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It’s better to have pictures
Genomics
Gregor Mendel figured out how the inheritance of traits worked by conducting experiments
with pea plants in the 1850s. But his work was ignored during his lifetime, until his principles
were re-discovered in the 1920s. Even though geneticists had a pretty good idea of the “rules”
governing inheritance, they still did not understand the physical mechanisms that actually
transmitted traits from one generation to another.
Geneticists and biochemists continued to make advances in their understandings of evolution
in the early 20th Century, but it was a piecemeal process . . .
1888 – Theodor Bovari notes that when you damage the chromosomes of a cell, that cell
becomes unable to reproduce.
1910 – Thomas Hunt Morgan verifies that chromosomes are the sites of genetic inheritance.
1944 – Oswald Avery and his colleagues confirm that of all the proteins and acids present in
chromosomes, it is DNA that encodes variations.
1953 – Francis Crick, James Watson, Maurice Wilkins, Rosalind Franklin, and Raymond
Gosling, discover the structure of DNA.
DNA and RNA are the molecules that are the physical vehicles for the inheritance of
variations in living things on our planet.
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Biological Anthropology Lab – DA Solomon
A. Get the Kids!: DNA Extraction in Your Own Kitchen EXTRA CREDIT
Pictured above is a plant cell (left) and an animal cell (right). All living things are made of cells,
and cells vary considerably across plants, animals, bacteria, fungus, and other living things.
But there are some important similarities.
Organelles are the tiny “organs” that make up the “body” of a cells. They are not actual
organs (which are made of millions of cells), but molecular machinery that functions inside the
cell as organs function in the body. You will notice that both the cells pictured have an
organelle called a nucleus. Inside the nucleus of the cells, there are even smaller organelles
known as chromosomes, which are made of bundles of DNA. In order to extract the DNA,
we must break apart the cells and the nucleus.
1. You’ll need a few things, so get ready. First you need a banana, but avocado, strawberries,
or kiwi might be used. Next, identify a jar or glass for you to use in extracting the DNA. It
should be about between one-half and 1 liter, smaller for a half-banana. It needs to be very
clean. You’ll also need a blender. If you don’t have a blender, don’t have any friends with
blenders, and don’t want to invest in a blender, then I have two suggestions, both
experimental. You might try beating the fruit into a puree the old fashioned way with a mixer or
patience and a mixing bowl, or you could buy a jar of all-natural banana flavored baby food. I
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suggest Earth’s Best Organic First bananas because it’s almost only bananas and water.
You’ll need to have some dish soap on hand too. A strainer or cheesecloth will be useful.
Read the questions before you carry out your DNA extraction – this is the data you should
keep track of as you carry out your experiment.
2. Cut your fruit into small pieces, drop it all in a blender, and add enough warm (not cold)
water to completely cover all the fruit pieces. Measure your water for reporting purposes, if
you can. Blend it until it is smooth and easily pourable. This will break apart the larger
structures of the fruit and prepare the cells to be broken down further in step 4.
3. Pour your puree through the strainer or cheesecloth, and into the jar or glass. Try to get all
the big chunks out. You want to have produced a fluid that is not too much thicker than water.
4. Add 1-2 teaspoons of dish soap to the puree, and gently stir it in. Do not stir fast enough to
make bubbles, just mix everything gently together. The soap will break down the cell walls,
releasing cell contents into the solution.
5. Once the soap is mixed into the fruit puree, pour rubbing alcohol very carefully down the
side of the jar onto the mixture. Your goal here is to pour the alcohol onto the top of the
mixture – you should not make any splashes, and the alcohol should not drop into the fruit-
soap-water solution fast enough to break the surface. Ideally, the lighter alcohol will sit in an
undisturbed layer on top of the fruit puree.
6. At this point, you may watch as the DNA that you have released from the banana cells
precipitates upward into the alcohol over a period of minutes, or you may continue on to the
next activity in today’s lab. In a few minutes you will see that a cloudy, milky substance has
accumulated in the alcohol. This is the actual DNA from the banana, which as it turns out
forms strands on the visible mechanical level as well as the molecular. If you have done this
right, you will be able to use a toothpick or paper clip to pull a strand of accumulated DNA out
of the solution.
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This is not a very exact process, but it is virtually the same as what scientists in laboratories
do to extract DNA.
Don’t expect it all to work out perfectly!
Prepare an account of your effort, and post it to the DNA extraction discussion forum. If you
have a smart phone or a computer with a camera, you should include a photograph of the
final product. Make sure your written account answers the following questions:
1) What kind/size jar or glass did you use?
2) What kind of fruit did you use?
3) Roughly how much fruit did you use?
4) How much water?
5) What did you use to make the puree?
6) What did you use to strain it?
7) How much fruit solution did you produce (roughly)?
8) What problems did you run into? What didn’t work out?
9) What did the DNA precipitate look like? How much did you produce?
