Molecular Biology Primer

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Molecular Biology Primer

• Lecture 1 September 1, 2005
• Algorithms in Biosequence Analysis
• Nathan Edwards - Fall, 2005

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Molecular Biology Primer

• DNA encodes the fundamental information required
  for life
• Biological function comes (mostly) from proteins
• Mutation selection create diversity
• Biotechnologies

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DNA

• Deoxyribonucleic Acid
• DNA molecules are stored in the nucleus of every
  cell, as chromosomes
• Each DNA strand is composed of nucleotide
  subunits, which consist of
• a deoxyribose sugar,
• a phosphate,
• one of four nitrogenous bases
• Adenine (A), Thymine (T), Cytosine (C), Guanine
  (G)

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DNA

• Two strands form bonds at complementary bases
• A with T
• C with G
• Strands are asymmetric
• 5 -gt 3
• Reversed with respect to one another.
• This stable conformation is the double helix

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5
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3
5
DNA
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DNA Replication

• Each strand of DNA also functions as a template.
• DNA polymerase extends the new complementary
  strand along the old one.
• Replication happens every time a cell divides!

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DNA Replication
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Chromosomes

• Humans have 46 chromosomes
• 22 pairs of autosomal chromosomes
• Numbered largest (1) to smallest (22)
• Two sex chromosomes
• XX for women, XY for men
• One chromosome of each pair comes from each
  parent
• The collection of chromosomes is called a genome

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Human Chromosomes
3 billion base-pairs
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Chromosomes
From chromosome 22

• AGTCCCACAACCTTTCTGGATTGATAGTTTGTGGTGAAATAAACAATTTT
  AGTTTGTTTGGAGAATCTTT
• TGTATACAAAATACAAATAAAACCTAAATCAAAGAAACAGAGCATGTCCG
  GAGAAGTCTGCCAACCCTTC
• TCCAGGCCATGGGGCTTCCCAAGCCAGGCCTGTACTCCTCATGTAGATTC
  CACACCCCGCCTTGATGTCT
• TTGGCTTTCACACTAGTGACTATAGCCTGGTGGGACGGGGTCTAGGGGCC
  ACAGTCCTGGTCCTGCGCAG
• GTGGCCCTGGAGAGAAGCCTTGGAGAACTTGGAGAAGCCCACGCGGCTGG
  CAGCATCATGGTGAGAGGCT
• GACACCTTGTGGCTGGCTGGCAGCATACGTCCTTCCTCCCCTAGGTCAGC
  TAGACGGCCAAAGCAGGGAT
• CTGCAAGCTCCTTCTGTGGCGGGCCAAAAAGTGAACATTCAGTGTGTCTG
  TTGCAGCTACTGTCATAGCA
• CTGAGGCACCCCTAGACAGTACAGAAACAAGCAGGTGTGGCCATGTTCCA
  GTGAAACCTTATGAATACTG
• AAATCTGAATCCATAATTTTCATGTATCACAAAGTAGTAATATTCTTTTA
  ATATGCAAAAACCGGCCAGG
• TGCGGTGGCTCATGCCTGTGACCTCAGCACTTTGGGAGGCCGAGGTGGGT
  GGATCACCTGAGGTCAGGAG
• TTCGAAACCAGCCTGGCCAACGTGGTGAAACCCTGTCTCTATTAAAAATA
  CAAAAATTAGCCTGGTGTGG
• TGGCACATGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCGTAGGAATT
  GCTTAAACCTGGGAGGCGGA
• GGTTGCAGTGAGCTGAGATCATGCCACTGCACTTCAGCCTGGGCAACAGA
  GCTAGACTCCATCTCAAAAA
• CAAACAAACAAAAAAACAAAAGCAAAAACCAGTCTTAGCTCACAGGCTGT
  GCCAAAACAGGCAGTGGGCT
• GGATTTGGTCCTCAAGCCTGGGCTTGCTGACCTCTGGCCTAGGACACCTC
  TCCTTTATGCCTCCGCTCCC

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Proteins

• Proteins do all the work!
• Examples
• DNA Polymerase
• Hemoglobin

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Proteins

• A polymer of 100s to 1000s of amino-acids
  strung together in long chains.
• Each chain folds into a specific 3D conformation
  determined by its amino-acids.
• The 3D shape of a protein determines its function

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Amino-Acids
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Amino-Acids
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Poes Cryptograms

• Edgar Allen Poe was a cryptogram enthusiast
• solved submitted cryptograms from readers in
  Atlantic Monthly
• claimed to have solved over 100 cryptograms
• Later, published two unsolved cryptograms
  supposedly by W.B.Tyler
• Both only solved recently

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Poes Cryptograms
"The soul secure in her existence smiles at the
drawn dagger and defies its point. The stars
shall fade away, the sun himself grow dim with
age and nature sink in years, but thou shalt
flourish in immortal youth, unhurt amid the war
of elements, the wreck of matter and the crush of
worlds."
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Poes Cryptograms

• It was early spring, warm and sultry glowed the
  afternoon. The very breezes seemed to share the
  delicious langour of universal nature, are laden
  the various and mingled perfumes of the rose and
  the essaerne (?), the woodbine and its
  wildflower. They slowly wafted their fragrant
  offering to the open window where sat the lovers.
  The ardent sun shoot fell upon her blushing face
  and its gentle beauty was more like the creation
  of romance or the fair inspiration of a dream
  than the actual reality on earth. Tenderly her
  lover gazed upon her as the clusterous ringlets
  were edged (?) by amorous and sportive zephyrs
  and when he perceived (?) the rude intrusion of
  the sunlight he sprang to draw the curtain but
  softly she stayed him. No, no, dear Charles,
  she softly said, much rather yould I have a
  little sun than no air at all.