Bioinformatics Workshop Journal

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Bioinformatics Journal Chasity Watt June 21 -25,
2004
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• DNA-The Molecule of Life

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DNA is short for deoxyribose nucleic acidThe
structure of DNA is a double helix. The outsides
of the molecule are made of deoxyribose sugars
alternating with phosphates. This part of the
molecule is sometimes called the "backbone". Note
that the strands run in opposite directions (this
is indicated by the 3-prime (3') and 5-prime (5')
notation), and are sometimes referred to as
"anti-parallel".
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DNA UP CLOSE
The inside of the molecule, the "steps" of the
staircase, are made of the nucleotide bases
Cytosine, Guanine, Adenine, and Thymine. C bonds
to G by three hydrogen bonds. A bonds to T by two
hydrogen bonds. A and G are double ringed
structures called "purines". C and T are single
ringed structures called "pyramidines". These
nucleotide bases are the information carrying
part of the molecule, and it is the differences
in the repeating sequence of Cs, Gs, As and Ts
that make us all unique.
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The human genome is the collective name for all
of the genes in the human body. The structure of
DNA was first described in 1953. Every cell in
the human body contains a copy of the genome, a
DNA blueprint which specifies how the cell was
built, how it will function and how it might
divide to produce a new, daughter cell.
Scientists from around the world are working
together on the human genome project, to get and
analyse the entire DNA sequence of the human
cell. With the entire DNA sequence available, it
will be possible to crack the DNA code and reveal
its secrets. We will have an understanding of how
healthy cells work, and how diseases can take
hold.
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Ethical, Legal, and Social Concerns about DNA
Databanking The primary concern is privacy. DNA
profiles are different from fingerprints, which
are useful only for identification. DNA can
provide insights into many intimate aspects of a
person and their families including
susceptibility to particular diseases, legitimacy
of birth, and perhaps predispositions to certain
behaviors and sexual orientation. This increases
the potential for genetic discrimination by
government, insurers, employers, schools, banks,
and others. Collected samples are stored, and
many state laws do not require the destruction of
a DNA record or sample after a conviction has
been overturned. So there is a chance that a
person's entire genome may be available
--criminal or otherwise..
Although the DNA used is considered "junk DNA"
(STRs-single tandem repeated DNA bases), in the
future this information may be found to reveal
personal information such as susceptibilities to
disease and certain behaviors
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Genetically Engineered Crops ---Very Controversial
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Ted Kisha Western Regional Plant Introduction
Station
Part of the National Plant Germplasm System whose
goal is to preserve the genetic diversity of
plants. The mission of the Western Regional Plant
Introduction Station (WRPIS) at Pullman,
Washington is to maintain the diversity and the
accessibility of plant germplasm resources.
Current trends indicate that diversification by
the agricultural and industrial communities will
benefit both producers and consumers. Reasons for
diversification include growing interest in
crops that are less demanding on renewable
resources crop diversification may reduce
farmer's financial risk growing interest in
alternative and sustainable agricultural systems
demands for new and exotic varieties of food from
consumers plants can supply raw materials for
industry. The agronomic community is encouraging
diversification by the growth and development of
new crops.
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Polymerase Chain Reaction
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Enzymes restricted entry of foreign DNA Cleaved
DNA at specific sequence Polymorphism could
arise through point mutation , insertion,
deletion, or inversion. Detected by probing a
known sequence of DNA with a labeled sequence
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AFLP (Amplified Fragment length
Polymorphism) AFLP is a highly sensitive method
for fingerprinting genomic DNA within any
organism. Applications of this technique range
far beyond agricultural applications, ranging
from agronomic trait analysis, diagnostics,
pedigree analysis, forensics, parental heritage
and may be used as a universal fingerprinting
system. AFLPs are based on the selective
amplification of a subset of genomic restriction
fragments using PCR(example) . Restriction
endonucleases such as Mse1, and EcoR1 are used to
digest the DNA before amplification, the
subsequent restriction site is then to be used as
a primer binding site for amplification using
PCR. These amplified fragments are then to be
analysed using denaturing polyacrylamide gel
electrophoresis which generates fingerprints to
be compared as polymorphisms. These polymorphisms
are typically inherited in a Mendelian genetics
fashion, enabling their use for typing,
identification and mapping of genetic
characteristics (15). Advantages 1. Many loci
are produced per assay 2. High levels of
polymorphisms are produced 3. Prefabricated kits
are available to buy, and are easy to use 4.
Results are reproducible, and stay constant over
time and between labs (some variation dependent
on thermocycler) 5. Cost is acceptable, ranging
between the costs of RAPDs and RFLPs 6.
Methodology is fast (5 days) 7. AFLPs have the
capacity to saturate the entire genome to locate
polymorphisms Disadvantages 1. Markers are
required, although radio isotopes may be avoided
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VNTR Variable Number Tandem Repeats VNTR's are
highly variable regions of DNA DNA samples are
cut with a restriction endonuclease The
phenotype for different alleles is a variable
length restriction fragment, which is detected by
agarose gel electrophoresis and Southern
hybridization.
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Advantages  of using RAPD technology 1. More
polymorphisms than RFLPs 2. Simple and quick 3.
Selective neutrality 4. Option not to use
radioisotopes 5. Differentially amplifies DNA
samples based on mutations 6. DNA quality may be
low (quick extraction possible) 7. A large
number of bands are produced per primer 8.
Primers are readily available
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NOTES Central DogmaDNAgtRNAgtProteingtFunction Repl
icationgttranscriptiongttranslationgtwork The cell
as a factory DNA-complete instructions for making
and maintaining the product.has to be kept safe
and accurateand organized. RNA- Portable copy of
one part of the instructions. Messenger RNA or
mRNAjust made when it is needed and then it is
disposable. Protein- tools and materials used for
actually building the productenzymes are
proteins that act polymerase is suppose to make
the mRNA as machinery to make something the cell
needsstructural proteins are proteins used to
form the structure DNA produces and RNA
transcriptthen sent out to cytoplasmribosome's
begin to read code. DNA must be unwound on
ribosome the mRNA is read and a protein is
created Only one strand of DNA serves as template
for making the RNA (transcription) Different
genes are transcribed from different
strands..Always go 3 to 5always add base to
3 end. Transcription Catalyzed by RNA
polymerasea complex, multisubunit enzyme that
catalyzes the formation of the phosphodiester
bonds that link together the nucleotides in an
RNA chain Gene Structure Promoter upstream the
coding sequence of genepromoter regulates when
the gene is codedProtein interacts with promoter
to turn on the gene encoding Translation-making
the proteinribosome looks for translation start
sitealways aug or atggtgtgttranslation stop
siteprotein is created and goes off to do the
work it is suppose to do Promoters-RNA polymerase
must end at the promoter to start making the mRNA
(transcription) Other proteins must bind to the
promoter to regulate when the RNA
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• Promoters regulate gene expression which DNA
  strand will serve as a templatewhen to start
  making the mRNA. Where to start making the mRNA
  TSPwhen to stop making the mRNA and how much to
  make
• Bacterial Gene Structure bacerial prokaryotic
  genesone mRNA can contain several coding
  regions..can have several cistronsdifferent
  genescoding for differerent proteins related in
  function
• Plant and Animal gene structureEukaryotic
  genesone mRNA contains a single coding region
  (ORF)
• DNA with one promotor controlling one gene
• Introns plant and animal genes often contain
  Extra DNA The coding region in some Eukaryotic
  genes is interrupted by non coding regions that
  have to be removed before the protein is made.
  The ORF in the gene are called exonsthe extra
  DNA chunks are called introns The preRNA also
  contains the sequence information that tell the
  cell where to trim out the extra DNA (splice
  junctions)
• Bioinformatics-LOTS and Lots of informationwhat
  do we do with it and how to we organize the
  information in a useful way.
• Mining fore useful information in that glut of
  information is what bioinformatics is about
• Steps to finding genes
• 1. Find ORFs..this is the biggest target, easiest
  to findlook for long stretches of triplet
  condons that dont have a stop codon
• Find the Start Codon-where the protein begins,
  always an atg
• Find promoter elements
• Gene StructureCodons
• 61 codons codes for amino acids, but only 20
  amino acids.
• All have carboxyl group and amino group....R
  groups give chemical propertiesmakes the
  molecule hydrophobic
• Tertiary structure-the protein all folded up nice
  and neat
• ORF-Open reading frame
• A human nucleus has 3 billion base pairs and
  about 35gs protein coding genes
• Steven Pechous NCBI
• NCBI Resources Sequence Database, Entrez,
  Genomic Resources, Blast

