The Molecular Nature of Genes

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The Molecular Nature of Genes

• Chapter 2

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The Nature of Genetic Material

• Miescher-1869
• Isolated nuclein from surgical bandages
• Phosphorus-bearing substance
• Mostly chromatin
• Complex of DNA and chromosomal proteins

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The Nature of Genetic Material

• Transformation in Bacteria
• Griffith
• Id DNA as genetic material in 1928
• Used transformation in Streptococcus pneumoniae
• Wild type is spherical with a mucus
  capsule-smooth
• -virulent .if injected caused lethal infections
• Mutant strain-lost ability to make capsule
• -avirulent-called rough
• Key to Griffith studies
• Heat-killed smooth could transform avirulent
  cells to virulent ones
• Neither heat-killed OR rough caused disease by
  themselves
• Together they are deadly

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The Nature of Genetic Material

• Transformation in Bacteria
• Griffith, cont.
• When together
• Caused disease
• Virulent trait passed to the live avirulent ones
• Capsule making ability passed to avirulent form
  and then conferred to descendants as a heritable
  trait
• MEANS that the transforming substance in the
  heat-killed bacteria was probably the gene for
  virulence itself
• What was the substance?

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The Nature of Genetic Material

• DNA The Transforming Material-Avery, MacLeod,
  and McCarty
• Used transformation similar to Griffith
• Defined chemical nature of transforming substance
  from virulent cells
• Removed protein
• Extract still transformed
• Subjected it to digestion with enzymes
• Trypsin and chymotrypsin
• Destroy protein
• No effect on transformation
• Neither did ribonuclease-degrades RNA
• Both ruled out protein and RNA as transforming
  agent
• Avery found DNase
• Breaks down DNA
• Destroyed transforming ability of virulent cell
  extract
• Suggested that DNA was the transforming substance

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The Nature of Genetic Material

• DNA The Transforming Material-Avery, MacLeod,
  and McCarty-analytical tools used
• 1. Ultracentrifugation
• Spun transforming substance at very highspeed to
  estimate size
• Transforming material sedimented rapidly
• Suggests high molecular mass
• Characteristic of DNA

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The Nature of Genetic Material

• DNA The Transforming Material-Avery, MacLeod,
  and McCarty-analytical tools used
• 2. Electrophoresis
• Placed transforming substance in an electric
  field
• High charge-to-mass ratio caused rapid movement
• 3. UV Absorption
• Absorbed strongly at 260nm
• Protein absorbs at 280nm

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The Nature of Genetic Material

• Further proof-Hershey and Chase
• Used T2 virus
• Infects E. coli
• Phage genes enter the host cell
• Directs synthesis of new phage particles
• Composed of protein and DNA
• Question was Do the genes reside in the protein
  or in the DNA?
• Hershey/Chase showed that
• On infection, most of the DNA entered the
  bacterium
• Only a small amount of protein enters cell
• Along with other evidence from previous
  experiments, it showed unequivocally the DNA is
  transforming substance!

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The Nature of Genetic Material

• Short Summary
• Genes are made of nucleic acid
• USUALLY DNA
• Some simple genetic systems have RNA
• Viruses

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The Chemical Nature of Polynucleotides

• DNA
• Four nitrogenous bases
• Purines and Pyrimidines
• ATGC
• Phosphoric acid
• Deoxyribose
• RNA
• Four nitrogenous bases
• Purines and Pyrimidines
• One different from DNA
• Phosphoric acid
• Ribose

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The Chemical Nature of Polynucleotides

• Connections
• Bases and sugars
• Called nucleosides
• Named from the DNA/RNA and the bases
• Adenosine (RNA)
• Deoxyadenosine (DNA)
• NOTE figures are denoted with chemical
  shorthand-not all of the Hs or Cs are noted for
  simplicity sake.

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The Chemical Nature of Polynucleotides

• Connections, cont.
• How nucleotides are connected
• Nucleotides
• Nucleosides phosphate
• Bond from the 5 (5 prime) of one phosphate to
  the 3 (3 prime) position of the next nucleotide
• Therefore, we say that the strand goes from 5 to
  3

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The Chemical Nature of Polynucleotides

• Summary
• DNA and RNA
• Chain-like molecules
• Made up of nucleotides
• Base linked to the 1-position of a sugar and
  phosphate group
• Phosphate joins the sugars in a DNA or RNA chain
  through their 5- and 3-hydroxyl groups by
  phosphodiester bonds

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Figure 2.12
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The Double Helix

• Spacing between adjacent bands in an arm of the X
  is inversely related to the overall repeat
  distance in the helix
• 34Å
• Spacing from top of X to the bottom inversely
  related to the spacing
• 3.4Å
• What does this mean?
• In order for the above to be true AND Chargaffs
  rules to be applied, then this is how the
  structure of DNA is found
• Sugar-phosphate backbones on outside
• Bases on the inside
• Bases must be paired-purine on one side with a
  pyrimidine on the other
• Eliminates bulges from two large paired purines
• Eliminates constrictions from two small
  pyrimidines

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Figure 2.13
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The Double Helix

• The Helix itself
• Likened to a twisted ladder
• Presented three ways
• Curving sides of the ladder
• Sugar-phosphate backbones of the two DNA strands
• Rungs of the ladder
• The base pairs
• Spacing between base pairs
• 3.4Å
• Helix repeat distance
• 34Å
• Means that there are about 10bp/turn of the helix
• B/c of 5 to 3 make-up of the strands
• Strands are antiparallel

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The Double Helix

• Summary
• DNA is a double helix
• Sugar-phosphate backbones on outside
• Base pairs on inside
• Bases pair in a specific way
• A with T
• G with C

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Physical Chemistry of Nucleic Acids (short
version)

• Three DNA structures
• A, B, and Z forms
• B form
• Structure proposed by Watson and Crick
• A form
• Plane tilts 20o away from horizontal
• 11bp/turn
• Each turn occurs in only 25Å instead of 34Å
• Hybrid of RNA strand and a DNA strand
• Double stranded RNA
• Z form
• Left handed helix
• Does exist but function unknown

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Physical Chemistry of Nucleic Acids

• Summary
• Common form of DNA is the B form
• Base pairs horizontal
• Very small is Z form
• Left-handed helix
• RNA-DNA hybrid
• A form
• Base pairs tilted away from the horizontal
• Separated DNA strands can be induced to anneal
• Temperature
• DNA concentration
• Time

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