Datasheet

 Finding all proteins that share a similar sequence (Chapter 7)

 Classifying proteins into families (Chapters 7, 8, and 9)

 Finding the best alignment between two or more proteins (Chapters 8

and 9)

 Finding evolutionary relationships between proteins, drawing proteins’

family trees (Chapters 7, 9, 11, and 13)

Analyzing DNA Sequences

During the 1950s, while scientists such as Kendrew and Perutz were still

struggling to determine the first 3-D structures of proteins, other biologists

had already acquired a lot of indirect evidence (via extremely clever genetics

experiments) that

deoxyribonucleic acid (DNA) — the stuff that makes up our

genes — was

also a large macromolecule. It was a long, chainlike molecule

twisted into a double helix, and each link in the chain was a pairing of two out

of four constituents called

nucleotides. (A nucleotide is made up of one phos-

phate group linked to a pentose sugar, which is itself linked to one of 4 types

of nitrogenous organic bases symbolized by the four letters A, C, G, and T.)

However, molecular biologists had to wait until much later — the 1970s, to be

more precise — before they could determine the sequence of DNA molecules

and get direct access to the sequences of gene nucleotides.

This was a revolution (earning A. Sanger his second Nobel Prize!) because the

small DNA sequence alphabet (4 nucleotides, as compared to 20 amino acids)

allowed a much simpler and faster reading — and quickly lent itself to complete

automation. Currently, the worldwide rate of determining DNA sequences is

faster (by orders of magnitude) than the rate of protein sequencing.

Reading DNA sequences the right way

As was the case for the 20 amino acids found in proteins, the 4 nucleotides

making DNA have different bodies but all have the same pair of hooks:

5' phosphoryl and 3' hydroxyl (pronounced five prime and three prime) by

reference to their positions in the deoxyribose sugar molecule, which is

part of the nucleotide chaining device. Figure 1-4 shows what free individual

nucleotides look like.

Forming a bond between the 5' and 3' positions of the constituent nucleotides

then makes the DNA molecule. Figure 1-5 shows a schematic representation

of the resulting DNA strand.

Chapter 1: Finding Out What Bioinformatics Can Do for You

05_089857 ch01.qxp 11/6/06 3:52 PM Page 17