Module 1 Outline: Genomics
http://www.ornl.gov/hgmis/posters/chromosome/chooser.html
1. Describe projects, tips for teamwork, team assignments (HANDOUTS) 10 min
2. Discuss questions brought up (open-ended issue); ask for questions (5 min)
3. Human genome (bring chart)
What does it mean?
How does our genome compare to a genome of a bacterium? Of a tree? Of a
salmon?
What can we do with a genome sequence?
What ethical issues does it bring up?
Over the next 2.5 weeks, we are going to use the information learned over the past week
about DNA and information processing, to delve into these questions (advertise Jeff’s
class).
a. Show movie (10 min)
b. Go over human genome facts (10 min)
Human genome stats:
3 x 109bp
23 pairs of chromosomes
30,000 genes
variability between individuals: 0.05%
1.4 x 106 differences
chromosome—like a hard disk
c. In class exercise: how extract information from genome sequence? (10/10
min)
d. If all cells have all the DNA, why are skin cells different from heart or bone
cells? (only a subset of the genes are expressed in each cell; like in a computer, a
program uses only a subset of the files, many programs on one computer; like, in a
factory that has the ability to make Widget A for home use or Widget B for commercial
use, the demand for Widget A goes down, they shut down that part of the plant and gear
up to maek Widget B.)
BREAK (10min)
4. Why are there so many different kinds of organisms: bacteria, fungi, plants, fish,
birds, mammals, etc.? All linked by commonalities: cells, information processing
(DNA, RNA, protein).
a. Discussion of natural selection (10 min). Compare to market selection of
products. Design space for biology very broad—natural selection chooses the successful
designs (like a consumer chooses the successful product designs). Human as the engineer
does not sample the entire design space—we make choices based on experience, design
constraints, market research, consumer research, etc. Nature as the engineer uses a
random design process with a powerful selection process to choose only the most fit.
Why is this desirable? If conditions change (design constraints change), the random
process ensures that the maximum design space is represented so that 1 out of a 100
million possibilities can still be chosen by selection.
b) Illustrate with the moth color example in London.
5. How does change occur? (10min + exercise—20min)
a) Any change in what an organism can do or what it looks like must be a result
of changes in the DNA sequence
b) in class exercise: Mutation (10min/10min)
c) Many paths to DNA changes
1) Errors by DNA polymerase
2) Chemical harm/repair (errors)
3) Gene duplication
4) Genetic exchange
d) Most changes are detrimental; once a protein works, most changes will make
it work less well; those don’t compete well, diluted out of the population
e) Adaptation to changing conditions requires some DNA sequence variability
f) Evolution of properties is an inevitable consequence
g) No adaptation: like a design becoming obsolete; powerful market selection
6. End result is: we are our DNA sequence (genome sequence); all organisms are
related at the DNA sequence level if we look at genes (functions) in all organisms
a) less closely related, less similar DNA sequence
b) build a matrix of relatedness based on comparisons of DNA sequences
c) called a tree (branches)
d) tree of life: relates ribosome RNA sequences (HANDOUT)
e) result: most of the sequence divergence has occurred in the single-celled
world
Evolution is the result of billions of years of natural selection (10 min)
a) Earth formed ~4.5 bya
b) fossil record tells us single-celled organisms were first, then small multicelled
organisms, then more complex, not until very recently, plants and animals
c) first evidence of life (bacterial): ~3.8 bya
d) first eukaryotes (protozoans): ~1.3 bya
e) first complex organisms: ~0.9bya
f) plants: ~0.2bya
g) dinosaurs: 50-100mya
h) mammals: 20-50 mya
i) first humans: 1 mya
7. Info on the Lab: sequence mitochondrial DNA, strictly voluntary, can use an
anonymous sample;
[prey/predator relationships]
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Cell as the fundamental unit of life—size is restricted by its ability to perform
essential functions (e.g., nutrient transport and diffusion limited by “size” of
gradient)
Multicellular systems have systems for moving around fluids—pipe it—
engineering analogy of increasing the size or number of pipes to get chemicals
transported to a site, restrictions due to load limits, using multiple or stronger
pumps (some of these represent design alternatives in order to meet an
important function)
Analogy of a tree as a living system and how nature has designed a system
that allows a tree to be tall (e.g., so that they can reach their energy source).