Chemistry Online: An Approach Based on Chemical Logic
List of Figures
07/02/2009
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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 -
b-mercaptoethanol and dithiothreitol
- Cleaving
Disulfide Bonds in Proteins
- 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
- Secondary
structure
- Tertiary
structure
- Quaternary
structure
- 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 -
- Summary of amino acids
propensities
-
Parallel
beta strands
-
Antiparallel
beta strands
-
Beta-pleated
sheets (antiparallel)
- 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
- Overview - Synthesis of
Protein Destined for Secretion
- Signal Recognition
Particle Complex
-
Translocon Equilbrium Model
-
GroEL and GroES.
-
Denaturation Curves for Proteins
- Diagram
showing relative contributions to the DG
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
DH for Protein
Denaturation by Differential Scanning Calorimetry
- Heat Capacity Changes:
A Molecular Interpretation
- Analogy between benzene
solubility in water and protein denaturation.
- Amino Acid Structure and
propensity for secondary structure
- Secondary structure prediction
- Helical wheel projection
- 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
- Typical isothermal titration calorimetry data and analysis
- Titration calorimetry determination of
Kd and DH 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
- alpha-beta interface
- 8 salt bridges
- C- or N- terminus
- F helix to shift
- 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
- 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)
- AT and GC base pairs have available
H bond donors and acceptors
- Lambda Repressor/DNA
Complex
- helix-turn-helix
in l repressor/DNA complex
- H Bond interactions between
l repressor and DNA
- Zinc
finger
- Leucine zippers
- Yeast Two-Hybrid
- Protein
Fragment Complementation
- Tandem
Affinity Purification
- Activation of p53 as a transcription
factor by phosphorylation and conformational change
- 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
- Eukaryotic promoters and
regulatory regions
- Eukaryotic
multisubunit general transcription apparatus
- 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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