Chapter 16: Molecular Genetics

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Chapter 16 Molecular Genetics

• AP Biology Ms. Rader

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DNA A brief history

• Researchers had established that DNA was the
  polymer that was responsible for genetic material
  and inheritance. (It was previously thought that
  proteins were responsible due to their high level
  of variability in structure and the infinite
  possible combinations of amino acids.)
• James Watson and Francis Crick used x-ray
  crystallography images obtained by Rosalind
  Franklin to determine the shape and eventually
  the structure of DNA. (1953)

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DNA Structure

• Watson and Crick determined that DNA was two
  strands of nucleic acids that were wound in a
  helix with nitrogenous bases strung between like
  rungs on a ladder. DNA shape is referred to as
  the double helix.

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DNA Structure

• The backbone of DNA is made up of deoxyribose
  sugar with an attached phosphate linked together
  by phosphodiester linkages
• The rungs of the ladder are paired nitrogenous
  bases that are suspended between the adjacent
  sugar molecules
• The bases are paired specifically Adenine
  Thymine and Cytosine Guanine (according to
  Chargaffs Rules)

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Base Pairing

• The bases pair with one purine to one pyrimidine.
  
• Adenine and Thymine form two hydrogen bonds
• Cytosine and Guanine form three hydrogen bonds

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DNA Form Facilitates Function

• The structure of DNA creates two complementary
  strands of nucleotides that can serve as
  templates for the ordering of nucleotides in the
  creation of new copies of DNA.
• The semiconservative model of DNA replication is
  the current accepted theory of how the parent
  strands of DNA create new copies of DNA. Each
  daughter strand will have one of the original
  strands.

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DNA Replication

• Origins of Replication are the sites of new DNA
  synthesis. In bacterial chromosomes there is only
  one origin of replication. In eukaryotic cells
  there can be thousands of origins of replication.
• The origin of replication opens up the DNA strand
  and creates two replication forks where new DNA
  is synthesized in a specific direction.

Replication bubbles
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Replication Forks

• Replication forks are the split section of the
  parent strand that allows the enzymes access to
  the DNA template for replication.

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DNA Directionality

• Directionality of DNA is determined by the
  anti-parallel arrangement of the DNA strand each
  end is labeled as either the 5 or 3 end.
• The 5 and 3 refer to the terminal carbons
  positional number in the deoxyribose ring. The 5
  carbon has a phosphate attached, whereas the 3
  carbon has a hydroxyl group attached

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DNA Synthesis

• New DNA is only made in the 5 to 3 direction.
  Meaning that new nucleotides are only added to
  the 3 end of the strand.

3 carbon
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Addition of Nucleotides

• The addition of a nucleotide to the emerging
  strand of DNA is accomplished by the formation of
  a phosphodiester bond between the 5end of a
  nucleoside triphosphate and the hydroxyl group of
  the 3 end of the adjacent nucleotide in the
  chain.

• The NTP loses a two-phosphate molecule
• called a pyrophosphate. The hydrolysis of the
  pyrophosphate releases the energy to drive the
• polymerization reaction.

Exergonic reaction
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Replication Enzymes

• DNA polymerases As their name suggests they
  polymerize DNA molecules. The DNA polymerases use
  the parent strand as a template to string
  together nucleotides in a complementary or
  daughter strand.
• Helicases Are enzymes that unwind the DNA double
  helix at the replication fork, so that the two
  strands are separated. Single stranded binding
  proteins then line along the two strands to keep
  them apart and accessible to the replication
  enzymes.
• Primases DNA polymerases can not start a DNA
  chain from scratch. They need a primer. The
  primer is a short stretch of RNA that is used to
  jump start the DNA synthesis process. Primases
  are responsible for creating this RNA segment
  from scratch at an origin of replication. Later
  another DNA polymerase will come along and
  replace this RNA segment with the DNA version.

