BSC 450 Exam 2 Study Guide
BSC 450 Exam 2 Study Guide BSC 450
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This 10 page Study Guide was uploaded by Jordana Baraad on Sunday October 11, 2015. The Study Guide belongs to BSC 450 at University of Alabama - Tuscaloosa taught by Dr. Ramonell in Summer 2015. Since its upload, it has received 198 views. For similar materials see Fundamentals of Biochemistry in Biological Sciences at University of Alabama - Tuscaloosa.
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Date Created: 10/11/15
Study Guide for Chapter 5 BSC 450550 1 Understand basic vocabulary dealing with enzymes ligand binding site etc Ligand molecule that binds to a protein dominated by noncovalent forces Binding site region in protein where ligand bonds Cofactor inorganic ion necessary to facilitate enzyme activity ex Cu2 Coenzyme organic or metaloorganic molecule necessary to facilitate enzyme activity Prosthetic group coenzyme or metal ion bound very tightly or covalently to enzyme protein Holoenzyme enzyme bound cofactorscoenzymes Apoenzyme apoprotein protein portion of holoenzyme Active site pocket of enzyme where enzyme catalyzed reaction occurs Substrate molecule bound at active site and acted upon by enzyme Binding energy energy derived from enzyme substrate interaction key noncovalent forces at ES complex major source of free energy to lower activation energies of reactions induced fit structural adaptation between protein and ligand 2 Identify weak aqueous forces used in protein ligand interactions a Hydrogen bonding b Electrostatic interactions c Hydrophobic interactions must ALL be hydrophilic or hydrophobic 3 Understand and be able to describe why there are differences in the oxygen binding curves of hemoglobin and myoglobin a theta v p02 b Hill plot nH 1 means no cooperativity i Myoglobin nH 1 throughout ii Hemoglobin nH l for most of plot narrow range when nH 3 l Signifies cooperative binding iii Sigmoidal oxygen binding curve for hemoglobin due to cooperative binding 1 Not possible in myoglobin bc only 1 subunit 4 Know the details of how the heme group operates a Protein bound heme binds with oxygen b Myoglobin monomeric structure alpha tertiary no quaternary c Hemoglobin heterotetramic structure i 2 subunits a2b2 each like myoglobin 5 Explain the terms KD and KA in terms of ligand binding a KD dissociation constant concentration of ligand at 50 binding 50 sites occupied KA association rate constant c Equilibrium when kA kD association and dissociation at same rate 10 ll Evaluate binding curves to estimate the KD value for an enzyme and be able to compare different enzymes based on their binding curves a Lower kD better affinity binding higher is lower affinitybinding b Point on x axis perpendicular to theta 50 Describe the evolutionary reasons that proteins like hemoglobin and myoglobin share certain 3D structures motifs ie the heme group a Free iron promotes damaging free radicals b Iron used in cells less reactive c Multicellular organisms requiring long distance oxygen transport use protein bound iron heme Explain the mechanisms of hemoglobin regulation pH C02 23 BPG in detail a pH i Metabolizing tissues release H lowering pH ii H binds to Hb I stabilizes T state T state has lower affinity than R state iii Reduced O affinity in lower pH tissues 0 deposited at tissues 1 Oz and H bound by Hb with inverse affinity b C02 i C02 produced by metabolic tissue must be exported ii Exported as carbamate H ion released I H increased so pH increased 1 See pH relationship to affinity above 2 Contributes to Bohr effect c 23 BPG i negative heterotropic regulator of Hb ii reduces hemoglobin affinity for O allosteric regulation iii binds to charge His amp Lys center between beta subunits iv stabilizes T state Explain at the molecular level how the single point mutation in hemoglobin results in sickle cell disease a Glu I Val in beta chain of Hb b Negative I hydrophobic amino acid c Red ag hydrophobic amino acid SHOULD NOT be facing outward d Hb has hydrophobic pocket that Val fits into e Forms dimers I fibers I sickle shape Understand the T and R states of hemoglobin a T state tense Hb has lower oxygen affinity typical state in tissues i More interactions more stable b R state relaxed Hb has higher affinity typical state in lungs i Fewer interactions more exible Understand and explain cooperativity in hemoglobin and the two models of enzyme cooperativity a Concerted model old i 2 state all T or R like or off ii In absence of O2 T state favored iii In biological systems 