Outlines

In this lesson you will outline a chapter which contains at least three sections with at least three paragraphs per section. Each paragraph must be identified by main topic and three supporting ideas must be included for each paragraph. The following example only has two sections. The first section has five paragraphs and the second section has four paragraphs. Three main points are provided for each paragraph.

For this assignment you will need to locate a biology text book. If you're lucky you will be currently enrolled in a biology course, otherwise you may need to get a book from your instructor (if he has one available) OR you will have to go to the library to locate one OR maybe you can borrow one from a biology teacher...

The sample is from Chapter 15 of Introduction to Protein Structure by Carl Branden and John Tooze. Only the introductory and first section of the chapter are outlined.
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Recognition of Foreign Molecules by the Immune System

1. Introduction
   1. Immune systems provide a defense mechanism against foreign parasites such as viruses and bacteria.
      1. Immune systems provide specific recognition of foreign molecules
      2. Immune systems have the ability to destroy foreign parasites
      3. Immune systems have a memory mechanism that allows a more rapid response to a second infection by the same microorganism
   2. Foreign invaders are recognized through specific and tight binding of the proteins of the immune system to molecules specific to the foreign organisms.
      1. The sites on foreign molecules that are recognized by the immune system are called antigenic determinants
      2. Antibodies, also known as immunoglobulins, are produced by B cells, which are stimulated by antigen binding to secrete antibodies into the bloodstream
      3. T-cell receptors, found on the surface of T cells, recognize and destroy virus-infected cells and play an important role in coordinating the immune response
   3. Antibodies secreted by B cells bind to foreign material (antigen) and serve as tags or identifiers for such material
      1. Antibody-tagged bacteria, pathogens, or other foreign objects are recognized and disposed of by macrophages and other effector cells in the immune system
      2. B cells rearrange the genes that code for their antibody proteins, so that each cell makes a unique antibody.
      3. B cells can display on their surface a membrane-bound form of their antibody
   4. T-cell receptors recognize antigenic determinants only when presented as part of a complex with MHC molecules
      1. MHC molecules fall into two classes: I and II
      2. These proteins are encoded by the major histocompatibility gene complex, a region of chromosome six (in humans) originally identified as the genetic element that controls transplant rejection
      3. Binding of a T-cell receptor to an MHC-antigen complex triggers activation of the T cell to kill the infected cell
   5. The three molecules directly involved in the specific recognition of antigen are immunoglobulins, the T-cell receptor, and the molecules of the MHC
      1. MHC proteins and T-cell receptors are cell surface proteins that occur naturally in low abundance
      2. The crystal structure of an immunoglobulin was solved long before the structure of the other two molecules and for this reason the structure shared by all three molecules is referred to as the immunoglobulin-like domain
      3. Structures have also been determined for soluble forms of MHC proteins and T-cell receptors
2. The Polypeptide Chains of Antibodies are Divided into Domains
   1. The basic structure of all immunoglobulin (Ig) molecules comprises two identical light chains and two identical heavy chains linked together by disulfide bonds
      1. There are two different classes, or isotypes, of light chains, lambda and kappa, but there is no known functional distinction between them
      2. Heavy chains have five different isotypes that divide the immunoglobulins into different functional classes: IgG, IgM, IgA, IgD, and IgE
      3. Each class of heavy chains can combine with either of the two different classes of light chains
   2. Immunoglobulins of the IgG class have the simplest structure
      1. Each chain of an IgG molecule is divided into domains of about 110 amino acid residues
      2. The light chains have two such domains
      3. The heavy chains have four such domains
   3. The amino-terminal domain of each IgG polypeptide chain is highly variable
      1. A light chain is built up from one amino-terminal variable domain (V_L) and one carboxyl-terminal constant domain (C_L)
      2. A heavy chain is built up from one amino-terminal variable domain (V_H), followed by three constant domains (C_H1, C_H2, C_H3)
      3. These differences are revealed by comparing the amino acid sequences from many different immunoglobulin (IgG) molecules
   4. The variable domains are not uniformly variable throughout their lengths
      1. There are three small regions that show much more variability than the rest of the domain - these are called the hypervariable regions or complementarity determining regions, CDR1 - CDR3
      2. The remaining parts of the variable domains have quite similar amino acid sequences
      3. All variable domains show significant overall sequence homology