Syllabus and Notes

Sept 4th, 2008

 

Lecture: Introduction and Principles of Structure
In this section we will describe the basic principles of structure with special emphasis on the non-bonded forces that underlie the conformation and interactions of biological macromolecules

HB
 

Lecture: Protein Structure
In these lectures, we will cover principles of protein structure (including physical and chemical properties of amino acids, primary structure, secondary structure, tertiary structure, and quaternary structure)

HB
  Exploring helices and sheets in proteins using Molecular Graphics SD
AttachmentSize
PrinciplesOfStructure.ppt676 KB
Protein Structure.ppt7.82 MB
secondary structure tutorial.doc36 KB

Sept 11th, 2008

 

Lecture: Nucleic Acid Structure
This section will cover the basic principles of nucleic acid structure including primary, secondary and tertiary structure. The Architecture of DNA and RNA will be reviewed and discussed.

HB
AttachmentSize
DNA structures.ppt1.38 MB
RNA structures.ppt2.26 MB
Principles of NA Structure.ppt1.35 MB

Sept 18th, 2008

 

Lecture: Protein Nucleic Acid Interactions
The principles of protein nucleic acids will be described.

HB
   Exploring nuceic acid structures SD
AttachmentSize
Protein Nucleic Acid08.ppt13.44 MB
NDB-tutorial-rev.doc36 KB

Sept 25th, 2008

 

Lecture: Visualization and Graphics
Students will learn how to use computer graphics programs to visualize protein structures

SD
  Introduction to RasMol SD
  Introduction to Chimera SD
  Making depositions (using Drupal) JC

 

AttachmentSize
Visualization-Fall-2008.ppt5.33 MB
RasMol-visualization-fall-2008.doc30 KB
RasMol-quick-ref.doc27 KB
Chimera_visualization-fall-2008.doc44.5 KB
HW_visualization-fall-2008.doc28.5 KB
Fall_2008_Deposition_Intro.ppt4.21 MB

Oct 2nd, 2008

 

Lecture: X-ray Crystallographic Methods
The basic principles of x-ray crystallography will be summarized and the procedures used for x-ray structure determination of biological molecules will be described.

HB
  Exercises in Symmetry HB
AttachmentSize
escher-drawings.ppt14.05 MB
X ray Lecture 2008.ppt6.1 MB

Oct 9th, 2008

 

Lecture: Electron Microscopy
Overview of EM methods used produce 3D volumes of biological specimens.

Exercise: fitting X-ray models into EM maps

CL
AttachmentSize
CryoEMLecture08.pdf5.79 MB

Oct 16th, 2008

 

Lecture: Calorimetry
Isothermal Titration Calorimetry

Differential Scanning Calorimetry

DP
AttachmentSize
BindingProfiles_ITC.pdf735.24 KB
MeltingCurves_DSC.pdf1.13 MB

Oct 23rd, 2008

 

Lecture: NMR Methords

GM
AttachmentSize
Montelione.NMR.Principles.ppt6.04 MB
Montelione.ProteinNMR-JC.ppt3.53 MB

Oct 30th, 2008

 

Lecture: Kinetics

SP
AttachmentSize
Introduction to enzymes.ppt8.63 MB

Nov 6th, 2008

 

Lecture: Kinetics

SP
AttachmentSize
Transition state theory.ppt2.8 MB

Nov 13th, 2008

 

Lecture: Kinetics
Description to be added

SP
AttachmentSize
Enzyme Kinetics.ppt528.5 KB
Transient State Kinetics Tutorial .pdf1.99 MB
kinetic simulation problem set.doc46.5 KB

Nov 20th, 2008

 

Lecture: Kinetics
Description to be added

SP
AttachmentSize
Transient state kinetics.ppt1.33 MB

Nov 27th, 2008

 

Thanksgiving holiday

 

Dec 04th, 2008

 

Lecture: Mass Spectrometry
Description to be added

PL