University Teaching

Course Instruction

• Chem 115/117: General Chemistry I
  
  

  PowerPoint Slides from Class Lectures (taken with modification from Chemistry: The Molecular Nature of Matter and Change by Martin S. Silberberg, McGraw Hill (3rd Edition, 2003)

  • Slides: Chapter 1
  • Slides: Chapter 2
  • Slides: Chapter 3
  • Slides: Chapter 4
  • Slides: Chapter 5
  • Slides: Chapter 6
  • Slides: Chapter 7
  • Slides: Chapter 8
  • Slides: Chapter 9
  • Slides: Chapter 10
  
  
  • Accessing Solutions to Problems
  • Learning Resource Center (LRC) Information
  • On Balancing Redox Equations
  
  
  • Undergraduate Research at Notre Dame: What, Where, How
  
  
  • Course Performance: Exam Profiles
  
  
• Chem 116/118: General Chemistry II
  
  

  PowerPoint Slides from Class Lectures (taken with modification from Chemistry: The Molecular Nature of Matter and Change by Martin S. Silberberg, McGraw Hill (3rd Edition, 2003)

  • Slides: Chapter 11
  • Slides: Chapter 12
  • Slides: Chapter 13
  • Slides: Chapter 15
  • Slides: Chapter 16
  • Slides: Chapter 17
  • Slides: Chapter 18
  • Slides: Chapter 19
  • Slides: Chapter 20
  • Slides: Chapter 21
  
  
  • Accessing Solutions to Problems
  • Learning Resource Center (LRC) Information
  
  
  • Undergraduate Research at Notre Dame: What, Where, How
  
  
  • Course Performance: Exam Profiles
  
  
  
• Chem 119L: General Chemistry Laboratory I
  
  
• Chem 120L: General Chemistry Laboratory II
  
  
• Chem 223: Elementary Organic Chemistry I
  
  
• Chem 224: Elementary Organic Chemistry II
  
  
• Chem 342: Intermediary Metabolism
  
  
• Chem 420: Principles of Biochemistry
• Chem 523: Macromolecular Structure and Function
  

