Term
| What is the difference between a cofactor & a coenzyme? |
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Definition
cofactor: one or more inorganic ions (ex. Fe2+, Mg2+, Mn2+, Zn2+)
coenzyme: a complex organic or metalloorganic molecule |
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Term
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Definition
| a coenzyme or metal ion that is very tightly or even covalently bound to the enzyme protein |
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Term
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Definition
| a complete, catalytically active enzyme together with its bound coenzyme and/or metal ions |
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Definition
| the protein part of a holoenzyme |
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Term
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Definition
| the confines of a pocket on the enzyme in which an enzyme-catalyzed reaction takes place |
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Term
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Definition
| the molecule that is bound in the active site & acted upon by the enzyme |
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Term
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Definition
| the starting point for either the forward or the reverse reaction; the contribution to the free energy of the system by an average molecule under a given set of conditions |
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Term
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Definition
| the difference between the energy levels of the ground state & the transition state |
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Term
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Definition
| transient chemical species that form & decay during the several steps of a reaction |
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Term
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Definition
| the step with the highest activation energy that determines the overall rate when several steps occur in a reaction |
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Term
| 2 things that determine the rate of any reaction |
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Definition
1. concentration of the reactant
2. rate constant (k) |
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Term
| binding energy (delta GB) |
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Definition
| the energy derived from enzyme substrate interaction |
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Term
| 2 fundamental principles for how enzymes use noncovalent binding energy |
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Definition
1. much of the catalytic power of enzymes is ultimately derived from the free energy released in forming many weak bonds & interactions between an enzyme & its substrate
2. weak interactions are optimized in the reaction transition state; enzyme active sites are complementary not to the substrates per se but to the transition states through which substrates pass as they are converted to products during an enzymatic reaction |
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Term
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Definition
| the ability to discriminate between a substrate & a competing molecule; an enzyme gets specificity from the same binding energy that provides energy for catalysis |
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Term
| 4 physical & thermodynamic factors contributing to the barrier to reaction |
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Definition
1. the entropy of molecules in solution (reduces the possibility that they will react together)
2. the solvation shell of hydrogen-bonded water that surrounds & helps to stabilize most biomolecules in aqueous solution
3. the distortion of substrates that must occur in many reactions
4. the need for proper alignment of catalytic functional groups on the enzyme |
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Term
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Definition
| a large restriction in the relative motions of two substrates that are to react |
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Term
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Definition
| happens to the substrate due to formation of weak bonds between substrate & enzyme |
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Term
| specific acid-base catalysis |
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Definition
| catalysis of the type that uses only the H+ or OH- ions preset in water |
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Term
| general acid-base catalysis |
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Definition
| proton transfers mediated by weak acids & bases other than water |
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Term
| What does maximum velocity (Vmax) look like on a graph? |
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Definition
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Term
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Definition
| when the enzyme is first mixed with a large excess of substrate & the concentration of ES builds up |
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Term
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Definition
| the point a reaction achieves when [ES] remains approximately constant over time |
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Term
| What does the Michaelis-Menten equation describe? |
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Definition
| the rate equation for a one-substrate enzyme catalyzed reaction |
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Term
| Michaelis-Menten kinetics |
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Definition
| all enzymes that exhibit a hyperbolic dependence of Vo on [S] |
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Term
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Definition
| the parameter that is the rate constant for the conversion of E + S to E + P |
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Term
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Definition
| competes with the substrate for the active site of the enzyme |
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Term
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Definition
| binds at a site distinct from the substrate active site & (unlike a competitive inhibitor) binds only to the ES complex |
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Term
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Definition
| binds at a site distinct from the substrate active site (like an uncompetitive inhibitor) but binds to either E or ES |
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Term
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Definition
| bind covalently with or destroy a functional group on an enzyme that is essential for the enzyme's activity or form a particularly stable noncovalent association |
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Term
| What type of inhibitors are suicide inactivators? |
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Definition
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Term
| mechanism-based inactivators |
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Definition
| hijack the normal enzyme reaction mechanism to inactivate the enzyme |
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Term
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Definition
| the hydrogen-bonding network in chymotrypsin where Ser195 is linked to His57 and Asp102 |
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Term
| What kind of virus is HIV identified as? |
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Definition
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Term
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Definition
| enzymes that cleave beta-lactam antibiotics (rendering them inactive); human use of penicillin & its derivatives has led to the evolutions of strains of pathogenic bacteria that express this |
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Term
| What type of enzymes exhibit increased or decreased catalytic activity in response to certain signals? |
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Definition
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Term
| How do allosteric enzymes function? |
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Definition
| through reversible, noncovalent binding of regulatory compounds called allosteric modulators (allosteric effectors) which are small metabolites or cofactors |
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Term
| Is covalent modulation reversible or irreversible? |
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Definition
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Term
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Definition
| when peptide segments are removed from an enzyme to activate it; unlike effector-mediated regulation, regulation by proteolytic cleavage is irreversible |
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Term
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Definition
| catalyze the attachment of phosphoryl groups to specific amino acid residues of a protein |
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Term
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Definition
| catalyze the removal of phosphoryl groups from target proteins |
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Term
| zymogen (proproteins) (proenzymes) |
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Definition
| an inactive precursor that is cleaved to form the active enzyme |
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Term
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Definition
| a mechanism that allows a very sensitive response to (and amplification of) a molecular signal; ex) formation of a blood clot |
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Term
| What is the makeup of fibrinogen? |
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Definition
| a dimer of heterotrimers with three different but evolutionarily related types of subunits |
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Term
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Definition
| a serine protease that catalyzes peptide removal |
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Term
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Definition
| a transglutaminase that catalyzes the condensation of Lys residues in one subunit with Gln residues in another to generate covalent cross-links that stabilize interactions |
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Term
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Definition
| when all components of a pathway are found in the blood plasma |
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Term
| Is the protein tissue factor (TF) found in the bloodstream? |
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Definition
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Term
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Definition
| circulating specialized cell fragments that lack nuclei whose activation begins blood clotting at the site of a wound |
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Term
| What is the relationship between factor VII & TF? |
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Definition
factor VII = a zymogen of a serine protease
TF = a regulatory protein that is required for its function |
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Term
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Definition
| the active form of factor VII; made from proteolytic cleavage carried out by factor Xa |
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Term
| What cleaves factor X to its active form factor Xa? |
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Definition
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Term
| tissue factor protein inhibitor (TFPI) |
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Definition
| the protein that quickly shuts down the TF-VIIa complex |
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Term
| When/how is factor IX converted to the active serine protease factor IXa? |
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Definition
| the TF-VIIa protease during initiation of the clotting sequence |
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Term
| What does factor IXa complex with in order to form a relatively stable alternative enzyme for the proteolytic conversion of factor X to factor Xa? |
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Definition
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Term
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Definition
| cleavage of factor XI zymogen by thrombin in a feedback loop |
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Term
| What cleaves the serine protease zymogen protein C? |
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Definition
| the thrombin-thrombomodulin complex |
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Term
| What is the function of the activated protein C-regulatory protein S complex? |
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Definition
| cleave & inactivate factors Va & VIIIa |
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Term
| What kind of protein is antithrombin III (ATIII)? |
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Definition
| a serine protease inhibitor |
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Term
| gamma-carboxyglutamate residues (Gla) |
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Definition
| the modification of multiple Glu residues near the amino terminus of each protein to form calcium-binding sites |
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Term
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Definition
| a vitamin K antagonist that works as a highly effective anticoagulant |
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Term
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Definition
| highly sulfated polysaccharides |
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Term
| What is aspirin effective as? |
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Definition
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