August 25

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August 25

• Review the idea of transformation-Griffiths,
  Avery
• Review pretest and testing strategy
• bonds
• Know your molecules
• The most important things about DNA-prep for
  reading
• Watson Crick paper (1 page) and questions for
  Tuesday

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1928 Frederick Griffiths Transformation Rou
gh strain-lacks polysaccharide coat
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1944 Avery, MacLeod, McCarty
Why was this such a good experiment? (And took 16
years to publish)
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1944 Avery, MaLeod, McCarty
1 part in 600,000,000 could transform. How does
this happen?
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This was one of the first experiments to show
that heritable information is carried by DNA To
think about How could you show that the S
polysaccharide phenotype and the virulence were
due to transformation of the same gene?
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Test strategies/hints

• For true-false-guess. Justify your answer.
• List more than one reason if you can, but dont
  write to fill up the space
• Use the logic of what you have learned and try to
  rationalize an answer
• There will always be at least one difficult
  question. If you dont try an answer you wont
  get any points
• Unlike the pretest, I wont give you anything you
  havent seen before

8
140 pretests

• between 9 and 12 out of 12
• Excellent
• between 5 and 8
• Good, theres more to be learned
• below 4
• You will need to make a commitment to catch up
  and work extra hard

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A few questions from the pretest

• The rest to come during the later two sections

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DNA is autocatalytic and heterocatalytic One way
flow of information
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A few definitions

• Transcription-copying of mRNA from DNA
• Translation-converting of mRNA to protein
• Most takes place in cytoplasm on ribosomes, a
  little appears to take place in the nucleus as
  part of proofreading/checking of messages

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Are there exceptions to the central dogma?
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Are there exceptions to the central dogma?
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True-False questions

• RNA is used by some viruses as genetic material
• DNA is found in all living organisms, viruses
  need their hosts
• Some changes in DNA do not affect changes in
  protein because of the redundancy of the genetic
  code
• Recombination between parental chromosomes
  ensures your chromosomes are not identical.
  Mutation might also contribute to differences

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Why review chemical bonds?

• Underlie the structure of DNA
• Basis of the stability of DNA
• Basis of replication and transcription
• Basis of methods that use DNA/RNA hybridization

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What would you want in a universal genetic
material?
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What would you want in a universal genetic
material?
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Valence matters
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Rules for making bonds The number of outermost
electrons determine reactivity If electron
shells is full, unreactive If unfilled-either
gain or lose electrons through ionic or covalent
bonds. Molecule cluster of atoms held together
by covalent bonds
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Double bonds- make molecules more planar
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Water weakens ionic bonds because it is polar
and surrounds the ions.
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• Hydrogen bonds
• Hydrogen shared
• weaker than covalent bonds
• Strongest when in a straight line

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Two additional types of bonds or intermolecular
forces
Van der Waals forces- shifts in charge due to
movement of electrons Stacking
effect Hydrophobic compounds in water like to
stick together
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What are the five major types of bonds?

• Rank these in order of strongest to weakest

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What are the five major types of bonds?

• Which would you use for designing something
  permanent in the cell to store information?
• What would you use if you wanted to provide
  access to that information?

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The peptide bond is an example of a covalent
bond. Another example is the phosphodiester
bond.
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Know your molecules

• Identify and label sugars, bases, nucleotides,
  amino acids
• Identify purines/pyrimidines, and specific amino
  acids if you can
• Consider the properties of the amino acid side
  chain-size, charge, hydrophobicity, polar or
  nonpolar.

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Six of the 12 most important things you should
know about DNA
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1
1)What are its components? 2-4) How do they fit
together?
Miescher -Nucleic acids, nuclein, 1869 from cell
nuclei Nucleotides Phosphate, pentose, base
(cyclic nitrogen- containing compound)
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2
Cyclic pentose (deoxyribose)- 5P 3OH 1base The
refore The sugar links everything
In RNA- 5P, 2OH, 3OH In chain terminating
nucleotides, just 5P
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Base- purine G,A pyrimidine T, C
3
Mmemonic purines have a short name and are
longer Pyrimidines have a long name and are
shorter G is a purine Isolated from bird GuAno
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4 Phosphate- Phosphodiester bond
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What was known before Watson and Crick wrote
their paper?
5 Chargaffs rule In the nucleus of an
organism, the amount of A and T are equal,
and the amount of G and C are equal
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What was known before Watson and Crick wrote
their paper?
Pauling proposed the alpha helix as a structure
for proteins Pauling Corey and Frasier had
proposed 3 chain models With phosphates on inside
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The players...

• James Watson
• Francis Crick
• Maurice Wilkins
• Rosalind Franklin

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Max Perutz on Watson he never made the
mistake of confusing hard work with hard
thinking he always refused to substitute the
one for the other.
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Watson and Crick, 1953
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Discovery consists of seeing what everybody has
seen and thinking what nobody has
thought.--Albert von Szent-Györgyi
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The contribution of Rosalind Franklin
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6
Rules for writing the code
What is the sequence shown here, read from 5 to
3?
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Rules for writing the code 5 GATC 3
What is the sequence of the complementary
strand written 5 to 3 ?
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Complement

• 5ATGGTGCAC3
• By convention, always read/write
• 5 to 3 and label the 5 and 3ends

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Are these molecules different or the same?

• 3TACCACGTG5
• 5GTGCACCAT3

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DNA polymerase
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Why only AT/GC base pairs?
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Why only AT/GC base pairs?