Biophysical Chemistry
Chemistry 537   Biochemistry 5537   Biomaps 501

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Project Information

 

 

Fall 2006 Schedule
Download: PDF | MS Doc
Last Updated: November 16, 2006
Texts
C. Branden and J. Tooze. Introduction to Protein Structure. Garland Publishing, Inc., 1999.
S. Neidle. Nucleic Acid Structure and Recognition. Oxford University Press, 2002.

Nov 21 Student presentations
Oral presentations will be made by each student on the assigned enzyme.
  1. Han, Hua – Avidin
  2. Wang, Jin – Oxygen sensor
  3. He, Xianglan – Peptide deformylase
  4. Yildirim, Evrim – SSB
The final presentations should each be 15 minutes long, followed by 5 minutes for questions or discussions. Please prepare accordingly.

All powerpoints for the presentations should be transferred to the class presentation laptop before the start of the class on the day of the presentation.


HB
Nov 28 Student presentations cont'd
Oral presentations will be made by each student on the assigned enzyme.
  1. Zang, Qingda – Uracil DNA glycosylase
  2. Delgado-Rivera, Roberto L. – IV protease
  3. Singh, Abhishek – DNA methyltransferase
  4. Chen, Yu-Jen – HCV NS3 helicase
The final presentations should each be 15 minutes long, followed by 5 minutes for questions or discussions. Please prepare accordingly.

All powerpoints for the presentations should be transferred to the class presentation laptop before the start of the class on the day of the presentation.


HB
Nov 30 Student presentations cont'd

Project Homework Due:
Enzyme/Protein complex depositions due on Mapdev (http://mapdev.rutgers.edu) site. (See Project Information page for details)

Oral presentations will be made by each student on the assigned enzyme.
  1. Mao, Lili – Glutathione reductase
  2. Schneider, Bill – HIV protease
  3. Paratkar, Swaroopa – Ras protein
  4. Ertekin, Asil – Adenylate kinase
The final presentations should each be 15 minutes long, followed by 5 minutes for questions or discussions. Please prepare accordingly.

All powerpoints for the presentations should be transferred to the class presentation laptop before the start of the class on the day of the presentation.


HB
Dec. 5 Student Presentations cont'd
Oral presentations will be made by each student on the assigned enzyme.
  1. Lapelosa, Mauro – Lactate dehydrogenase
  2. Nguyen, Tung – Rab4A Ras-related protein
  3. Landers, John M. – ATP-dependent DNA ligase
  4. Jongjin, Jung – Dihydrofolate reductase
The final presentations should each be 15 minutes long, followed by 5 minutes for questions or discussions. Please prepare accordingly.

All powerpoints for the presentations should be transferred to the class presentation laptop before the start of the class on the day of the presentation.


SP
Dec. 7 Student Presentations cont'd
Oral presentations will be made by each student on the assigned enzyme.
  1. Tao, Yuan – Nitrophorin
  2. Zheng, Guohui – Chemotaxis receptor methyltransferase
  3. Goel, Shivani – EcoRV endonuclease
  4. Hua, Xia – Dihydrofolate reductase
The final presentations should each be 15 minutes long, followed by 5 minutes for questions or discussions. Please prepare accordingly.

All powerpoints for the presentations should be transferred to the class presentation laptop before the start of the class on the day of the presentation.


SP
Dec. 12 Student Presentations cont'd
Oral presentations will be made by each student on the assigned enzyme.

Project Homework Due:
Enzyme/Protein complex depositions due on Mapdev (http://mapdev.rutgers.edu) site by Nov. 30.
All corrections to deposition must be finalized before this date. (See Project Information page for details)

  1. Chen, Hsin-Yi – HCV NS3 protease
  2. Ho, Sau Chum (Eric) – GFP like protein
  3. Haq, Omar – ABC transporter
  4. Annavarapu, Srinivas – DNA polymerase beta
The final presentations should each be 15 minutes long, followed by 5 minutes for questions or discussions. Please prepare accordingly.

All powerpoints for the presentations should be transferred to the class presentation laptop before the start of the class on the day of the presentation.


