Supplemental Material for Bio 401/501

Nucleic Acids

Fall 2010

 

Readings

A partial list of literature that will be discussed in class is given here

Homework/Problem Sets

Nucleic Acids

Problem Set

Homework I  Answers

Homework II Answers

Homework III Answers

Homework IV Answers

1998 Exam Questions 1 & 2

Enzyme Kinetics

Problem Set 1 (Lectures 1-3) Answers (Corrected for log error)

           Problem Set 2          "  Answers

               Extra Homework Problem (CORRECTED!)Solution
           Problem Set 3 (Lectures 4 & 5) Answers
       Problem Set 4 (Lectures 5 & 6) Answers

 

 


Structural Biology Links

Much of the Nucleic Acids section of the course is based on analysis of how structure determines function. It is helpful for students in the class to develop the skills of analyzing structural data.


 


Simple Molecular Structure Viewers

1. A simple program that I will use for some of the class presentation is called Kinemages.

Kinemage can be also be obtained for free for the MAC, PC or UNIX systems for use on your home computer. Download Kinemage here. Instructions for using Kinemage are here.

The individual images that I use in the Bio 401/501 class can be downloaded here.

NOTE: TWO ADDITIONAL  KINEMAGEStRNA

-PHE and Nucleosome

 

 

2. A free, small, useful (but somewhat cumbersome) program for viewing images from the PDB directly is called ProteinExplorer (requires a helper application call CHIME).

 

 

3. For those with more disk space, the DS_ViewerProviewer program can also be used to view PDB files directly.

 

 

Data Depositories and Other On-line Resources

The US repository for all structural data is the Protein Data Bank(PDB) at the Research Collaboratory for Structural Bioinformatics (RCSB) at Rutgers and the San Diego Supercomputer Center.

The repository for data and tools specific to the analysis of the structures of nucleic acids and complexes of nucleic acids with drugs and proteins is the Nucleic Acids Database (NDB)

For those who are interested in a protein structure self-study course, there is a very good on-line one given by Birkbeck College in the UK. This course uses technology similar to that used in the courses I teach. The link to that course is here

A general biochemistry website that collects a number of useful links is here