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Replication Enzymes

• Ligases These enzymes are responsible for
  linking together the Okazaki fragments in the
  lagging strand. The ligases string together the
  Okazaki fragment after the DNA polymerases have
  replaced the RNA primers with DNA.
• Nucleases A DNA cutting enzyme. This enzyme is
  used in repair of DNA damage. The nuclease cuts
  out the damaged section so that polymerases can
  fill it in with the proper nucleotides.
• Telomerases These enzymes are responsible for
  elongating telomeres. They are special enzymes
  that contain a short RNA segment to use as its
  own template to elongate the telomere.

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DNA Replication

• The fact that new nucleotides are only added to
  the 3 end of the strand adds a unique challenge
  to the process of DNA replication. The double
  stranded DNA is opened up to allow the enzymes
  access to the template and give space for the
  generation of new DNA. Only one of the parent
  strands will start with the 3 end and can
  therefore be continuously elongated toward the
  replication fork. This strand is referred to as
  the leading strand.
• The other strand starts with the 5end and the
  enzymes must backtrack and build the new DNA
  strand from the 3ends of the nucleotides.
  Resulting in elongation away from the replication
  fork. This strand is referred to as the lagging
  strand.
• The enzymes will string about 100-200 nucleotides
  together and then back to the opening of the
  replication fork to begin another section. These
  sections are not yet connected and are called
  Okazaki fragments.

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Leading Strand Elongation

• The leading strand can be continuously elongated
  toward the replication fork because it is
  continuously adding nucleotides to the 3 end of
  the strand. This means that the parent strand
  begins with the 3 end and the complementary
  strand or daughter strand starts with the 5end.

5 end of new daughter strand
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Lagging Strand Elongation

• Elongation of the lagging strand is a little more
  problematic as the parent strand starts with the
  5 end. This means the nucleotides must be made
  toward the start of the template. The DNA
  polymerase works in the opposite direction on the
  lagging strand, polymerizing away from the
  replication fork instead of toward it. The
  polymerase creates a short segment of DNA and as
  the replication bubble grows another short strand
  can be made. Each segment of DNA that is created
  is called an Okazaki fragment. Each Okazaki
  fragment requires a RNA primer be made by a
  primase. Once DNA ploymerases replace the RNA
  primer with DNA a ligase comes along and
  ligates (joins together) the sugar-phosphate
  backbone of the daughter strand creating one long
  complementary DNA strand.

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Lagging Strand Elongation
Okazaki Fragments
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Ligase Joins Okazaki Fragments
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When it all goes wrong DNA Repair

• The DNA polymerase self corrects by proofreading
  the newly created daughter strand and replacing
  incorrectly paired bases.
• If a base pair error is missed or occurs as a
  result of some sort of nucleotide damage a
  mismatch repair occurs. Special enzymes are
  employed to remove the incorrect bases and
  replace them with the correct ones. (Aside Colon
  cancer has been linked to a hereditary defect in
  one of these special enzymes that does not
  correct the mismatch and allows cancer causing
  errors to accumulate in the DNA.)
• Damage that needs repair can also occur to
  existing DNA. Chemical and physical damage
  (toxins, x-rays, UV radiation, etc) can cause
  changes in the DNA. Spontaneous chemical changes
  to the bases also occur in the cell under normal
  conditions. This typically calls for nucleotide
  excision repair, where a nuclease (an enzyme that
  cuts out sections of DNA) cuts out the damaged
  section and then a DNA polymerase replaces the
  cut out section, then the sugar-phosphate
  backbone is repaired by a ligase.

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Telomeres

• The fact that the DNA polymerase can only add new
  nucleotides to the 3 end of existing nucleotides
  is a limitation that can cause a potential
  problem for organisms with linear DNA. The DNA
  polymerase can not finish the lagging strand.
  This would result in the deletion of genes.
• To combat this problem eukaryotic chromosomes
  have telomeres at the ends of their DNA strands.
  Telomeres are sequences of non-coding nucleotides
  that will not create any defects in the organism
  if they are deleted.
• In order to keep the telomeres from becoming
  increasingly shorter over time some cells have
  enzymes called telomerases that have their own
  template that allows them to elongate DNA at the
  3 end of the strand, then the polymerases extend
  the 5 end in the usual fashion.