Term
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Definition
A place in the protein's structure where the substrate binds and the reaction occurs
May contain non-amino acid molecules called cofactors (either metal ions or coenzymes) that are essential for the enzyme's function |
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Term
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Definition
| Enzymes are specific for the reaction they catalyze, specific enzyme will catalyze a specific substrate |
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Term
| Regulation (How substrate binds enzyme, 2 ways) |
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Definition
Lock and Key: active site and substrate structures are complementary
Induced fit (more common): enzyme changes shape to fit substrate |
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Term
| Enzymes affect on thermodynamics |
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Definition
| Enzymes do not affect thermodynamics (Free energy) |
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Term
| How enzymes increase the kinetics of a reaction |
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Definition
They decrease the kinetics (activation energy) of a reaction
May completely change pathway by which reactant becomes product, this pathway has a TS molecule with a lower free energy making it more stable
In the presence of enzyme, pathway is the same as without the enzyme, but the enzyme stabilizes the TS molecule (lower free energy of TS molecule) |
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Term
| Three general ways enzymes help reactions |
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Definition
Acid-base catalysis (donates or accepts proton)
Covalent catalysis (enzyme covalently attached to either reactant or TS)
Metal ion catalysis (enzyme that contains metal ion where that ion is somehow involved in the reaction) |
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Term
| What reaction does Chymotrypsin catalyze? |
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Definition
| it catalyzes the hydrolysis of peptide bonds after Phe, Tyr, Trp |
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Term
| What are Chymotrypsin's active site residues? |
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Definition
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Term
| Change to the first tetrahedral intermediate of chymotrpsin |
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Definition
| His 57 works does base catalysis and donates a H+ to Ser 195, Ser 195 breaks its bond between O and H to connect O to the substrate and the extra e are added to the double bonded O |
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Term
| Change from first tetrahedral intermediate to Acyl-enzyme intermediate (covalent intermediate) |
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Definition
| O- donates its extra e to make a double bond with C of the substrate again, The bond between C and N of the subtrate is broken to bind N with the H on His 57, The N on His 57 becomes the e sink |
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Term
| Change from Acyl-enzyme intermediate with added water |
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Definition
| Water enters the active site and H-bonds with His 57 |
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Term
| Change into second tetrahedral intermediate |
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Definition
| Water donates a proton to His 57 (base catalyst), leaving a hydroxyl group that attacks the carbonyl group of the remaining substrate, then the O on the substrate acts like the e sink |
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Term
| Last step of chymotrypsin |
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Definition
| Substrate O double bonds with C again, the bond between Ser 195 and the substrate is broken |
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Term
| The first product of chymotrypsin |
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Definition
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Term
| The second product of chymotrypsin |
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Definition
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Term
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Definition
Oxyanion hold, N-H bonds H-bond with substrate to stabilize it
H-bonds with O- stabilizes TS which lowers the free energy, which lowers the activation energy which increases the rate
NH of Serine and Gly 193 |
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Term
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Definition
firm fit for substrate, varies based on enzymes
Gly, Ser, and Gly for large aromatics |
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Term
| pH affects enzyme activity |
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Definition
Place pka of a.a. residues on 50% points
If it needs to be unprotonated to function then the curve goes up
If it needs to be protonated to function then the curve goes down |
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Term
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Definition
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Term
| Rate of formation = rate of ES going away |
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Definition
| K1[S][E] = K-1[ES] + K2[ES] |
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Term
| Enzyme can be in free form or complexed to substrate |
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Definition
| [Etotal] = [Efree] + [ES] |
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Term
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Definition
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Term
| Velocity rate when [S] >>>>>>>>> [E] |
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Definition
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Term
| Michaelis-Menten equation |
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Definition
| Vo = (Vmax[S])/(Km + [S]) |
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Term
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Definition
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Term
| Draw a lineweaver-burk plot |
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Definition
Y-intercept = 1/Vmax
X-intercept = -1/Km
Slope = Km/Vmax |
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Term
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Definition
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Term
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Definition
| measure of the number of substrate molecules converted to product within a single enzyme in a certain amount of time |
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Term
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Definition
| molecule that binds reversibly to the enzyme |
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Term
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Definition
| molecule that binds at the active site of the enzyme, it increases the Km value, but does not affect the Vmax, decreases the affinity between the enzyme and the substrate |
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Term
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Definition
alpha = 1 + [I]/KI
alpha = Vmax with I / Vmax w/o I OR Km with I/ Km without I |
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Term
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Definition
| molecule that binds to the enzyme (somewhere other than the active site) and decreases the Vmax, but doesn't affect the Km |
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Term
| General functions that change when you change an active site residue |
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Definition
If the Vmax drops, but the Km stays the same: the a.a. was important in converting the substrate to product
If the Vmax stays the same, but the Km increases: the a.a. was important in binding the substrate |
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Term
| Specific functions figured out by changing an a.a. |
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Definition
Is it a acid or base catalyst?
Does it play a part in stabilizing a molecule |
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Term
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Definition
| lipid bilayer: two layers of lipids, hydropillic outside, hydrophobic inside (nonpolar), Proteins embedded in membrane, Carbohydrates. |
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Term
| Integral protein structure |
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Definition
| alpha helices or Beta barrel |
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Term
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Definition
| Voltage gradient forms K+ flowing into the cell, concentration gradient favors K+ flowing out of the cell. |
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Term
| Equation to determine if ions flow in or out of the cell |
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Definition
| G=RTln(concentration where going/concentration where from) + ion charge(F)(membrane potential where going - membrane potential where it is from) |
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Term
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Definition
| Na+ floods in, K+ slowly moves out after membrane potential goes positive, C=O guides K+ out of the cell |
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Term
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Definition
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Term
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Definition
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Term
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Definition
Na+ goes into the cell, K+ exits the cell, now too many K+ outside and too many Na+ inside, pump 3 Na+ out/ 2 K+ in per 1 ATP
When using the equation times the end product by how many are pumped |
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Term
| Mechanism of Na+/K+ channel |
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Definition
1) 3 Na+ bind ATPase
2) ATP - ADP and P binds to ATPase
3) P changes ATPase confirmation
4) Release of Na+
5) 2 K+ binds and H2O clips off P
6) confirmation changed and K+ let off inside the cell |
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Term
| Na Glucose Transporter/Pump |
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Definition
| From intestinal space 1:1 glucose and Na, then Glucose goes out glucose transporter, Na goes out Na+/K+ ATPase, charges part of mechanisms doesn't matter for neutral ions |
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