Biology 2581B Study Guide - Final Guide: Peptide, Genetic Linkage, Penetrance

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26 Jan 2013

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Genetics Study Notes
DNA, the Molecule of Heredity and Biological Information
INFORMATION: is “that which reduces uncertainty”
How do you quantify information?
Uncertainty = log2(M), where M is the # of possible symbols. Maximum information
content of any sequence = L[log2(M)], where L is the length of the sequence
- For DNA: 4 possible symbols A,G,C, or T
- Uncertainty= log2(4) =2 bits
- Bits is the unit for information
How DNA was experimentally shown to carry information
Goal: figure out what in the cellular debris was actually conveying the message
- First they showed that this whole system was independent of the mouse. Could
do the same thing in vitro.
- Started purifying cellular debris into different components DNA, protein and,
- Found it was the DNA component that could transform cells to S form.
- Some scientists were skeptics, and said it wasn’t purified. And therefore they
couldn’t know for sure.
- Used enzymes to destroy certain components.
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DNA is the Genetic Material
What was the phage injecting? DNA or protein?
- Two experiments
- 1. Take phage, infect E.coli, grow them in media that has radioactive P,
- 2. Same thing, but phages labeled with radioactive S.
- Why P-32 and S-35?
- P is found in DNA, not protein, Sulfur is found in protein but NOT DNA.
- 1. Infect E.coli- create new phage. DNA is labeled. Radioactivity was not
associated with the ghosts. It was found inside the cells. Phage are introducing
DNA into the cell…
- 2. Same routine- this time radioactivity is associated with ghosts and not
The Eukaryotic Chromosome
Grooves (major and minor) are as a result of the geometry of the base pairings.
o The angle between the glycosidic bonds of the minor groove is 120
degrees. The angle between the glycosidic bonds of the major groove is
240 degrees.
B-DNA represents only one possible conformation that a DNA double helix can
Other forms of DNA also exist e.g. A-DNA. However, they do not form under
physiological conditions and are thus not biologically relevant. Only B and Z are
physiologically relevant.
Biological Function of Z-DNA
The Biological role of Z-DNA remains mysterious, but some evidence suggests
that Z-DNA may have a functional role within cells:
o Z-DNA is formed transiently in association with transcription
o Several proteins identified with highly specific Z-DNA binding activities
e.g. Vaccinia virus E3L protein: essential for virulence
o Antibodies to Z-DNA bind transcriptionally active regions
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Flexibility in helical structure
A crucial property of the double helix is its ability to separate the two strands
without disrupting covalent bonds. This makes it possible for the strands to
separate and reform under physiological conditions.
o This is important for the processes of DNA replication, transcription, and
also for DNA repair mechanisms.
Base Flipping
o Enzymes involved DNA repair may scan for DNA lesions by flipping out
Flexibility in DNA Organization
Linear, circular, single stranded or double stranded. Lots of variety.
Flexibility in DNA Topology
Topology: 3d organization of a molecule in space.
Topologically constrained: if you were to denature the strands, you wouldn’t be
able to separate strands- they are interwoven
No Topological Constraint: If you denature the strands you could separate
For a constrained double helix, torsional stress introduces… supercoiling
DNA does (-) supercoiling, makes it more compact
Supercoiling can be induced if the DNA molecule is underwound before the circle
is made.
This destabilizes the helix (260 bp/23 turns= 11.3 bp/turn).
There are now two ways to stabilize the DNA molecule: 1) partially separate the
strands, or 2) introduce supercoils.
Why do Living Cells store DNA with Negative Superhelicity?
Many advantages in storing energy in this way
Can be called on when needed for processes that require strand separation e.g.
DNA replication, transcription
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