Overheads for Secton 1

 

 Scientific Method

 Pope and evolution

 Vatican & ID_1/19/06

 

 Chapter 1

         Life it's own self

         Cell fractionation

         Phylogeny of Kingdoms

         Organism classes

         Procaryotes

         Eucaryotes

         Cytoskeleton

         Isolating organelles

 

         Biochem Organization

         Chemical Composition of cells

         Noncovalent Interactions

         Functional Groups

         Chemical properties

         Chirality

         Protein Interactions

        

         Physical concepts  

 

         DNA complementarity

         Molecular Biology Paradigm

         DNA point mutations

         Genetic Diversity

 

         Prebiotic Evolution
         Evolutionary Time Line

         Acquistion of mitochondria?

         Genomic Data

          
 

Chapter 2

    Weak bonds

    Water structure

    water Clathrates

    Dissolution of ions

    Hydrogen bonding

    Nonpolar interactions

    Solute interactions

    Colligative properties
    water has unusal properties

    Logarithms

    Acids and pH

    Ionization of water
    proton hopping

    estimate Ka

    acid species and pH

    Common acids

    titration of acids

    table of pKs

    pKa with dielectric

    Buffer example

    Practical buffer calculations

    Blood buffering

    Ionization of protein side chains

 


 
 

Chapter 3

          Amino acid nomenclature

          The RS system

          The 20 standard amino acids

          Titration of AA

          Opical absorbance

          Aromatic absobance

Table of AA properties

          Nonstandards AAs

          Chemical Reactions

          Peptide formation

          Levels of protein structure

          Protein assays

          Acrylamide gels

          PAGE-1

PAGE-2
           Animation of SDS run

          MW from PAGE

          Salt fractionation and Dialysis

          Ion exchamge chromatography

          Molecular seive chromatography

          MW from gel filtration

          Affinity chromatography

          2D gels

          ELISA assays

          The Edman reaction

          Chemical sequencing of proteins

          A simple example of overlapping peptides

          Cytochrome C sequences

          Species relations

          Evolutionary trees

 

          Aligning protein sequences
 
 

Chapter 4

 

          Peptide Bond

          Phi/Psi definitions

          Extended chain

          Phi/Psi Demo

          Ramachandran Plot

          Peptide helices

          a-helix

          b-sheets

Peptide turns

Propensities

Fibrous Proteins

Keratins

Collagen

Collagen bonding

Globular Proteins

Simple motifs

Helix interactions

Motifs to domains

Four-helix Bundle

antiparallel beta barrel

Beta Sandwhich

Simple Greek Key Barrel

Jelly-roll beta barrel

The beta-alpha barrel

The NAD binding domain

Domain structure

Table of composition

Protein Structure Demo

X-ray Structure Determination-1

X-ray Structure Determination-2

Electron density

Protein folding forces

Examples of atom distribution

Quaterary Structure

Simple quaternary structure

Molecular Symmetry

Virus symmetry

Protein Folding

Folding

Folding Barnase

Chaperones 

 
 
 

Chapter 5

 

Nonenzyme protein examples

 

Globins
Oxygen transport

Myoglobin

Hemes

O2 binding to Mb

Hemeoglobin structure

Cooperative binding

Hill Plots

A simple cooperative model

Two states for Hb

Heme interaction with O2

Hb quaterary shifts1

Hb quaterary shifts2

Simple Hb quat. model

The Bohr Effect

Hb allosteric effectors

BPG binds T state Hb

Molecular evolution

Example of deamination

Sickle cell anemia

Trait inheritance

Evolution and expression of globins

 

Antibodies

Humoral immunity

Ig G Antibody structure

IgG sequences

Antigen binding

Binding a small antigent to an antibody

   A deep antibody pocket

   Some chemical interactions

Antibody binding to a protein

Antibody-like domains are common in the immune response

Clonal selection

Cellular immunity

MHC sytem

Immune response

 

Motor proteins: actin & myosin

Skeletal muscle

Myosin and actin

Actin-myosin assembly

Sliding filament model of muscle contraction

Molecular mech of power stroke