleic acid" href="http://en.wikipedia.org/wiki/Nucleic_acid">nucleic acids</a>, proteins are essential parts of all living organisms and participate in every process within <a title="Cell (biology)" href="http://en.wikipedia.org/wiki/Cell_%28biology%29">cells</a>. Many proteins are <a title="Enzyme" href="http://en.wikipedia.org/wiki/Enzyme">enzymes</a> that <a title="Catalysis" href="http://en.wikipedia.org/wiki/Catalysis">catalyze</a> biochemical reactions, and are vital to <a title="Metabolism" href="http://en.wikipedia.org/wiki/Metabolism">metabolism</a>. Other proteins have structural or mechanical functions, such as the proteins in the <a title="Cytoskeleton" href="http://en.wikipedia.org/wiki/Cytoskeleton">cytoskeleton</a>, which forms a system of <a title="Scaffolding" href="http://en.wikipedia.org/wiki/Scaffolding">scaffolding</a> that maintains cell shape. Proteins are also important in <a title="Cell signaling" href="http://en.wikipedia.org/wiki/Cell_signaling">cell signaling</a>, <a title="Antibody" href="http://en.wikipedia.org/wiki/Antibody">immune responses</a>, <a title="Cell adhesion" href="http://en.wikipedia.org/wiki/Cell_adhesion"><font color="#810081">cell adhesion</font></a>, and the <a title="Cell cycle" href="http://en.wikipedia.org/wiki/Cell_cycle">cell cycle</a>. Protein is also a necessary component in our diet, since animals cannot synthesise all the amino acids and must obtain <a title="Essential amino acid" href="http://en.wikipedia.org/wiki/Essential_amino_acid">essential amino acids</a> from food. Through the process of <a title="Digestion" href="http://en.wikipedia.org/wiki/Digestion">digestion</a>, animals break down ingested protein into free amino acids that can be used for <a title="Protein biosynthesis" href="http://en.wikipedia.org/wiki/Protein_biosynthesis">protein synthesis</a>.</p>

<p>The word <em>protein</em> comes from the <a title="Greek language" href="http://en.wikipedia.org/wiki/Greek_language">Greek</a> <em>&pi;&rho;ώ&tau;&alpha;</em> (&quot;prota&quot;), meaning &quot;<em>of primary importance</em>&quot; and these molecules were first described and named by <a title="Jöns Jakob Berzelius" href="http://en.wikipedia.org/wiki/J%C3%B6ns_Jakob_Berzelius">J&ouml;ns Jakob Berzelius</a> in <a title="1838" href="http://en.wikipedia.org/wiki/1838">1838</a>. However, proteins' central role in living organisms was not fully appreciated until 1926, when <a title="James B. Sumner" href="http://en.wikipedia.org/wiki/James_B._Sumner">James B. Sumner</a> showed that the enzyme <a title="Urease" href="http://en.wikipedia.org/wiki/Urease">urease</a> was a protein.<sup class="reference" id="_ref-0"><a title="" href="http://en.wikipedia.org/wiki/Protein#_note-0">[1]</a></sup> The first protein to be sequenced was insulin, by <a title="Frederick Sanger" href="http://en.wikipedia.org/wiki/Frederick_Sanger">Frederick Sanger</a>, who won the Nobel Prize for this achievement in 1958. The first protein structures to be solved included <a title="Haemoglobin" href="http://en.wikipedia.org/wiki/Haemoglobin">haemoglobin</a> and <a title="Myoglobin" href="http://en.wikipedia.org/wiki/Myoglobin">myoglobin</a>, by <a title="Max Perutz" href="http://en.wikipedia.org/wiki/Max_Perutz">Max Perutz</a> and <a title="John Kendrew" href="http://en.wikipedia.org/wiki/John_Kendrew">Sir John Cowdery Kendrew</a>, respectively, in 1958.<sup class="reference" id="_ref-1"><a title="" href="http://en.wikipedia.org/wiki/Protein#_note-1">[2]</a></sup><sup class="reference" id="_ref-2"><a title="" href="http://en.wikipedia.org/wiki/Protein#_note-2">[3]</a></sup> Both proteins' three-dimensional structures were first determined by x-ray diffraction analysis; the structures of myoglobin and haemoglobin won the 1962 <a title="Nobel Prize in Chemistry" href="http://en.wikipedia.org/wiki/Nobel_Prize_in_Chemistry">Nobel Prize in Chemistry</a> for their discoverers.</p>

