Links (mostly) at the top of the lecture Web pages are compiled below. The title or brief annotation indicates whether they are a Chime page, quiz, animation, etc. Several do not appear on the printed lecture handouts.
- Each link is ranked by its importance to a thorough understanding of Biochemistry I material using the following icons:
- Important! These pages are an integral part of the course. They go beyond what is provided in the text.
- Supplementary. Worthy of at least a look, these pages provide alternative presentations of the important items; they complement the text.
- Optional? Interesting or related topics, but not necessary for a mastery of course material. Comparable to Campbell's "Biochemical Connections".
- Topics for Exam 1 (Lectures 1-8):
Review Quizzes Index of self-quizzes for each lecture's topic. The multiple choice questions from Exam 1, 2000-2003 are also available.
- Lecture 1: Introduction & Organic Functional Groups
- How to to make Hard Copies
- Molecular Models for Biochemistry
- Organic Nomenclature
- Introduction to Basic Organic Nomenclature at Okanagan University College.
- Chromatin & Nucleosome Structure
- Constants and Conversion Factors
- Lecture 2: Water & Hydrogen Bonds
- Chime display of a Water Cluster
- Lecture 3: Acid-Base Equilibria & Buffers
- Ratios & Fractions in the Henderson-Hasselbalch Equation
- The pH titration animation shows a typical weak acid titration.
- The Phosphate Titration Curve shows a typical polyprotic acid titration (cf. Campbell, Fig. 3.7b).
- Graphing Quiz: pH Titration Determine pKa and the acid concentration.
- Lecture 4: Structure & Properties of Amino Acids
- Self-guided tour of the amino acids
- Amino Acid Identification Quiz (Chime Images)
- Amino Acid Structure Quiz (GIF images)
- The Histidine Titration Curve shows a typical polyprotic acid titration
(cf. Campbell, Fig. 3.7b: What's wrong with the Campbell graph?).
- Lecture 5: Peptides
- Ionization of Amino Acids and Proteins Class handout
- "pKa Values of Common Amino Acids" Summary and condensed version of Campbell's Table 3.2
- Graphing Quiz: Dibasic & Tribasic pH Titration Determine pKa's and the acid concentration.
- Alanine Titration Key features for determining pKa's and concentration.
- Frogs Legs and Parasitic Tales The magainin peptide story (at Columbia Univ.)
- Lecture 6: Protein Primary & Secondary Structure
- The Protein Architecture Tutorial introduces the basic principles of protein 3-D structure using Chime images of Protein G
- Conformational Elements of Protein Structure provides side-by-side Chime images of peptides in several secondary structure conformations.
- Pauling, et al. (1951): The classic paper that anounced the structure of the a-Helix.
- Lecture 7: Protein Tertiary & Quaternary Structure
- The CMU Chime Tutorial, covered previously in cluster sesssions, can also be accessed this week. Be sure you understand the operation of this visualization tool.
- The Protein Architecture Tutorial introduces the key principles of protein 3-D structure using Chime-generated images of Protein G.
- The "Alpha_bet Helix" shown in lecture today as an example of an ideal a-helix. But note the lack of one H-bond and the steric clash that is seen at the Pro residue.
- Lecture 8: Protein Folding & Viewing
- Test your understanding of protein architecture with the Protein Structure Quiz. It uses GIF images that are taken from the Protein Architecture Tutorial
- Protein Structure Examples: Links to Chime images of the proteins shown in Campbell, Ch. 4 (and other representative structures).
- Protein Viewing (in-class demonstrations)
- Disulfide Bonds in RNaseA Chime page
- Topics for Exam 2 (Lectures 9-20):
Review Quizzes Index of self-quizzes for each lecture's topic. The multiple choice questions from Exam 2, 2000-2003 are also available.
- Lecture 9: Biochemical Energetics 1
- Lecture 10: Biochemical Energetics 2
- Protein Folding-Unfolding Transition: a Shockwave movie of an "aa structure" that allows you to set the reaction temperature and view the results on a transition curve graph.
- Protein G Chime page highlighting the location of residue 53.
- Lecture 10 Supplement The hydrophobic effect can be measured as a DG of transfer.
- Lecture 11: Immunoglobulin Structure and Function
- Human Immunoglobulin Structure Diagram
- Aspects of Immunoglobulin Structure shows Chime images of antibodies and antibody-antigen complexes:
Side-by-side images on one page (1,950K).
One image per page (248K).
Molecular Mass Scales, (220K) shows a selection of eight superimposed structures ranging in molecular weight from 18 Da (H2O) to 2.6*106 Da (70S Ribosome). The IgG molecule is ~1.4*105 Da (140 kDa).
