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57 Cards in this Set
- Front
- Back
What can enzymes be made out of?
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Protein or RNA
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Scissile bond-
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a bond of a substrate that is subject to enzymatic cleavage
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Cofactors-
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small molecules bound to the enzyme
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apoenzymes-
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enzymes without their associated cofactors
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holoenzymes-
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enzymes with their cofactors
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coenzymes-
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small organic cofactors
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What are the 4 reaction groups in organic chem? biochem?
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Organic - rearrangement, elimination, addition, substitution
Biochem Isomerase, Lyase, Ligase, Oxidoreductase, Transferase, Hydrolase |
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What enzyme group does proteases belong?
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hydrolases
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How do enzymes work?
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Make it easier for the substrate to turn into the transition state
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What does the velocity of the reaction depend on?
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on the energy of activation
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Through what interactions are substrates bound to the enzyme?
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Through multiple weak interactions- H bonds, van der waals, ect
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What are the 2 different models for substrates binding? which is more correct?
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Lock and key and induced fit
induced fit |
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K_m-
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concentration of S at which the reaction rate is half the maximal rate (V_max)
- the concentation of S at which half of all active sites are occupied -the dissociation constant for the breakdown of the ES complex |
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What does michaelis -menten model assume?
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-no P reverts back to S
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What is constant in steady-state? What changes
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constant- ES
changed - S and P |
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What is the rate of breakdown
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breakdown of the ES - can go either way forward or backwards
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E_T
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enzyme total - made of both the bound and unbound enzymes
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What is the X and Y axis in a Lineweaver-Burk plot?
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X axis- 1/S concentration
Y axis- 1/V |
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What is the slope?
X intercept Y intercept on a Lineweaver-Burk plot |
Slope- K_m/V_max
X intercept - -1/K_m Y intercept- 1/V_max |
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What does a small Km mean?
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the smaller the number the tighter the binding of ES
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Turnover number-
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the number of substrate molecules converted to product per second when enzyme is fully saturated with substrate K_2
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Kinetic perfection-
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every single times a substrate hits the enzyme a reaction takes place - Or - the diffusion-controlled encounter of enzyme and substrate
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What does K-cat include?
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all the catabolic steps of an enzyme - K1, K2 ect
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What does Kcat/Km measure?
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the effectiveness of the enzyme - the bigger the number the more effective the enzyme
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What are the 2 classes of multiple substrate reactions?
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sequential displacement and double displacement
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What are the 2 subclasses of a bisubstrate reaction?
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sequential ordered and random sequential
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sequential ordered mechanism for multiple substrates-
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the order of the binding of the substrates and the release order of the products matter
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Multiple substrates - random sequential mechanism
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the order of the substrate binding and product release doesnt matter
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Multiple substrates -double displacement-
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one the of products is released before all the substrates are bound -- has a substituted enzume intermediate
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What are the 2 types of reversible inhibition?
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competitive and noncompetitve
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What is the results of the Vmax and Km in competitive inhibition?
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Vmax- is unchanged
Km- increases |
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How can competitive be overcome?
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by increasing substrate concentration
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What is the results of the Vmax and Km in non-competitive inhibition?
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Vmax decreases
Km unchanged Can be overcome by increasing enzyme not substrate |
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What does a competitive inhibitor look like on a lineweaver burk plot?
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Competitive - still crosses at the same Y intercept (1/Vmax)
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What does a noncompetitive inhibitor look like on a lineweaver burk plot?
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Still keeps the same Xaxis (-1/Km)
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IC_50 value-
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the effectiveness of drugs as inhibitors
- the concentration of inhibitor at which half of max enzyme activity is inhibited - very dependent upon the conditions under which they are measured |
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Where do irreversible inhibitors often bind?
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to the catalytic site residues
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What are the 3 types of irreversible inhibition and how do they work?
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group specific - bind to specific side chains
affinity labels-structurally similar to substrate molecules, and covalently modify the active site suicide inhibitors- modified substrates and are the most specific for labeling an active site |
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Besides looking like substrate what is something else to look like and inhibit?
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The substrate transition state
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How does penicillin inhibit bacterial growth? through what type of inhibition?
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interfers with bacterial cell wall growth through irreversible inhibition
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What is bacterial cell wall made out of? what does that consist of?
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peptidoglycan - polysaccharide chains cross linked by short peptides and sugars
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What specific part of the bacterial wall does penicillin interfere with? what enzyme catalyzes this and that penicillin bindsto?
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blocks the cross links of the polysaccharide chains - glycopeptide transpeptidase
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What are vitamins often precursors to?
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essential coenzymes (small organic cofactors)
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enzyme strategy - Binding energy-
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the free energy released in the formation of numerous weak interactions between an enzyme and its substrate
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enzyme strategy covalent catalysis-
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active site contains a reactive group that is temporarily covalently modified
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enzyme strategy General acid-base catalysis-
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a molecule/residue (not water) plays the role of proton donor/acceptor
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enzyme strategy Metal-ion catalysis
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uses a bound metal ion
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enzyme strategy - catalysis by approximation-
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involves 2 substrates that are brought together on a single binding surface to enhance the rate of the reaction
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What is the delta G of peptide bond breaking?
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negative -happens spontaneous -has to if enzymes speed it up- but very slow
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Where does chymotrypsin cleave? What protease family is it apart of/
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on the carboxyl side of aromatic or large hydrophobic groups -(trp, tpr, phe, met, leu) - the serine protease family
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What enzyme strategy does chymotrypsin use?
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covalent modification - the substrate has to be bound
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How many steps does chymotrypsin use? What are the phases called?
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2 - burst phase (acylation) and steady state phase (deacylation)
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What is the active site of made of in chymotrypsin?
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catalytic triad - his, asp, and the reactive ser
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What does the catalytic triad do the ser?
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Help pull proton away from the ser - creating a reactive alkoxide ion - a powerful nucleophile
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What does the oxyanion hole stabilize?
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the very unstable tetrahedral intermediate in the chymotrypsin catalytic mechanism
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What are the 3 main other classes of proteases besides serine?
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1. Cystein proteases
2. Aspartyl proteases - no catalytic triad 3. Metalloproteases- use a bound metal ion to activate water |
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Why is the aspartyl proteases asp so reactive?
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2 asp share a proton - a 1/2 charge on each = very reactive
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