This lecture is about ways of looking at DNA sequences in complete genomes and chromosomes, in terms of symmetry elements. There are two parts to this talk. In Part 1, I will discuss the fact that we simply have "Too Much Information" becoming available, and the problem will only get worse in the near future. There are ways of cataloging and organising the data, of course. I have found that the true diversity of genome sizes in Nature is often neglected, so we'll talk for a few minutes about the "C-value paradox", along with some possible ideas for WHY certain organisms have so much DNA.
I would like to think that one way of dealing with the explosion of sequence information, in terms of DNA sequences, is to think about it in biological terms, in particular in physical-chemical terms of structure and function of symmetry elements. For example, there are specific DNA sequences which "code" for a telomere, and different DNA sequences which are specific for centromeres. Specific DNA sequences, their structures, and biological functions will be discussed.
I have also made a separate file, containing specific LEARNING OBJECTIVES for this lecture, as well as a "self-test quiz", which I recommend having a look at, BEFORE the lecture, if possible. I've incorporated the answers to questions 1 and 2 into PART 1 of the lecture notes.
Part 1: The Problem: Too Much Information
and Too Many TLA's
Brevis esse laboro, Obscuro fio. - Horace
Some philosophical thoughts about Information and the Size of Genomes.
The information in GenBank is doubling every107 months.
What are the implications of this?
A look at genome sequencing over the past five years:
| YEAR | # GENOMES Sequenced |
| 1995 | |
| 1996 | |
| 1997 | |
| 1998 | |
| 1999 | |
| 2000 |
The "C-value" paradox"
Although the number of genomes being sequenced is increasing rapidly, one has to this into perspective - the genomes of organisms fall very roughly into four different classes:
| Organism group | Size (bp) | No. sequenced |
| viruses | ~1000 bp - 70,000 bp | 534 |
| bacteria | ~500,000 - 8,000,000 bp | 30 |
| "simple" eukaryotes |
~12,000,000 - 270,000,000 bp | 2 |
| "complex" eukaryotes most animals and some plants |
~700,000,000 - ~10,000,000,000 bp |
0 |
| "other" eukaryotes plants and amoeba |
~10,000,000,000 - 670,000,000,000 bp | 0 |
Discussion
Why does amoeba have more than 200x as much DNA as humans?
Think about it for a discussion in class. I have a possible explanation, although I'm not sure anyone really knows the answer to this, to be honest.
This brings us to the first question on the quiz:
Answers to the self-test quiz which you are supposed to do BEFORE the lecture:
1. The short answer - a very long time. About 2.4x1012 years.
That's about 160 times longer than the estimated age of the universe!
2. The piece of paper would be quite thick - it would reach outside the earth's
atmosphere and beyond the orbit of the planet Mars.
Part 2: DNA Symmetry Elements and DNA Structures
Today's lecture will cover:
Next Tuesday's lecture will cover:
A "Z-DNA" Atlas for Leishmania major, chromosome 4
Link to more atlases for Leishmania major chromosomes
A "DNA repeats" Atlas for Escherichia coli, pO157
Friday (10 November, 2000)
Link to a list of recent papers and talks on DNA structures.
Sinden,R.R., Pearson,C.E., Potaman,V.N., Ussery,D.W., "DNA: STRUCTURE and FUNCTION", Advances in Genome Biology, 5A:1-141, (1998).
Calladine,C.R., Drew,H.R., "Understanding DNA: The Molecule and How It Works", (2nd edition, Academic Press, San Diego, 1997).
A List of more than a thousand books about DNA
Last modified Thursday, 9 November, 2000 by David Ussery
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