<p><a id="Biochemistry" name="Biochemistry"></a></p>

<h2><span class="mw-headline">Biochemistry</span></h2>

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<a title="Resonance (chemistry)" href="http://en.wikipedia.org/wiki/Resonance_%28chemistry%29">Resonance</a> structures of the <a title="Peptide bond" href="http://en.wikipedia.org/wiki/Peptide_bond">peptide bond</a> that links individual amino acids to form a protein <a title="Polymer" href="http://en.wikipedia.org/wiki/Polymer">polymer</a>.</div>

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Section of a protein structure showing serine and alanine residues linked together by peptide bonds. Carbons are shown in white and hydrogens are omitted for clarity.</div>

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<div class="noprint"><em>Main article: <a title="Protein biosynthesis" href="http://en.wikipedia.org/wiki/Protein_biosynthesis">Protein biosynthesis</a></em></div>

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<p>Proteins are assembled from amino acids using information encoded in <a title="Gene" href="http://en.wikipedia.org/wiki/Gene">genes</a>. Each protein has its own unique amino acid sequence that is specified by the <a title="Nucleotide" href="http://en.wikipedia.org/wiki/Nucleotide">nucleotide</a> sequence of the gene encoding this protein. The <a title="Genetic code" href="http://en.wikipedia.org/wiki/Genetic_code">genetic code</a> is a set of three-nucleotide sets called <a title="Codon" href="http://en.wikipedia.org/wiki/Codon">codons</a> and each three-nucleotide combination stands for an amino acid, for example AUG stands for <a title="Methionine" href="http://en.wikipedia.org/wiki/Methionine">methionine</a>. Because <a title="DNA" href="http://en.wikipedia.org/wiki/DNA">DNA</a> contains four nucleotides, the total number of possible codons is 64; hence, there is some redundancy in the genetic code and some amino acids are specified by more than one codon. Genes encoded in DNA are first <a title="Transcription (genetics)" href="http://en.wikipedia.org/wiki/Transcription_%28genetics%29">transcribed</a> into pre-<a title="Messenger RNA" href="http://en.wikipedia.org/wiki/Messenger_RNA">messenger RNA</a> (mRNA) by proteins such as <a title="RNA polymerase" href="http://en.wikipedia.org/wiki/RNA_polymerase">RNA polymerase</a>. Most organisms then process the pre-mRNA (also known as a <em>primary transcript</em>) using various forms of <a title="Post-transcriptional modification" href="http://en.wikipedia.org/wiki/Post-transcriptional_modification">post-transcriptional modification</a> to form the mature mRNA, which is then used as a template for protein synthesis by the <a title="Ribosome" href="http://en.wikipedia.org/wiki/Ribosome">ribosome</a>. In <a title="Prokaryote" href="http://en.wikipedia.org/wiki/Prokaryote">prokaryotes</a> the mRNA may either be used as soon as it is produced, or be bound by a ribosome after having moved away from the <a title="Nucleoid" href="http://en.wikipedia.org/wiki/Nucleoid">nucleoid</a>. In contrast, <a title="Eukaryote" href="http://en.wikipedia.org/wiki/Eukaryote">eukaryotes</a> make mRNA in the <a title="Cell nucleus" href="http://en.wikipedia.org/wiki/Cell_nucleus">cell nucleus</a> and then translocate it across the <a title="Nuclear membrane" href="http://en.wikipedia.org/wiki/Nuclear_membrane">nuclear membrane</a> into the <a title="Cytoplasm" href="http://en.wikipedia.org/wiki/Cytoplasm">cytoplasm</a>, where <a title="Protein biosynthesis" href="http://en.wikipedia.org/wiki/Protein_biosynthesis">protein synthesis</a> then takes place. The rate of protein synthesis is higher in prokaryotes than eukaryotes and can reach up to 20 amino acids per second.<sup class="reference" id="_ref-Dobson_0"><a title="" href="http://en.wikipedia.org/wiki/Protein#_note-Dobson">[6]</a></sup></p>

<p>The process of synthesizing a protein from an mRNA template is known as <a title="Translation (genetics)" href="http://en.wikipedia.org/wiki/Translation_%28genetics%29">translation</a>. The mRNA is loaded onto the ribosome and is read three nucleotides at a time by matching each codon to its <a title="Base pair" href="http://en.wikipedia.org/wiki/Base_pair">base pairing</a> <a title="Anticodon" href="http://en.wikipedia.org/wiki/Anticodon">anticodon</a> located on a <a title="Transfer RNA" href="http://en.wikipedia.org/wiki/Transfer_RNA">transfer RNA</a> molecule, which carries the amino acid corresponding to the codon it recognizes. The enzyme <a title="Aminoacyl tRNA synthetase" href="http://en.wikipedia.org/wiki/Aminoacyl_tRNA_synthetase">aminoacyl tRNA synthetase</a> &quot;charges&quot; the tRNA molecules with the correct amino acids. The growing polypeptide is often termed the <em>nascent chain</em>. Proteins are always biosynthesized from N-terminus to C-terminus.</p>

