Term
| How is the THI stabilized during in the enzyme Chymotrypsin? |
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Definition
| The oxyanion hole stabilizes the charge. Glycine-193 and Serine-195 donate hydrogen bonds to stabilize the negatively charged oxygen. |
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Term
| What is DIPF and TCPK and what are their significance? |
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Definition
| DIPF= Diisopropylphosphofluoridate and it reacts with the active site serine-195 on Chymotrypsin to elucidate it's catalytic importance. TCPK is another inhibitor of chymotrypsin that binds to the active site histine-57 to show its enzymatic importance. |
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Term
| How was the 2 step mechanism determined for chymotrypsin? |
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Definition
| A chromogenic substate called N-acetyl-L-phenylalanine-p-nitrophenyl ester was introduced to chymotrypsin and the absorbance of the yellow product produced was measured. The results showed an initial burst phase followed by a steady phase suggesting the second step is the rate limiting step. |
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Term
| Name the properties of starch and glycogen: |
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Definition
| Starch and glycogen are polysaccharides of glucose molecules. They are bound by a(1,4) linkages which cause them to adopt a helical shape. Glycogen is also highly branched with a(1,6) linkages every 8-12 residues. |
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Term
| Why is ASP-102 so conserved in the structure of chymotrypsin? |
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Definition
| It stabilizes the rotatable bonds on the histidine, pointing it in the optimum direction to interact with SER-195. |
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Term
| How is Glycogen branched? |
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Definition
| a (1,4) for linear glycosidic bonds, a (1,6) for branching bonds |
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Term
| How are N-linked carbohydrates attached to proteins? |
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Definition
| Theough linkage with amide nitrogen of asparginine. This always results in a core of 2-N-acetylglucosamine linked with a mannose triad. |
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Term
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Definition
| Galactopyranosyl is bound to glucopyranose through a b(1,4) linkage. |
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Term
| Name the four strategies that enzymes use to accomplish chemistry: |
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Definition
| 1. Covalent Catalysis, 2. General acid/base catalysis, 3. Metal Ion Catalysis, 4. Catalysis by approximation, |
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Term
| What is the consequence of a(1,4) linkages? |
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Definition
| It constrains the polymer to be curved creating helices. |
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Term
| How are O-linked carbohydrates attached to proteins? |
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Definition
| Linked to the hydroxyl group of either serine or threonine usually by N-acetylgalactosamine. |
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Term
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Definition
| Glucose is bound to fructose in an a(1,2) glycosidic bond. |
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Term
| In sucrose, what is the configuration of the anomeric carbon of the fructose constituent? |
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Definition
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Term
| The larger the Kcat/Km ratio does what to the catalytic efficiency of an enzyme? |
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Definition
| Increases catalytic efficiency. |
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Term
| Since the peptide bond is kinetically favorable, how are enzymes able to cleave the bond? |
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Definition
| Enzymes use 3 tools: 1. Active site uses a potent nucleophile to attack the carbonyl carbon, 2. The peptide carbonyl is further polarized to make the carbonyl carbon even more susceptible to nucleophilic attack, 3. Stabilize the intermediates in order to drive the reaction forward. |
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Term
| What sugar contributes to a RBC being an A antigen? |
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Definition
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Term
| What are the consequences of glycogen's branching? |
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Definition
| The structure is highly dense and has multiple ends available for enzymatic degredation |
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Term
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Definition
| Glucopyranosyl is linked to glucopyranose through an a(1,4) linkage |
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Term
| What sugar contributes to a RBC having a B antigen? |
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Definition
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Term
| Name the properties of cellulose? |
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Definition
| Cellulose is a polysaccharide that is made up of b(1,4) linkages between glucose molecules. The linearity allows the glucose molecules to hydrogen bond with one another in strands giving cellulose great tinsile strength. |
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Term
| In ABC Transporters, how is the substrate transported across the membrane? What role does ATP play in this process? |
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Definition
| ATP binds to the binding casette to create a conformational change in the transporter to release the substrate. ATP hydrolysis resets the transporter to its original state. |
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Term
| Why is adding phosphate an effective means of regulating protein activity? |
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Definition
| 1. Its -2 charge allows for a conformational change, 2. The phosphoryl group can accept 3 or more hydrogen bonds, 3. The free energy of phosphorylation is rather high and is a good means of keeping the signal on or off, 4. The timescale that phosphorylation lasts is controlable to seconds up to hours, 5. Amplification, 6. ATP links phosphorylation to energy metabolism to signaling |
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Term
| What is CTP and what is its significance? |
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Definition
| CTP is an allosteric effector of aspartate transcarbamoylase and is not a substrate analog. It affects the regulatory subunit and thus affects the T/R state transition. |
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Term
| What mechanism do NMP kinases use? |
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Definition
| Catalysis by approximation and metal ion catalysis |
