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in âintelligentâ laboratory ware. Cells are engineered with their own âsmartâ apparatus that contains and controls the chemical reactions that keep you alive. A cellâs smart apparatus is made of massive, intricately structured molecules called proteins. Unlike the inert, unrective glassware used in chemistry labs, each piece of protein apparatus is a chemist in its own right, carefully controlling a specific set of chemical reactions inside the cell. Evolution has selected and refined this smart âproteinwareâ to intelligently manage the millions of reactions that drive your metabolismâ¦Teams of chemists, using the very latest technology to run a reaction sequence are no match for smart proteins. These molecules are âinformation rich.â Like pieces of specialized software, they only respond to very specific sets of commands. Each protein is specific to the reaction it initiates and controls. Itâs a case of one protein, one structure, one effectâ (p. 1). The quote in the main text is by Miller (1997, p. 328).

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P. 144: PROTEINSâ CAPACITY TO RECOGNIZE

Modlin (2000) writes: âInnate immunity enables an organism to respond rapidly to invading microorganisms. To do this, the innate immune system uses receptor proteins that can recognize a microbial pathogen by the molecular pattern it displaysâ (p. 659). Kolodner (2000) writes: âProteins of the MutS family are remarkable sensors of DNA damage. The eukaryotic MSH2-MSH6 complex can detect several types of errors in DNA, with different consequences. For example, mispaired bases that arise as a result of DNA-replication errors are recognized by this complex, and repaired by mismatch repairâ¦Finally, eukaryotic MutS proteins can recognize chemical damage in DNA, including that caused by some drugs used for chemotherapy. This can activate cell-death pathways rather than DNA repair. Defects in this process result in cellular resistance to these drugs, and the resistance of cancer to chemotherapy. So, if we can unravel how the MutS proteins distinguish between so many types of problematic DNA structure, and communicate specifically with so many downstream pathways, we will not only gain greater insight into a fundamental biological process, but may also learn more about stumbling blocks to the effectiveness of chemotherapy. Several different models for the basic process of mismatch repair have been proposed, all of which conceivably include a âsignalingâ element. In bacteria, MutS binds to a mispair and then interacts with MutL, signaling the activation of at least two other proteins. One of these proteins makes a break in the DNA strand containing the incorrect base. The other unwinds this segment of the DNA strand so it can be destroyed. The resulting gap in the strand will then be repairedâ (pp. 687, 689).

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P. 145: UBIQUITIN, THE VERSATILE PROTEIN

Marx (2002) writes: âA small protein called ubiquitin is turning out to be the Clark Kent of cell biology. Like Supermanâs alter ego, ubiquitin has long been regarded as worthy but somewhat dull, a player in the cast of characters that carry out housekeeping functions for the cell. But recent findings are beginning to reveal it as a kind of superhero, performing feats that few suspected. Early work showed that ubiquitin, which was discovered in the mid-1970s, is part of the cellâs janitorial services. It binds to other proteins, tagging them for destruction by a large multiprotein complex called the proteasome. This kiss of death eliminates damaged proteins, an essential job but perhaps not one to catch the eye of Lois Lane. But ubiquitin-mediated protein disposal soon turned out to have a more glamorous role: helping regulate such key cellular processes as the cell division cycle. Now researchers are finding that ubiquitinâs functions go far beyond even these crucial activitiesâ¦Ubiquitin tagging directs the movement of important proteins in the cell, determining, for example, whether they end up on the cell membrane or in an internal vacuole, where they are destroyed without the proteasomeâs helpâ¦Other work indicates that ubiquitin