FARMINGDALE STATE COLLEGE DEPARTMENT OF CHEMISTRY. April CONTACT HOURS: Lecture: 3 Laboratory: 3

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1 FARMINGDALE STATE COLLEGE DEPARTMENT OF CHEMISTRY COURSE OUTLINE: COURSE TITLE: Prepared by Dr. Glen Hinckley April 2017 Biochemistry COURSE CODE: CHM 380 CREDITS: 4 CONTACT HOURS: Lecture: 3 Laboratory: 3 CATALOG DESCRIPTION: A one semester course covering the fundamentals of biochemistry. Topics covered include: the structure and function of important biomolecules such as carbohydrates, lipids, amino acids, proteins and nucleic acids; enzyme kinetics and the use of cofactors & coenzymes; and metabolic pathways including glycolysis, TCA, electron-transport system, fatty acid and amino acid pathways. Laboratory work includes current biochemical laboratory techniques such as chromatography and electrophoresis, application of specific topics described above, and analysis of data from laboratory experiments. PREREQUSITE: CHM 260 or CHM 271. IMPORTANT NOTE: BOTH THEORY AND LABORATORY PARTS OF THIS COURSE MUST BE TAKEN CONCURRENTLY IN ORDER TO RECEIVE CREDIT. REQUIRED FOR: ELECTIVE FOR: Medical Laboratory Technology Bioscience 1

2 REQUIRED TEXT: OPTIONAL TEXT: Experiments in Biochemistry by Dr. Glen Hinckley. Biochemistry, by Garrett & Grisham, 5th Edition, Brooks/Cole REQUIRED SUPPLIES: Lab coat and safety glasses 2

3 FARMINGDALE STATE COLLEGE DEPARTMENT OF CHEMISTRY CHM 380 Biochemistry Lecture Schedule I. Biology Review Major organelles in the cell, Organization of the cell, Major organs in the body 1. Identify the major organelles of the cell and their function. 2. Identify the major organs of the body and their functions 3. Reproduce the structure of the cell at a schematic level II. General Chemistry Review Thermodynamics, Equilibrium, Acid / Base theories, Kinetics At the end of the section, the student should be able to: 1. Define spontaneity and correlate it with Gibbs free energy 2. Interpret an equilibrium equation and perform calculations of concentrations 3. Define the acid base theories of Arrhenius and Bronsted-Lowry and identify into which classification specific compounds fall 4. Interpret a rate equation and perform calculations of rates and rate constants III. The Nature of Water Polar and non-polar substances, Hydrogen bonds, strong and weak acids and bases, Henderson-Hasselbalch equation, buffer solutions. 1. Distinguish between polar and non-polar compounds 2. Draw a hydrogen bond schematic between donor and acceptors 3. Calculate concentrations, ph, and pka using the Henderson-Hasselbalch equation 4. Identify important regions, especially the buffering region, in the titration of a weak acid 3

4 IV. Organic Chemistry Review Functional groups in organic chemistry, Lewis Acid / base theory, fundamentals of organic reactions & mechanisms, acidity of the alpha carbon to carbonyls V. Lipids 1. Identify organic functional groups by name and structure 2. Identify compounds as Lewis acids or bases 3. Identify nucleophiles and electrophiles in organic reactions 4. Predict the product of biochemically relevant organic reactions 5. Draw the tautomerization of a ketone Classification, fatty acids, triglycerides, terpenes & steroids, phosphoand sphingolipids, physical properites of lipids 1. Identify and classify lipids by structure and name 2. Draw the structure of fatty acids (lauric, myristic, palmitic, stearic, oleic, linoleic, linolenic) 3. Draw the structure of triglycerides and phospholipids 4. Predict relative melting and polarity properites of lipids 5. Identify function of each type of lipid VI. Carbohydrates Classification by length and type, stereoisomerism, cyclic forms, anomers, di- and polysaccharide structures and linkages, typical polysaccharide structures and functions, reducing sugars and tests for. 1. Classify sugars by length, type, and stereoisomers 2. Draw the cyclic form of sugars from their straight chain structure, and visa-versa 3. Identify and define major di and polysaccharides, including their functions and digestion 4. Define reducing sugars and predict results of tests for reducing sugars. 4