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Term
| What is the role of the divalent cations in NMP kinases? |
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Definition
| Mg2+ and Mn2+ have 3 roles: 1. Neutralize the negative charges of the substrate, 2. Properly position the substrate, 3. Provide additional interactions with the enzyme |
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Term
| Name the common covalent modifications of protein activity: |
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Definition
| 1. Phosphorylation, 2. Acetylation, Myristoylation (lipidation), 3. ADP-ribosylation, 4. Farnesylation, 5. gamma-Carboxylation, 6. sulfation, 7. Ubiqitination |
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Term
| Where does glycosylation occur? |
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Definition
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Term
| Which amino acid residues are sugars commonly linked in glycoproteins? |
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Definition
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Term
| What are the 6 major classes of enzymes? |
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Definition
| 1. Transferase, 2. Oxidoreductase, 3. Hydrolase, 4. Lyase, 5. Isomerases, 6. ligases |
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Term
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Definition
| catalyze group transfer reactions. ex: NMP kinases |
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Term
| What do oxidoreductases do? |
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Definition
| Catalyze oxidation/reduction reactions. Ex: lactate dehydrogenase |
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Term
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Definition
| Catalyze hydrolysis reactions. Ex: chymotrypsin |
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Term
| What do lyase reactions do? |
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Definition
| Catalyze the addition or removal of double bonds. Ex: fumarase |
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Term
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Definition
| Catalyze intramolecular group transfer. Ex: triose phosphate isomerase |
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Term
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Definition
| Join two substrates. Requires ATP. |
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Term
| What does Keq tell us? Kcat? |
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Definition
| Keq tells us how favoable a reaction is. Kcat tells us how fast the reaction is. |
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Term
| What does an enzyme have the highest affinity for: the substrate, the transition state, the product? |
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Definition
| The transition state because if it was completely complementary to either the substrate or the product, it would not catalyze a reaction and would be stuck in the ES or EP complex. |
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Term
| How can we neglect k-2 reverse reaction in the formulation of kcat? |
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Definition
| In early points during the reaction, we can assume that product levels are low and the reverse reaction can be neglected. |
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Term
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Definition
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Term
| In a lineweaver-burke plot, what do the x and y axis' represent? |
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Definition
| Y axis: 1/V0, X axis: 1/[S]. This means that the greater value on the Y axis, the slower the initial velocity and the greater the number on the x-axis represents the lower the concentration of the substrate. |
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Term
| What do the y and x intercept represent on the lineweaver burke plot? The slope? |
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Definition
| y intercept is 1/Vmax; x intercept is -1/Km; Slope= Km/Vmax |
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Term
| What factors does Km depend on? |
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Definition
| pH, temperature and ionic strength |
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Term
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Definition
| 1. It is the concentration at which half of the active sites are filled for catalysis. 2. It tells us about the stability of the ES complex. If Km is high it tells us that the ES compex is unstable and vice-versa. |
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Term
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Definition
| It is the max amount of product that is formed when the enzyme is saturated. |
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Term
| How do we measure catalytic efficiency? |
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Definition
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Term
| What does kcat/Km tell us? |
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Definition
| kcat/Km tells us about the catalytic efficiency under typical cellular concentrations. Sinc cellular concentrations rarely approach those to reach Vmax, kcat/Km tells us both about the rate of ES formation and catalytic rate. The larger this number, the better the enzyme is at performing under cellular conditions. This can also tell us the preferace toward certain substrates for a particular enzyme. |
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Term
| What are the types of enzyme inhibition? |
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Definition
| 1. Competitive, 2. Uncompetitive, 3. Mixed, 4. Irreversible |
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Term
| What are the characteristics of competitive inhibition? |
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Definition
| It occcurs only at the active site. It essentially removes enzyme from the solution. Does not affect Vmax since adding more and more substrate will eventually lead to reaching Vmax. It increases the apparent Km value due to the need of more substrate. |
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Term
| What are the features of uncompetitive inhibition? |
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Definition
| It only binds to the ES complex away from the active site. |
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Term
| What does a LWB plot look like of a competitively inhibited enzyme? |
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Definition
| It changes the Km but not the Vmsx, so therefore it will change the slope to make the graph steeper with the same y-intercept. |
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Term
| What does a LWB plot look like of an uncompetitvely inhibited enzyme? |
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Definition
| Since both the Km and Vmax are affected, the graph is shifted up with a larger y intercept and more negative x intercept. The slope, however, is not changed. |
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