A program of ITEST (Information Technology
Experiences for Students and Teachers) funded
by the National Science Foundation
Background Session #1
May 3, 2008
Henrik Kibak
Associate Professor of Biology
California State University, Monterey Bay
Nucleic Acid Structure
Review
 Laboratory techniques we will use this
summer:
Purification of DNA from tissue
Polymerase Chain Reaction
DNA sequencing
 Analytical techniques we will use this
summer:
Obtaining DNA sequence from chromatographic
traces
Multiple sequence alignment
Preparing phylogenetic trees from alignments
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DNA & RNA are the two
important nucleic acids in cells
 Chromosomes carry the genetic information
and are composed of DeoxyriboNucleic Acid
 Many important structural molecules in cells
such as the Ribosome and the Signal
Recognition Particle are composed of
RiboNucleic Acid
 Information carriers such as tRNA and
mRNA are also composed of ribonucleic acid
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Nucleotides are the building
blocks of nucleic acids.
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RNA & DNA are polymers of
ribonucleotides or deoxyribonucleotides
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Nucleic Acids have
directionality.
We say, “5’ to 3’ direction,”
because the chains can only
polymerize by adding new
nucleotides to a 3’ hydroxyl.
This concept is very important
for the experiments we will do
this summer!
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 CHECK YOUR UNDERSTANDING
Nucleotides are monomers that consist of a
sugar, a phosphate group, and a nitrogencontaining base.
Nucleotides polymerize to form nucleic acids
through formation of phosphodiester linkages
between the 3' carbon on one nucleotide and
the 5' carbon on another.
You should be able to draw a simplified cartoon
of a nucleotide and a cartoon version of two
nucleotides joined by a phosphodiester
linkage…
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Whereas the sugarphosphate backbone
is a covalent linkage,
the base-pairing in
the double helix is
only hydrogen
bonding.
This is another
important concept
for our research this
summer.
Because hydrogen
bonding is weaker,
DNA strands can
“melt” apart and reanneal, simply by
heating and cooling.
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The pairs of bases form
a “base sequence” or
sequence of nucleotides.
Because each strand is
complementary to the
other, if you know one
sequence of bases, you
also know the other.
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Animated Lectures
 To complete your homework, we have
provided three animated lectures:
 http://marinebiotech.net/workshop/bioinformatics/May_sessions.html
DNA Structure Review –
You will need to do the
interactive exercise at the end of this lecture in order to
complete your homework assignment.
The Cell Cycle –
You will only need to review the first
section of this lecture for your assignment.
DNA Replication –
You will only need to review the first
section of this lecture for your assignment.
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Animated Lectures
Pause
and Play
frequently
to get the
full
benefit of
these
animated
lectures.
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