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Colonie High BIOCHEMISTRY/MOLECULAR BIOLOGY Goldberg
DNA The Genetic
Material
Replication, Amplification,
and Sequencing
Scientific History
The march to understanding that DNA is
the genetic material
T.H. Morgan (1908)
Frederick Griffith (1928)
Avery, McCarty & MacLeod (1944)
Hershey & Chase (1952)
Watson & Crick (1953)
Meselson & Stahl (1958)
Genes are on chromosomes
T.H. Morgan
working with Drosophila (fruit flies)
genes are on chromosomes
but is it the protein or the DNA of the chromosomes that are the genes? through 1940 proteins
were thought to be genetic material… Why?
1908 | 1933 The “Transforming Factor”
1928
Frederick Griffith
Streptococcus pneumonia bacteria was working to find cure for
pneumonia
harmless live bacteria mixed with heat-killed infectious bacteria causes disease in mice
substance passed from dead bacteria to live bacteria = “Transforming Factor”
The “Transforming Factor”
Transformation?
something in heat-killed bacteria could still transmit
disease-causing properties
live pathogenic strain of bacteria
live non-pathogenic strain of bacteria
mice die mice live
heat-killed pathogenic bacteria
mix heat-killed pathogenic &
non-pathogenic bacteria
mice live mice die
A. B. C. D.
DNA is the “Transforming Factor”
Avery, McCarty & MacLeod
purified both DNA & proteins from
Streptococcus pneumonia bacteria
which will transform non-pathogenic bacteria?
injected protein into bacteria
no effect
injected DNA into bacteria
transformed harmless bacteria
into virulent bacteria
1944
Colonie High BIOCHEMISTRY/MOLECULAR BIOLOGY Goldberg
Avery, McCarty & MacLeod
Oswald Avery
Maclyn McCarty
Colin MacLeod
Confirmation of DNA
Hershey & Chase
classic “blender” experiment
worked with bacteriophage
viruses that infect bacteria
grew phage viruses in 2 media,
radioactively labeled with either
35S in their proteins
32P in their DNA
infected bacteria with
labeled phages
1952 | 1969
Hershey & Chase
Alfred Hershey Martha Chase
Protein coat labeled with 35S
DNA labeled with 32P
bacteriophages infect bacterial cells
T2 bacteriophages are labeled with
radioactive isotopes S vs. P
bacterial cells are agitated to remove viral protein coats
35S radioactivity found in the medium
32P radioactivity found in the bacterial cells
Which molecule
carries viral genetic info?
Hershey
& Chase
Which radioactive marker is
found inside the cell?
“Blender” Experiment
Radioactive phage & bacteria in blender
35S phage
radioactive proteins stayed in supernatant
therefore protein did NOT enter bacteria
32P phage
radioactive DNA stayed in pellet
therefore DNA did enter bacteria
Confirmed DNA is “transforming factor”
Colonie High BIOCHEMISTRY/MOLECULAR BIOLOGY Goldberg
Chargaff
DNA composition: “Chargaff’s rules”
varies from species to species
all 4 bases not in equal quantity
bases present in characteristic ratio
humans:
A = 30.9%
T = 29.4%
G = 19.9%
C = 19.8%
1947 Structure of DNA
Watson & Crick
developed double helix model of DNA
other scientists working on question:
Rosalind Franklin
Maurice Wilkins
Linus Pauling
1953 | 1962
Franklin Wilkins Pauling
Watson and Crick Rosalind Franklin (1920-1958)
Double Helix Structure of DNA
the structure of DNA suggested a mechanism
for how DNA is copied by the cell
Directionality of DNA
You need to
number the
carbons!
it matters!
OH
CH2
O
4
5
3 2
1
PO4
N base
ribose
nucleotide
Colonie High BIOCHEMISTRY/MOLECULAR BIOLOGY Goldberg
The DNA Backbone
Putting the DNA
backbone together
refer to the 3 and 5
ends of the DNA
the last trailing carbon
OH
O
3
5
PO4
base
CH2
O
base
O
P
O
C
O –O
CH2
Base Pairing in DNA
Purines
adenine (A)
guanine (G)
Pyrimidines
thymine (T)
cytosine (C)
Pairing
A : T
C : G
Anti-parallel Strands
Phosphate to sugar bond
involves carbons in 3 & 5
positions
DNA molecule has
“direction”
complementary strand
runs in opposite direction
“It has not escaped our notice that
the specific pairing we have
postulated immediately suggests
a possible copying mechanism for
the genetic material.” Watson & Crick
Bonding in DNA
….strong or weak bonds?
How do the bonds fit the mechanism for copying DNA?
hydrogen
bonds
3’
5’ 3’
5’
phosphodiester
bonds
Copying DNA
Replication of DNA
base pairing allows
each strand to serve
as a pattern for a
new strand
Models of DNA Replication
Alternative models so how is DNA copied?
