AP Biology Discussion Notes
Wednesday 1/27/2016
Goals for Today
• Be able to say what the central dogma of
biology is.
• Be able to describe the structure of DNA
and its associated terms
• Be able to describe the process &
players in DNA replication
• Be able to “build” a strand of DNA
Question of the Day 1/27
• What is DNA replication & what can be said
about this process & what does that mean?
(Is it liberal?)
Question of the Day 1/27
• What is DNA replication & what can be said
about this process & what does that mean?
(Is it liberal?)
Figure 16.9-1
Semiconservative Replication
A
T
C
G
T
A
A
T
G
C
(a) Parent molecule
Figure 16.9-2
Semiconservative Replication
A
T
A
T
C
G
C
G
T
A
T
A
A
T
A
T
G
C
G
C
(a) Parent molecule
(b) Separation of
strands
Figure 16.9-3
Semiconservative Replication
A
T
A
T
A
T
A
T
C
G
C
G
C
G
C
G
T
A
T
A
T
A
T
A
A
T
A
T
A
T
A
T
G
C
G
C
G
C
G
C
(a) Parent molecule
(b) Separation of
strands
(c) “Daughter” DNA molecules,
each consisting of one
parental strand and one
new strand
Chapter 16 in your book
Figure 16.10
(a) Conservative
model
(b) Semiconservative
model
(c) Dispersive model
Parent
cell
First
replication
Second
replication
• Experiments by
Matthew Meselson
and Franklin Stahl
supported the
semiconservative
model
• They labeled the
nucleotides of the old
strands with a heavy
isotope of nitrogen
15N, while any new
nucleotides were
labeled with a lighter
isotope, 14N
Figure 16.11a
EXPERIMENT
2 Bacteria
transferred to
medium with
14N (lighter
isotope)
1 Bacteria
cultured in
medium with
15N (heavy
isotope)
RESULTS
3 DNA sample
centrifuged
after first
replication
?
4 DNA sample
centrifuged
after second ?
replication
Less
dense
More
dense
Figure 16.11b
CONCLUSION
Predictions:
First replication
Conservative
model
Semiconservative
model
Dispersive
model
Second replication
DNA Replication: A Closer Look
• The copying of DNA is remarkable
in its speed and accuracy
–E.coli has about 4.6 Million
nucleotide/base pairs and replicates
DNA, then divides into 2 new cells in
less than an hour!
–Humans have ~6 Billion
nucleotide/base pairs and replicate
their DNA in a few hours
Getting Started
• Replication begins at particular sites called
origins of replication, where the two DNA
strands are separated, opening up a replication
“bubble”
• A eukaryotic chromosome may have hundreds or
even thousands of origins of replication
• Replication proceeds in both directions from each
origin, until the entire* molecule is copied
Figure 16.12a
(a) Origin of replication in an E. coli cell
Origin of
replication
Parental (template) strand
Daughter (new) strand
Doublestranded
DNA molecule
Replication
bubble
Replication fork
Two
daughter
DNA molecules
0.5 m
Synthesizing a New DNA Strand
• Enzymes called DNA polymerases catalyze the
elongation of new DNA at a replication fork
• The rate of elongation is about 500
nucleotides per second in bacteria and
50 per second in human cells
• How do we speed this up in our cells?
Figure 16.12b
(b) Origins of replication in a eukaryotic cell
Double-stranded
Origin of replication DNA molecule
Parental (template)
strand
Bubble
Daughter (new)
strand
Replication fork
Two daughter DNA molecules
0.25 m
Can you answer these questions:
• In which direction is each strand being
built?
• How is it built?
• Where is it moving towards?
• What enzymes are involved and what
are their roles?
Figure 16.15a
Leading
strand
Overview
Origin of replication
Lagging
strand
Primer
Lagging
strand
Overall directions
of replication
Leading
strand
DNA Replication
• At the end of each replication bubble is a
replication fork, a Y-shaped region where new
DNA strands are elongating
• Helicases are enzymes that untwist the double
helix at the replication forks
• Single-strand binding proteins bind to and
stabilize single-stranded DNA
• Topoisomerase corrects “over winding” ahead of
replication forks by breaking, swiveling, and
rejoining DNA strands
Figure 16.15a
Leading
strand
Overview
Origin of replication
Lagging
strand
Primer
Lagging
strand
Overall directions
of replication
Leading
strand
What enzyme?
• What enzyme will build the new DNA
strand (the new polymer of DNA)?
There is a small problem…
• Besides ONLY being able to build in the 5’ to 3’
direction, DNA polymerases cannot initiate
synthesis of a polynucleotide; they can only add
nucleotides to the 3 end
The Solution….
