Lecture 1 Basics of Molecular Biology January 4 , 2000 Notes :

We begin with a review of the basic molecules responsible for the functioning of all organisms' cells. Much of the material here comes from the introductory textbooks by Drlica [2], Lewin [4], and Watson et al. [8]. Later in the course, when we discuss the computational aspects of molecular biology, some useful textbooks will be those by Gusfield [3], Salzberg et al. What sorts of molecules perform the required functions of the cells of organisms? Cells have a basic tension in the roles they need those molecules to fulfill: 1. The molecules must perform the wide variety of chemical reactions necessary for life. To perform these reactions, cells need diverse three-dimensional structures of interacting molecules. 2. The molecules must pass on the instructions for creating their constitutive components to their descendents. For this purpose, a simple one-dimensional information storage medium is the most effective. We will see that proteins provide the three-dimensional diversity required by the first role, and DNA provides the one-dimensional information storage required by the second. Another cellular molecule, RNA, is an intermediary between DNA and proteins, and plays some of each of these two roles. Proteins have a variety of roles that they must fulfill: 1. They are the enzymes that rearrange chemical bonds. 2. They carry signals to and from the outside of the cell, and within the cell. 3. They transport small molecules. 4. They form many of the cellular structures. 5. They regulate cell processes, turning them on and off and controlling their rates. This variety of roles is accomplished by the variety of proteins, which collectively can assume a variety of three-dimensional shapes. A protein's three-dimensional shape, in turn, is determined by the particular one-dimensional composition of the protein. Each protein is a linear sequence made of smaller constituent molecules called amino