Exam 3 Study Guide
Exam 3 Study Guide BSC 450
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This 0 page Study Guide was uploaded by Jordana Baraad on Tuesday November 10, 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 134 views. For similar materials see Fundamentals of Biochemistry in Biological Sciences at University of Alabama - Tuscaloosa.
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Date Created: 11/10/15
StudV Guide for Chapter 10 Lipids 1 Understand basic fatty acid structure and nomenclature a Structure combinations of CH2 units 4 36 carbons carboxylic acid i Saturated all CH2 units unsaturated containing double bonds ii Cis configuration typical for double bonds b Nomenclature i Standard V nutritional nomenclature 1 Standard start numbering left I right from carboxylic carbon 2 Nutritional terminal double bond is chief concern a Start numbering rightl left from carbon on terminal double bond ii Longhand monounsaturated 1 Con guration C of double bond prefix oic acid Ex ciS 9 Octadecanoic acid iii Shorthand monounsaturated 1 Carbons Double Bonds dlocation Ofdoublebond 2 ex 181 d9 1V Shorthand monounsaturated 1 Carbons Double B Duds dlocation of double bonds location location 2 ex 20 5 d5 8 11 14 17 2 Understand the term amphipathic and be able to recognize an amphipathic molecule a Amphipathic possessing both hydrophilic and hydrophobic elements b Recognition i Hydrophilic contains polar functional groups ii Hydrophobic contains long nonpolar stretches often long carbon chains 3 Understand the effect of fatty acid structure on its chemical properties a Weak forces at play hydrophobic effect and Van der Waal s Forces i The longer the chain the greater their impact ii Increased melting point proportional to increased C chain length b Saturated fat lack of conjugation I tight packing c More double bonds I more exible membrane less susceptible to rupture when melts after freezing 4 Know the various functions of fatty acids a Waterproofing ex wax layer of cuticle b Defense ex cuticle can have poisons bad tasting compounds mixed in c Structural adaptations ex buoyancy in spermaceti whale 5 Compare energy storage of fatty acids VS sugars a Fatty acids more efficient storage molecules than sugars Fatty acids store 2x more energy g sugar C s more oxidized downsiede slower access to long term stored energy b Fatty acids result in energy stored in more lightweight encironment i Due to lack of water 1 TAGS are hydrophobic sugar attracts water 2 TAGs gtkcompletely excludedlt water 3 Each g of sugar associates w 2 g water 6 Know the basic structures of triglycerides phospholipids sphingolipids glycolipids and sterols a Triglyceride glycerol backbone 3 long chain alkyl groups ester linked FA s i Neutral storage lipid no polar head group b Phospholipids l or 2 long chain alkyl groups glycerol backbone polar head group attached by phosphodiester linkake i Indcludes glycerophospholipids and some sphingolipids ii polar membrane lipid l attachment of phosphate group gives chirality c Sphingolipids 1 FA chain amide linkage to sphingosine backbone i Polar phosphate headgroup in phospholipid shingolipids not all ii Mono or oligosaccharide headgroup in glyclopid sphingolipids not all iii Polar membrane lipid d Glycolipid l or 2 FA chains sphingosine or glycerol backbone polar head group containing mono or oligosaccharide i Includes galactolipids and some sphingolipids ii Marks blood type iii Polar membrane lipid e Sterols polar head group alkyl side chain 4 ring planar steroid nucleus i Sterol hormones cholesterol derivitives 7 Know the basic functions of the lipid soluble vitamins A D E and K a Vitamin A vision particularly light sensitivity and night vision i Rods and cones cis I trans configuration when dark I light b Vitamin D calcium uptake i Activated in 2 steps in skin by UV light ii Cholecalciferol Vit D3 activated inside the body c Vitamin E antioxidant i Interact w free radicals to inactivate them I quenching ii more prevalent in mitochondria due to greater oxidation susceptibility d Vitamin K essential to blood clotting activates prothrombin Study Guide for Chapter 11 Biological Membranes 1 Know the various functions of biological membranes a Define the boundaries of the cell b Allow import and export i Selective import of nutrients eg lactose ii Selective export of waste and toxins eg antibiotics C Retain metabolites and ions within the cell i Against concentration gradient Sense external signals and transmit information into the cell 6 Provide compartmentalization within the cell i separate energy producing reactions from energy consuming ones ii keep proteolytic enzymes away from important cellular proteins f Produce and transmit nerve signals Store energy as a proton gradient Support synthesis of ATP i H ATPase is membrane protein P QQ 2 Understand the levels of 3D structure of lipids Fig 