Introduction to Bioinformatics: CMSC54610-1, Spring quarter 2006.

Lecture 1 Overview and book review

Our text:

Fundamental Concepts of Bioinformatics (Paperback)

by Dan E. Krane, Michael L. Raymer

• Amazon offers a small discount
• but there are also used copies that are cheaper.

• Missing from the text is the periodic table showing the essential elements
• from a chemistry web site with lots more information available

• The Genetic Material
  • The structure of DNA is based on the nitrogenous bases
  • and the deoxyribose sugar
  • come together to form, e.g., dA deoxyribose sugar (see Figure 1.1 in the text)
  • Two DNA subunits merge to form a phosphodiester bond (see Figure 1.2 in the text)
  • The structure of hydrogen bonds in DNA and RNA shows how A-T and C-G are complementary (see Figure 1.3 in the text)
  • The DNA subunits stack and twist to form
  • the 3-D structure of DNA. Color code: G (green), C (red), A (yellow), T (blue)
• Gene Structure and Information Content
  • Promoters turn on protein creation
  • Genetic code: how do 64 things describe 20 things? Or is it twenty-one? See this paper for more information on the amino acid selenocystein (SeC).
  • Open reading frames (ORFs), introns, exons and splicing
  • Excellent opportunity for automatic detection by various means [special lecture] including computational linguistics
• Protein Structure and Function
  • Primary structure: sequence
  • Secondary structure: helices and sheets (and parallel side chains) is discussed in several places
  • Tertiary structure: the protein folding problem [special lecture]
  • Quaternary structure: protein-protein interactions
• Nature of chemical bonds
  • Hydrogen bonds are dominant in nature and come from lone pairs of negative charge.
  • Water is the best maker of hydrogen bonds
  • Some hydrogen bonds are vulnerable to water if they are not protected by hydrophobic groups. These hydrogen bonds benefit by attachment of a third party.
  • Hydrophilicity and Hydrophobicity
• Molecular Biology Tools (please read)
• Genomic information content
  • The C-value paradox and increasing interactivity

• Homework problems: 1.2, 1.5, 1.6, 1.7, 1.9, 1.10 in the text
• Homework is due by the beginning of the next class.
  • Preferred: Homework should be turned in physically before the start of the class
  • Emergency: send it to me electronically in standard formats.