5 VII. Amino acids and peptides Structures, names, and three letter & one letter codes of all 20 common amino acids, Zwitterion, ioniziation states of amino acids at different ph values, the structure of the peptide bond. 1. Identify all amino acids by structure, name, three letter, and one letter code 2. Determine the charge and ionization state of all ionizable groups on an amino acid given a specific ph 3. Construct a peptide from a sequence and given amino acid structures VIII. Proteins Four levels of protein structure, factors that affect each level of protein structure, including hydrogen bonding and the hydrophobic effect, types of proteins (fibrous, globular, membrane), major features of keratin and collagen, denaturation, glycosylation and lipoylation 1. Define each level of protein structure 2. Identify and interpret major factors affecting protein structure 3. Distinguish the fundamentals, strengths, and weaknesses in X-ray Crystallography and NMR protein structure determinations. 4. Catagorize proteins by type and characteristics 5. Recite major features of keratin and collagen 6. Define denaturation and intepret means of denaturation 7. Define glycosylation and lipoylation and define their importance to protein structure and function 5

6 IX. Myoglobin / Hemoglobin Gross structure of myoglobin & hemoglobin, structure, states, and function of heme, ligand binding equations, cooperativity, effects of ph, CO2, and BPG on oxygen binding to hemoglobin. X. Enzymes 1. Identify heme structure 2. Recite and define three oxidation states of heme 3. Define ligand 4. Define K D and calculate using appropriate equations 5. Define cooperative binding and sketch a binding curve 6. Name and interpret the three factors that affect oxygen binding to hemoglobin 7. Use the given equilibria with hemoglobin to interpret changes in oxygen binding to hemoglobin Classifications, catalytic theory, mechanisms of catalysis, Michaelis- Menten equation, types of inhibition, coenzymes and cofactors 1. Define activation state, catalysis, and activation state stabilization 2. Define and explain the three mechanisms of catalysis 3. Write the Michaelis-Menten equation and define V max & K M 4. Calculate V max & K M from a given Michaelis-Menten curve 5. Draw a Lineweaver-Burke plot given V max and K M 6. Define three types of inhbition 7. Interpret changes in V max & K M as they apply to inhibition types 8. Identify major coenzymes and their functions 6

7 XI. Nucleic Acids Purines and Pyrimidines, Nucleosides and Nucleotides, structure and function of DNA, relationship between DNA / RNA sequence and peptide / protein sequence 1. Identify the four bases from their structures 2. Identify the three phosphorylated versions and abbreviations of nucleic acids 3. Define RNA & DNA and identify structural and functional differences 4. Define base pair and how many hydrogen bonds in each base pair 5. Draw a 2 to 3 base length, single stranded nucleic acid 6. Use a genetic code to translate from an RNA sequence to a protein sequence XII. Metabolism Introduction Anabolism & Catabolism, ATP & high energy phosphate compounds, electron carriers (NAD + & FAD), Metabolic control by flux & regulation. 1. Define anabolism & catabolism and identify given reactions as such 2. Calculate free energy changes for two combined reactions 3. Define ATP, NAD +, & FAD and what their functions are 4. Define allostery and its function in regulation 5. Describe the necessity of multiple enzymes at flux control points. 7

8 XIII. Glucose Metabolism Glycolysis, Gluconeogenesis, Glycogen metabolism, Pyruvate dehydrogenase, Citric acid cycle 1. Assemble all intermediate structures and names in proper order in the glycolysis/gluconeogenesis and citric acid cycle pathways 2. Define substrate level phosphorylation & oxidative decarboxylation 3. Calculate ATPs, NADHs, and FADH 2 s derived at each step. 4. Define protein phosphorylation, its function and consequences 5. Recite the effects of insulin and glucagon on all pathways in glucose metabolism XIV. Electron Transport Reduction / oxidation reactions, electron transport pathway, F1-F0 ATPase, decoupling, conversion values for NADH & FADH 2 to ATP. 1. Assemble the components in the electron transport pathway and define the function of each. 2. Recite which components of the pathway pump protons across the mitochondrial membrane 3. Calculate total ATPs from NADH & FADH 2 values. 4. Define decoupling and its purpose 8