  Supplementary Biochemistry Lecture Material

  • Covalent and Noncovalent Bond Energies
  • Noncovalent Interactions
  • Induced Dipole and Dispersion Forces
  • Noncovalent Interaction Energy
  • Dipole Moments of Some Molecules
  • Electrostatic Interactions Between Macroions
  • Hydrogen Bond Lengths in Biomolecules
  • Structure of Ice
  • Exchange of Hydrogen Bonds
  • Small Ion-Macroion Interactions
  • Protein Solubility and pH
  • Constant Volume and Constant Pressure Reactions
  • Reaction Enthalpy and Entropy
  • Amphipathic Molecules and Water
  • Particle Mobility in Gel Electrophoresis
  • Isoelectric Focusing
  • Base Tautomerization
  • Nucleotide Conformation
  • Furanose and Hydroxymethyl Conformation
  • UV Spectra of Nucleotides
  • The Meselson-Stahl Experiment
  • Base Pairing in DNA
  • A- and B-DNA: Top and Side Views
  • DNA Structure
  • Hoogsteen Base Pairing in DNA
  • Palindromic DNA
  • Structure of H-DNA
  • 16S rRNA Secondary Structure
  • Thermal Denaturation of DNA
  • Cloning Basics
  • Ribonucleotide Reductase
  • Maxam-Gilbert Sequencing of DNA
  • Chemistry of the Maxam-Gilbert DNA Sequencing Method
  • Solid-Phase DNA Synthesis
  • Chemistry of Solid-Phase DNA Synthesis
  • Amino Acid Titration Curves
  • Chemical Modification of Cysteine
  • Fibrous and Globular Proteins: Examples
  • Mechanisms of Amide Bond Hydrolysis
  • Cyanogen Bromide: Reaction with Met
  • Edman Degradation of Polypeptides
  • Sequencing of Insulin
  • Cis and Trans Peptide Bonds
  • Globular Proteins: Polypeptide Folding
  • Definition of the Phi and Psi Torsions in Peptides
  • Phi/Psi Angles and Nonbonded Interactions
  • Idealized Protein Helices
  • Right-Handed Alpha-Helix
  • Beta-Pleated Sheet
  • Silk Fibroin
  • Beta Turns in Proteins
  • Gamma Turns in Proteins
  • Intrachain H-Bonding in Globular Proteins
  • Proproteins and Preproproteins
  • A Ramachandran Plot
  • Protein-DNA Recognition
  • DNA Binding Protein, Cro
  • The Globins and Oxygen Transport/Storage
  • Molecular Dynamics of Myoglobin
  • Iron Coordination in Hemoglobin
  • Oxygen Binding Curves: Storage vs Transport
  • Oxygen Binding by Hemoglobin
  • 2,3-BPG Binding by Hemoglobin
  • Allosterism: Two Structural Models
  • Thermal Denaturation of Ribonuclease
  • Thermal Denaturation of BPTI: Effect of Disulfides
  • Protein Folding: Proposed Steps
  • Protein Folding: Structural Model
  • Structure of a Protein Dimer: Prealbumin
  • Symmetry in Multisubunit Proteins
  • Protein Dynamics: Timescales of Motions
  • Carbohydrate Terminology
  • Ring-Closure of Glucose and Fructose
  • Solution Composition of Sugars
  • Aldose-Ketose Isomerization: Enediol Intermediate
  • Helical Structure of Amylose
  • Structure of Amylopectin
  • Structure of Cellulose
  • Cell Surface Oligosaccharides
  • ABO Blood Group Antigens
  • O- and N-linked Glycoproteins: Covalent Bonds to the Protein
  • Sequencing Oligosaccharides with Glycosidases
  • Biosynthesis of Blood Group Oligosaccharides
  • Structure of Cartiliage Proteoglycan
  • Structures of a Saturated and Unsaturated Fatty Acid (Stearic and Oleic Acids)
  • Structures of Some Phospholipids
  • Phosphoglyceride Structure
  • Sphingomyelin Structure
  • Examples of Glycosphingolipids
  • Biosynthesis of PGG₂: PGH Synthase
  • Induction of PGG₂ and PGH₂ Biosynthesis
  • Micelles and Bilayers
  • Structure of the Plasma Membrane
  • A Membrane Integral Protein
  • Lipid-Anchored Membrane (Peripheral) Proteins
  • The Sodium-Potassium Pump
  • The Sodium-Glucose Pump
  • The PEP-Dependent Phosphotransferase System in Bacteria
  • In Vivo Transport Processes: An Overview
  • Enzyme-Substrate Complementarity
  • Enzyme-Substrate Recognition: Enthalpic and Entropic Factors
  • Enzyme Recognition of Prochiral Substrates
  • Two Models for Enzyme-Substrate Interactions
  • Free Energy Diagrams: Boat-Chair Interconversion
  • Enzyme Catalysis: Intermediates Along the Reaction Coordinate
  • Entropic and Enthalpic Factors in Enzyme Catalysis
  • Enzyme Catalysis: An Energy Bar Diagram
  • First-Order Reaction Kinetics
  • The Steady-State Approximation in Michaelis-Menten Enzyme Kinetics
  • Irreversible Enzyme Inhibition: Diisopropylfluorophosphate (DFP)
  • Enzyme Inhibition: Competitive
  • Enzyme Inhibition: Noncompetitive
  • Active Site Residues of Chymotrypsin
  • Enzyme Mechanisms: Chymotrypsin
  • Catalytic Mechanism of Pancreatic RNase
  • A Competitive Inhibitor of Ribonuclease
  • Lysozyme: X-Ray Structure
  • Lysozyme: Substrate Structure
  • Lysozyme: Half-Chair Conformation of Substrate
  • Lysozyme: Catalytic Mechanism
  • CN-Catalyzed Decarboxylation of an alpha- Ketoacid
  • Reactions of Thiamine Pyrophosphate
  • Catalytic Mechanism: Pyruvate Dehydrogenase Reaction
  • Reactions of Pyridoxal Phosphate
  • Reaction Mechanism: PLP-Catalyzed Transamination
  • Tetrahydrofolate Coenzymes
  • Reactions of Vitamin B₁₂
  • Intracellular Locations of Metabolic Pathways
  • Overview of Metabolism
  • Thermodynamics of the Ice-Water Phase Transition
  • Thermodynamics of Some Chemical Reactions
  • Free Energies of Hydrolysis of Biological Phosphates
  • Free Energy Change: Phosphoglucoisomerase
  • Overview of Glycolysis I
  • Overview of Glycolysis II
  • Phase I of Glycolysis
  • Phase II of Glycolysis
  • Regulation of Glycolysis
  • Free Energy in Glycolysis
  • Other Substrates for Glycolysis
  • Roles of Glycolytic Intermediates in Anabolism
  • Distinction Between Hydrolysis and Phosphorolysis of a Glycosidic Linkage
  • Hormone Regulation Cascade for Glycogen Catabolism
  • Alternate Pentose Phosphate Pathways
  • Mechanisms of the Pyruvate Dehydrogenase Complex
  • Carbon Fate in the TCA Cycle
  • Metabolic Roles of TCA Intermediates
  • Three Stages of Respiration
  • Location of Respiratory Processes in Mitochondria
  • Complexes I-IV of the Electron Transport Chain
  • Chemical Structures of Some Inhibitors of Electron Transport and Oxidative Phosphorylation
  • ATP Synthase: Relationship to the Electron Transport Chain
  • ATP Synthesis Driven by Light and Bacteriorhodopsin
  • Structure of the FoF1 Complex
  • An Energy Balance Sheet for Gluconeogenesis and Glycolysis
  • Overview of the Fatty Acid Oxidation Pathway

  PowerPoint Slides from Class Lectures (taken with modification from Biochemistry by Donald Voet and Judity G. Voet, Wiley (3rd Edition, 2004)

  • Slides: Chapter 2
  • Slides: Chapter 3
  • Slides: Chapter 4
  • Slides: Chapters 5/29
  • Slides: Chapter 6
  • Slides: Chapter 7
  • Slides: Chapter 8
  • Slides: Chapter 9
  • Slides: Chapter 10
  • Slides: Chapter 11
  • Slides: Chapter 12
  • Slides: Chapter 13
  • Slides: Chapter 14
  • Slides: Chapter 15
  • Slides: Chapter 16
  • Slides: Chapter 17
  
  
• Chem 439L: Physical Chemistry Laboratory
  
  
• Chem 621: Seminar in Biochemistry
  
  

  The following PowerPoint presentations were given in this course in the Fall 2002. The seminar date and speaker are identified for each entry. Seminar attendees are welcome to download these files if they wish to follow up on the details of each presentation.

  • Seminar on September 27, 2002: Matthew Feldman
  • Seminar on October 11, 2002: Gergana Ugrinova
  • Seminar on October 18, 2002: Michael Evans
  
  
• Chem 624: Advanced Biochemical Techniques
  
  
• Chem 626: NMR Spectroscopy in Chemistry and Biochemistry
  
  
• Special Topics (Graduate): Carbohydrates in Chemistry and Biology
  
  
• Special Topics in Biochemistry (Graduate): Ethics in Research