Chemistry Online: An Approach Based on Chemical Logic
List of Figures
04/17/16
I have created most of the images found in BC Online, using programs such
as Power Point, Paint Shop Pro, and ChemDraw. Some of these figures
have been modeled after those found in various biochemistry textbooks.
I have also used other figures which are already available on the web.
For those, I have referenced those by including the url for the site
directly on the figure.
Some of the figures in this online book are used, by permission, from
Science, Nature, and the Proceedings of the National Academy of Science.
The specific reference for each figure is shown on the figure. For
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Introduction
Chapter 1: Lipid Structure
Chapter 2: Protein Structure
-
Table: Structure and Property of the Naturally-Occurring Amino Acids
-
Amino Acids React to Form Proteins
- Review:
Comparison of protein, carbohydrate and nucleic acid synthesis
-
Different Representations of a Polypeptide (heptapeptide rep)
-
Stereochemistry of Amino Acids
-
Titration curves for Gly, Glu, and Lys
-
A review of the chemistry of aldehydes, ketones, and carboxylic acid
derivatives
-
Understanding the properties of proteins: low to high resolution
-
Lysine Reactions 1
-
Lysine Reactions 2
-
Lysine Reactions 3
-
Cysteine Reacions 1
-
Cysteine Reactions 2
-
Sulfur redox chemistry
-
Disulfide - Cystine - Reactions
-
Disulfide Oxidizing Agents - β-mercaptoethanol, dithiothreitol and
phosphines
- TCEP
reduction of disulfides
-
Cleaving Disulfide Bonds in Proteins
-
Redox state of Cysteine
-
Reactions of Histidine
-
Where is the H on His? Where is the Charge?
-
His reacts with reasonably high selectivity with diethyl pyrocarbonate
-
Post-translational modification of proteins
-
Understanding the properties of proteins: low to high resolution
-
Amino Acid absorbance profiles.
-
Edman Degradation
- ESI
Mass Spectrum of Apo-Myoglobin
-
Linear and 3D Quadrupoles
-
Peptide Fragmentation and Sequencing by MS/MS
-
Annotated MS/MS spectra of
human Glu1- fibrinopeptide B
-
Secondary structure
-
Tertiary structure
-
Quaternary structure
- Peptide
Bonds - MOs and Huckel Diagram
-
The CD Spectra of Alpha-Helix, Beta-Sheet, and Random Coils
-
X-Ray Structures and the Parthenon
-
1D NMR spectra of a protein
-
2D NOSEY spectra of a protein
-
Extended Polypeptide Showing Planes and Phi/Psi Angle
-
Trans arrangement of the alpha C's
-
Ramachandran Plot
-
Ramachandran plots showing Phi, Psi angles for Gly, Ala, Tyr, and Pro in
actual proteins
-
Lennard-Jones potential (6-12 potential)
-
Right Handed Alpha helices -
-
Parallel beta strands
-
Antiparallel beta strands
-
Twisted Beta Sheet/Saddle
-
Beta Barrel
-
Beta strand connections
-
Reverse Turns
-
Type I and Type II Reverse Turns
-
Twisted sheets or saddles as well as beta barrels
-
Why do amino acid propensities for secondary structure differ?
-
Helix-loop-helix
-
EF hand.
-
Beta-hairpin, or beta-beta
-
Greek Key motif:
-
Beta-alpha-beta:
-
Beta Helices
-
Socks and protein folding
-
Anfinsen Experiment: Folding of RNase
-
Catalytic Shuffling of Disulfides with beta-mercaptoethanol
-
Kinetic and thermodynamic measurements of proteins stability and folding
-
Protein Folding Landscape:
-
Reversible denatuation,
-
Addition of iodoacetamide
-
Bovine pancreatic trypsin inhbitor (BPTI): Folding Kinetics
-
BPTI: Folding Pathway In Vitro
-
Lactalbumin
-
NMR in protein folding: exchange of all C's with ionizable protons,
including, the amide H's
-
Experimental data on model proteins
-
Unfolding of RNase H with Optical Tweezers
-
RNaseH Folding Transitions: Optical Trap
-
Folding Lanscape of RNase H: Optical Tweezers
-
Characteristics of Intrinsically Disordered Proteins
-
The Protein Trinity: Ordered, Collapsed and Extended States
-
Comparison of cytosolic prokaryotic and eukaryotic chaperone pathways
-
Overview - Synthesis of Protein Destined for Secretion
-
Signal Recognition Particle Complex
-
Sec Dependent Pathway for Post-translational translocation
-
Translocon Equilbrium Model
-
GroEL and GroES.