11 4 a Micelle smallest lowest energy favorable delta G i wedge shaped individual units cross section head gt side Chain ii polar head 1 FA tail b Bilayer intermediate size complexity i cylindrical individual units cross section head side Chain ii 2 FA tails prevent micelle formation too much steric hindrance iii main weak forces hydrophobic effect amp Van der Waal s iv lipid majority of structure 1 holds membrane together v minor polar head interactions C Vesicle largest least favored formation need other proteins not formed by Chance controlled process i I folding in on self ii aqueous core iii studied for drug delivery 3 Know the weak forces that are involved in membrane formation a 2 main weak forces hydrophobic effect amp Van der Waal s interactions i in hydrophobic tails b minor force hydrogen bonding btwn polar groups in heads 4 Describe the common features of membranes a impermeable to ions i problem charge b asymmetric not same composition on both sides i with respect to phospholipids and proteins c dynamic constant motion i replacement cycling of phospholipids receptor proteins etc 5 Understand why membranes are impermeable to charged polar molecules Desolvation requires breaking all hydrogen bonds Raises activation barrier highly unfavorable wo transporter 6 Understand and describe the Fluid Mosaic model a Fluid lipids i Contribute to membrane uidity exibility ii Skate along surface due to weak forces b Mosaic proteins i Different types embedded within and throughout phospholipid bilayer 7 Understand the concept of membrane lea et asymmetry a Innerouter membranes have distinct protein and lipid composition i Phosphatidylserine almost all in 1 important in cell death ii Phosphatidylinositol 4 phosphate always inside 1 Involved in cell signaling will be cleaved 2 I motion in cell pathway iii sphingomyelin almost all out b Sugars always outside c Positiveinside rule positively charged His Arg and Lys more commonly in cytoplasmic inner lea et 8 Predict changes in membrane composition based on environment a Liquidordered L0 v liquiddisordered Ld state degree of allowed lateral lipid motion i 2040 degrees Celsius I L0 polar head grops uniformly arrayed at surface regularly packed nearly motionless acyl chains 1 sterol content increases rigidity in unsaturated FA chains ii heat 40 degrees C I thermal motion I Ld much thermal motion no regular organization 1 sterol content increases uidity in saturated FA chains b Regulate membrane uidity by changing ratio saturated to unsaturated lipids c The more unsaturated the more uid more saturation I increased rigidity d Fluidity important to survive colder temperatures i Rigidity I rupturing upon thawing ii As temperature drops ratio of unsaturated saturated lipids increases 9 Understand the concept of lipid rafts and why they are important a b Formed in membrane from cholesterol sphingolipid association A k a microdomains thicker and more ordered than surrounding monolayer of PM lea ets Enriched by 2 classes of integral membrane proteins i GPI anchored proteins outer ii Cys attached proteins w 2 long chain saturated FA s inner I vesicle formation important for endocytosis i caveolin eX Cys attached recruits claithrin I endocytosis role in signalling 10 Understand why the ability to curve the membrane form vesicles and fuse them to other membranes is essential in the cell 8 Fusion i gt Sperm egg ii Endosomes lysosomes iii Small vacuoles I larger vacuoles plants only Membrane curvature i Vesicle formation budding from Golgi compleX ii Exocytosis iii Endocytosis l Mechanism of viral infection iv gt kcell division separation of 2 plasma membranes Both neurotransmitter release Studv Guide for Chapter 12 Biosignaling 1 Understand the basic types of membrane proteins and their structure a Integral membrane proteins Hydrophilic portions interact with the extracellular matrix ECM and cytoplasm Hydrophobic portions spanning membrane Alpha helices Beta motifs also sometimes present FepA OmpLA Maltoportin KEY to cell functioning transport b GPI anchored proteins Glycophosphatidylinositol anchored proteins Sugar protein phosphatidylinositol anchor Signal cleaved I sugar protein released to act in cell Anchor added post translationally ex of post translational modification c Peripheral membrane proteins Inner or outer lea et Weak force interaction with phospholipid heads and membrane Dominant force hydrophobic interactions hold in membrane 2 Understand how a hydropathy plot is generated and what it tells you a Generated hydropathy index V residue number i hydropathy index free energy change when residue moved from hydrophobic solvent to water 1 determined experimentally 2 range from highly exergonic to highly endergonic b Number of peaks number of hydrophobic regions endergonic c Many peaks I inference protein is an integral membrane protein 3 Describe the general steps in a signal