Download 1. Explain why researchers originally thought

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Chapter 16 sec 1 & 2 RQ
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What is a virus that infects
bacteria called? bacteriophage
Who actually took the X-ray
diffraction photo of DNA’s
structure? Rosalind Franklin
What are the bonds between
nitrogenous bases? Hydrogen bonds
What does the “semiconservative
model” describe? DNA replication
What does “topoisomerase” do?
Relieves the strain of replicating DNA molecules;
breaks, swivels, and rejoins DNA strands
Why researchers originally thought
protein was the genetic material.
• Proteins are macromolecules with great
heterogeneity and functional specificity
• Little was known about nucleic acids
• The physical and chemical properties of
DNA seemed too uniform to account for
the multitude of inherited traits 
The experiment that led to the discovery
that DNA was the genetic material in cells.
• Frederick Griffith in 1928
• Trying to find a vaccine to fight pneumonia
• Experimented with the two strains of
pneumococcus; smooth & rough
• Smooth caused the disease, rough did not
• When dead S strain was mixed with live R,
the mice DID die, indicating an acquired
ability 
Transformation and viruses and their
effects on bacteria.
• Change in
phenotype due to
the assimilation of
external genetic
material by a cell
• Viruses can inject
their information
into cells and cause
drastic changes in
behavior 
Hershey & Chase experiment
The three components of a nucleotide.
1. Pentose
(5-C sugar)
2. Phosphate
3. Nitrogenous
base 
The nitrogenous bases found in DNA;
pyrimidines and purines.
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Pyrimidines
Purines
6 membered ring of • 5 membered ring
carbon and
with 6 membered
nitrogen
ring
C – cytosine
• A – adenine
T – thymine (DNA) • G – guanine 
U – uracil (RNA)
How Watson and Crick deduced the structure
of DNA and what evidence they used.
• Built models to
conform to x-ray
data
- sugar phosphate
backbone
- nitrogenous base
interior 
The “base-pairing rule” and it’s significance.
• A – T : 2 hydrogen
bonds
• G – C : 3 hydrogen
bonds
• Suggests the
mechanisms for DNA
replication
• Dictates combination
of complementary
pairs 
The structure of DNA and the kind of chemical bond
that holds the two strands together.
• Hydrogen bonds hold the nitrogen
bases together
• Van der Waals forces help keep helix
spiral shape
• Covalent bonds link the sugarphosphate backbone 
Semiconservative replication and the
Meselson-Stahl experiment.
Chapter 6 Sections 2 & 3 RQ
1. What does primase synthesize? A primer
2. Okazaki fragments make up which
replicating strand? lagging
Telomeres are special nucleotide sequences
3. _____
found at the ends of eukaryotic
chromosomal DNA molecules.
4. Which proteins make up almost half of
chromatin? histones
5. The less compacted, more dispersed,
euchromatin
“true chromatin” is called _______.
The process of DNA replication and the role of helicase, single
strand binding protein, DNA polymerase, ligase, and primase.
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The helical molecule untwists while it copies its 2
antiparallel strands simultaneously
Very rapid – 50 nucleotides are copied per second
Very accurate – one in ten billion nucleotides are
incorrect
Helicase  catalyzes the unwinding of the parental
double helix to expose the template
Single strand binding protein  keeps the
separated strands apart and stabilizes the
unwound DNA
Topoisomerase – relieves twisting strain
Polymerase and ligase  catalyze the filling-in
process
Primase  the enzymes that polymerize the short
segments of RNA (primers) to get the DNA
replication started 
The energy source that drives the
endergonic synthesis of DNA.
• It is the hydrolysis of nucleoside
triphosphates, which are nucleotides with a
triphosphate covalently linked to the 5’
carbon of the pentose
• Exergonic hydrolysis of this phosphate
bond drives the endergonic synthesis of
DNA  it provides the required energy to
form the new covalent linkages between
nucleotides 
Antiparallel DNA strands and why continuous
synthesis of both is not possible.
• Antiparallel  the sugarphosphate backbones of the 2
complementary DNA strands
run in opposite directions
• DNA can only elongate in the
5’ to 3’ direction due to
polarity issues
- 3’ end has a hydroxyl group
- 5’ end has a phosphate 
The leading strand and the lagging strand.
• Leading  continuous
DNA synthesis, it is
synthesized as a single
polymer in the 5’ to 3’
direction towards the
replication fork
• Lagging  the DNA
strand that is
discontinuously
synthesized against
the overall direction
of replication 
The lagging strand is synthesized when DNA
polymerase can add nucleotides only to the 3’ end.
• The lagging strand is
produced as a series
of Okazaki fragments
in the 5’  3’ direction
• Fragments are ligated
by DNA ligase which
catalyzes the
formation of a
covalent bond between
the 3’ end of each
fragment to the 5’ end
of the chain 
The role of DNA polymerase, ligase, and repair
enzymes in DNA proofreading and repair.
• DNA polymerases and ligase catalyze
the filling-in process of the new DNA
strands
• Repair enzymes excise ( remove) the
damaged segments and the gap is
filled in by the correct nucleotides 
Pictures 
the role of telomeres in solving the endreplication problem with the lagging DNA
strand.
• Telomere  series of short tandem repeats
at the ends of eukaryotic chromosomes;
prevents chromosomes from shortening with
each replication cycle
• Telomerase  enzyme that periodically
restores this repetitive sequence to the ends
of DNA molecules 
prokaryotic and eukaryotic genomes.
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Prokaryotic
Usually circular
Smaller
Found in the
nucleoid region
Less elaborately
structured and
folded
Eukaryotic
• Complexed with a large
amount of protein to
form chromatin
• Highly extended and
tangled during
interphase
• Found in the nucleus 
the current model for progressive levels of
DNA packing.
• Nucleosome  basic unit of DNA packing [formed
from DNA wound around a protein core that
consists of 2 copies each of the 4 types of histone
(H2A, H2B, H3, H4)]
• A 5th histone (H1) attaches near the bead when
the chromatin undergoes the next level of packing
• 30 nm chromatin fiber  next level of packing;
coil with 6 nucleosomes per turn
• the 30 nm chromatin forms looped domains, which
are attached to a nonhistone protein scaffold
(contains 20,000 – 100,000 base pairs)
• Looped domains attach to the inside of the nuclear
envelope 
how histones influence folding in eukaryotic DNA.
• Histones  small proteins rich in
basic amino acids that bind to DNA,
forming chromatin
• Contain a high proportion of positively
charged amino acids which bind
tightly to the negatively charged
DNA 
heterochromatin and euchromatin.
Heterochromatin
• Chromatin that
remains highly
condensed during
interphase and is
NOT actively
transcribed
Euchromatin
• Chromatin that is
less condensed
during interphase
and IS actively
transcribed
• Becomes highly
condensed during
mitosis 