B. The genetic code.
You probably already know that “the genetic code” can be represented as a series of four
letters, A, G, T, and C. But what does this mean?
DNA (deoxyribonucleic acid) is a double helix, which is like a spiraling ladder shape. Like a
ladder, it is composed of two long backbones which are connected by a series of rungs. The
backbones of the ladder are composed of sugar molecules and phosphate molecules. The
rungs of the ladder are composed of molecules called nucleotides. They come in four
flavors: Adenine, Guanine, Cytosine, and Thymine. These are the “letters” in the genetic
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code.
Another molecule that works alongside DNA is RNA (ribonucleic acid). RNA is extremely
similar to DNA. For our purposes, there is one important difference. In RNA, Thymine is
replaced by Uracil, represented by the letter U.
The nucleotides in RNA (AGUC) and DNA (AGTC) occur in sets of three. These sets are
known as codons. A codon is like a three-letter word spelled with nucleotides. We say that
these four molecules make up a genetic “code” because they are literally the physical
blueprints from which our bodies are built. Just as patterns of ink on paper or patterns of
vibrations in the air can transmit information between people (in the form of language),
codons are molecular words that cells translate into the proteins from which our bodies are
made. There are sixty-four possible codons (combinations of A,G,C, and T/U).
As a cell begins to divide, the DNA in the nucleus of the cell unzips along its rungs. Each half
of the DNA ladder is copied into an RNA format known as mRNA or “messenger RNA.” Later,
the codons of mRNA are captured by an organelle called a ribosome and matched to a
different kind of RNA known as tRNA. Unlike DNA and mRNA, which occur in long strings,
tRNA molecules are only one codon long each. Each molecule of tRNA is attached to one of
twenty kinds of amino acid. In a process called protein synthesis, the sixty-four possible
codons of DNA/mRNA are matched with tRNA molecules until the amino acids that the tRNA
molecules carry are strung together into protein chains. These chains are the materials from
which living cells are made.
Finally, some codons translate into “commands” to the cell’s machinery to “STOP READING.”
This way cells know when to begin and end the process of building proteins.
This is quite complicated, and we will discuss protein synthesis next week. Next week we’re
going to go into depth about the biological processes that take us from DNA to bodies, but
today we’re just going to play with the “code.” What you need to know:
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a) DNA’s code (AGTC) transcribes into mRNA’s code (AGUC).
b) mRNA’s code (AGUC) translates into tRNA’s code (AGUC).
c) tRNA translates into amino acids.
You should also take note of which nucleotides match.
Adenine copies into Uracil A –> U
Guanine copies into Cytosine G –> C
Cytosine copies into Guanine C –> G
Thymine and Uracil copy into Adenine T and U –> A
C. Mapping the Human Genome
The discovery of DNA’s double helix structure in 1956 was momentous because it
represented a step towards more precise, more far-reaching manipulation of evolutionary
forces than had ever been achieved by thousands of years of careful animal and plant
breeding. However, with greater understanding of these mechanisms also came the
realization that the DNA of humans and other organisms has the potential to be quite large
and complex. It took further innovations in statistical analysis, imaging technology, and
biochemistry before it became possible to effectively map genomes in such a way that would
allow scientists to correlate phenotypic outcomes with genotypic sequences. In the 1990s and
2000s, there were two main efforts to map the human genome, The Human Genome Project
and Celera Genomics.
Human Genome Project Celera Genomics
began 1989 began 1998
cost US taxpayers $3 billion cost private funders $300 million
international effort headed by the United private project headed by genomics mogul
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States National Institutes of Health Craig Venter
partial draft in 2000 ?
complete draft in 2002 complete draft in 2002
the work was done at universities like UCSC work done in corporate laboratories
developed their own techniques used HGP techniques + shotgun sequencing
created all original data used HGP data for its drafts
made complete human genome publicly
available for free at UCSC’s Genome
Browser
released some of its data for free; kept most
of it secret; lobbies for the right to copyright
genetic sequences
Celera completed its draft of the human genome first, less expensively, and faster than the
government project. There are some obvious reasons for this, given in the above chart, but
some of Celera’s success was also due to innovative genetic sampling techniques devised by
Craig Venter, notably “shotgun sequencing,” which allowed larger sequences of DNA to be
mapped simultaneously. Yet, they did make use of the HGP’s freely available data, and
despite this they have reserved the right to keep most of their results private so that they may
profit from their work.
Now that “the” human genome has been mapped, scientists are working to understand where
the “genes” are. That is, research is now focused on trying to identify what everything does!
One basic purpose to which our new knowledge of the human genome has already been put
is towards reconstructing evolutionary relationships. Through various DNA sequencing
techniques, researchers may analyze genomic sequences for homologies on the genetic
level, which may be useful in reconstructing evolutionary relationships. (If you have the
Human Evolution Coloring Book, refer to plate 2-7 for more.)
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