Course Outline: Biochemistry (CHM380)

Course Information

Credits: 4

Contact Hours:

  • Lecture: 3
  • Lab: 3

Note on Laboratory: Both Lecture and Laboratory must be taken simultaneously; separate grades will not be given for either. Students must pass the laboratory section to receive a passing grade in the entire course.

Semesters Offered: Fall, Spring, & Summer

Prerequisites: CHM 260 or CHM 271

Catalog Course 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.

Elective Course for: Bioscience

Course Texts: Experiments in Biochemistry by Dr. Glen Hinckley.

Other Required Course Materials

Lab coat and safety glasses

Course Learning Objectives

I. Biology Review

Major organelles in the cell, Organization of the cell, Major organs in the body

At the end of this section, the student should be able to:

  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 concentration.
  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.

At the end of this section, the student should be able to:

  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

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

At the end of this section, the student should be able to:

  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

V. Lipids

Classification, fatty acids, triglycerides, terpenes & steroids, phospho- and sphingolipids, physical properites of lipids

At the end of this section, the student should be able to:

  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.

At the end of this section, the student should be able to:      

  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.

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. 

At the end of this section, the student should be able to:

  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
 
At the end of this section, the student should be able to:
  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

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. 

At the end of this section, the student should be able to:

  1. Identify heme structure
  2. Recite and define three oxidation states of heme
  3. Define ligand
  4. Define KD 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

X. Enzymes

Classifications, catalytic theory, mechanisms of catalysis, Michaelis-Menten equation, types of inhibition, coenzymes and cofactors

At the end of this section, the student should be able to:

  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 Vmax & KM
  4. Calculate Vmax & KM from a given Michaelis-Menten curve
  5. Draw a Lineweaver-Burke plot given Vmax and KM
  6. Define three types of inhbition
  7. Interpret changes in Vmax & KM as they apply to inhibition types
  8. Identify major coenzymes and their functions

XI. Nucleic Acids 

Purines and Pyrimidines, Nucleosides and Nucleotides, structure and function of DNA, relationship between DNA / RNA sequence and peptide / protein sequence

At the end of this section, the student should be able to:

  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.

At the end of this section, the student should be able to:

  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.

XIII. Glucose Metabolism 

Glycolysis, Gluconeogenesis, Glycogen metabolism, Pyruvate dehydrogenase, Citric acid cycle

At the end of this section, the student should be able to:

  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 FADH2s 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 & FADH2 to ATP. 

At the end of this section, the student should be able to:

  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 & FADH2 values.
  4. Define decoupling and its purpose

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. 

At the end of this section, the student should be able to:

  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

At the end of this section, the student should be able to:

  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.

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.
  3. spectrophotometry
  4. electrophoresis
  5. protein analysis
  6. enzyme assays & activities
  7. ion exchange and size exclusion chromatographies
  8. high performance liquid chromatography
  9. thin layer chromatography
  10. micropipetting
  11. To perform experiments which are biochemically related:
  12. pH
  13. proteins
  14. lipids
  15. carbohydrates
  16. enzymes
  17. To obtain & analyze data for the above methods/experiments:
  18. Hand in laboratory reports showing the data and conclusion drawn from the data.
  19. The reports are graded as to neatness, accuracy of data and/or results, and conclusions.
  20. 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.

Laboratory Schedule

  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

NOTE: This course outline supersedes any course syllabus provided by a professor.