Module 6: Protein structure and function



Final Exam Review Objectives: Module 1: ThermodynamicsA.?Relate?Gibbs free energy changes to equilibrium constants and?solve?the free energy equation ΔG = ΔG° + RT*ln(Q).Define?ΔG, ΔG°, and ΔG°'.Predict?how changes in temperature or reactant and product concentrations affect ΔG.B.?Differentiate?between enthalpically and entropically-driven reactions.Predict?the sign of ΔS° based on balanced equation.C.?Use?Hess’s law to obtain ΔG°, ΔH°, or ΔS°.D.?Solve?the Nernst Equation.Determine?the oxidation state of atoms in molecules.Identify?redox reactions, reducing agents (reductants), and oxidizing agents (oxidants).Determine?electrical potential from standard reduction potentials of half reactions and?relate?this electrical potential to ΔModule 2: Non-covalent interactions, water, and buffersA. Predict?the solubilities of molecules in water, polar, or non-polar solvents.Assess?regions of molecules that can participate in covalent bonds or weak interactions.Differentiate?between?H-bond donors and pare?the distance dependence and relative strengths of non-covalent interactions.Explain?the driving force of the hydrophobic effect and the self-assembly of amphiphilic/amphipathic molecules.B. Interpret?pKa values and their role in dictating weak interactions.Assign?acid/conjugate base and base/conjugate acid pairs.Solve?the Henderson-Hasselbalch equation.Interpret?titration curves.Explain?why buffers are important for biochemical experiments and?predict?buffering ranges.Predict?how pH can affect weak interactions such as hydrogen bonding.C. Discuss?the many functions of water in biological systems.Module 3: Amino acidsA. Identify and name?amino based on their molecular structure and?classify?their molecular properties.Draw?the general structure and stereochemistry of amino acids.Identify?chiral centers and?assign?R/S-stereochemistry to these centers.Classify?amino acid side chains as aromatic, charged polar, uncharged polar, or nonpolar groups.Calculate?the pI of amino acids and polypeptides and predict their charge at a given pH.Assign?the structure of amino acids given only their three- or one-letter codes.Module 4: Protein Primary Structure and PurificationA.?Draw?the structures of short peptide sequences with correct stereochemistry.Identify?peptide bonds and?understand?how they are formed.Understand?the chemical properties of the peptide bond.B.?Predict?physical properties of peptides and proteins to their primary structures. Important physical properties includeIsoelectric point (pI)UV absorbanceMolecular weightC.?Propose?methods to detect and separate mixtures of amino acids or peptides (e.g. chromatography, salting out, SDS-PAGE, etc.)Explain?how the pH of the solution and the primary structure dictates the charge of the protein.Select?an appropriate buffer, and other buffer components for any discussed separation technique.Predict?elution order of a mixture of peptides given the primary sequence of the peptides in the mixture and the composition of the stationary and mobile phases.Differentiate?between denaturing and non-denaturing separation techniques.D.?Interpret?electrospray ionization (ESI) coupled mass spectrometry (MS) data to determine the molecular weight of peptides or proteins.E.?Predict?if peptides can form intra- or intermolecular disulfide bonds and?know?the conditions in which they are formed and broken.Module 5: Protein 3D StructureA.?Differentiate?between primary, secondary, tertiary, and quaternary structural features of proteinsB. Identify?the covalent and non-covalent interactions and enthalpic and entropic driving forces that stabilize protein structure and influence protein folding.H-bondsElectrostatic interaction (ion pairs)Hydrophobic effectVan der Waals (London) forcesDisulfide crosslinksC. Contrast?structural differences between alpha helices and beta sheets.D. Evaluate?how amino acid mutations, changes in pH and temperature, or addition of non-polar or chaotropic substances affect protein structure and stability.E. Identify?and differentiate?cofactors and co-substrates.Module 6: Protein structure and functionA.?Define?and?differentiate?between?equilibrium and rate constantsRelate?rate constants to equilibrium constants.B. Extract?equilibrium parameters from experimental data.Solve?hyperbolic and sigmoidal ligand binding equations and?interpret?their plots to determine the parameters?Kd?and the Hill coefficient,?n.Interpret?Hill plots to determine if proteins exhibit positive or negative cooperativityC.?Correlate?protein structure with function.Identify?protein structural features important for ligand binding and selectivity.Relate?changes in rate constants and binding parameters to structural