Agriculture A fruit grower raised two crops, apples and peaches. Each of these crops is shipped to three different outlets. The shipment levels are represented by Outlet 123 The profits per unit are represented by the matrix Compute and interpret the result.
Study Guide for BIOC 4331 Final Exam Noncovalent interactions Different types of noncovalent interactions Electronegativity and hydrogen bonds ( what is required to make a hydrogen bond) Acids and bases Definition of pH Definition of acid dissociation constant (pKa) Relationship between pKa and pH (General Rule of Thumb: proportions of ionized or unionized molecules) Amino acids and peptides Chemical structure of Lamino acids Know and be able to draw the structures of amino acid side chains, and chemical characteristics (acids, bases, hydrophobic etc.) Know the one and three letter codes Know the chemical structure of the peptide bond Acid and base characteristics of amino acid side chains: which side chains generally act as acids or bases and their ionization state given their pKa value at a specific solution pH value Be able to draw and recognize a graph of pH vs. % protonated or % unprotonated Protein primary structure Definition of protein primary structure Steps involved in determining primary structure SDSPAGE and proteins: how it works Basic concepts of protein evolution (hypervariable, invariant, conservative amino acids) Protein secondary structure Characteristics of helices (how many amino acids per turn) Definition and characteristics of amphipathic helices Characteristics of –sheets (how many amino acids per turn Which is more favorable: antiparallel or parallel Why) Characteristics of turns Protein tertiary structure (which amino acids are found in betaturns) Definition of a motif and domain Difference between convergent and divergent evolution Types of membrane proteins: integral, peripheral, transmembrane Amphipathic helices as membrane proteins Characteristics of protein glycosylation Protein quaternary structure Naming conventions (monomer, dimer, homo vs hetero etc.) Differences between globular and fibrous proteins; examples of fibrous proteins Thermodynamics and Equilibrium First and second laws of thermodynamics Free energy, enthalpy (exothermic vs. endothermic) and entropy and equations relating these variables G and spontaneity of reactions; exergonic versus endergonic Additive G values for reactions sharing common intermediates Relationship between free energy change (ΔG) and concentration Definition of ΔG’ (a constant!) Calculating the actual G and its relationship to ΔG’ Relationship between K’eq and ΔG’ protein folding Concepts of protein folding; chaperones and what they do Cofactors/coenzymes NAD/FAD coenzymes and redox Basics of redox equations; carbon oxidation Know equation relating G and E Know the Nernst equation and how to use it protein purification Know the fundamentals of the different purification methods discussed (isoelectric focusing, ion exchange chromatography, gel filtration/size exclusion, affinity chromatography) Methods for detecting proteins and peptides Hemoglobin and allostery Concepts to know: allostery, cooperative binding of hemoglobin, sigmoidal binding curve for Hb vs. hyperbolic curve for Mb, Bohr effect, BPG Protein binding Ka and Kd Know how to interpret the plots for noncooperative ligand binding multiple sites of a protein How to interpret a Hill plot; the Hill coefficient nH Enzyme kinetics Know MichaelisMenten equation Know how Vmax is defined and its relationship to Kcat and Et Define Kcat Know what the Km is and what it measures Know how to draw a plot of [S] versus V0 when given appropriate information Know how to interpret a doublereciprocal plot of a MichaelisMenten enzyme Enzyme inhibition Know how to draw a plot of [S] versus V0 for uninhibited or inhibited enzyme when given appropriate information Know how to recognize double reciprocal plots for different types of inhibitors covered in class and how to read these plots Study table summarizing affects of different inhibitors (slide 19, p. 163 in Griffin course packet) know interactions between Vmax, Km, and inhibitor for each plot (competitive, pure noncompetitive, mixed noncompetitive) Know what the and ’ term is Bisubstrate reactions Know how to recognize and name multisubstrate reactions (Bi bi etc., sequential vs. ping pong) Know how to interpret/draw shorthand enzyme diagrams for sequential (ordered/random), ping pong reactions Know how to recognize from double reciprocal plots for bi bi sequential vs. ping pong reactions Enzymatic catalytic mechanisms Know the different mechanisms discussed (general acid/base, metal catalyzed etc.) and how to recognize these for a given mechanism Know how to recognize the specific enzymes and their mechanisms discussed in class: carbonic anhydrase, enolase, chymotrypsin (serine proteases), lysozyme , HIV protease know which mechanisms exhibit ping pong or sequential reactions Know types of protein regulation and details underlying each of these (6 different types of regulation but focus on allosteric regulation, protein degradation via ubiquitination, zymogen activation, and covalent modification via phosphorylation) Know the concepts of phosphoryl group transfers (e.g. glutamine synthetase) and the thermodynamics of these reactions Carbohydrates Recognize the sugars glyceraldehyde, ribose, glucose, galactose, fructose, glycerol, 2 deoxy ribofuranose, glucosamine, amylose, amylopectin, glycogen and cellulose. Know what epimers and anomers are and how to tell alpha vs. beta. Know the ring closure reactions for glucose and fructose. Understand alpha and beta linkages in polysaccharides including amylose, amylopectin, glycogen, cellulose, and chitin. Know the storage and structural polysaccharides: examples, structure, significance, Hbonding. Glycolysis Be able to recognize all structures, know the names of all enzymes and cofactors, and which steps involve energy and carbon gain or loss. Know the importance of phosphorylating glucose and how key enzymes are regulated. Know how NAD+ is regenerated under anaerobic conditions in