Lecture 7Cell Biology lecture notes Chapter 3 p.128-144

General formula for an amino acid

Dehydration synthesis to form peptide bond

20 amino acids: 10 = polar; 10 = nonpolar (glycine[R=H] and cysteine[R=CH₂-SH] = nonpolar?) 21^st a.a: selenocysteine. 22^nd: pyrrolysine (see below) both = rare

Look at structure of proline (not free to swivel) : check CD picture

cysteine and disulfides (CD)

Domains: structural units that fold independently. Hydrophobic inside, hydrophilic on surfaces.

Chaperones prevent temporarily exposed hydrophobics from associating during synthesis.

Lysozyme; an intensively studied, abundant, cheap protein.

helix (intrachain, cross membrane), sheets (interchain) maximize backbone H-bonds

Primary, secondary, tertiary, quaternary structures, and domains describe levels of organization.

Coiled-coil: helices with hydrophobics on one side coil around each other. (CD)

Protein fold: particular combination of helices and sheets; 1,000 identified of 10,000 proteins

polypeptides adopt single, stable config. How done? Natural selection. (Proven?)

Yeast 2 and Drosophila engrailed = different sequences, similar 3D structures.

Serine proteases: chymotrypsin, trypsin, elastase: serine residue in catalytic site. Roles in sequencing proteins.

Neutral mutations: affect sequence, not function. Rates indicate years entities separated.

Analyze large proteins based on domain analyses, because 3D protein structure = nontrivial

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=1828528

Mol Microbiol. 1991 Mar;5(3):515-20. Selenocysteine: the 21st amino acid.

Bock A, Forchhammer K, Heider J, Leinfelder W, Sawers G, Veprek B, Zinoni F.

Lehrstuhl fur Mikrobiologie, Universitat Munchen, Germany.

Great excitement was elicited in the field of selenium biochemistry in 1986 by the parallel discoveries that the genes encoding the selenoproteins glutathione peroxidase and bacterial formate dehydrogenase each contain an in-frame TGA codon within their coding sequence. We now know that this codon directs the incorporation of selenium, in the form of selenocysteine, into these proteins. Working with the bacterial system has led to a rapid increase in our knowledge of selenocysteine biosynthesis and to the exciting discovery that this system can now be regarded as an expansion of the genetic code. The prerequisites for such a definition are co-translational insertion into the polypeptide chain and the occurrence of a tRNA molecule which carries selenocysteine. Both of these criteria are fulfilled and, moreover, tRNASec even has its own special translation factor which delivers it to the translating ribosome. It is the aim of this article to review the events leading to the elucidation of selenocysteine as being the 21st amino acid.

http://pubs.acs.org/cen/topstory/8021/8021notw1.html

22nd AMINO ACID IDENTIFIED

Methanogen uses stop codon

to genetically encode l-pyrrolysine

Nature uses only a handful of amino acid building blocks to generate immense complexity from a relatively simple genetic code. There are just 20 genetically encoded amino acids in mammalian cells; a few organisms use 21. Now, researchers at Ohio State University have discovered a 22nd [Science, 296, 1459 and 1462 (2002)].

The team, led by microbiology professor Joseph A. Krzycki and chemistry and biochemistry professor Michael K. Chan, calls the amino acid l-pyrrolysine. The novel residue is an amide-linked 4-substituted pyrroline-5-carboxylate lysine derivative.

Chan and graduate student Bing Hao identified pyrrolysine in the 1.55-Å crystal structure of monomethylamine methyltransferase (MtmB) from the microbe Methanosarcina barkeri, found at the bottom of freshwater lakes. An enzyme in the pathway that makes methane from methylamine, MtmB has a barrel protein fold with pyrrolysine tucked into the bottom. Pyrrolysine (right) was identified in a methyltransferase of a methane-generating microbe. The substituent at C-4 could not be conclusively determined from the electron density map. But finding a novel amino acid in a protein structure doesn't necessarily mean the residue is genetically encoded. In the protein collagen, for example, 4-hydroxyproline and 5-hydroxylysine are introduced by modification of the appropriate amino acid after the polypeptide chain has been synthesized. To qualify as genetically encoded, amino acids must be directly inserted into the growing peptide chain by a dedicated transfer RNA (tRNA) that recognizes a specific three-nucleotide codon in the messenger RNA (mRNA) transcript.

New findings on lysozyme and circumcision:

Summary of evidence that the foreskin and lysozyme may protect against HIV infection By George Hill http://www.foreskin.org/lysozyme.htm

Laumann et al. report that about 77 percent of adult American males are circumcised. ⁴ Thus, these circumcised males have no sub-preputial wetness and no lysozyme protection. Laumann finds that circumcised men are slightly more likely to have both a bacterial and a viral STD in their lifetime.

The high incidence of HIV in the United States and its correlation with the high rate of circumcision has been noted by Storms⁹ and Nicoll. ¹⁰ Furthermore, Tanne reports a general epidemic of STD, including chlamydia and HIV, in the United States.