02 always present RT transition based on relative O l EX lungs I tissue high 0 I low RI T b Sequential Model new i Each site acts independently each site affects site it s closest to ii hemoglobin s cooperation as 1 subunit binds 0 next subunit s affinity for 0 increases 12 Be able to apply your knowledge of hemoglobin to other situations involving heme containing proteins Study Guide for Chapter 6 1 Be familiar with enzyme nomenclature and the 6 major classes of enzymes a 4 classification class name subclass Type of acceptor Type of acceptor b l Oxidoreductase transfer electrons 2 transferase group transfer reactions 3 hydrolase hydrolysis reactions 4 lyase cleaves CC CO CN leaves double bonds or rings or addition of groups to double bonds 5 isomerase transfer of groups within molecules to yield isomers 6 ligase formation CC CS CO CN Via condensation typically coupled to cleavage of ATP 2 Describe common features of enzymes and enzymecatalyzed reactions a Act by binding substrates b Generally noncovalent bonding c Bonding I binding energy I transition state TS stabilized i Enzyme active sites bind TS better than substrates I better catalysis induced fit model d 4 main catalytic methods i AcidBase Catalysis Givetake of protons 1 Most common for enzymes a Asp Glu Lys very common Cys Tyr more rare 2 2 types a General enzyme uses anything but water b Specific only water used as proton donor acceptor ii Covalent change reaction paths 1 transient covalent bond between E amp intermediate 2 Enzyme type not as important as ability to stage nucleophilic attack 3 Transfer intermediate to active site a Hold or attach to E to form good leaving group iii Metal Ion l Redox changed oxidation state 2 Shift pka a EX Zn lowers pka of water b Fe w heme and Cu most common 3 Redistribute electron cloud density w charge 4 Stabilize charge a Typical in ATP Mg stabilizes charge iv Entropic Reduction preferential interactions w TS 1 Hold in rigid position to force rxn 2 Catalysis by overcoming entropy 3 Describe enzyme catalysis in terms of thermodynamics ie what is different from an energetics standpoint between an enzymecatalyzed and uncatalyzed reaction a Increases reaction rate k by reducing activation barrier AG i Top of activation barrier transition state stabilized by enzyme 1 VERY short lifetime NOT an intermediate b Equilibrium AG not changed c P v time graph i enzyme slope steeper ii if going to infinity end at same plane 4 Interpret enzymatic data in terms of the common mechanisms of enzyme catalysis a See practice problems 5 Understand the MichaelisMenten equation what assumptions are made in this equation and what information it gives us regarding enzyme activity a Means of comparing 2 enzymes catalyzing same rxn compare curves b Vmax effected by E E ltlt S assumed c Assumptions i Formation of products is fastest nonreversible step 1 Binding is reversible ii Steady state assumption rate ES formation rate ES dissociation 1 allows k2E to be considered constant 2 v k2EtS km S becomes V0 S km S a if vmax known can calculate km at any point in rxn 6 Understand the difference between a MichaelisMenten plot and a LineweaverBurk plot a MichaelisMenten v0 vs S hyperbolic i 2 portions 1 beginning linear v dependent on S 2 end hyperbolic I plateau v not dependent on S b LineweaverBurke double reciprocal lvo v 1 S linear i Xintercept llltm ii Yintercept lvmax 7 Understand and be able to mathematically describe Km and Vmax a Km K1 K2 K1 S V0 5 X Vmax i K1 describes ES formation ii K4 describes ES breakdown iii k2 describes product formation irreversible ratedetermining b vm maximum velocity plateau of hyperbola on Michaelis plot as S is increased i reached when all enzyme activates sites are filled with substrate forming ES complex doesn t count if it s an ESI complex c km Vmax slope of LineweaverBurk plot d decreasing km I better enzyme i less substrate needed to get to same velocity e increasing vmax I better enzyme f kcat km specificity constant good measure of enzyme efficiency i catalytic perfection specificity constant 108109M391S391 8 Understand the basic concept of Kcat and what it describes a Kcat k2 describes product formation irreversible ratedetermining step i Measure of enzyme efficiency ii How much substrate can be converted to product at a given active site over a period of time 9 Be able to determine Km and Vmax from data in a table or on a plot a Vmax highest value of v b Km S corresponding to half that value 10 Understand and be able to recognize the different enzyme kinetic mechanisms sequential