The first section of the course focuses on the chemistry of DNA, the interaction of DNA with proteins, and the mechanisms by which the genetic material is copied.  The readings for each section are outlined below with links to the specific web pages.  There is also a link to the online review page for this exam, practice exam problems and their answers.

Exam I Review Page

Exam I Practice Problems: Exam 1 Practice.pdf

Exam I Practice Problem Answers: Exam 1 Practice Answers.pdf

Lecture 1: The Central Dogma

The Cold Spring Harbor DNA Learning Center has some amazing flash driven movies that capture the classic experiments in Molecular Biology better than any paper text could.  Go to their DNA Interactive Timeline and explore the multimedia history.  The individuals and experiments we discuss in class are all listed.  Start with Avery in the 40's and move through time to the 60's.  You do not have to explore topics that are not mentioned in class, but feel free to do so if the something catches your eye.

Animations and Movies:

A wonderful introduction to the big ideas in Molecular Biology and their impact on biology:

Lecture 2: DNA Structure and Chemistry

Readings:

• Molecular Cell Biology: DNA Structure
• Interactive Concepts in Biochemistry: DNA Structure (Click on the continue button at the bottom right for the best DNA structure tutorial I have seen)

Animations and Movies:

An animation that covers all of the major points of DNA structure

An animation that demonstrates the principles of Gel Electrophoresis

A second animation that discusses both Gel Electrophoresis and Blotting. There is a quiz at the end to test your understanding.

A clever animation showing how the length of DNA molecules affects their ability to move through a gel.

Hear about the discovery of DNA from Watson (Right) and Crick (Left)

Lecture 3: Protein-DNA Interactions

Readings:

• Molecular Biology of the Cell: Major and Minor Groove Contacts (Particularly Figure 7.7 and Figure 7.8, rest of section is a good overview of DNA Binding Domains)
• Interactive Concepts in Biochemistry: Protein Domains that bind DNA (Click on the continue button at the bottom right for the structure tutorial)
• Techniques: Gel Mobility Shift Assay

Lecture 4: DNA Topology and Nucleosomes

Readings:

Biochemistry: Topology

Molecular Cell Biology: Topoisomerase I and II Mechanisms

Animations and Movies:

Two animations which demonstrate how DNA is wrapped around nucleosomes with the cell's nucleus.  Only the beginning of the second movie is relevant to our discussion of nucleosomes.

Lecture 5: DNA Replication I (The Replication Fork)

Readings:

• Molecular Biology of the Cell: DNA Replication Mechanisms
• Biochemistry: Chemistry of Nucleotide Addition

Animations and Movies:

Different pieces of the replication machinery:

The Biochemitsry of DNA polymerase's Enzymatic Activity: DNA_polymerase.mov 

The Biochemical Activity of the Helicase: Helicase Animation

The structure of the sliding clamp: Sliding_clamp.mov

Loading the Sliding Clamp: Animation

Putting the steps together:

A step-by-step review of the basic steps created by Dr. Richard Losick at Harvard.

Animation of the Basic Replication Mechanism

The following two movies provide two different perspectives on the repliation process.  The first movie is a cartoon animation that reviews all of the important proteins and their functions during the replication of the leading and lagging strands.  The second movie uses the three dimensional crystal structures of all the proteins to recreate a more true to life real-time view of the replication fork.