The DNA Structure

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The DNA Structure
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Three Major Approaches

• Structural (architecture of the molecules)
• Biochemical (interactions between cell metabolism
  and heredity)
• Informational (transfer of information,
  translation of information)

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The Discovery of DNA

• Friedrich Miescher (Swiss, 1844-1895)
• Intelligent from early age but very shy
• His father was a professor of anatomy
• Studied at the University of Göttingen under
  Ernst Felix Immanuel Hoppe-Seyler, considered the
  father of biochemistry

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• He examined used bandages obtained from a
  hospital caring for the wounded of the Crimean
  War in hope of finding something interesting
• He discovered a substance containing both
  phosphorus and nitrogen, made up of molecules
  that were apparently very large, in the nuclei of
  white blood cells found in pus

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• Named the substance nuclein because it seemed to
  come from cell nuclei. In 1874 when Miescher
  separated it into a protein and an acid molecule.
  It is now known as deoxyribonucleic acid (DNA)
• This substance was so unusual that Hoppe-Seyler
  repeated the work himself before allowing
  Miescher to publish the paper on the discovery

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• He found an excellent (and more pleasant) source
  of nuclear material in the sperm of the salmon
• The nuclei are large in any sperm cells,
  remarkably so in the salmons
• From these he first extracted a pure DNA
• In 1889 a pupil of his, the German
  pathologist Richard Altmann (1852-
  1900) introduced the term nucleic
  acid

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Inborn Errors of Metabolism

• Archibald Garrod (British, 1857-1936)
• His father was a physician
• Received his medical training at St.
  Bartholomew's Hospital, London

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• The relationship between genes and proteins was
  first proposed by Garrod in 1908
• Garrod, a prominent physician at St.
  Bartholomew's Hospital in London, understood both
  the new science of biochemistry and the emerging
  discipline of genetics

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• He studied a harmless but rare disorder in the
  general population but frequent in children of
  first-cousin marriages alkaptonuria
• A patient with this disorder produces urine that
  when exposed to air turns distinctively dark,
  because these people lack the enzyme found in
  normal individuals who are able to convert the
  reddening agent, alkapton, to another substance

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• Following Mendels laws, Garrod concluded that
  alkaptonuria is a congenital disorder, not the
  result of a bacterial infection as was commonly
  thought

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• He observed that inherited diseases reflect a
  patient's inability to make a particular enzyme,
  which he referred to as inborn errors of
  metabolism
• Garrod's hypothesis was ahead of its time
• In the 1930s George Beadle and Boris Ephrussi
  linked the synthesis of pigments to eye color in
  fruit flies to specific mutations

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1910-1925 Development of Cytological Genetics

• Cytogenetics is the study of chromosomes and
  chromosome abnormalities

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X-ray Crystallography

• X-ray crystallography is a technique that
  exploits the fact that X-rays are diffracted by
  crystals
• It is not an imaging technique X-rays have the
  proper wavelength to be scattered by the electron
  cloud of an atom of comparable size
• Based on the diffraction pattern obtained from
  X-ray scattering off the periodic assembly of
  molecules or atoms in the crystal, the electron
  density can be reconstructed

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• In 1912 Max von Laue reported the diffraction of
  X rays by a crystal (for which he received a
  Nobel Prize in physics in 1914)

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• For progress in pharmaceutical research the
  structure of complex organic molecules has to be
  understood
• By studying the chemical reactions that a
  compound and its degradation products could enter
  into with other compounds of known structure,
  chemists were able to deduce the structures of
  many complex organic molecules

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• X-ray crystallography allowed to determine
  molecular structure from the compound itself. In
  this method, structural information is obtained
  by mathematical analysis of the intensity of X
  rays scattered (or diffracted) from parallel
  planes in a crystal, as recorded photographically
  or by an electronic detector
• In 1915 a unique father-son team, William Henry
  Bragg (18621942) and his son, William Lawrence
  Bragg (18901971), won the Nobel Prize in physics
  for their seminal roles in X-ray crystallography

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William Lawrence Bragg (left) and William Henry
Bragg
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• William Henry's original interest was in what
  diffraction showed about the nature of X-rays,
  and he was a skilled experimenter and designer of
  instruments
• William Lawrence was more concerned with what
  X-rays revealed about the crystalline state, and
  he possessed a powerful ability to conceptualize
  physical problems and express them mathematically
• Until electronic computers were developed during
  World War II, these calculations were incredibly
  laborious

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Transforming Principle

• In 1928, Frederick Griffith (British, conducted
  an experiment that showed the transformation of
  living cells by a transforming principle, which
  was later discovered to be DNA

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Tetranucleotide Hypothesis

• Phoebus Levene (Russian-American, 1869-1940)
• He worked with Albrecht Kossel and Emil Fischer,
  the nucleic acid and protein experts at the turn
  of the 20th. century

