F BICH 410 Study Guide 3 Lectures 18 24 Lectures 18 What are the three types of enzymes and what are they known to do o Oxidoreductase oxidation reduction reaction that typically uses NAD NADH o Lyase breaks molecule and generates double bonds o Ligase brings two molecules together typically ATP or energy source o Isomerase changes the structure of a molecule o Transferase transfers groups o 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 ion o A coenzyme is an organic cofactor o A cosubstrate is a coenzyme that transiently binds o A prosthetic group is a coenzyme that permanently binds Which are true and false o Enzymes do not change the free energy TRUE o Enzymes accelerate the rate of the reaction TRUE o Enzymes do not affect the activation energy FALSE o Enzymes effect Keq FALSE o 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 k2 o 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 protein o 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 keq o If keq S than Vo Vmax 2 o 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 Vmax o Km equals the x intercept at 1 km o 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 inhibitors o 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 numbers o 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 binding Lecture 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 releasedintersecting 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 reduction o Desolvation of substrates eliminates water interfering with the reaction o 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 catalysis o 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 nucleophile o 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 proteases o 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 proteolytically cleaved 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 membrane o Can determine transmembrane location by hydropathy plots because TMD are hydrophobic Lecture 24 What are the types of lipid linked proteins typically on cytoplasmic side o Amide linked myristoyl anchors ie n myristoylation o Thioester linked fatty acyl anchors cysteine with generally palmitate and reversible ie spalmitoylation o Thioether linked prenyl anchors on isoprene units C15 farnesyl and C20 geranylgeranyl residues o Glycosyl phosphatidylinositol GPI anchors