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45 Cards in this Set
- Front
- Back
trypsin and thrombin specificity
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Trypsin--must have Lys or Arg side chain
Thrombin--must have Arg side chain |
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apoenzyme
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free form of an enzyme that uses a cofactor
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holoenzyme
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apoenzyme plus cofactor
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coenzymes
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mostly small molecules derived from amino acids
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larger Keq=_________change in energy
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more negative
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cofactor of cytP450
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heme
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active site residues are usually made up of______________ residues
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noncontiguous
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Emil Fisher
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lock and key
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Dan Koshland
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induced fit
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Michaelis Menten kinetics
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assumes [S]>>[E]
stability of ES is defined by KM=(Ksub-1 + Ksub2)/Ksub1 |
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Michaelis Menten equation
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Vo=Vmax*([S]/([S]+Km))
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Lineweaver-Burk Plot
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1/Vo=1/Vmax+Km/Vmax*1/[S]
end up with straight line instead of hyperbolic y intercept=Vmax x intercept=km |
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Km=dissociation constant (Kd) only when
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ksub2<<ksub-1
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Ksub2 is the same as
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Kcat (turnover number or max)--how fast when saturated with substrate
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Kcat can never be
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>Ksub1 because Ksub1 is the association constant
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allosteric enzymes
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don't follow Michaelis Menten kinetcs--the binding of one substrate can alter other active sites
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Kcat/Km
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catalytic efficiency allows a comparison of different enzymes or substrates
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example of a multi-substrate ordered sequential reaction
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lactate dehydrogenase--NADH must bind then pyruvate must bind the lactate is released then NAD+ is released
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example of multi-substrate random sequential reaction
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creatine kinase--ATP or creatine can bind first and phosphocreatine or ADP can be released first
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example of multi-substrate double displacement reaction
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aspartate aminotransferase--aspartate binds, enzyme retains NH3 and oxaloacetate is released, alpha-ketoglutarate binds and glutamate is released (with NH3 bound to it)
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RNA enzymes
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ribosymes
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competitive inhibitors
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compete for active sites
km changes, but no Vmax |
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uncompetitive inhibitors
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binds after substrate has bound--next to active site
decreases apparent Vmax and Km |
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Ki
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=[E][I]/[EI]; dissociation constant for inhibitor--small Ki mean potent inhibitor
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noncompetitive inhibitor
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binds not at the active site
decreases Vmax but not Km |
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irreversible inhibitors
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modify enzymes by formation of new covalent bonds
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2 examples of group specific reagents
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DIPF forms covalent bond with OH on serine residue (acetylcholinesterase=enzyme)
iodoacetamide binds covalently to S in Cysteine |
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affinity labels
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aka reactive substrate analogs
molecules that are structurally similar to substrate for enzyme and covalently bind to active-site residues |
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group specific reagents
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react with specific side chains of amino acids
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example of affinity label
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TPCK inhibits chymotrypsin by binding at active site and reacting irreversibly with His residue
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suicide inhibitors
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aka mechanism-based inhibitors--inhibitor binds to enzyme and is initially processed by normal catalytic mechanism--this generates a chemically reactive intermediate that inactivates enzyme through covalent modification
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example of suicide inhibitor
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N, N-dimethylpropargylamine inhibits MAO
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treatment for parkinsons and depression
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(-) deprenyl (MAO inhibitor)
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transition state analogs
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compounds resembling transition state of a catalyzed reaction inhibit enzymes
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example of transition-state analog
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pyrrole 2-carboxylic acid binds to proline racemase (changes L-Proline to D-Proline). Transition state of Pro is trigonal as is pyrrole 2-carboxylic acid--binds 160 times more tightly than Pro
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peptidoglycan
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cell-wall macromolecule of bacteria--consists of linear polysaccharide chains that are cross-linked by short peptides
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glycopeptide transpeptidase
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catalyzes final step in peptidoglycan synthesis--amino group at one end of pentaglycine chain attacks peptide bond between 2 D-alanine residues in another peptide unit forming a peptide bond between glycine and on D-alanine residue (other is released)
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penicillin
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inhibits glycopeptide transpeptidase--binds ot active site because it mimics D-Ala-D-Ala moiety of normal substrate--then forms covalent bond with serine residue at active site (penicillin has highly strained 4-membered ring makes it reactive)
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6 major categories of enzymes
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oxidoreductases
tranferases hydrolases lyases isomerases ligases |
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oxidoreductase
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oxidation-reduction reactions
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trasnferases
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group transfer
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hydrolases
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hydrolysis reactions (transfer of functional groups to water)
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lyases
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addition or removal of groups to form dbl bonds
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isomerases
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isomerization (intramolecular group transfer)
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ligases
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ligation of 2 substrates at the expense of ATP hydrolysis
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