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• DNA-Base pairs-G, T, A, C
• Double helix-base pairs same shapestack on top
  of each other and twist around
• DNA- a script to be passed from cell to cellthe
  secret to life
• Watson and Crick discover the double helix
• Genetic code a story the has evolved over
  millions of years
• Examining and interpreting the genetic code Key
  to understanding disease and curing
  diseaseheredity
• How can u read what's inside a molecule?
  Cytosine, Guanine,
• 1 of genes active?
• Revolution- computerization of genetic decoding
• Human Genome Project-J. Craig Vender-1990
  Decoding proteins and genes. Machine that cuts
  the DNAlabels it and reads it with a laseris
  able to read G T A Ccodes must be arranged
  againAUTOMATION
• Francis CollnsHuman Genome Projectthousand base
  pairs a second! Out of university labs directly
  onto the internetSolara used information.was a
  race to get the genome sequenced the fastest.
• Population from Africa about a hundred thousand
  years ago.not much genetic variationpeople very
  similar
• Proteinsshape defines what it does and how it
  interacts with other proteins
• Mutations in proteins can cause very serious
  consequenceschanges in shape make it not able to
  interact with other proteinsprotein in three
  dimensional shape.much more complex then linear
  DNA
• Human Genes 30,000
• Genes make a message but can be spliced in
  different waysmodifications to proteins can make
  them function differently.
• Starting with the same raw ingredients, different
  arrangements can produce many different
  complexity
• Finding Genes. If it has an ORF like a genehas
  a promoter like a gene and has a function like a
  gene
• Can use restriction enzymes to cut dna into
  different sizes and run through gel

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Something For My Ladies!
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The End