vs pingpong a Sequential substrates bond to enzyme concurrently forming noncovalent ternary complex i Random substrates bind in either order ii Ordered necessary that l binds for the next to bind efficiently b Pingpong ie double displacement first substrate converted to product before 2nd substrate binds to transformed enzyme release of 2nd enzyme regenerates original enzyme no temarny complex 11 Be able to draw a Cleland diagram to represent a specific kinetic mechanism 12 Be able to predict the pattern you would see in a LineweaverBurk plot if you were given various enzyme kinetic mechanisms a intersection of slopes at single point ternary complex i ordered or random ii intersection away from yaxis b parallel slopes pingpong double displacement 13 Be able to identify the different types of enzyme inhibition i Irreversible permanent shutdown l Suicide ie mechanismbased irreversible covalent bonding hijack enzyme s normal mechanism to produce inactive form useful in rational drug design 2 Transitionstate analogs very tight noncovalent binding Resembles transition states fits enzyme active site better than substrate ii Reversible 1 Competitive bind to active site of E 2 Uncompetitive bind to TS on another site once ES complex has formed 3 Noncompetitive mixed binds at site that isn t the active site can bind to either E or ES 14 Be able to compare and contrast the different kinetic mechanisms of enzyme inhibition a Competitive inhibits substrate binding no effect on catalysis i No change vmax increase in km ii no change in kcat b Uncompetitive inhibits catalysis does not affect substrate binding i Decrease in vmax decrease in km no change vmax km ii No change in kcat c Noncompetitivemixed inhibits substrate binding and catalysis i Decrease in vmax no change in km ii Reduced kcat 15 Be able to predict and eXplain Lineweaver Burk plots for the different mechanisms of enzyme inhibition a Competitive slopes intersect at yaXis b Uncompetitive parallel slopes c Noncompetitivemixed slopes intersect left from yaXis 16 Be able to recognize different mechanisms of enzyme inhibition from LineweaverBurk plots Study Guide for Chapter 7 Carbohydrates 1 Be able to identify stereochemistry in Carbohydrate structures a Chiral center 4 different molecules attached to a Carbon C b Enzymes recognize only 1 stereoisomer stereospeci city 2 Understand carbohydrate naming triose tetrose ketone aldehyde etc and vocabulary epimers anomers pyranose furanose a Aldoketo pre x quotosequot i Pre x triose 3C tetrose 4c pentose 5C hexose 6c heptose 7C ii Epimer 1 of 2 isomers with different con gurations around 1 asymmetrical C iii Anomer speci c type of epimer 1 of 2 stereoisomers w differing con guration only at hemiacetalacetal carbon aka anomeric carbon iv Pyranose 6membered carbohydrate ring w 5 C s 1 O v Furanose 5membered carbohydrate ring 2 4 C s 1 O 3 Be able to draw the structures of glucose and ribose 4 Be able to identify the reactivities of carbohydrates hemiacetal amp hemiketal reactions cyclization of sugars nucleophile and electrophile a Alcohol nucleophilic attacks aldehyde electrophilic D hemiacetal b Alcohol attacks ketone l hemiketal 5 Be able to draw or recognize a cyclized sugar structure if given a linear sugar structure a Linear sugars w 6 C s can cyclize D furanosepyranose rings i Attack on carbonyl C by OH attached to C5 D furanose ii Attack on carbonyl C by OH attached to C6 D pyranose 6 Be able to identify glycosidic linkages and reducing nonreducing ends of carbohydrates a Rxn hemiacetal OH on anomeric C w alcohol b Forward rxn condensation reverse hydration c Reducing end end w anomeric C not involved in glycosidic bond i hemiacetalcontaining reactive add to chain on this end d Nonreducing end no hemiacetal 7 Be able to name glycosidic linkages a Determine con guration of each sugar prelinkage i When linear L v D look C furthest from carbonyl C 1 OH on left L OH on right D ii Alpha v beta look at anomeric C 1 Alpha anomeric OH on opposite side of OH on C6 2 Beta anomeric OH on same side of OH on C6 b Name left right nonreducing l reducing i 1 Nonreducing con guration LDaphabeta 2 Nonreducing name cutting off at quotoquot furanosyl puranosyl 3 quotC of original hemiacetal l C of original alcoholquot most common 14 4 Reducing con guration 5 Reducing name 8 Understand the major concepts discussed regarding the nutritional polysaccharides starch and glycogen a Main storage polysaccharides starch for plants glycogen for animals b Starch mixture of 2 homopolysaccharides of glucose amylose and