transduction pathway Beta andrenergic receptor prototypical GPCR indicative of GPCR signal transduction a Ligand binding to receptor I conformational change in receptor s intracellular domain I activation of GPCR b G protein exchanges bound GDP for GTP then binds to nearby effector enzyme altering its activity Activated enzyme generates 2nd messenger d 2 messenger affects downstream target 0 4 Describe the six basic types of signal transducers in the cell a G proteincoupled receptor GPCR see 6a for more detail i External ligand binds to receptor I intracellular GTP binding protein activation ii Activation I regulation of enzyme that generates intracellular 2nd messenger iii Best studied receptor targets 50 of drugs 1 Ex beta blocker suppresses fight ight response I reduced anxiety b A Receptor tyrosine kinase ligand binding I tyrosine kinase activity autophosphorylation i Kinase I transcription factor alteration I altered gene expression ii Predominant in animals SerThr more common in plants c Receptor guanylyl cyclase ligand binding to extracellular domain I formation cGMP 211d messenger d Gated ion channel openscloses based on signal ligand concentration or membrane potential i Specific response to extracellular ligand ii Simplest type of bonding e Adhesion receptor integrin binding molecules in ECM I altered conformation I changed interaction w cytoskeleton i tails for clamping onto cytoskeleton ii physical transduction across membrane 1 bent off straight on recruits adapters f Nuclear receptor hormone binding I regulation of specific genes Describe the five factors that contribute to the sensitivity unique properties of signal transduction pathways a Specificity ONLY particular signaling molecule fits complementary binding site on receptor b Ampli cation enzymes affecting enzymes I geometric increase in affected molecules I enzyme cascade c Modularity proteins w multivalent affinities form diverse signaling complexesmodules from interchangeable parts i multivalent affinites affinity for multiple signaling molecules ii KEY for building phosphorylation 1 Forms new binding sites 2 Provides reversible points of interaction d Desensitization feedback inhibition i Activated receptor triggers shutdown of receptor or removal from cell surface ii Expression turned off or down e Integration cross talk between pathways i Antagonistic addition of 2 pathways w opposing effects on a metabolic characteristic ii Regulatory outcome integrated input of both pathways 1 Some cancellation 2 Net result reveals which pathway predominates iii Responsible for generalized immune response evolutionarily conserved Understand and be able to describe the basic structure of a G protein coupled receptor and its associated heterotrimeric G protein a GPCR i 3 outer loops bind epinephrine ii 3 inner loops associate with G protein iii alpha unit GDP bound off GTP bound on iv Dissociation I active effector typically an enzyme v Beta unit no lipid tail b G protein guanosine nucleotide binding protein i Heterotrimeric 3 subunits Gsalpha Gheta and Ggamma l Gsalpha contains pocket for GDP binding a Activated by epinephrine binding Be able to describe the B adrenergic receptor BZAR signaling pathway from the binding of epinephrine to the formation of cAMP a Epinephrine binds to specific receptor I formation hormone receptor compleX b CompleX causes GTP to replace GDP I activation Gsalpha c Activated Gsalpha moves from Gsbemgamma to adenylyl cyclase I activation adenylyl cyclase i One compleX may activate many Gsalpha s d Adenylyl cyclase catalyzes formation of cAMP using ATP Know the specific changes that occur to the BZAR when epinephrine binds and the changes that this causes in the GO subunit a Binding I changes in TMS TM6 i TMS shifts down ii New loop formed in TM6 new 2ndary structure b Alpha subunit on G protein intimately associated w receptor change shape receptor I new interaction w alpha subunit i TMS shift I new hydrophobic pocket created so Galpha can shift up c F139 phenylalanine i critical in messagement movement ii without it epinephrine still binds but no signaling 1 Gsalpha not activated Understand and be able to describe the multiple mechanisms that are involved in terminating the BZAR signaling pathway a Breakdown cAMP 2ndary messenger i Hydrolysis I 5 AMP inactive form by cyclic nuceleotide phosphodiesterase b Gsalpha can hydrolyze GTP I turn self off i Gsalpha is a GTP ase ii Converting bound GTP I GDP favors return of Gsalpha to beta and gamma subunits I G protein inactive cannot interact w adenylyl cyclase c Internalize receptor desensitization step i Gsalpha can t hear signal even if epinephrine binds ii Phosphorylation of receptor creates binding site for protein betaarrestin l Betaarrestin adapter protein that recruits claithrin I vesicles for internalization coated pits Study Guide for Chapter 13 Bioenergetics and Biochemical