- Antibodies are the September "Molecule of the Month" at the Protein Data Bank. Short descriptions with graphics in a series by David Goodsell.
- Lecture 12: Ligand Binding Measurements
- Background reading: "Ligand Binding" Equations and Analysis by Dr. Gordon Rule.
This more extensive treatment is available as an eight-page PDF image.
- Simulation of Molecular Motion at Binding Equilibrium (The animation requires the Shockwave plug-in.).
- Graphing Quiz: Ligand Binding Scatchard Plots: Determine stoichiometry (n) and Kd.
- Lecture 13: O2 Binding by Myoglobin & Hemoglobin
- Myoglobin & Hemoglobin: Side-by-side Chime Images. -by Dr. Gordon Rule, CMU
- Cooperative Ligand Binding Measurements Class hand-out
- Graphing Quiz: Cooperative Binding Hill Plots: Determine Hill coefficient (nH) and Kd.
- Oxygen Binding Simulation that shows the differences between the "concerted" and "sequential" mechanisms of allosterism applied to hemoglobin.
- Hemoglobin Gallery of still pictures and animations. -by Dr. John Lukin (C. Ho Laboratory, CMU)
- Lecture 14: Enzyme Kinetics
- Substrate Saturation Kinetics shows various graphs used to analyze kinetic data.
- Graphing Quiz: Michaelis-Menten Kinetics Determine Vmax and KM.
- Lecture 15: Enzyme Inhibition
- Data Analysis for Competitive Inhibition The class handout shows enzyme inhibition curves.
- Structure of a Trypsin-Inhibitor Complex: "Must-viewing" of an enzyme-inhibitor complex on a Chime page.
- Carbonic Anhydrase Structure: Another enzyme-inhibitor complex on a Chime page.
- ATCase Architecture: Chime images of T-State & R-State Aspartate Transcarbamoylase with and without bound ATP (activator) and CTP (inhibitor).
- Graphing Quiz: Enzyme Inhibition Kinetics Lineweaver-Burk Plots: Determine Vmax, KM and KI.
- Lecture 16: Purification of Proteins
- Example Graphs for Gel Filtration and SDS-PAGE analysis.
- Example Problem: SDS-PAGE Gel.
Example Problem: Answer.
- Lecture 17: Nucleic Acid Structures
- Class handouts for this lecture:
1. Backbone & Bases and 2. Base Pairs
- Nucleic Acid Structures is a page of JPEG images to accompany this lecture.
- Lecture 18: DNA Replication & Repair
- DNA Replication Tutorial Flash animation of prokaryotic replication.
- Enzymes & Proteins that act on DNA is a worksheet to accompany this lecture.
Answers for the above worksheet.
- Lecture 19: DNA Transcription
- DNA Transription Tutorial Flash animation of prokaryotic transcription.
- Review of some Molecular Genetics Terminology
- RNA Polymerase-Promoter Complex: The bacterial enzyme architecture. (Chime, 188K)
- RNA Polymerase Elongation Complex: The yeast enzyme architecture. (Chime, 80K)
- Lecture 20: Transcription Regulation
- CAP-cAMP & CREB Activation Comparison of prokaryotic vs. eukaryotic features.
- Protein-Nucleic Acid Interactions A page of JPEG images to accompany this lecture.
- Structural Motifs in DNA-Binding Proteins (Campbell, Section 10.5):
    CREB-DNA Complex: Human bZIP Protein. (Chime, 44K)
    E. coli CAP-cAMP-DNA Complex: Helix-turn-Helix Activator. (Chime, 109K)
    Zif268-DNA Complex: Human Zinc-Finger Protein. (Chime, 32K)
- Topics for Exam 3 (Lectures 21-30):
Review Quizzes Index of self-quizzes for each lecture's topic. The multiple choice questions from Exam 3, 2000-2003 are also available.
- Lecture 21: Protein Synthesis: tRNA Structure & Charging
- Protein Synthesis Tutorial : Flash animation for Lectures 21 and 22.
- Features of tRNAPhe Structure: JPEG images to accompany this lecture.
- Lecture 22: Protein Synthesis: Ribosomes & Peptide Bond Formation
- Recap of Gene Expression Lectures (#17-22) Handout for this lecture
- Structure of the 50S Ribosome Subunit A page of images to accompany this lecture.
- Polypeptide Elongation Cycles is an animation of polypeptide chain elongation.
- Ribosome Structures: Overview of the 70S crystal structure and a Chime animation of steps in translation. Separate pages show selected features of the 30S and 50S subunits.
- Lecture 23: Lipids
- Structures of Lipids: Chime images of the building blocks.