-
Denaturation Curves for Proteins
-
Diagram showing relative contributions to the ΔG for protein folding.
-
Denaturation temperature vs pH for proteins
-
Thermodynamic cycle for formation of a H-bonded dimer of
N-methylacetamide in a nonpolar solvent
-
Free energy of transfer of amino acids from water
-
Hofmeister Series
-
Free energy of transfer of the nonpolar amino acids into 8M urea
-
Reagents might interact with the surface of the protein.
-
Thermodynamic cycle for urea denaturation of proteins
-
Water Accessible Surface Area in Protein Unfolding
-
Change in G, H and -TS for taking benzene from pure benzene to water.
-
Heat of fusion, heat of vaporization, and heat capacity of water
-
Thermal Denaturation of a protein using differential scanning
calorimetry
-
Heat capacity of proteins vs temperature
-
Determination of ΔH for Protein Denaturation by Differential Scanning
Calorimetry
-
Heat Capacity Changes: A Molecular Interpretation
-
Analogy between benzene solubility in water and protein denaturation
-
Stabilization of Carbocations by Hyperconjugation
-
Orbital involvement in H-bonds and n to pi* interactions in alpha
helices
-
Ramachandran plots of n to pi* interactions.
-
Amino Acid Structure and propensity for secondary structure
-
Secondary structure prediction
-
Helical wheel projection
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Hydrophathy plot for chymotrypsinogen
-
Types of membrane proteins
-
Hydropathy plot for bovine rhodopsin
-
Seven transmembrane helices for bovine rhodopsin
-
Nanodisc with membrane protein
-
3-helix bundle
-
Helices form early
-
Simultaneous and quick partial helix formation and collapse
-
Engrailed homeodomain 3 helix bundle protein
-
Complete Folding Pathway of Engrailed Homeodomain by Experiment and
Simulation
-
Alzheimer's protein: beta amyloid protein and mutations
-
Cartoon Models of PrPc and PrPsc
-
Potential energy functions in protein mechanics and dynamics
calculations
Chapter 3: Carbohydrates
Chapter 4: DNA, Genomics, and Proteomics
Chapter 5: Binding
-
M is free macromolecule, L is free ligand, and ML is
macromolecule-ligand complex,
-
ML vs L at Varying Kd's
-
ML vs L at Even Lower Kd's
-
ML vs L at a Very Low Kd!
-
Y vs L and Y vs Lo when Lo is not >> Mo
-
Comparison of Covalent Binding of Protons vs Noncovalent Binding of
Ligand
-
Saturation binding curve for dimerization of a macromolecule
- Isothermal
Titration Calorimeter Cells
-
Typical isothermal titration calorimetry data and analysis
-
Titration calorimetry determination of Kd and ΔH for the interaction of
gp120 and CD4
-
Binding Curves that Explain Sigmoidal Titration Calorimetry Data for
gp120 and CD4
-
Surface Plasmon Resonance
-
Negatively charged phospholipids in biological membranes
-
Hyperbolic plot: Y vs L
-
Double-reciprocal plot: 1/Y vs 1/L
-
Scatchard plot: Y/L vs Y
-
Semilog plot: Y vs log L
-
Y vs log L: Differing Kd values
-
Heme
-
Heme-O2 Octahedral Complex
-
Plots of Y (fractional saturation) vs L (pO2) are hyperbolic for Mb, but
sigmoidal for Hb,
-
Bohr Effect - Hemoglobin
-
Conformation Changes on Oxygen Binding to Deoxy-Hemoglobin
-
Salt Bridges in Deoxy Hb
- Salt
Bridges in DeoxyHb
-
C- or N- terminus
-
4 Ways to plot Mb and O2 plots
-
Plots of Y vs L for Hb with varying degrees of cooperativity: n = 1,
2.8, and 4
-
Hill Plot for Mb (n =1)
-
Hill Plots: n = 1, 2.8, and 4
-
Hill Plots For Hb Showing straight lines for n=2.8 and for n's=1 which
model the low and high affinity sites.