Reaction types BSC 450550 1 Solve problems using equations describing free energy equilibrium constants and Q a Worked examples in class Tuesday 2 Apply common mechanisms used to alter the free energy of a reaction to new situations a changing initial concentrations i 1 M I Q mass action ratio ii Q mass action ratio Pt T iii Concentrations at SPECIFIC TIME in rxn iv Actual AG AG 0 RTan 1 Q substituted for keq V Modifying AG by using different concentrations of reactants and products b coupling rxns unfavorable W favorable i favorable eX hydrolysis of ATP ii eX 3 steps of glycolysis power all 10 steps iii I net free energy AG 0 hydrolysis breaking of bonds water released d isomerization moving functional groups particularly phosphate transfer 3 Understand the structure of ATP and Where the free energy of hydrolysis comes from in chemical terms a Structure i adenosine purine nitrogenous base ii ribose pentose sugar iii triphophate b Free energy of hydrolysis comes from relative stability of products i 3 main traits 1 electrostatic strain of reactants 2 resonance stabilized product 3 ionization of product ADP Pi inorganic phosphate ii also destabilized reactant 1 lots of negative charges close together I destabilization 2 Mg2 temporarily stabilizes by balancing charge 4 Explain the general chemical reasons that ATP is the energy currency of the cell a ATP H20 x ADP P1 30 kJ mol i high energy molecule large energy release b VERY stable kinetically AG lt O BUT very unstable thermodynamically i high activation barrier enzyme NECESSARY for rxn to proceed ii products more stable ATP wants to hydrolyze c Destabilized reactant I relatively stable product i See 3 d Mass action ratio Q e AT P perfect intermediate for high amp low energy compounds based on AG O hydrolysis f Provides energy through group transfer reactions i 2 step phosphate transfer 5 Understand and be able to eXplain the reasons why phosphoesters Phosphoenolpyruvate and thioesters Acetyl CoA can be used as energy currency similar to ATP a Phosphoesters phosphoenolpyruvate PEP i Very negative AG O ii T automerization I product stability 1 Similar to resonance iii So high energy that can donate P to make ADP I ATP in glycolysis 1 Direct donation substrate level phosphorylation 2 PEP I pyruvate ATP b Thioesters Acetyl CoA i Ionization in product ii Resonance on acetate iii Sulfate high energy portion 6 Be able to recognize the mechanisms for Aldol and Claisen condensation isomerization group transfer and NAD oxidatior reduction reactions Drawing these out to follow the electrons will be helpful for full understanding of these processes a Aldol condensation Base catalysed condensation H II ESEIT 13HI V HEM H313 39 H E Acid catalysed condensation H l H o o 39 m H o D 39 H2 I Jl 390 i gt H J M H39 CH3 H CH3 H C113 H b Claisen condensation C Isomerization F fj fiah 311 r par 5 o m I manquot E mayij f ieig infquot minim1 H o a glucjn if phasgjh ze E39icmse I5 uhjsphaie Fig 13 6 d Group transfer i Phosphoryl group transfer Fig 13 8 e NAD oxidatior reduction Radium211 qu39 aIJrr E E39iu39u quotuu 1 m1emamnmlwn 1e G NH 7 Know the classes of enzymes involved in phosphate group transfer and oxidatior reduction reactions involving cofactors like NAD a Primary phosphate group transfers W ATP as donor kinases b Carry phosphoryl groups from ATP to other nucleotides nucleoside diphosphate kinase i I reversible formation of non ATP nucleoside triphosphates GTP UTP etc i j Hydrolysis of PR I 2 Pi inorganic pyrophosphatase Catalyzes lowering of ADP concentration adenylate kinase i Simultaneously replenishes ATP Rapid ATP synthesis from phosphocreatine PCr creatine kinase i When demand for ATP too sudden urgent for standard catabolic pathways Reversible phosphoryl storage in ATP synthesis from polyP in bacteria polyphosphate kinase1 Reversible GTP ATP synthesis polyphosphate kinase2 NADP linked enzymes dehydrogenases i Oxidation reactions using NADP as coenzyme NADP accepts hydride 0r NADPH donates hydride oxidoreductase Light receptors photolyases 8 Describe how carbonyl groups can be used in biological reactions 8 b Delocalization of electrons stabilizes carbanion necessary for forming C C bond i Makingbreaking C C bond occurs in 3 major rxn classes 1 Aldol condensations 2 Claisen ester condensations 3 decarboxylations Acts as electrophile to react w nucleophilic carbanion i Electronegativity of oxygen I oxygen becomes electron withdrawing group I carbon takes on partial positive Charge ii Electrophilic capacity often augmented by metal ion e g Mg2 or general acid 9 Compare and contrast NADPH and Flavin chemistry 8 b NADPH i Associate wdehydrogenases freely diffusible coenzymes ii Accept 2 electrons l proton Flavins FAD amp FMN i Associate w avoproteins tightly bond prosthetic groups ii Accept l or 2 electrons protons
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