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 pK_a 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 pK_a's and the acid concentration.

Alanine Titration Key features for determining pK_a'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 K_d.

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 (n_H) and K_d.

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 V_max and K_M.

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 V_max, K_M and K_I.

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 tRNA^Phe 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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