{"id":4206,"date":"2019-08-05T11:53:26","date_gmt":"2019-08-05T18:53:26","guid":{"rendered":"https:\/\/integrativewellnessandmovement.com\/iwmbasicscience\/?p=4206"},"modified":"2019-08-05T20:12:41","modified_gmt":"2019-08-06T03:12:41","slug":"amino-acids","status":"publish","type":"post","link":"https:\/\/integrativewellnessandmovement.com\/iwmbasicscience\/biochemistry\/amino-acids\/","title":{"rendered":"Amino Acids."},"content":{"rendered":"\n<p>[Study guide covering chapter 6, <a href=\"http:\/\/www.integrativewellnessandmovement.com\/iwmstudentresources\/biochem\/biochem-ch6.pdf\" target=\"_blank\" rel=\"noreferrer noopener\" aria-label=\"PDF (opens in a new tab)\">PDF<\/a>]<\/p>\n\n\n\n<p>Last edited: 08.05.2019<\/p>\n\n\n\n<p class=\"has-medium-font-size\">Structure.<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>Phosphate group.<\/li><li>Nitrogen\/amino group: attached to the alpha carbon of the carboxylate.<\/li><li>Carboxylate group.<\/li><li>R-side chain.<\/li><li>Concept of zwitterion.<\/li><li>Amine group pH ~9.5<\/li><li>Physiological pH ~7.5<\/li><li>Alpha carbon is chiral except in glycine.<\/li><li>Glycine, the carbon is achiral (has two H).<\/li><li>Mammalian AA are L configuration  (as opposed to D).<\/li><li>Alpha aminos are AA attached to alpha carbon.<\/li><li>Primary structure: sequence of AAs.<\/li><li>AA joined via peptide bonds betw. COO- of one AA and the NH3+ of the other.<\/li><li>Backbone &gt;&gt; carbolxylate, alpha carbon, and amino group.<\/li><li>AA are the side chains.<\/li><li>Binding sites.<\/li><li>Ligand-receptor pairs.<\/li><li>N-terminal (where the amino group is).<\/li><li>C-terminal (where the carboxylate is).<\/li><\/ul>\n\n\n\n<p class=\"has-medium-font-size\">Classification of Amino Acids.<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>pKa<\/li><li>Hydropathic index: a scale to describe hydrophobicity of the side chain.<\/li><li>Glycine is a special case where its R-group is just H. Has the least steric hinderance. Can be found in the &#8220;nooks and crannies&#8221;.<\/li><li>Nonpolar: alanine, valine, leucine, isoleucine; aliphatic; very hydrophobic; typically form the hydrophobic cores.<\/li><li>Proline is another special case as it&#8217;s attached to the backbone twice. It has both an alpha carbon and alpha amino group. Proline is an imino acid. Rigid and forms kinks. Restricted conformations.<\/li><li>Aromatic acids: 6-member ring of C and H; conjugated double bonds. H on the ring doesn&#8217;t participate in H-bonding. The substituents on the ring influence side chains characteristics &amp; determine what action takes place (e.g. hydrophilic or hydrophobic).<\/li><li>Aliphatic, polar, uncharged AA: has amide group (asparagine, glutamine); or hydroxyl group (serine, threonine); form H-bonds with water. Typically found on surfaces.<\/li><li>AA with sulfur: cysteine and methionine. Can form disulfide bridges via oxidation of the sulfhydral groups, but it doesn&#8217;t always do that. The action\/function depends on it&#8217;s surrounding environment and &#8220;what else&#8221; there is.<\/li><li>Acidic AA: carboxylic acid groups; e.g. aspartate and glutamate. Their negative charge can form ionic bonds with cations.<\/li><li>Basic AA: have side chains containing N (+)  and tends towards basicity; e.g. histidine, lysine, arginine. Their positive charges can form ionic bonds with anions. Lysine and arginine can form bonds to anionic compounds w\/protein binding sites (i.e. those protein binding sites can become incorporated into a new compound as well as become altered). Those ligand-receptor sites can become &#8220;grandfathered in&#8221;.<\/li><li>Acidic\/basic characteristics can allow AAs to participate in H-bonds and salt bridge formations.<\/li><li>Carbon positions can be described using the Greek letters: alpha, beta, gamma, delta, epsilon).<\/li><li>If pH &lt; pKa then it favors the protonated form (-COOH, -NH3+). If pH&gt;pKa, then it favors the deprotonated form (-COO- and -NH2).<\/li><li>Imidazole ring. C3N2H4 (compound).<\/li><li>In proteins, only the side chains, N-terminal, and C-terminal are dissociateable. Other C, N, H that form part of the backbone do not participate in acidic\/basic characteristics.<\/li><li>Electrophoresis: separate proteins via charge differences. Helps to identify proteins and components.<\/li><\/ul>\n\n\n\n<p class=\"has-medium-font-size\">Variations in Protein Structure.<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>Protein structure and characteristics can vary between different individuals and different ages. This variant nature is called variant regions.<\/li><li>Hypervariable describes a situation where variation is tolerable within reason.<\/li><li>Invariant regions, in contrast, do NOT vary between individuals, species, etc. Variation is NOT tolerated.<\/li><li>Polymorphisms: when allele variations occur with great frequency.<\/li><li>Homologous proteins: these belong to the same ancestral proteins.