Colonie High BIOCHEMISTRY/MOLECULAR BIOLOGY Goldberg
Semi-conservative Replication
Meselson & Stahl label nucleotides of “parent” DNA strands with
heavy nitrogen = 15N
label new nucleotides with lighter isotope = 14N
“The Most Elegant Experiment in Biology”
1958
parent replication
Semi-conservative replication
Make predictions…
15N strands replicated in 14N medium
1st round of replication?
2nd round?
DNA Replication
Large team of enzymes coordinates
replication
Replication: 1st step Unwind DNA
helicase enzyme unwinds part of DNA helix at ori
forms replication forks
stabilized by single-stranded binding proteins
single-stranded binding proteins
Replication: 2nd step Bring in new nucleotides to
match up to template strands
single-stranded binding proteins
energy
Energy of Replication Where does the energy for the bonding come
from?
ATP ADP AMP GTP TTP CTP GMP TMP CMP
Colonie High BIOCHEMISTRY/MOLECULAR BIOLOGY Goldberg
Energy of Replication The nucleotides arrive as nucleosides
DNA bases with P–P–P
DNA bases arrive with their own energy source for bonding
bonded by DNA polymerase III
ATP GTP TTP CTP
DNA
P III
energy
energy
energy
Replication
Adding bases
can only add
nucleotides to 3
end of a growing
DNA strand
strand grow 5'3’
energy
5'
3'
3'
5'
leading strand
Priming DNA Synthesis
DNA polymerase III
can only extend an
existing DNA molecule
cannot start new one
cannot place first base
short RNA primer is
built first by primase
starter sequences
DNA polymerase III can
now add nucleotides to
RNA primer
Leading & Lagging Strands
Leading strand - continuous synthesis
Lagging strand
- Okazaki fragments
- joined by ligase - “spot welder” enzyme
Okazaki
Okazaki Fragments Cleaning Up Primers
DNA polymerase I removes sections of RNA primer and replaces with DNA nucleotides
Colonie High BIOCHEMISTRY/MOLECULAR BIOLOGY Goldberg
Replication Enzymes
helicase
DNA polymerase III
primase
DNA polymerase I
ligase
single-stranded binding proteins
And in the end…
Ends of
chromosomes
are eroded with
each replication
an issue in
aging?
ends of
chromosomes
are protected by
telomeres
Telomeres
Expendable,
non-coding sequences
at ends of DNA
short sequence of
bases repeated 1000s
times
TTAGGG in humans
Telomerase enzyme in
certain cells
enzyme extends
telomeres
prevalent in cancers
Why?
Replication Bubble
Adds 1000 bases/second!
Which direction does DNA build?
List the enzymes & their role
DNA Polymerase Review
DNA polymerase III
1000 bases/second
main DNA building enzyme
DNA polymerase I
20 bases/second
editing, repair & primer removal
DNA polymerase III enzyme
1000 bases/second =
lots of typos!
DNA polymerase I
proofreads & corrects
typos
repairs mismatched bases
excises abnormal bases
repairs damage
throughout life
reduces error rate from
1 in 10,000 to
1 in 100 million bases
Editing & Proofreading DNA
Colonie High BIOCHEMISTRY/MOLECULAR BIOLOGY Goldberg
Fast & Accurate!
It takes E. coli <1 hour to copy
5 million base pairs in its single
chromosome
divide to form 2 identical daughter cells
Human cell copies its 6 billion bases &
divide into daughter cells in only few
hours
remarkably accurate
only ~1 error per 100 million bases
~30 errors per cell cycle
1
2
3
4
What’s it really look like?
protein RNA
The “Central Dogma”
DNA
transcription translation
replication
flow of genetic information within a cell
Polymerase Chain Reaction (PCR)
What if you have to
copy DNA with not a
lot to begin with?
PCR is a method for
making many
copies of a specific
segment of DNA
~only need 1
molecule of DNA to
start
PCR Process PCR Process It’s copying DNA in a test tube!
What do you need?
template strand
DNA polymerase enzyme
nucleotides
primer
Thermocycler
Colonie High BIOCHEMISTRY/MOLECULAR BIOLOGY Goldberg
Kary Mullis
development of PCR technique
a copying machine for DNA
1985 | 1993 PCR Process What do you need to do?
in tube: DNA, enzyme, primer, nucleotides
heat (90°C) DNA to separate strands (denature)
cool to hybridize (anneal) & build DNA (extension)
The Polymerase Problem
Heat DNA to denature it
90°C destroys DNA polymerase
have to add new enzyme every cycle almost impractical!
