Chapter 3: read pp' 4156

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Chapter 3 read pp. 41-56 skim the
rest Problems1, 2 Chapter 23 read pp.
725-732, 737-751, 761-770 skim the
rest Problems 2, 6 Chapter 24 read pp.
773-789, 797-799 skim the rest Problems 2,
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VVP Fig. 23-41 T4
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VVP Fig. 23-2
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VVP Fig. 23-15
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VVP Fig. 23-16
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VVP FIG. 23-17
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VVP p. 749
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VVP Fig. 23-29
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VVP Fig. 23-29
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Each human cell has 2 meters of DNA. (E. coli
has 1.4 mm.)
The total length of DNA in an average person is
2 x 1010 km--
compare that to the earth's diameter of 4 x 104
km!!
A human liver cell nucleus has a diameter of µm
and must contain 46 chromosomes each ca. 4.3 cm
long. Since the largest human chromosome
contains 2.4 x 108 bp it would have a length of
8.2 cm if the DNA were stretched out in the B
conformation.
In fact, the length of this chromosome during
metaphase (when it is most condensed) is about
10 µm or about 1/8000 the length it could have
as B DNA!!!
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MVA Fig. 28.7 A mitotic chromosome
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VVP Fig. 23-43
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VVP Fig. 23-47
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prolate ellipsoid 100 x 70 Angstroms.
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Properties of histones
residues MW arg lys
H1 215 23.0 1 29 H2a 129 14 9 11 H2b 125 13.8 6 16
H3 135 15.3 13 10 H4 102 11.3 14 11
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VVP Fig. 23-45
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VVP Fig. 23-44b
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MVA Fig. 28.12
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VVP Fig. 27-31 Chromosome Puffs where
transcription is occurring.
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VVP Fig. 24-25
Chemical mutagenesis
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VVP Fig. 24-23
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VVP Fig. 24-28
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VVP Fig. 24-29
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VVP Fig. 24-30
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VVP Fig. 24-25
Chemical mutagenesis
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VVP Fig. 24-28
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VVP Fig. 24-29
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VVP Fig. 24-30
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VVP Fig. 23-32b
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VVP Fig. 23-32c
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VVP Fig. 23-32a
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VVP p. 790
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VVP Fig. 24-1 Meselson and Stahl Experiment
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VVP Fig. 24-2
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DNA replication requires 1.A DNA template to
be replicated. 2.DNA helicase - this enzyme
unwinds the helical DNA at replication forks.
3.Primase - this enzyme lays down the primers
that are necessary for DNA polymerase activity.
The primers are composed of RNA. 4.DNA
polymerase III - this is the polymerase that does
the bulk of the DNA replication using its 5'(3'
polymerase activity. 5.DNA polymerase I -
the function of this polymerase during
replication is to remove the RNA primers (after
they have done their job of initiating
DNA replication) using a 5'---gt3' exonuclease
activity. It then uses its 5'---gt3' polymerase
activity to fill in the resulting gaps (Figure
5.23). 6.DNA ligase - this enzyme seals
nicks in DNA by linking up 3' hydroxyl groups
with adjacent 5' phosphate groups (Figure 5.23).
DNA Ligase will connect DNA to DNA but not DNA
to RNA - so there is never a danger of RNA
primers being stitched into the nascent DNA.
7.SSB single-strand DNA binding protein - this
protein binds single-stranded DNA at the
replication fork and physically blocks potential
hybridization - i.e. it makes sure that the DNA
is single-stranded when the polymerization
machinery is ready to replicate it.
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DNA polymerases are unable to melt duplex DNA
(i.e., break the interchain hydrogen bonds) in
order to separate the two strands that are to be
copied. All DNA polymerases so far discovered
can only elongate a preexisting DNA or RNA
strand, the primer they cannot initiate
chains. The two strands in the DNA duplex are
opposite (5-3 and 3-5) in chemical polarity,
but all DNA polymerases catalyze nucleotide
addition at the 3-hydroxyl end of a growing
chain, so strands can grow only in the 5-3
direction.
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VVP Fig. 24-3 Replication Eye
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VVP Fig. 24-4
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Consensus sequence of the minimal bacterial
replication origin based on analyses of genomes
from six bacterial species. Similar sequences
constitute each origin the 13-bp repetitive
sequences (orange) are rich in adenine and
thymine residues. The 9-bp repetitive sequences
(brown) exist in both orientations that is, the
lower-right sequence, read right to left, is the
same as that of the upper-left sequence, read
left to right. These sequences are referred to as
13-mers and 9-mers, respectively. Indicated
nucleotide position numbers are arbitrary. See
J. Zyskind et al., 1983, Proc. Nat'l. Acad. Sci.
USA 801164.
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Model of initiation of replication at E. coli
oriC. The 9-mers and 13-mers are the repetitive
sequences. Multiple copies of DnaA protein bind
to the 9-mers at the origin and then melt
(separate the strands of) the 13-mer segments.
The sole function of DnaC is to deliver DnaB,
which is composed of six identical subunits, to
the template. One DnaB hexamer clamps around each
single strand of DNA at oriC, forming the
prepriming complex. DnaB is a helicase, and the
two molecules then proceed to unwind the DNA in
opposite directions away from the origin.
Adapted from C. Bramhill and A. Kornberg, 1988,
Cell 52743, and S. West, 1996, Cell 86177.
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VVP Fig. 24-11 SSB
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Staged assembly of the replisome occurs at the
DnaA-oriC complex. IHS - Integration host
factor FIS - Factor for inversion stimulation
DnaB - helicase DnaC - helicase associated
factor SSB - single stranded binding protein
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VVP p. 787 Replication of ?X174. Big bubbles
are the primase!
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Dna polymerases
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VVP Fig. 24-14b
ß-subunit
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VVP Fig. 24-14a
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VVP Fig. 24-5
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VVP Fig. 24-12
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VVP Fig. 24-7
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VVP Fig. 24-8
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VVP Fig. 24-10a E. coli Pol I Klenow
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VVP 24-10b
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MVA Fig. 28.17
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VVP Fig. 24-13 Ligase
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VVP Fig. 24-9
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VVP Fig. 24-29
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VVP Fig. 24-22
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Alfonse, Biochemistry makes my head hurt!!
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