both yeast and humans Draw fructose and galactose entry into glycolysis. TCA cycle Know all structures, names of all enzymes and cofactors, and which steps involve energy and carbon gain or loss. Know how pyruvate dehydrogenase works. Understand the three conceptual phases. Know which steps involve oxidative decarboxylation Electron transport and oxidative phosphorylation Know the functions of the complexes, electron carriers, how compounds enter, how molecules move, understand the reaction. Be able to draw e transport and oxidative phosphorylation at the ‘blob’ level. Understand standard reduction potential and the significance of the proton gradient. Know the process of ATP synthesis by ATP synthase. Be able to describe ironsulfur centers and cytochrome proteins. Gluconeogenesis and Glycogen synthesis Be able to recognize all structures, know the names of all enzymes and cofactors, and which steps involve energy. Know the steps that differ between glycolysis and gluconeogenesis, and understand why some enzymes are used for both pathways and some are not (which step involves oxidative decarboxylation) Understand energy charge and reciprocal regulation. Know how glycolysis, gluconeogenesis, glycogen synthesis and glycogen breakdown are regulated by the metabolic state of the cell and by hormones. Understand insulin, glucagon, and protein kinase A. Metabolic Regulation Be able to describe the coordinated control and reciprocal regulation of glycolysis and gluconeogenesis, the regulatory role of fructose 2,6bisphosphate. How is Fructose2,6bisphosphate regulated by glucagon How does glucagon affect its phosphorylation states Case Studies and Metabolic Diseases Review the case studies and be able to describe a disease caused by loss of a metabolic enzyme or vitamins. Lipids Know the basic types, structural and chemical properties of lipids Know how to name fatty acids standard vs. PUFA omega Know the properties of fatty acids including trans fat, the properties of triacylglycerides, the properties of phospholipids and lipid bilayer. Be able to explain fluid mosaic model of membrane and identify the types of lipids and their derivatives as signaling molecules. Explain the mechanism of Aspirin and why it could reduce risks for heart disease. Lipids catabolism Understand the lipid digestion and uptake process. Know the lipolysis process in adipose cell and its hormonedependent regulation. Know the process of fatty acid activation into fatty acylCoA, where and why it happens, and the enzymatic process. Understand the carnitine shuttle system. Understand each step in betaoxidation including the compound structure, enzyme names and cofactors. Know the properties and composition of ketone bodies. Understand the general process of ketone bodies generation, when and why they are generated. Lipids biosynthesis Understand the general properties of lipid biosynthesis. Know the properties, regulation and function of acetyl CoA carboxylase and the reaction catalyzed by acetyl CoA carboxylase. Clearly understand the enzymatic processes of fatty acid synthesis including the compound structure, enzyme names and cofactors. Know the processes of producing NADPH and acetyl CoA for lipid biosynthesis. Know the regulation of lipid biosynthesis pathway. Cholesterol Know the facts about cholesterol and the four stages of cholesterol synthesis. Understand the steps in the synthesis of mevalonate in comparison to the ketone bodies synthesis pathways. Know the ratelimiting step in cholesterol biosynthesis and the principle of statin drug. Know the properties and functions of four lipoprotein particles. Understand the role of LDL receptor and the link between LDL and atherosclerosis. Know the differences between HDL, LDL, and VLDL Amino acid metabolism Know the basic facts about nitrogen metabolism and amino acid oxidation. Understand the general process of amino acids uptake in digestive system. Know the transamination reaction – enzymes, substrates, key cofactor and cellular function. Know the functional roles of glutamate, glutamine and alanine in amino group metabolism, including the general process and the enzymes involved. Know the enzymatic process of the synthesis of carbamoyl phosphate. Clearly understand the urea cycle – compounds involved, where each reaction occurs and if energy is consumed. Understand the connection between the urea cycle and TCA cycle. Understand glucogenic/ketogenic amino acids and the ones exclusively ketogenic. Diabetes Know the symptoms of different types of diabetes (mellitus vs. insipidus) and be able to explain these symptoms. Clearly understand the roles of hormone (insulin, glucagon and epinephrine) during Fed and Fasted/diabetic states – their regulation of blood glucose, glycolysis/gluconeogenesis, glycogen and lipid metabolism. Know the mechanism of insulin stimulation of glucose uptake and the mechanism of insulin secretion from pancreatic beta cells in response to high glucose. Know the acute and chronic diabetes conditions. Understand protein glycation in diabetes and Hemoglobin A1c test. Photosynthesis Know the basic facts of photosynthesis and the properties of chlorophyll. Clearly understand the light reaction process, both cyclic and noncyclic oxidative phosphorylation. What is generated in each and what is not Know the similarities and differences between noncyclic light reaction and mitochondria electron transport chain (Complex I, III, IV). Understand the basic concepts about dark reactions (Calvin cycle) and what each step is similar to. Know the three phases of Calvin cycle and their similarities/differences with the three phases of TCA cycle. Know the enzyme in the first step of Calvin cycle and the general process of regenerating ribulose1,5 bisphosphate – how carbons are shuffled from 6C and 3C compounds to generate 5C compounds Cancer metabolism Know the Warburg hypothesis – its definition and comparison between cancer and normal cells. Know the principles of FDGPET scanning. Understand how Warburg effect is advantageous and the cause of altered metabolism. Understand the role of mitochondria in Warburg effect.