Need enzyme that can withstand 90°C…
Taq polymerase from hot springs bacteria
Thermus aquaticus
PCR Primers
The primers are critical!
need to know a bit of
sequence to make proper
primers
primers bracket target
sequence
start with long piece of DNA
& copy a specified shorter
segment
primers define section of
DNA to be cloned 20-30 cycles
3 steps/cycle
30 sec/step
Sanger method
determine the base sequence
of DNA
dideoxynucleotides
ddATP, ddGTP, ddTTP, ddCTP
missing O for bonding of next
nucleotide
terminates chain
DNA Sequencing DNA Sequencing
Sanger method
synthesize complementary DNA strand in vitro
in each tube:
“normal” N-bases
dideoxy N-bases
ddA, ddC, ddG, ddT
DNA polymerase
primer
buffers & salt
2
1
3
4
2
Colonie High BIOCHEMISTRY/MOLECULAR BIOLOGY Goldberg
Reading the Sequence Load gel with sequences from
ddA, ddT, ddC, ddG in separate lanes
read lanes manually & carefully
polyacrylamide gel
Fred Sanger 1978 | 1980
This was his 2nd Nobel Prize!!
1st was in 1958 for the
structure of insulin
Advancements to Sequencing
Fluorescent tagging
no more radioactivity
all 4 bases in 1 lane each base a different color
Automated reading
Advancements to Sequencing
Fluorescent tagging sequence data
Computer read & analyzed
Applied Biosystems, Inc
(ABI) built an industry on
these machines
Advancements to Sequencing Capillary tube electrophoresis
no more pouring gels
higher capacity & faster
384 lanes
PUBLIC
Joint Genome Institute (DOE)
MIT
Washington University of St. Louis
Baylor College of Medicine
Sanger Center (UK)
PRIVATE
Celera Genomics
Big labs!
economy of scale
Colonie High BIOCHEMISTRY/MOLECULAR BIOLOGY Goldberg
Automated Sequencing Machines
Really BIG labs!
Human Genome Project U.S government project
begun in 1990 estimated to be a 15 year project
DOE & NIH initiated by Jim Watson
led by Francis Collins
goal was to sequence entire human genome 3 billion base pairs
Celera Genomics
Craig Venter challenged gov’t
would do it faster, cheaper
private company
Different Approaches
3. Assemble DNA sequence using overlapping sequences.
“map-based method” gov’t method
“shotgun method” Craig Venter’s method
1. Cut DNA from entire chromosome
into small fragments and clone.
2. Sequence each segment & arrange
based on overlapping nucleotide
sequences.
1. Cut chromosomal DNA segment into
fragments, arrange based on
overlapping nucleotide sequences,
and clone fragments.
2. Cut and clone into smaller fragments.
Human Genome Project
On June 26, 2001, HGP published the “working
draft” of the DNA sequence of the human genome.
Historic Event! blueprint
of a human
the potential to
change science
& medicine
Sequence of 46 Human
Chromosomes
3 billion base pairs
3G of data
Raw Genome Data
Colonie High BIOCHEMISTRY/MOLECULAR BIOLOGY Goldberg
GenBank
Database of
genetic
sequences
gathered
from
research
Publicly
available!
Organizing the Data
And we didn’t stop there… The Progress
Dec-82
Dec-83
Dec-84
Dec-85
Dec-86
Dec-87
Dec-88
Dec-89
Dec-90
Dec-91
Dec-92
Dec-93
Dec-94
Dec-95
Dec-96
Dec-97
Dec-98
Dec-99
Dec-00
Dec-01
Dec-02
J
un-03
S1
0.E+00
5.E+09
1.E+10
2.E+10
2.E+10
3.E+10
3.E+10
4.E+10
First 2 bacterial genomes
complete
122+ bacterial
genomes
Data from NCBI and TIGR
(www.ncbi.nlm.nih.gov and www.tigr.org )
first eukaryote complete
(yeast)
first metazoan complete
(flatworm)
17
eukaryotic
genomes
complete or
near
completion
including
Homo
sapiens,
mouse and
fruit fly
Official “15 year”
Human Genome Project:
1990-2003.
# of DNA base pairs
(billions)
in GenBank
How does our genome stack up?
Organism
Genome Size
(bases)
Estimated
Genes
Human (Homo sapiens) 3 billion 30,000
Laboratory mouse (M. musculus) 2.6 billion 30,000
Mustard weed (A. thaliana) 100 million 25,000
Roundworm (C. elegans) 97 million 19,000
Fruit fly (D. melanogaster) 137 million 13,000
Yeast (S. cerevisiae) 12.1 million 6,000
Bacterium (E. coli) 4.6 million 3,200
Human Immunodeficiency Virus (HIV) 9700 9
…you will certainly find something!
0 25 50 75 100 125
0
25
50
75
100
Millions of years ago
Horse/ donkey
Sheep/ goat
Goat/cow
Llama/ cow
Pig/ cow
Rabbit/ rodent
Horse/cow
Human/rodent
Dog/ cow
Human/ cow
Human/kangaroo
Nu
cle
oti
de s
ub
sti
tuti
on
s