<\/li><li>Paralogs: proteins that have similar structure and function that have evolved from the same gene after gene duplication.<\/li><li>Divergent evolution: when one gene performs it&#8217;s expected function yet a copy mutates into a different function or have different characteristics.<\/li><li>Superfamily: large family of homologous proteins.<\/li><li>Isoforms: 2+ functionally similar proteins with similar structure (but not identical) or AA sequence; isoforms of a protein have the same function.<\/li><li>Isozymes: 2+ enZ w\/similar functions but differ in structure; isozymes catalyze the same reactions.<\/li><li>Developmental variation: structures and functions differ at different developmental stages.<\/li><li>Tissue-specific isoforms: proteins that function &#8220;the same&#8221; but they vary in structure\/characteristics from tissue group to another tissue group.<\/li><li>Tissue-specific isozymes: enZ that function &#8220;the same&#8221; but they vary in structure\/function from tissue group to tissue group.<\/li><li>Species variation: proteins and enzymes (and their structure and function) can vary from species to species.<\/li><\/ul>\n\n\n\n<p class=\"has-medium-font-size\">Modified Amino Acids.<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>Post-translational modification. Post-protein synthesis, some AA residues in the primary sequence may be modified. These changes may or may not serve\/enhance function or characteristics. Usu. occur after protein has already folded into its specific conformation.<\/li><li>Glycosylation: the addition of carbohydrates to a molecule.<\/li><li>Fatty acylation: the addition of lipid group(s) to a molecule. These types of changes (N- or O-) can enhance barrier\/surface protection (e.g. N-linked oligosaccharides). O-linked oligosaccharides can enhance secretions.<\/li><li> <a rel=\"noreferrer noopener\" aria-label=\" (opens in a new tab)\" href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC4975971\/\" target=\"_blank\">https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC4975971\/<\/a> <\/li><li> <a rel=\"noreferrer noopener\" aria-label=\" (opens in a new tab)\" href=\"https:\/\/www.nature.com\/articles\/nrm.2015.11\" target=\"_blank\">https:\/\/www.nature.com\/articles\/nrm.2015.11<\/a> <\/li><li>Prenylation: the addition of farnesyl or geranylgeranyl groups via thioether linkate to specific cysteine residues of membrane proteins.<\/li><li>Regulatory modifications. Phosphorylation, acetylation, and adenosine diphosphate (ADP)-ribosylation of some AAs can alter bonding characteristics of the AA.<\/li><li>Other amino acid posttranslational modifications: can alter the activity of the protein.<\/li><li>Selenocysteine: found in a few enZ and is required to activate those enZ.<\/li><\/ul>\n\n\n\n<p>Resources.<\/p>\n\n\n\n<p>References.<\/p>\n\n\n\n<p>\n\nLieberman,&nbsp;M., &amp; Peet,&nbsp;A. (2017).&nbsp;<em>Marks&#8217; basic medical biochemistry: A clinical approach<\/em>(5th&nbsp;ed.). Philadelphia, PA: LWW.\n\n<\/p>\n","protected":false},"excerpt":{"rendered":"<p>[Study guide covering chapter 6, PDF] Last edited: 08.05.2019 Structure. Phosphate group. Nitrogen\/amino group: attached to the alpha carbon of the carboxylate. Carboxylate group. R-side chain. Concept of zwitterion. Amine group pH ~9.5 Physiological pH ~7.5 Alpha carbon is chiral except in glycine. Glycine, the carbon is achiral (has two H). Mammalian AA are L [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[48],"tags":[],"class_list":["post-4206","post","type-post","status-publish","format-standard","hentry","category-biochemistry"],"_links":{"self":[{"href":"https:\/\/integrativewellnessandmovement.com\/iwmbasicscience\/wp-json\/wp\/v2\/posts\/4206","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/integrativewellnessandmovement.com\/iwmbasicscience\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/integrativewellnessandmovement.com\/iwmbasicscience\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/integrativewellnessandmovement.com\/iwmbasicscience\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/integrativewellnessandmovement.com\/iwmbasicscience\/wp-json\/wp\/v2\/comments?post=4206"}],"version-history":[{"count":5,"href":"https:\/\/integrativewellnessandmovement.com\/iwmbasicscience\/wp-json\/wp\/v2\/posts\/4206\/revisions"}],"predecessor-version":[{"id":4224,"href":"https:\/\/integrativewellnessandmovement.com\/iwmbasicscience\/wp-json\/wp\/v2\/posts\/4206\/revisions\/4224"}],"wp:attachment":[{"href":"https:\/\/integrativewellnessandmovement.com\/iwmbasicscience\/wp-json\/wp\/v2\/media?parent=4206"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/integrativewellnessandmovement.com\/iwmbasicscience\/wp-json\/wp\/v2\/categories?post=4206"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/integrativewellnessandmovement.com\/iwmbasicscience\/wp-json\/wp\/v2\/tags?post=4206"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}