differences between wild-type and mutant proteins.Propose?single amino acid mutations to test structure function relationships in proteins.Predict?how changes in pH or temperature will affect ligand-binding parameters.Identify?allosteric contributions to protein function.Module 7: EnzymesA. Classify?enzymes by their reaction type.B. Analyze enzyme structure functions relationships.Identify?enzyme structural features needed to impart substrate specificity and increase the rate of reaction.Propose single amino acid mutation experiments to test structure-function relationshipsC. Interpret?reaction coordinate diagramsLabel?reaction coordinate diagrams with ΔG, Ea, intermediates, and transition pare?and contrast?catalyzed and uncatalyzed reaction coordinate diagrams.Analyze?reaction coordinate diagrams to predict if product formation is under kinetic or thermodynamic control.D. Understand influences on rate constantsUnderstand?molecularity and how it relates to the units of the rate constants.Relate?rate constants to equilibrium constants.Predict?how changes in pH or temperature will affect enzyme rate .Relate?activation energy to rate constants.Module 8: Enzyme kinetics, inhibition, and controlA.?Interpret?kinetic plots including Michaelis-Menten plots and integrated rate equations.Interpret?kinetic plots including Michaelis-Menten plots and integrated rate equations.Extract?kinetic parameters?Vmax,?kcat,?KM?from a Michaelis-Menten or Lineweaver-Burk plot.Determine?if experimental protocols will provide usable kinetic parameters in accordance with the assumptions made to derive rate equations, including the Michaelis-Menten equation.B. Classify?the mode of inhibition by?interpreting?series of Michaelis-Menten or Lineweaver-Burk plots at varying inhibitor concentrations.Determine?the inhibition constant (KI).C. Classify?mechanisms of enzyme control.Module 9: CarbohydratesA.?Identify?structural features of carbohydrates critical for their chemistries and stereoconfigurations.Draw?and identify?monosaccharides and polysaccharides in both their linear and ring forms.Differentiate?between epimers and anomers.Identify?anomeric carbons and glycosidic bonds.Differentiate?between reducing and non-reducing sugars.B. Evaluate?how stereospecificity of enzymes is critical for their catalysis of carbohydrate reactions.Module 10: Nucleic AcidsIdentify and label?the phosphate, sugar, and nitrogenous base components of a nucleotide.Draw and identify?all DNA and RNA nucleotides (i.e., A, T, G, C, and U)Connect?Chargaff’s rules and the H-bonding observed between Watson-Crick base pairs.Relate?structural differences of ribo- and deoxyribonuclotides with differences in reactivities and differences in macromolecular structures of RNA and DNA.Explain?the purpose of each step in PCR (denaturation, annealing, polymerization) and the purpose of all PCR reaction components.Interpret?DNA electrophoresis data used for DNA sequencing (Sanger method).Design?primers for DNA amplification by PCR.Module 11: LipidsIdentify?and?differentiate?between lipids and other membrane components, for example:Fatty acidsTriglyceridesGlycerophospholipidsGangliosidesSphingolipidsSteroidsIdentify?head groups of glycerophospholipids (Table 9-2).Predict?from lipid structure, if they will self-assemble into micelles or bilayers in water.Predict?how changes in the lipid composition of the lipid bilayer will affect its fluidity and transition temperature.Draw?a fatty acid based on its lipid number.Relate?structural features of integral membrane proteins to their amphipathic nature.Module 11: Membrane transportDifferentiate?between mediated and non-mediated transport and passive/facilitated and active transport.Determine?the electrochemical potential across a membrane.Understand?different biological strategies for transporting ions and other molecules across the membrane. Examples:IonophoresPorinsIon channelsDifferentiate?between uniport, symport, and antiport systems.Explain?how electrochemical gradient or ATP can be used to drive active transport.Interpret?data to determine if transport is mediated or non-mediated.Module 13: BiosignalingRelate?conformational changes, hormones, enzymes, DNA, RNA, lipids) to biosignaling pathways.Identify?when DNA, proteins, and lipids interact with each other in biosignaling pathways.Predict?if the receptor for a signaling molecule is on the membrane surface or cytosolic.Classify?signal cascades as kinase or secondary messenger cascades.Differentiate?between unique components of RTK and GPCR pathways.Identify?regulatory mechanisms for these signaling pathwaysGAP proteins (RTK)Kinases/phosphatasesPhosphodiesterases ................
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