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Three possible representations of the three-dimensional structure of the protein <a title="Triose phosphate isomerase" href="http://en.wikipedia.org/wiki/Triose_phosphate_isomerase">triose phosphate isomerase</a>. Left: all-atom representation colored by atom type. Middle: simplified representation illustrating the backbone conformation, colored by secondary structure. Right: Solvent-accessible surface representation colored by residue type (acidic residues red, basic residues blue, polar residues green, nonpolar residues white).</div>

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NMR structures of the protein <a title="Cytochrome c" href="http://en.wikipedia.org/wiki/Cytochrome_c">cytochrome c</a> in solution show the constantly shifting dynamic structure of the protein. <a title="Image:Protein Dynamics Cytochrome C 2NEW small.gif" href="http://en.wikipedia.org/wiki/Image:Protein_Dynamics_Cytochrome_C_2NEW_small.gif">Larger version</a>.</div>

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<p>Proteins are not entirely rigid molecules. In addition to these levels of structure, proteins may shift between several related structures in performing their biological function. In the context of these functional rearrangements, these tertiary or quaternary structures are usually referred to as &quot;<a title="Chemical conformation" href="http://en.wikipedia.org/wiki/Chemical_conformation">conformations</a>,&quot; and transitions between them are called <em>conformational changes.</em> Such changes are often induced by the binding of a <a title="Substrate (biochemistry)" href="http://en.wikipedia.org/wiki/Substrate_%28biochemistry%29">substrate</a> molecule to an enzyme's <a title="Active site" href="http://en.wikipedia.org/wiki/Active_site">active site</a>, or the physical region of the protein that participates in chemical catalysis. In solution all proteins also undergo variation in structure through thermal vibration and the collision with other molecules, see the animation on the right.</p>

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Molecular surface of several proteins showing their comparative sizes. From left to right are: <a title="Antibody" href="http://en.wikipedia.org/wiki/Antibody">Antibody</a> (IgG), <a title="Hemoglobin" href="http://en.wikipedia.org/wiki/Hemoglobin">Hemoglobin</a>, <a title="Insulin" href="http://en.wikipedia.org/wiki/Insulin">Insulin</a> (a hormone), <a title="Adenylate kinase" href="http://en.wikipedia.org/wiki/Adenylate_kinase">Adenylate kinase</a> (an enzyme), and <a title="Glutamine synthetase" href="http://en.wikipedia.org/wiki/Glutamine_synthetase">Glutamine synthetase</a> (an enzyme).</div>

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<p>Proteins are the chief actors within the cell, said to be carrying out the duties specified by the information encoded in genes.<sup class="reference" id="_ref-Lodish_2"><a title="" href="http://en.wikipedia.org/wiki/Protein#_note-Lodish">[5]</a></sup> With the exception of certain types of <a title="RNA" href="http://en.wikipedia.org/wiki/RNA">RNA</a>, most other biological molecules are relatively inert elements upon which proteins act. Proteins make up half the dry weight of an <em><a title="Escherichia coli" href="http://en.wikipedia.org/wiki/Escherichia_coli">Escherichia coli</a></em> cell, while other macromolecules such as DNA and RNA make up only 3% and 20% respectively.<sup class="reference" id="_ref-Voet_0"><a title="" href="http://en.wikipedia.org/wiki/Protein#_note-Voet">[13]</a></sup> The set of proteins expressed in a particular cell or cell type is known as its <a title="Proteome" href="http://en.wikipedia.org/wiki/Proteome">proteome</a>.</p>

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The enzyme <a title="Hexokinase" href="http://en.wikipedia.org/wiki/Hexokinase">hexokinase</a> is shown as a simple ball-and-stick molecular model. To scale in the top right-hand corner are its two substrates, <a title="Adenosine triphosphate" href="http://en.wikipedia.org/wiki/Adenosine_triphosphate">ATP</a> and <a title="Glucose" href="http://en.wikipedia.org/wiki/Glucose">glucose</a>.</div>

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<h3><span class="mw-headline">Cell signalling and ligand transport</span></h3>

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A <a title="Mouse" href="http://en.wikipedia.org/wiki/Mouse">mouse</a> antibody against <a title="Cholera" href="http://en.wikipedia.org/wiki/Cholera">cholera</a> that binds a <a title="Carbohydrate" href="http://en.wikipedia.org/wiki/Carbohydrate">carbohydrate</a> antigen.</div>

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<h3><span class="mw-headline">Cellular localization</span></h3>

