F BICH 410 Study Guide 3: Lectures 18-24Lectures 18- What are the three types of enzymes and what are they known to do?o Oxidoreductase- oxidation/reduction reaction that typically uses NAD/NADHo Lyase- breaks molecule and generates double bondso Ligase- brings two molecules together- typically ATP or energy sourceo Isomerase- changes the structure of a moleculeo Transferase- transfers groupso Hydrolase- hydrolysis reaction- What is the difference between a cofactor, coenzyme, cosubstrates, and prosthetic groups?o A cofactor is a small molecule that facilitates a reaction- can be a metal iono A coenzyme is an organic cofactoro A cosubstrate is a coenzyme that transiently bindso A prosthetic group is a coenzyme that permanently binds - Which are true and false?o Enzymes do not change the free energy- TRUEo Enzymes accelerate the rate of the reaction- TRUEo Enzymes do not affect the activation energy- FALSEo Enzymes effect Keq- FALSEo A catalyst lowers the activation barrier equally for both the forward and reverse reaction- TRUE- What is the equation for the rate enhancement?o Rate enhancement= e^(activation energy/RT)= kcat/kuncat- How do you calculate the free energy?o deltaG=-RTlnKeq keq=k1/k2o deltaG=-RTln[vh/kBT]Lecture 19- What is the Michaelis-Menten Kinetics?o E+S <-> ES -> P+E- How do you calculate specific activity or turnover rate?o Specific activity= vmax/amount of proteino Specific activity= vmax/amount of protein x molecular weight- What is the equation for velocity and how can [S] and [E] effect it?o Vo=Vmax[S]/(keq+[S])o If [S] is significantly less than Km than the eqn is Vo=Vmax[S]/keqo If keq=S than Vo=Vmax/2o If [S] is significantly greater than Km than Vo=Vmax- How do you plot a Lineweaver-Burk plot?These notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.o It is a plot of 1/V versus 1/[S]o Slope= Km/Vmaxo Km equals the x-intercept at -1/kmo Vmax equals the y intercept at 1/Vmax- What are the different inhibition patterns and mechanisms and how do they differ?o Reversible (dead end or product) or irreversible inhibitorso Competitive E(binds here)+S <-> ES -> P+E Same Vmax for all plots- intersecting lines Can be overcome with increase in [S] Ki=[I]/(slope w I/slope wo I -1)  Ki=[I]/(Km w I/Km wo I -1) o Uncompetitive E+S <-> ES(binds here) -> P+E Same slope for all- parallel lines  Ki=[I]/(yint w I/yint wo I -1)  Ki=[I]/(xint w I/xint wo I -1) o Mixed  E+S(binds here) <-> ES(binds here) -> P+E Ki=[I]/(slope w I/slope wo I -1) AND Ki=[I]/(yint w I/yint wo I -1)  2 different numberso Noncompetitive E+S(binds equally here) <-> ES(binds equally here) -> P+E Ki=[I]/(slope w I/slope wo I -1) AND Ki=[I]/(yint w I/yint wo I -1)  same number Same km for all - What does a smaller Ki mean?o Tighter bindingLecture 20- Bisubstrate reactions are quite common, what is the most common type?o Transferase and oxidation-reduction reactions- What are the 2 kinetic mechanisms?o Sequential- all substrates bound together before rxns then products are released- intersecting lines on lineweaver-burk plot Ordered and randomo Ping-pong- one or more products are released before all substrates released- parallel linesLecture 21- How are the effects of substrate binding?o Reduces the entropy reductiono Desolvation of substrates- eliminates water interfering with the reactiono Formation of weak interactions between enzyme and substrate- What is the transition state optimization and stabilization?o The transition state analog with the best geometric and electronic binding to the ligand is the transition state. The transition state stabilization says that the tighter the enzyme binds to the transition state the faster the catalyzed reaction occurs- What are the 2 binding motions for enzymes?o Lock and key and induced fit- What are the three types of catalytic mechanisms?o Acid-base catalysiso Can be general acid (enzyme protonated, substrate deprotonated), general base (enzyme deprotonated, substrated protonated), or concerted acid-base o For concerted acid-base the ph plot has the active form between the pKa of the base and the pka of the acid o Covalent catalysis- involves formation of covalent bond with electrophile and nucleophileo Metal ion catalysis- very common 1/3 of enzymes Metalloenzymes-tightly bound Metal activated- loosely bound- What are the enzymatic mechanisms we should be familiar with for the test?o Ribonuclease A (2 His), carbonic anhydrase (metal ion catalysis Zn with 3 His), serine proteases (trypsin, chymotrypsin, elastase), aspartic proteases (2 active sites of Asp), carboxypeptidase- What is the Catalytic triad?o When the active sites of typsin, chymotrypsin, and elastase are made of His, Asp and Ser- What are other examples of important enzymes to the body?o Serine proteaseso Aspartic proteases- HIV-1 protease (cleaves HIV1 genome allowing growth and infection)Lecture 22- How are enzyme regulated?o Availability of substrates and products, rate of synthesis/decomp, allosteric rxns (do not obey Michaelis-menton kinetics because has hyperbolic curve- T and R form exist- multi subunit), covalent modifications, zymogens (precursor of enzyme must be proteolyticallycleaved in order to work), isozymes (similar to enzyme but is not the same bc differs in kinetics with different kmax and vmax)Lecture 23- What are the functions of membranes?o Barrier to toxins, help accumulate nutriens, facilitate cell motion, assist in reproduction, modulate signal transduction, mediates cell-cell interaction, modulate signal transduction- What kind of movements can a phospholipid bilayer undergo?o Membranes are asymmetrical and the phospholipids can rotate and move laterally but not across the layers- this movement requires proteins such as flippase (moves from outer to inner), floppase (moves inner to outer), or scramblase (movement achieves equilibrium and moves from inner to outer)- What are characteristics of transmembrane proteins?o Typically helical with Cterm on inside and Nterm on outside but can be composed of sheet barrel proteins (also novel helical barrels)o Carbohydrates are attached to outside of membraneo Can determine transmembrane location by hydropathy plots because TMD are hydrophobicLecture 24- What are the types of lipid linked proteins (typically on cytoplasmic side)?o Amide linked myristoyl