• The initial nucleotide strand is a
short RNA primer
Figure 16.15a
Leading
strand
Overview
Origin of replication
Lagging
strand
Primer
Lagging
strand
Overall directions
of replication
Leading
strand
Antiparallel Elongation
• The antiparallel structure of the double helix
affects replication
• DNA polymerases add nucleotides only to the free
3end of a growing strand; therefore, a new DNA
strand can elongate only in the 5to 3direction
• This creates a “leading” and a “lagging” strand
Let’s try to understand this….
Can you answer these questions:
• In which direction is each strand being
built?
• How is it built?
• Where is it moving towards?
• What enzymes are involved & what are
their roles?
Figure 16.15a
Leading
strand
Overview
Origin of replication
Lagging
strand
Primer
Lagging
strand
Overall directions
of replication
Leading
strand
Antiparallel Elongation
• Along one template strand of DNA, the DNA
polymerase synthesizes a leading strand
continuously, moving toward the replication fork
Figure 16.15
Leading
strand
Overview
Origin of replication
Lagging
strand
Primer
Lagging
strand
Leading
strand
Overall directions
of replication
Origin of
replication
3
5
RNA primer
5
3
3
Sliding clamp
DNA pol III
Parental DNA
5
3
5
5
3
3
5
Figure 16.15b
Origin of
replication
3
5
RNA primer
5
3
3
Sliding clamp
DNA pol III
Parental DNA
5
3
5
5
3
3
5
Antiparallel Elongation
• To elongate the other new strand, called the
lagging strand, DNA polymerase must work in the
direction away from the replication fork
• The lagging strand is synthesized as a series of
segments called Okazaki fragments, which are
joined together by DNA ligase
Figure 16.16
3
Overview
5
Template
strand
3
Leading
strand
3
Origin of replication
5
RNA primer
for fragment 1
Lagging strand
2
5
1
3
5
3
5
Okazaki
fragment 1
RNA primer
for fragment 2
5
Okazaki
3
fragment 2
2
Lagging
strand
1
3
5
1
5
3
5
3
2
1
3
5
5
3
2
1
3
5
Overall direction of replication
1
Overall directions
of replication
Leading
strand
Figure 16.16a
Overview
Leading
strand
Origin of replication
Lagging
strand
Lagging strand
2
1
Overall directions
of replication
Leading
strand
Figure 16.17
Overview
Origin of
replication
Leading
strand
Leading strand
Lagging
strand
Overall directions
of replication
Lagging
strand
Leading
strand
DNA pol III
5
3
3
Parental
DNA
Primer
5
3
Primase
5
DNA pol III
4
Lagging strand
DNA pol I
35
3
2
DNA ligase
1 3
5
Figure 16.17a
Overview
Leading
strand
Lagging
strand
Origin of
replication
Lagging
strand
Leading
strand
Overall directions
of replication
Leading strand
DNA pol III
5
3
3
Parental
DNA
Primer
5
3
Primase
Figure 16.17b
Overview
Origin of
replication
Leading
strand
Leading strand
Lagging
strand
Overall directions
of replication
Lagging
strand
Leading
strand
Primer
5
DNA pol III
4
3
Lagging strand
DNA pol I
35
3
2
DNA ligase
1 3
5
Figure 16.18
The DNA Replication Complex
DNA pol III
Parental DNA
5
3
5
3
3
5
5
Connecting
protein
3
Helicase
3
DNA
pol III 5
Leading strand
3
5
Lagging strand
Lagging
strand
template
Proofreading and Repairing DNA
• DNA polymerases proofread newly
made DNA, replacing any incorrect
nucleotides
Figure 16.19
5
3
3
5
Nuclease
5
3
3
5
DNA
polymerase
5
3
3
5
DNA
ligase
5
3
3
5
Evolutionary Significance of Altered DNA
Nucleotides
• Error rate after proofreading repair is low but not
zero
• Sequence changes may become permanent and
can be passed on to the next generation (when
would they be passed on?)
• These changes (mutations) are the source of the
genetic variation upon which natural selection
operates
“The Players”
in DNA Replication
• The Enzymes
– Helicase (“Hacks”)
– DNA Polymerase (“Pastes”)
– Ligase (“Links”)
•
•
•
•
•
•
Nucleotides (A,T,C,G)
Origin(s) of Replication
Leading Strand
Lagging Strand
5’  3’
Okazaki Fragments
Summary of DNA Replication
Helicase unwinds and unzips DNA at O.O.R.
LOTS of OOR’s/Chrom. in Euk’s: ONE in Prok’s.
DNA Polymerase jumps in at O.O.R. and adds new
nucleotides from 5’3’
LEADING and LAGGING strands formed from
each template strand
LAGGING strand Okazaki Fragments are
connected by Ligase
Now have two copies of the same DNA!
Can you answer these
questions:
• In which direction is each strand being
built?
• How is it built?
• Where is it moving towards?
• What enzymes are involved?
DNA assignment