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Proteins in different <a title="Cellular compartment" href="http://en.wikipedia.org/wiki/Cellular_compartment">cellular compartments</a> and structures tagged with <a title="Green fluorescent protein" href="http://en.wikipedia.org/wiki/Green_fluorescent_protein">green fluorescent protein</a> (here, white).</div>

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<div class="references-2column">

<ol class="references">

<li id="_note-1"><strong><a title="" href="http://en.wikipedia.org/wiki/Protein#_ref-1">^</a></strong> <cite style="FONT-STYLE: normal">Muirhead H, Perutz M (1963). &quot;Structure of haemoglobin. A three-dimensional fourier synthesis of reduced human haemoglobin at 5.5 A resolution&quot;. <em>Nature</em> <strong>199</strong> (4894): 633-8. <a class="external" title="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=14074546" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=14074546">PMID 14074546</a>.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Structure+of+haemoglobin.+A+three-dimensional+fourier+synthesis+of+reduced+human+haemoglobin+at+5.5+A+resolution&amp;rft.jtitle=Nature&amp;rft.date=1963&amp;rft.volume=199&amp;rft.issue=4894&amp;rft.au=Muirhead+H%2C+Perutz+M&amp;rft.pages=633-8&amp;rft_id=info:pmid/14074546">&nbsp;</span> </li>

<li id="_note-2"><strong><a title="" href="http://en.wikipedia.org/wiki/Protein#_ref-2">^</a></strong> <cite style="FONT-STYLE: normal">Kendrew J, Bodo G, Dintzis H, Parrish R, Wyckoff H, Phillips D (1958). &quot;A three-dimensional model of the myoglobin molecule obtained by x-ray analysis&quot;. <em>Nature</em> <strong>181</strong> (4610): 662-6. <a class="external" title="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=13517261" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=13517261">PMID 13517261</a>.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=A+three-dimensional+model+of+the+myoglobin+molecule+obtained+by+x-ray+analysis&amp;rft.jtitle=Nature&amp;rft.date=1958&amp;rft.volume=181&amp;rft.issue=4610&amp;rft.au=Kendrew+J%2C+Bodo+G%2C+Dintzis+H%2C+Parrish+R%2C+Wyckoff+H%2C+Phillips+D&amp;rft.pages=662-6&amp;rft_id=info:pmid/13517261">&nbsp;</span> </li>

<li id="_note-8"><strong><a title="" href="http://en.wikipedia.org/wiki/Protein#_ref-8">^</a></strong> Walian P, Cross TA, Jap BK. (2004). Structural genomics of membrane proteins <em>Genome Biol</em> 5(4): 215. </li>

<li id="_note-Voet">^ <a title="" href="http://en.wikipedia.org/wiki/Protein#_ref-Voet_0">^{<em><strong>a</strong></em>}</a> <a title="" href="http://en.wikipedia.org/wiki/Protein#_ref-Voet_1">^{<em><strong>b</strong></em>}</a> Voet D, Voet JG. (2004). <em>Biochemistry</em> Vol 1 3rd ed. Wiley: Hoboken, NJ. </li>

<li id="_note-10"><strong><a title="" href="http://en.wikipedia.org/wiki/Protein#_ref-10">^</a></strong> <cite style="FONT-STYLE: normal">Radzicka A, Wolfenden R. (1995). &quot;A proficient enzyme.&quot;. <em>Science</em> <strong>6</strong> (267): 90-931. <a class="external" title="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=7809611" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=7809611">PMID 7809611</a>.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=A+proficient+enzyme.&amp;rft.jtitle=Science&amp;rft.date=1995&amp;rft.volume=6&amp;rft.issue=267&amp;rft.au=Radzicka+A%2C+Wolfenden+R.&amp;rft.pages=90-931">&nbsp;</span> </li>

<li id="_note-Zhang"><strong><a title="" href="http://en.wikipedia.org/wiki/Protein#_ref-Zhang_0">^</a></strong> Zhang Y, Skolnick J. (2005). The protein structure prediction problem could be solved using the current PDB library. <em>Proc Natl Acad Sci USA</em> 102(4):1029-34. </li>

<li id="_note-Kuhlman"><strong><a title="" href="http://en.wikipedia.org/wiki/Protein#_ref-Kuhlman_0">^</a></strong> Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D. (2003). Design of a novel globular protein fold with atomic-level accuracy. <em>Science</em> 302(5649):1364-8. </li>

<h2><span class="mw-headline">External links</span></h2>

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<p><a id="Databases_and_projects" name="Databases_and_projects"></a></p>

<h3><span class="mw-headline">Databases and projects</span></h3>

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<p><a id="Tutorials_and_educational_websites" name="Tutorials_and_educational_websites"></a></p>

<h3><span class="mw-headline">Tutorials and educational websites</span></h3>

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