{"id":1789,"date":"2016-04-04T10:16:59","date_gmt":"2016-04-04T17:16:59","guid":{"rendered":"http:\/\/blogs.oregonstate.edu\/psquared\/?page_id=1789"},"modified":"2021-03-27T14:57:22","modified_gmt":"2021-03-27T21:57:22","slug":"protein-chains","status":"publish","type":"page","link":"https:\/\/blogs.oregonstate.edu\/psquared\/protein-chains\/","title":{"rendered":"Protein chains"},"content":{"rendered":"

Chains with backbones<\/h2>\n

Proteins are\u00a0chains of amino acids, and if we ignore the uniquene brought by the amino acids we find that one protein chain is a lot line another. \u00a0They all have a backbone consisting of 3 atoms in a row: \u00a0nitrogen, carbon, carbon. \u00a0Repeat as many times as needed. \u00a0That’s the backbone of the protein. \u00a0It’s what’s connected to the backbone that gives each protein its uniqueness in the world of proteins.<\/p>\n

Protein manufacture<\/h2>\n

Here’s series\u00a0of nicely artistic textbook figures illustrating the key aspects of protein manufacture. \u00a0They are copied from Dealing with Genes<\/a> by Berg and Singer, and illustrated by Georg Klatt (their book is sadly out of print and is a real steal if you find it at a used book store). \u00a0Note how according to the central dogma of molecular biology, genetic information is first transcribed\u00a0from DNA chains into messenger RNA chains, and is then translated by ribosomes from messenger RNA chains into protein chains using transfer RNA to bring each newly added amino acid to the growing protein chain.<\/p>\n

\"The<\/a><\/p>\n

\"The<\/a><\/p>\n

\"The<\/a><\/p>\n

Amino acids: \u00a0Elements\u00a0of a charm bracelet.<\/h2>\n

Each protein chain is a linear polymer having two distinct ends (N and C). \u00a0The units (the 20 aa’s) are joined by peptide bonds. \u00a0The “sequence” of a protein chain is given as the list of amino acids in its chain, from N to C. \u00a0The illustration below (also from Berg and Singers textbook) lists the twenty amino acids, complete with their generic amino group and carboxyl group (shaded in gray) and their unique side-chain (shaded in yellow). \u00a0The full name and the three-letter abbreviation are given for each amino acid. \u00a0Each amino acid is also commonly abbreviated by a\u00a0single letter<\/a>. \u00a0The only letters of the English language that are not associated\u00a0with an amino acid are B, J, O, U, X and Z.<\/p>\n

\"Berg<\/a><\/p>\n

The amino acids can be described according to three main chemical characteristics<\/a>:<\/p>\n

    \n
  1. Is the side-chain oil-like (hydrophobic)?<\/li>\n
  2. Is it wettable by water (hydrophilic)?<\/li>\n
  3. Is it positively or negatively charged?<\/li>\n<\/ol>\n

    In addition, some of the amino acids play special roles. \u00a0For example, a cysteine can form a cross-link with another cysteine. \u00a0Glycine is special because it has such a tiny side-chain. \u00a0Proline is special because its side-chain is locked into a small ring that restricts flexibility.<\/p>\n

    Practice exercises<\/h2>\n

    Practice exercise 1<\/em>: \u00a0Jot down the one-letter abbreviation for each amino acid. \u00a0Here’s a flashcard quiz<\/a> to help you memorize the amino acid abbreviations.<\/p>\n

    Practice exercise 2<\/em>: The following is a numbered list\u00a0of the twenty side-chains. \u00a0Can you assign each number with the name of the amino acid?<\/p>\n

    \"twenty_side-chains\"<\/a><\/p>\n

     <\/p>\n","protected":false},"excerpt":{"rendered":"

    Chains with backbones Proteins are\u00a0chains of amino acids, and if we ignore the uniquene brought by the amino acids we find that one protein chain is a lot line another. \u00a0They all have a backbone consisting of 3 atoms in … Continue reading →<\/span><\/a><\/p>\n","protected":false},"author":196,"featured_media":0,"parent":0,"menu_order":112,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-1789","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/pages\/1789","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/users\/196"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/comments?post=1789"}],"version-history":[{"count":29,"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/pages\/1789\/revisions"}],"predecessor-version":[{"id":2723,"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/pages\/1789\/revisions\/2723"}],"wp:attachment":[{"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/media?parent=1789"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}