9 XV. Lipid Metabolism β-oxidation, fatty acid synthesis, regulation of fatty acid metabolism by insulin / glucagon system, ketone bodies and ketosis, synthesis of cholesterol from acetyl-coa, lipid transport through the body. 1. Calculate total acetyl-coa, NADH, and FADH2 produced in the β-oxidation of any saturated fatty acid 2. Calculate total acetyl-coa, NADPH, and FADH2 required for the synthesis of any fatty acid. 3. Identify the actions of insulin and glucagon on fatty acid synthesis, storage, and β-oxidation 4. Define ketone bodies, their function, and consequences of their production. 5. Identify the major intermediates in the cholesterol pathway 6. Identify the lipoproteins involve in lipid transport, their origins, and their functions. XVI. Amino acid Metabolism Deamination and transamination, Urea cycle, glucogenic vs. ketogenic, essential and non-essential amino acids 1. Predict the result of a deamination on an amino acid 2. Assemble all intermediate structures and names in proper order in the urea cycle 3. Define glucogenic and ketogenic amino acids 4. Identify all amino acids as either essential or nonessential. 9

10 FARMINGDALE STATE COLLEGE DEPARTMENT OF CHEMISTRY CHM 380 Biochemistry The aims of the laboratory section: 1. To have the students become familiar with biochemical methods or techniques. 2. To use the following biochemical methods: a. spectrophotometry b. electrophoresis c. protein analysis d. enzyme assays & activities e. ion exchange and size exclusion chromatographies f. high performance liquid chromatography g. thin layer chromatography h. micropipetting 3. To perform experiments which are biochemically related: a. ph b. proteins c. lipids d. carbohydrates e. enzymes 4. To obtain & analyze data for the above methods/experiments: 5. Hand in laboratory reports showing the data and conclusion drawn from the data. 6. The reports are graded as to neatness, accuracy of data and/or results, and conclusions. 7. The students are also given a test at the end of the semester testing their theory and practical knowledge of biochemistry they learned during the semester. 10

11 FARMINGDALE STATE COLLEGE DEPARTMENT OF CHEMISTRY CHM 380 Biochemistry Laboratory Manual: Supplies Required: Laboratory Period Experiments in Biochemistry, by Dr. Glen Hinckley Safety glasses or goggles, other materials may be required by the instructor. LABORATORY SCHEDULE Experiment Title 1 Calibration of Pipettes 2 Spectroscopy 3 Buffer Construction 4 Carbohydrate Analysis 5 Determination of Protein Concentration 6 Size Exclusion Chromatography 7 Spectroscopy of Hemoglobin 8 Michaelis-Menten Kinetics 9 Thin Layer Chromatography of Lipids 10 Lysozyme Purification Project: Batch Chromatography 11 Lysozyme Purification Project: Enzyme Analysis 12 Lysozyme III: Denaturing Protein Gel Electrophoresis 13 Practical Examination 11

12 FARMINGDALE STATE COLLEGE DEPARTMENT OF CHEMISTRY CHM 380 Biochemistry Grading Policies Components of Grade Examinations 58% Homeworks 17% Laboratory 25% Examinations Three unit examinations are given during the semester. No makeups are given for any examination. A comprehensive final is optional for students to take, but can be used to replace a missed or poor examination grade. Homeworks Six homeworks are given during the semester, covering concepts and objectives outlined for the sections covered. Late homeworks will be accepted with a point deduction up until one week late. After one week, a late homework is not accepted. Laboratory 12 Laboratory experiments are performed and a short written report is required for each laboratory, with the lowest scoring experiment being dropped. Absences are counted as no credit, and can be dropped as the lowest laboratory experiment. A laboratory final is given, consisting of a written examination covering basic practical laboratory concepts. The laboratory score percentages are given as follows: Laboratory Reports 60% Purification Project 25% Laboratory Practical 15% 12

FARMINGDALE STATE COLLEGE DEPARTMENT OF CHEMISTRY

FARMINGDALE STATE COLLEGE DEPARTMENT OF CHEMISTRY COURSE TITLE: Advanced Biochemistry COURSE CODE: CHM 381 CREDITS: 3 CONTACT HOURS: Lecture: 3 CATALOG DESCRIPTION: A continuation of the concepts covered in Biochemistry. Students will examine the pathways,