HHMI Notes

1. Basic Genetics
1. A human cell all cells (except red blood cells) contain the entire human
genome all the genetic information necessary to build a human being.
Information is encoded in 6 billion base pairs of DNA; egg and sperm cells contain
3 billion base pairs of DNA
2. Cell nucleus 6 feet of DNA are packaged into 23 pairs of chromosomes
3. Chromosome each of the 46 human chromosomes contains the DNA for
thousands of individual genes, the units of heredity
4. Gene each gene is a segment of double-stranded DNA that holds the recipe
for making a specific molecule
5. Protein essential components of all organisms and chemical activities
2. The Yeast Genome
1. Instructions were spelled out in 12 million base pairs, or subunits, of DNA
encoding ~6,000 genes
2. Simpler organisms can be grown rapidly, and their genes can be mutated at will
1. This quality is essential since mutations that stop a particular gene from
functioning make it possible to figure out what the genes function is
3. In 1985, Michael Wigler rescued a mutant yeast cell that lacked an essential
developmental gene, the yeast equivalent of the human Ras gene, by inserting
the human gene into it
4. The genes that regulate growth and development cycles in yeast are almost
identical to the human cell cycle
3. The Microarray
1. A microarray is a robot whose pointed tip can deliver up to 20,000 bits of DNA,
each representing a different gene, to specific spots on microscope slides
1. Printed DNA strands remain fixed on the slides
2. When samples of fluorescently tagged DNA made from a cells active genes are
washed over the glass slides, any sample that complements a fixed strand of DNA
that will stick to it, making it glow
1. The location of the glowing spots reveals which genes are active in the cell
at the time
3. This method works because the tagged DNA is a copy of mRNA, which is
produced only when a gene is expressed and actively making protein
4. Glowing spots represent only the genes that are turned on in the cell at the
moment
5. This technique enables researchers to compare the activity of genes in 2
different cells simplify by tagging their DNA with 2 different types of fluorescent
dye
6. The brighter green a dot glows, the higher level of expression of a gene from the
cell whose DNA is labeled green
7. The brighter red, the lower that genes level of expression compared to an
identical gene from the other cell
8. When 2 genes are expressed to the same extents, dots glow in yellow
9. Scientists can see the activity of genes in different cells or at different times by
examining color pattern
4. The Sexual Development of Yeast
1. Yeast comes in two mating types a and alpha along with a slightly larger
diploid cell that carries both a and alpha

2. When a diploid cell runs out of food, it morphs into spores of the 2 different
mating types, which remain enclosed in a tough shell
3. Spores then burst and look for mates to fuse together with
4. Yeasts development is similar to the development of human sperm and eggs
1. Egg or sperm cells carry only one copy of the genome
2. Diploid cells have to go through meiosis
5. It was found that more than 1,000 yeast genes showed changes in mRNA levels
during sporulation
5. Guilt By Association
1. Guilt by association we can guess their function based on the fact that
other genes whose function we do know are turned on at the same time
2. Genes tend to expressed when their products have important roles to play
3. Assumptions was tested in yeast
1. Knocking out the gene revealed the function
6. Breast Cancer
1. Studying the characteristics of different kinds of cancer cells allows precise
therapy
1. You can do clinical trails in which you treat people who have exactly the
same disease
2. DNA chips made by Affymetric use the technique, photolithography; each chip
is a square of glass on which thousands of short filaments of DNA have been
imprinted
1. DNA filaments are synthesized from labs and represent known DNA
sequences
3. Liquid that contains chopped up genes or mRNA is poured over the chip and bits
of genetic material complement the synthetic filament on the chip, making it glow
4. A scanner then reads the pattern
7. Spreading the Benefits
1. Pat Brown posted a DIY genome analysis; it provides a list of necessary
materials for a microarray and showers where to order parts and explains how to
put it together
2. Printing a microarray that contains the yeast genome is only $10
3. Being able to do experiments with microarrays is the main benefit of having
genome sequences
8. Building Microarrayers
1. Pat Brown and Joseph DeRisi helped a program that would build DNA
microarrayers form spare parts
2. They brought a container of yeast genomic DNA so that the scientists could
make multiple copies of it and learn how to print it onto class microscope slides in
the arrayers
3. Scientists then installed the microscope slides and assembled the printing
robots, each with 16 vertical, sharp tipped pins that would deliver DNA spots to
precise locations on the slides
4. The 16 pins would be dunked into a cleaning solution and dried before picking
up new DNA
5. The pins would move to a slightly different position over the glass slides and,
acting like the tips of fountain pens, the pins would deposit small, measured
volumes of the new DNA onto new spots
6. Students performed experiments by washing out samples of DNA over the
printed spots on the glass slides to see where the DNA would bind

1. Binding indicated that a certain gene was expressed in the cell that
provided the samples
7. They learned how to measure and interpret these differences, using a special
scanner for measurement
8. The hope is to identify the genes by comparing levels of gene expression in
normal and diabetic mice and to identify the genes pathways
9. This is used to study the mechanisms of memory, breast cancer, leukemia, and
the cell division cycle
9. More on Yeast
1. Yeast can make bread rise, produce wine when added to squashed grapes, and
cause beer to foam
1. They produce fermentation bubbles the bubbles that cause dough to
rise/beer to foam
2. Yeast is easy to grow it doubles every 90 minutes when food is available, and
billions can fit in petri dishes
3. They are alive (until heat kills them), can transmit signals from cells surface to
its nucleus, manufacture thousands of proteins, create cellular scaffolding, repair
DNA in the nucleus, etc.
4. It is the best model organism for studies of anything that does on inside a cell
5. You can stitch bits of DNA from a normal yeast cell onto a plasmid, the plasmid
will carry this DNA into a mutant yeast cell, and the normal yeast gene will replace
the mutant one at precisely the right place
6. Yeast genes have very few introns that interrupt the coding sequences of
mammalian genes
1. This makes it easy to recognize where the genes are in yeast and what
their boundaries are
2. 70% of the yeast genome codes for protein
7. They produce nearly identical proteins
10. Yeasts Cell-Division Cycle
1. Abnormal yeast cells stop growing while their food supply is plentiful
2. Leland Hartwell studied the basic cycle through which a cell grows and divides
into 2 daughter cells
1. He used the cells of bakers yeast which never grow bigger than they are
at maturity
2. A little knob, or bud, starts to protrude from the cells surface, breaking its
symmetry as the cell enters its reproductive cycle. Bud grows larger and
later splits off
3. Any mutation that affects cell division makes the bud stop growing
4. The bigger the bud when growth stops, the father the cell had progressed
along the division cycle
5. Cells whose buds stop at different sizes have mutations that affect
different stages of the cell cycle
3. Hartwell used this bud size as a guide to identify the first mutant gene, cdc or
cell division cycle mutant, which was responsible for blocking the cell cycle
4. These human genes turned out to play a crucial role in the development of
cancer