Genomes, DNA Structure and Topology

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Lecture 16

• Genomes, DNA Structure and Topology

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Replication
DNA
Transcription
mRNA and other RNA
Translation
Protein
Degradation
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Types of Genomes

• Viral
• Prokaryotic
• Eukaryotic
• Humanestimate 32000 genes (as of 2/16/01)
• Only 3x as many as yeast

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DNA structure/topology

• Genomes are longer than the cells in which they
  are packaged
• Most cellular DNA is supercoiled
• DNA topology is defined by a linking number (LK)
• Enzymes known as topoisomerases underwind DNA

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Comparison of genome sizes
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Review of Watson/Crick DNA Structure
B form of DNA (Relaxed)
(36 Å)
(10.5 bp/turn)
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BForm DNA

• Watson-Crick, 1953
• Franklin and Wilkins X-ray
• Chargaff
• A G T C
• Helix
• Antiparallel
• Complementary
• Base-stacking and H-bonds

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Other Possible Secondary Structures of DNA
A 11bp/turn
Z 12 bp/turn
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Supercoiling can eliminate strain
Fewer helical turns than in B DNA
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Methods to study DNA Topology
Electron Microscopy
Centrifugation
Electrophoresis
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Linking number(LK)

• Defined for covalently closed DNA circles
• No change in linking number unless a
  phosphodiester bond of one backbone is broken.
• Always an integer.
• Made up of 2 componentsTwists (TW) and writhes
  (Wr)

LKTwWr
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Topoisomerase I changes the linking number
27.5 Å diameter hole for DNA double helix
Tyr that become covalently bonded to DNA
Catalyzes relaxation of negatively supercoiled DNA
Linking number increase 1
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DNA Gyrase introduction of negative supercoils
Uses ATP (introduction of an additional
supercoil9 kcal/mol)
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HistonesProteins associated with DNA
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Histones are highly basic proteins
The two copies of each of the core histones
(H2A, H2B, H3, and H4) form the basic core
particle, known as a nucleosome, around which a
160 - 240 bp of DNA is wrapped
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Nucleosomefundamental organization of chromatin

• Repeating unit of chromatin
• 140 bp of DNA wound around histone octamer
• Protects regions of DNA from digestion
• Linker regions bind H1
• Topoisomerases necessary to assemble chromatin
  (supercoiling)

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Chromatin assemblyIntroduction of negative
supercoils