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UKCD Biochem Lec 8
Terms from Biochem lecture 8
| Question | Answer |
|---|---|
| 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
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