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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