In the first part of the takehome exam, the unknownprotein had ______ domains.A. 1B. 2C. 3D. 4E. More than 4A domainA. is synonymous with “motif”.B. is a subsection of a single polypeptidechain.C. is an independently folded portion of apolypeptide chain, usually consisting ofat least 50 a.a.D. A, B and CE. B and CIf the only information you had about aprotein was its primary sequence, you’dwant toA. Search for all proteins with similar primarysequences in the PDB database.B. Search for all proteins with similar primarysequences in the NCBI database.C. Search for all proteins with similar primarysequence and similar length in the NCBIdatabase.D. Search for all proteins with similar primarysequence and similar length in the PDB database.E. Search for similar proteins from the sameorganism in either database.Fig. 5-32 LehnFig. 5-29LehnFig. 5-29LehnFig. 5-29LehnFig. 5-30 LehnFig. 5-30 LehnSome Recombinant DNAtechniques that can be usedto facilitate the study ofproteins.A. Site-directed mutagenesisB. Protein expression in bacteriaC. Transgenic organismsSite-directed mutagenesis• Alters the DNA sequence of a gene in adirected way such that amino acids arechanged in the protein productaccording to the experimenter’s needs.• Used to test “what if the proteinsequence was different from the normalsequence?”Protein expression in bacteria• Many proteins are not present in highenough quantities (in their normalcellular environment) for us to purifyand study them.• By moving the gene coding for thisprotein into bacteria, we can producelarge quantities of the protein to study(enough to crystallize, for example).Fig. 5-32 LehnFig. 5-30 LehnFig. 5-29LehnFig. 14-15B and TFig. 5-30 LehnFig. 5-33LehnFig. 14-15B and TFig. 5-33LehnFig. 5-33LehnFig. 5-33LehnFig. 5-33LehnFig. 14-16B and TISOFORM-SPECIFICDOMAINS OF MYOSIN ANDPHOSPHORYLATION OFPARAMYOSIN REGULATESKELETAL MUSCLEFUNCTIONSANDY BERNSTEINDEPARTMENT OF BIOLOGYMOLECULAR BIOLOGY INSTITUTESDSU HEART INSTITUTESAN DIEGO STATE UNIVERSITYELCRLCActin bindingsitesATP entryDROSOPHILA MYOSIN ISOFORMS VARY INDISCRETE LOCATIONSNear N-teminusRelay loopConverter• NEAR SITE OFNUCLEOTIDE EXCHANGE• NEAR N-TERMINUS/PIVOT POINT• RELAY LOOP• CONVERTER• HINGE OF ROD• C-TERMINUS OF RODEmbryonicIFI7d11e3b9a7a9b11c3aELCRLCATP entry2 MHC ISOFORMS DIFFER IN ALL ALTERNATIVE REGIONSTransgenic organisms• In a whole animal or plant, genes can beadded or replaced with a sequence of theexperimenter’s choosing.• Dr. Bernstein used this technique to switchmyosin proteins in the fly Indirect Flightmuscles.• Used to test “what if this tissue contained adifferent protein from the one usuallypresent?”Some Recombinant DNAtechniques that can be usedto facilitate the study ofproteins.A. Site-directed mutagenesisB. Protein expression in bacteriaC. Transgenic organismsAn experimental strategy will often usemore than one of these molecular biologytechniques.• Site-directed mutagenesis might be used toalter a gene before it is reintroduced into atransgenic organism.• If you wanted to use X-ray crystallography toexamine how alteration of the amino acidsequence of a protein affected its structure,you would first alter the gene encoding thisprotein through site-directed mutagenesis.• Then, you would produce the mutant proteinin bacteria, so that you could produce enoughof it to
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