SP

Sept. 5 Introduction and Principles of Structure
Lecture:
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.
Download 'Principles of Structure' - lecture [PPT]
HB
Sept. 7 Protein Structure
Lecture:
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)
Download 'Protein Structure' - lecture [PPT]
HB
Each student will be assigned a Cytokine, a nucleic acid, and an enzyme for study
(See Project Information page for details)

Sept. 12 Protein Structure cont'd
Download 'Protein Structure' - lecture [PPT]

HB
Homework:
Review PDB tutorial
http://www.pdb.org/pdbstatic/tutorials/tutorial.html

Sept. 14 PDB tutorial
Lecture:
Students will learn how to navigate the PDB site to learn about proteins. This will be hands on.

Download 'PDB Tutorial' [PPT]

Download 'Tutorial Exercise 1' [DOC] (Lysozyme)
Download 'Tutorial Exercise 2' [DOC] (Myoglobin/Hemoglobin)

SD
Sept. 19, 21 Nucleic Acid Structure
Lecture:
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.

Download 'Nucleic Acid Structure: Principles' lecture [PPT]

Download 'DNA Structures' lecture [PPT]

Download 'RNA Structures' lecture [PPT]
HB
Sept, 26 Visualization and graphics tutorial
Lecture:
Students will learn how to use computer graphics to visualize protein structure

Download 'Visualization' lecture [PPT]
Download 'Chimera Visualization' handout [DOC]

SD
Sept. 28 Protein nucleic acid interactions
Lecture:
The principles of protein nucleic acids will be described.
Download 'Protein Nucleic Acid Interactions' lecture [PPT]
HB
Oct. 3. 5 X-ray crystallographic methods
Lecture:
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.
Download 'X-ray Crystallography: Theory and Practice' lecture [PPT] (* Revised 10/04/06)
HB
Oct 10 Cryo electron microscopy
Lecture:  
Overview of the cryo electron microscopy technique for structure determination of biological assemblies
Download 'CryoEM Lecture' [PPT] (* Revised 10/06/06)
CL
Oct 12 Nuclear Magnetic Resonance
Lecture:
Download 'NMR STUDIES OF STRUCTURE AND FUNCTION OF BIOLOGICAL MACROMOLECULES' [PDF]
Download 'Biomolecular NMR spectroscopy' [PDF]
JB
Oct. 17 Computational Biology
Lecture:
What Is Computational Biology?
Download 'What Is Computational Biology?' [PPT]
RL
Oct 19 The PDB Pipeline
Lecture:
The way in which data are archived and distributed by the PDB will be described. Students will learn how to validate structures.
Download 'The PDB Pipeline ' lecture [PPT]

RCSB PDB Validation Tutorial: http://pdb-linux-37.rutgers.edu/validemo/index.html

Download 'Validation Tutorial' lecture [PPT]

HB
Validation Homework:
http://pdb-linux-37.rutgers.edu/validemo/jsp/mail/index.jsp

Oct. 24 Use of editing tools to describe protein structures
Lecture:
Introduction to the Molecular Anatomy Project development site.

Students will be introduced to the MAPdev editing and submission tools.

During this week students will sign up for 3-hour slots to finalize their papers on the assigned macromolecules
Sign Up Form: http://rcsb-class.rutgers.edu/cgi-bin/signup/index.cgi
All papers will be on Mapdev site. (http://mapdev.rutgers.edu)
SD
Oct.31 Calorimetry
DP
Project Homework Due:
All depositions on Nucleic Acids and Cytokines due in Mapdev
http://mapdev.rutgers.edu (See Project Information page for details)

Nov. 2 Enzyme Kinetics
Lecture:
Principles of enzyme kinetics, steady state kinetics, introduction to rapid mixing methods (rapid quench-flow and stopped-flow), analysis of pre-steady state kinetics, kinetics of ligand binding and determination of the kinetic pathway of enzymatic reactions reveals enzyme mechanisms.

Download 'Enzyme Kinetics Lecture 1' [PDF]
Download 'Enzyme Kinetics Lecture 1' [PPT]
SP
Nov. 7 Enzyme Kinetics cont'd
Download 'Enzyme Kinetics Lecture 2' [PDF]
Download 'Enzyme Kinetics Lecture 2' [PPT]
SP
Nov. 9 Enzyme Kinetics cont'd
Download 'Enzyme Kinetics Lecture 3' [PDF]
Download 'Enzyme Kinetics Lecture 3' [PPT]
SP
Nov. 14 Protein Ligand Interaction, Circular Dichroism

NG
Nov. 16 Enzyme Kinetics cont'd
Download 'Enzyme Kinetics Lecture 4' [PDF]
Download 'Enzyme Kinetics Lecture 4' [PPT]
SP