Kmill104 Week 12

1. Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own citation, to a book or URL. Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
   • Online Biological Dictionaries
     • Web sites
       • biology-online.org dictionary
       • Gene Ontology
       • NCI Dictionary of Cancer Terms
     • eBooks
       • Oxford Dictionary of Biochemistry and Molecular Biology eBook
       • Dictionary of Biology Oxford Reference eBook
       • Dictionary of Cell and Molecular Biology eBook
       • Dictionary of Genetics Oxford Reference eBook

1. proteasome: Proteasomes are large multi‐subunit protease complexes that selectively degrade intracellular proteins that are tagged for destruction by ubiquitination. They control cellular processes, such as metabolism and the cell cycle, through signal‐mediated proteolysis of key enzymes and regulatory proteins. They also operate in the stress response, by removing abnormal proteins, and in the immune response, by generating antigenic peptides. The proteolytic activity is due to a 26S protease (a 2 MDa complex), whose ability to degrade proteins generally depends on both the ubiquitination of the substrate and the presence of ATP. At the core is a 20S particle that carries the catalytic activity. When first isolated, it was called ‘multicatalytic proteinase’ because of its ability to cleave peptide bonds carboxy‐terminal to basic, hydrophobic, and acidic residues. The 20S particle does not require ATP for activity. The crystal structure of this core from the archaean Thermoplasma acidophilum has been determined. The core alone is inactive because it requires two specific subunits of a 19S particle to mediate recognition of ubiquitin‐protein conjugates. The core subunits are arranged in four heptameric rings, stacked to form a hollow cylinder with the protease activity on the inside. The active site nucleophile is threonine. The protein substrate first must be unfolded and the disulfide bonds reduced before entry into the cylinder. In Thermoplasma, the two outer rings are composed of seven α subunits, and each inner ring contains seven β subunits. The enzyme catalyses the cleavage at Xaa‐|‐bonds in which Xaa carries a hydrophobic, basic, or acidic side chain. Components of the human proteasome include: c2, c3, c5, c7, c8, c9, β chain, c13, δ chain, ε chain, mecl‐1, τ chain, and ζ chain. (Oxford, 2008).
2. leucine zipper: a domain in a protein structure in which two alpha helices containing leucines (normally four or five) repeating every seventh amino‐acid residue, interdigitate in zipper fashion to stabilize the structure. Such an arrangement was originally found in DNA‐binding proteins, but it is now known to occur also in other proteins, especially adjacent to proposed transmembrane regions, mediating dimerization. The abbreviation ZIP is used, e.g., in designating the bZIP family of proteins. (Oxford, 2008).
3. chromatin immunoprecipitation: abbr.: ChIP; a method used to demonstrate the association between transcription factors or other DNA‐binding proteins and specific regions of genomic DNA. Chromatin is isolated from preparations of nuclei, chemically cross‐linked, and sheared to provide short fragments. Antibodies are used to immunoprecipitate the specific DNA‐binding protein and with it the fragment of DNA to which it is bound. Polymerase chain reaction (PCR) is then used to identify the presence of specific DNA fragments. (Oxford, 2008).