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UKCD Biochem Lec 8

Terms from Biochem lecture 8

QuestionAnswer
Binding energy free energy released in formation of many weak interactions b/w enzyme and substrate, imparts specificity and increases catalytic efficiency, only correct substrate will participate, promote transition state formation
Covalent catalysis active site contains a reactive group that is temporarily covalently modified
General acid-base catalysis active site contains a reactive group that is temporarily covalently modified
Metal-ion catalysis uses a bound metal ion
Catalysis by approximation involved two substrates that are brought together on a single binding surface to enhance the rate of rxn
Protein turnover important process where proteins are continually synthesized and degraded
Proteases (proteinases) catalyze the hydrolysis of peptide bonds, degrading protein
Proteases (Chymotrypsin) mammalian digestive enzyme, catalyzes hydrolysis at peptide bonds on carboxyl side of aromatic/large hydrophobic groups, member of serine protease family, requires covalent attachment of substrate during rxn
Chromogenic substrate changes color upon cleavage
Pre-steady state kinetics two stages implying two steps in rxn acylation and deacylation
Catalytic triad three chains of amino acids in chymotrpsin, has a serine h-bonded to a histidine h bonded to a aspirate which help pull proton away from serine creating alkoxide ion which is a powerful nucleotide
Oxyanion hole helps stabilize the very unstable tetrahedral intermediates
S1 pocket hydrophobic pocket within serine proteases that determines specificity
Cysteine proteases similar to serine proteases, but use a cysteine in place of the serine to form covalent intermediate ex. papain
Aspartyl proteases use two aspartate groups plus a water molecule to hydrolyze peptide bonds, no covalent intermediate ex rennin, HIV-1 protease
Metalloproteases use a bound metal ion, usually zinc, to activate water that can then attack peptide bonds, no covalent intermediate ex. Thermolysin and carboxypeptidase A
Carbonic anhydrases speed up interconversion of CO2 and HCO3-, contains zinc essentially for catalytic activity, zinc activates water ligand viewed from pH dependence of activity, activated water acts as a nucleophile
Proton shuttle rxn like carbonic anhydrases require quick replenishment of protons available from a buffer
Convergent evolution carbonic anhydrases show because alpha, beta and gamma anhydrases present that all use zinc to activate water
Restriction enzymes (restriction endonucleases) cleave DNA in a highly specific manner, found in bacteria and prokaryotes evolved to protect organism from foreign DNA ex viruses, catalyze the hydrolysis of the phosphodiester backbone of DNA,
Cognate DNA (recognition sites) specific short sequences recognized by restriction enzymes
Methylases DNA protected by these enzymes in bacteria by placing methylate adeneine bases within host recognition sequences
Covalent intermediate caused by the double displacement retention configuration (SN2) present in restriction enzymes cleavage
Inverted repeats type of sites recognized by restriction enzymes, give 3D structures recognition sites in 2fold rotational symmetry
Restriction enzymes Type II common catalytic core, prevalent in Archaea and Eubacteria, related evolutionarily, most likely obtained by horizontal gene transfer
Horizontal gene transfer passing of pieces of DNA b/w species, providing new host a selective advantage, relatively common event in microorganisms
Nucleoside Monophophate (NMP) catalyze the transfer of a terminal phosphoryl group from a nucleoside triphosphate (usually ATP) to a nucleoside monophosphate, must be done promoting transfer of a phosphoryl group from NTP to water
NTP binding domain NMP kinases belong to this homologous family, contains central beta sheet surrounded by alpha helicies,
P-loop loop b/w first beta strand and 1st helix is highly conserved sequence is Gly-X-X-X-X-Gly-Lys, interacts with phosphoryl groups in bound nucleotide
Created by: wiechartm