amylopectin i Amylose unbranched polymer of a1 a 4 ii Amylopectin branched a1 a 6 linkers every 2430 residues iii Hbonding D Spiral when packed iv Reducing and nonreducing ends 1 Enzymes work on nonreducing side c Glycogen branched homopolysaccharide of glucose i a1 a 4 linked chains ii Branchpoints with 051 a 6 linkers every 8 12 residues Understand the major concepts discussed regarding the structural polysaccharides cellulose and chitin as well as glycosaminoglycans hyaluronic acid chondroitin sulfate and heparin a Cellulose structural polysaccharide for plants rigid water insoluble i branched glucose homopolysaccharide ii 31 a 4 linked chains 1 animals lack enzyme to hydrolyze this linkage cellulose not used as animal fuel source 2 fungi and protozoans get around this by secreting cellulase a ruminants and termites symbiotic w cellulose secreting microorganisms b cellulase may be future of fermenting biomass for fuel iii Hbonds between monomers and between chains iv EXAM Q most abundant polysaccharide in nature b Chitin structural polysaccharide for animal exoskeletons insects spiders crabs etc and mushroom cell walls i Nacetylglucosamine monomers form 31 a 4linked chains ii extended bers similar to cellulose 1 tough but exible waterinsoluble indigestible by vertebrates iii Structure is tough but exible and waterinsoluble c Glycosaminoglycans GAG linear polymers of repeating disaccharides i One monomer Nacetylglucosamine ex chitin OR Nacetyl galactosamine ii Negatively charged iii Uronic acids C6 oxidation iv Sulfate esters 1 Ex chondroitin sulfate sulfated GAG a Chain Of 100 alternating sugars N acetylgalactosamine and glucuronic acid b component of collagen prevents compression dietary supplement for osteoarthritis 2 Ex heparin highly sulfated GAG a Highest known charge density of any biomolecule b Common use as anticoagulant v Extended hydrated molecule to minimizes charge repulsion vi Forms meshwork with brous proteins to form extracellular matrix 1 Ex hyaluronic acid component of extracellular matrix involved in proliferation and migration a Unique nonsulfated VERY heavy Study Guide for Chapter 8 BSC 450550 1 Know the basic structural details of individual nucleotides DNA and RNA a Nucleotide contains i Nucleoside 1 nitrogenous heteroaromatic nucleobase a 16 pyrimidine CTU or 19 purine AG 2 pentose sugar a 1 5 b RNA Dribofuranose DNA 32 deoxyD ribofuranose i Lack of 2 OH D tight packing possible ii phosphate 1 typically attached to 5 ATP GTP 39ITP CTP 2 Know the role of weak forces in DNARNA structure a Hbonding speci c base pairing complimentary strands b Hydrophobic interactions stacking of 2 bases w rings parallel 3D structure i Minimizes contact w water c Van der Waals assists w base stacking 3 Understand the functions of DNA and RNA and be able to compare and contrast them a DNA storage of genetic info b RNA expression of DNA S genetic information many cellular functions i mRNA messenger transmission of genetic info 1 codes for 1 protein 2 genetic information from DNA El protein ii rRNA part of enzyme protein synthesis iii tRNA adapter molecules in protein synthesis 1 bind to amino acid on one end mRNA on other iv siRNA regulates gene expression v ribozyme acts as enzyme processing of genetic info 4 Know the other functions of nucleotides in biological systems NAD ATP FAD etc a ATP energy for metabolism i Hydrolysis D chemical energy ii Alternate nucleoside triphosphates used similarly UTP GTP CTP b Adenosine crucial component of many enzyme cofactors i Evolutionary advantage of using one compound for multiple roles ii EX NAD NAD hydride transfers iii EX FAD active form Vitamin Bz electron transfers iv Ex CoA acyl transfers c cAMP signal transduction i quotsecondary messengerquot ii hormones chemical signals D ATP w adenylyl cyclase catalysis D cAMP 5 Understand the various molecular mechanisms responsible for DNA mutagenesis a Oxidative more easily repaired by cellular processes i Spontaneous 1 Deamination a Slow daily process 100 CU per day 2 Depurination a Hydrolysis of betaNglycosyl bond oss base form AP site b Signi cant for purines 10k ost per day c Repaired by baseexcision repair ii Reactive chemicals 1 Oxidation by hydroxyl radical a Hydroxylation of guanine b Mitochondrial DNA most susceptible 2 Methylation of guanine on carbonyl O b Radiation i UV dimerization of thymidine 1 Main mechanism for skin cancer ii Xray break covalent bonds l ring opening strand breaking 1 Ionizing 2 Worst kind most dif cult to repair
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