Information Transfer in Cells

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Information Transfer in Cells

• Information encoded in a DNA molecule is
  transcribed via synthesis of an RNA molecule
• The sequence of the RNA molecule is "read" and is
  translated into the sequence of amino acids in a
  protein.

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Review of DNA Structure

• What is a nucleoside?
• What is a nucleotide?
• What forces hold DNA together as a helix?
• Why are there two kinds of grooves in a B DNA
  helix?
• What are the differences between A, B and Z forms
  of DNA

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DNA (deoxyribonucleic acid)
Building blocks deoxyribonucleotides
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Ribose
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1
4
2
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Ribose - a pentose sugar - a furanose ring - in
RNA - in nucleotides for energy metabolism (ATP)
2 deoxyribose - a pentose sugar - a furanose
ring - in DNA
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(11.2 Pentoses of Nucleotides)

• D-ribose (in RNA)
• 2-deoxy-D-ribose (in DNA)
• The difference - 2'-OH vs 2'-H
• This difference affects secondary structure and
  stability

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11.1 Nitrogenous Bases

• Pyrimidines
• Cytosine (DNA, RNA)
• Uracil (RNA)
• Thymine (DNA)
• Purines
• Adenine (DNA, RNA)
• Guanine (DNA, RNA)

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Naturally occurring purine derivatives
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Properties of Pyrimidines and Purines

• Keto-enol tautomerism
• Strong absorbance of UV light

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Guanine
Guanine
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Nucleoside
A purine/pyrimidine deoxyribose or ribose
Cytosine
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5
3

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2
1




Cytidine
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11.3 Nucleosides

• Linkage of a base to a sugar
• Base is linked via a glycosidic bond
• Named by adding -idine to the root name of a
  pyrimidine or -osine to the root name of a purine
  
• Sugars make nucleosides more water-soluble than
  free bases

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11.4 Nucleotides

• Nucleoside phosphates
• Know the nomenclature
• "Nucleotide phosphate" is redundant!

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Deoxyribonucleic acid
DNA is a nucleotide polymer linked by a 3 to 5
phosphodiester bond
5 phosphate
3 hydroxyl
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Single-stranded DNA Has polarity Has a
hydrophilic side Has a hydrophobic side
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RNA versus DNA - Stability issues
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Double-stranded DNA
1) Pair of DNA chains in an antiparallel
arrangement
2) Sugar-P backbone outside, aromatic rings
(bases) inside
3) Bases pair specifically by H-bonding
A pairs with T G pairs with C A T and G
C purines pyrimidines
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The canonical base pairs

• The canonical AT and GC base pairs have nearly
  identical overall dimensions
• A and T share two H-bonds
• G and C share three H-bonds
• GC-rich regions of DNA are more stable
• Polar atoms in the sugar-phosphate backbone also
  form H-bonds

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Why a helix? Why not a ladder?

• A side view of base pairs shows they are
  perpendicular to the helix axis
• The heterocyclic bases have flat surfaces which
  are hydrophobic
• To exclude water from between the rings, we
  should bring the bases closer together
• One way to model them closer together is to
  twist the ladder into a helix

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Right-handed twist 10 base pairs per turn B form
DNA helix
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Summary What holds DNA together?

• Sugar-phosphate backbone outside
• (1) minimizes electrostatic repulsion,
• (2) interacts with water
• Bases inside
• (3) hydrogen-bonded
• (4) plus base stacking by hydrophobic interactions

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Major and minor grooves

• The "tops" of the bases (as we draw them) line
  the "floor" of the major groove
• The major groove is large enough to accommodate
  an alpha helix from a protein
• Regulatory proteins (transcription factors) can
  recognize the pattern of bases and H-bonding
  possibilities in the major groove

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Comparison of A, B, Z DNA

• A right-handed, short and broad, pitch is 2.3 A,
  11 bp per turn
• B right-handed, longer, thinner, pitch is 3.4
  A, 10 bp per turn
• Z left-handed, longest, thinnest, pitch is 3.8
  A, 12 bp per turn

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Picture of E. coli DNA outside of the cell
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DNA Packaging

• Human DNA total length is 2 meters
• Is packaged into a nucleus that is 5 microns in
  diameter
• This represents a compression of more than
  100,000 fold
• It is made possible by wrapping the DNA around
  protein spools called nucleosomes and then
  packing these into helical filaments

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We reviewed Chapter 11, Sections 11.1, 11.2,
11.3, 11.4, 11.5 and the DNA parts of
11.6 Chapter 12, Sections 12.2, 12.5