-
Hill Plot for Hb: Black line showing hypothetical actual curve
-
Linked equilibrium in he MWC model
-
Y Vs alpha with varying L and c - MWC MODEL
-
Hb binding curves: Experimental, vs Theoretical Hill and MWC Equations
-
Cooperativity as transition between two hyperbolic binding curves with
different Kd's
-
Equilbria in KNF Model
-
Conformational Selection vs Induced Fit Binding
-
Types of Molecular Recognition Features in Intrinsically Disordered
Proteins
-
Linked equilibrium: binding of H+, CO2 and O2 to hemoglobin
-
A review of thermodynamic cycles - linked equilibria
-
C2 Symmetry
-
D2 Symmetry
-
Mutations causing Dimer with C2 symmetry or Infinite Helix
-
Equilibria in KNF Model
-
Conformational Selection vs Induced Fit Binding
-
Inhibitor-DNA-enzyme (IDE) - an engineered allosteric enzyme
-
A combination of MWC and KNF: a modern structure view of structural
changes in Hb on ligand binding
-
Of mice and oxygen
-
Receptor agonists/antagonist I
-
Receptor agonists/antagonist II
-
Process that affect the steady state concentration of a protein
-
Positive and Negative Regulation of Gene Transcription
-
Function of proteins in galactose utilization
-
IPTG and Lactose Structures
-
Induction of the Lac Operon
-
Control of globin gene transcription
-
Example of transcription complexes
-
Upon absorbing red light, a phytochrome photoreceptor is converted from
the inactive Pr form to the active Pfr form (permission)
-
Enhancers of Transcription
-
Eukaryotic promoters and regulatory regions
-
Eukaryotic multisubunit general transcription apparatus
-
AT and GC base pairs have available H bond donors and acceptors
-
Lambda Repressor/DNA Complex
-
helix-turn-helix in λrepressor/DNA complex
-
H Bond interactions betweenλ repressor and DNA
-
Zinc finger
-
Leucine zippers
-
Arg in T3c Transposase binding in Narrowed Minor Grove of T3c
Transposon
-
Yeast Two-Hybrid
-
Protein Fragment Complementation
-
Tandem Affinity Purification
-
Activation of p53 as a transcription factor by phosphorylation and
conformational change
-
Canonical sequence for both activating and repressing p53RE
-
Transcription Factors: Functional Classification
-
Kinetics of protein-DNA binding
-
Two proteins, A and B,
-
Cooperative binding of B to the protein A-DNA complex.
-
Chromatin
-
Nucleosome
-
Remodeling of Chromatin and Control of DNA Transcription
-
Methylation of CpG
-
RNA Interference: Antisense and Silencing
-
RNAi-mediated gene silencing in mammals using short haripin RNA genes.
-
Endosomal TLR3 Interaction with foreign RNA and DNA
-
Recognition of PAMPs by TLRs
-
An Overview of the Regulation of Gene Expression in Eukaroytes
-
DNase I Sensitivity of Nucleosome Bound and Free DNA
-
Combinatorial Drug Development.
-
Test tube and in situ synthesis of triazole inhibitors.
-
Antisense
RNA forms a dsRNA
-
Cells can be made to make an antisense RNA within the cells
-
Triple helix formation: binding to exposed H bond donors and acceptors
of bases not involved in Watson-Crick H-bonding interactions.
-
Peptide:nucleic acid hybrids
-
Detection of Differential Gene Expression in Tumors and Normal Cells
Using Microarray Chip
-
Multivalent inhibitor of flu virus
-
Multivalent Ligand Binding Models
Chapter 6: Transport and Kinetics
Chapter 7: Catalysis
Chapter 8: Oxidation/Phosphorylation
Chapter 9: Signal Transduction
Capstone: Origin of Life
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Biochemistry Online Table of Contents
Biochemistry Online by Henry Jakubowski is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.