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• He conducted experiments that in 1931 suggested
  that the four components of DNA occur in
  approximately equal ratios
• He suggested the possibly that DNA was made of a
  repeating tetramer
• If so, the implication was that the structure of
  DNA was too simple and too regular to contribute
  to genetic variation attention thereafter
  focused on protein as the probable hereditary
  substance

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One gene-One enzyme Hypothesis

• This proposal of the one gene-one enzyme
  hypothesis was developed by the Americans George
  Beadle (1903-1989) and George Wells Tatum
  (1909-1975) in 1938

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• Beadle and Tatum hypothesized that if there
  really was a one-to-one relationship between
  genes and specific enzymes, it should be possible
  to create genetic mutants that are unable to
  carry out specific enzymatic reactions
• They exposed spores of Neurospora crassa (a bread
  mold) to X-rays or UV radiation and studied the
  resulting mutations
• The mutant molds had a variety of special
  nutritional needs. Unlike their normal
  counterparts, they could not live without the
  addition of particular vitamins or amino acids to
  their food
• Normal Neurospora requires only one vitamin
  (biotin), but mutants were created that also
  required thiamine or choline

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• Genetic analysis showed that each mutant differed
  from the original, normal type by only one gene
• Biochemical studies showed that the mutants
  seemed to be blocked at certain steps in the
  normal metabolic pathways
• Their cells contained large accumulations of the
  substance synthesized just prior to the blockage
  point, just as Garrod's patients had accumulated
  alkapton

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• As Beadle and Tatum had predicted, they created
  single gene mutations that incapacitated specific
  enzymes, so that the molds with these mutations
  required an external supply of the substance that
  the enzyme normally produced, and the substance
  that the enzyme normally used, piled up in the
  cell
• These results confirmed their one gene-one enzyme
  hypothesis
• They received the 1958 Nobel Prize in Physiology
  and Medicine

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Transforming Principle identified as DNA

• In the early 1940s Oswald T. Avery and Maclyn
  McCarty, a colleague at the Rockefeller Institute
  Hospital, began concentrating on the problem of
  pneumococcal transformation

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• Avery's work focused first on purifying the
  transforming substance. Using refined versions of
  Colin M. MacLeod's preparation techniques, Avery
  and McCarty isolated biologically active
  transforming principle from samples of
  pneumococci

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• Then attention turned to its chemical analysis.
  Proteases (enzymes that deactivate proteins) and
  lipases (enzymes which destroy lipids) were found
  not to inactivate the transforming principle
• Avery concluded that the substance was
  essentially protein and lipid free. He found that
  the substance was rich in nucleic acids, but
  ribonuclease, an enzyme that destroys ribonucleic
  acid (RNA), did not inactivate the substance
  either

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• It was not a carbohydrate like the polysaccharide
  capsular material, as carbohydrates are not
  precipitated by alcohol (the transforming
  principle was)
• Alcohol was, however, a well-known precipitant
  for deoxyribonucleic acid (DNA). Further, the
  transforming substance had a high molecular
  weight, as did DNA, and gave a strong reaction to
  the Dische test for DNA. Thus, the transforming
  substance, producing permanent, heritable change
  in an organism, was DNA

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What is Life?

• By the end of WWII, many physicists, saddened by
  the prospects of atomic bombs, turned their
  attention toward biology
• One of them was Erwin Schrödinger (Austrian
  1887-1961)

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• Schrödinger published in 1945 a book titled What
  is Life? that planted the idea for searching the
  secret of life
• This marked the beginning of reductionism in
  biology

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Base Ratios

• In 1951 Edwin Chagraff (1905-2002) noted
  regularities in the base composition of nucleic
  acids, which reflected the existence in all DNA
  preparations of certain structural principles
• In particular, for duplex DNA he identified the
  constant proportion of bases A T and C G

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X-ray Crystallography Applied to Nucleic Acids

• Between 1940's and 1950's Maurice Wilkins
  (1916-) and Rosalind Franklin (1920-1958) worked
  on X-ray/DNA

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The Hershey-Chase Experiment

• The Americans Alfred Hershey (1908-1997) and
  Martha Chase (1930-2003) published in 1952 a now
  classical paper

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• They showed DNA to be the carrier of genetic
  information in virus reproduction, working with
  T2 phage
• They demonstrated by labeling the capsid proteins
  and nucleic acid of bacteriophage T2 with
  different radioactive isotopes that only the DNA
  of the phage had to enter the cell for virus
  replication to occur

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Enter Watson and Crick

• James Watson (American, 1928-)
• Francis Crick (British, 1916-)

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What did Watson and Crick Really Contribute?

• Major original breaks by W C were the A-T and
  C-G having the same molecular shape
• That lead to understanding constancy for the
  diameter of the DNA molecule, the use of
  Chargaffs ratios
• The application of model building which lead to
  the complementary model

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