- Lipid Micelle Structure (68K): Chime image of a theoretical model.
- Lipid Bilayer Structures (258K): Chime images of the gel and liquid-crystal phases.
- Lecture 24: Biological Membranes
- Biological Membranes : Flash animation of key features.
- Examples of integral membrane proteins on Chime pages:
Bacteriorhodopsin Maltoporin
Hemolysin.
- Lecture 25: Membrane Transport
- Lactose Permease : Flash animation of the mechanism.
- Na+-K+ Pump : Part of the Flash animation on membranes.
- Lactose Permease: Structure of the inward-facing conformation. Chime page (92K).
- Lecture 26: Enzyme Mechanism: Serine Proteases
- Structure of a Trypsin-Inhibitor Complex: "Must-viewing" of an enzyme active site on a Chime page.
- Serine Protease Mechanism : Flash animation of the separate steps.
- Serine Protease Mechanism: a JavaScript animation of the separate steps.
- Serine Protease Structures: Chymotrypsin, trypsin, & elastase superposed; Chime page.
- A Catalytic Triad at High Resolution: JPEG of the Asp-His H-bond in a serine protease.
- Effects of pH on Enzyme Mechanism: a derivation and application to serine proteases.
- Trypsin: "Molecule-of-the-Month" (Oct, 2003) an introduction and graphics by David Goodsell at the PDB.
- Lecture 27: Carbohydrates
- Structures of Sugars: Chime images of the building blocks.
- Boat to Chair Conformers of Glucose: Chime animations of the conversion.
- D-glucose: from Fischer projection to 3D hemiacetal: Animations of the linear to the ring forms of glucose. (Chime & ChemSymphony, Java Applets are used.)
10.25.04: A 1/3-speed version of the above Chime page by Dr. Hens Borkent might display better, depending on your computer.
- Lecture 28: Carbohydrates 2
- Lysozyme Chemical Mechanism: Handout for Lecture 28.
- Trypsin and Lysozyme Mechanisms Compared: Handout for Lecture 28.
- Lysozyme Binding & Catalysis: Structure is related to function on a Chime page.
- Lecture 29: Glycolysis
- Glycolysis Pathway Summary: Class handout on the 10 reactions in the pathway.
- Free Energy Profile of Glycolysis: in the Human Red Blood Cell
- Glycolysis Intermediates: Chime images of the 10 reactions in the pathway.
- Hexokinase Induced Fit: Chime images of the two conformations.
- Protein Structure Examples: Chime images of Triose Phosphate Isomerase, Pyruvate Kinase, and Lactate Dehydrogenase.
- Glycolytic Enzymes: "Molecule-of-the-Month" (Feb, 2004) an introduction and graphics by David Goodsell at the PDB.
- Lecture 30: Glycogen Metabolism/Gluconeogenesis
- Muscle Glycogen Phosphorylase: Chime page showing the R and T state conformations.
- Glycogen Phosphorylase: "Molecule-of-the-Month" an introduction and graphics by David Goodsell at the PDB.
- Topics included in the Final Exam (Lectures 31-34):
Review Quizzes Index of self-quizzes for each lecture's topic. The multiple choice questions from Final Exams, 2000-2003 are also available.
- Lecture 31: Citric Acid Cycle
- Citric Acid Cycle Summary Class handout on the reactions in the pathway.
- Metabolic Pathway Simulation and the effects of an inhibitor
- Citric Acid Cycle Intermediates: Chime images of the reactions in the pathway.
- Lecture 32: Oxidative Phosphorylation
- Redox Chemistry in Biological Processes: Review of Chapter 12.8-12.9 topics.
- ATP Synthesis : Flash tutorial of the FoF1 ATP synthase.
- ATP Synthase Overall architecture of the FoF1 complex (Chime).
- Succinic Dehydrogenase: Chime page showing the only membrane-bound enzyme in the TCA cycle, Complex II (104 KB).
- Cytochrome c Oxidase: Chime page showing the dimeric Cyt a/a3 complex Complex IV (256 KB).
- ATP Synthase: A detailed lecture by Antony Crofts, University of Illinois.
(Be sure to watch the movie of the rotating F1 ATPase.)
- Lecture 33: Catabolism of Fatty Acids
- Lecture 34: Integrated Metabolism
- Protein Kinase/Phosphatase Cascades: Handout on epinephrine and cAMP regulatory effects.
- Protein Kinase/Phosphatase Cascades Same as above as a GIF image.
- Signaling via G Proteins Flash tutorial: how receptor binding leads to cAMP synthesis.
- Muscle Glycogen Phosphorylase: Chime page showing the R and T state conformations.
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