Download The molecular basis of inheritance

Ch. 16 Warm-Up
1. Draw and label a nucleotide.
2. Why is DNA a double helix?
3. What is the complementary DNA strand to:
DNA: A T C C G T A T G A A C
Ch. 16 Warm-Up
1. What was the contribution made to science by these
people:
A.Hershey and Chase
B.Franklin
C.Watson and Crick
2. Chargaff’s Rules: If cytosine makes up 22% of the
nucleotides, then adenine would make up ___ % ?
3. Explain the semiconservative model of DNA
replication.
Ch. 16 Warm-Up
1. What is the function of the following:
A. Helicase
B. DNA Ligase
C. DNA Polymerase (I and III)
D. Primase
E. Nuclease
2. How does DNA solve the problem of slow replication on the
lagging strand?
3. Code the complementary DNA strand:
3’ T A
G C T A A G C T A C 5’
4. What is the function of telomeres?
THE MOLECULAR BASIS OF
INHERITANCE
Chapter 16
What you must know





The structure of DNA.
The major steps to replication.
The difference between replication, transcription,
and translation.
The general differences between the bacterial
chromosome and eukaryotic chromosomes.
How DNA is packaged into a chromosome.
Problem:
Is the genetic material of organisms made of
DNA or proteins?
Frederick Griffith (1928)
Frederick Griffith (1928)
Conclusion: living R bacteria transformed into
deadly S bacteria by unknown, heritable
substance
Oswald Avery, et al. (1944)
 Discovered that the transforming agent was
DNA


Their conclusion was based on experimental evidence that only DNA
worked in transforming harmless bacteria into pathogenic bacteria
Many biologists remained skeptical, mainly because little was known
about DNA
Hershey and Chase (1952)

Bacteriophages: virus that infects bacteria; composed of
DNA and protein
Protein = radiolabel S
DNA = radiolabel P
Hershey and Chase (1952)
Conclusion: DNA entered infected bacteria  DNA must
be the genetic material!
Edwin Chargaff (1947)
Chargaff’s Rules:
 DNA composition varies
between species
 Ratios:
 %A = %T and %G = %C
Rosalind Franklin (1950’s)




Worked with Maurice Wilkins
X-ray crystallography = images of DNA
Provided measurements on chemistry of DNA
The width suggested that the DNA molecule was
made up of two strands, forming a double helix.
James Watson & Francis Crick (1953)

Discovered the
double helix by
building models to
conform to
Franklin’s X-ray
data and
Chargaff’s Rules.
James Watson & Francis Crick (1953)




Watson and Crick built models of a double helix to
conform to the X-rays and chemistry of DNA
Franklin had concluded that there were two
antiparallel sugar-phosphate backbones, with the
nitrogenous bases paired in the molecule’s interior
At first, Watson and Crick thought the bases paired
like with like (A with A, and so on), but such pairings
did not result in a uniform width
Instead, pairing a purine with a pyrimidine resulted
in a uniform width consistent with the X-ray
LE 16-UN298
Purine
Purine++purine:
purine:too
toowide
wide
Pyrimidine
+ pyrimidine:
too
narrow
Pyrimidine
+ pyrimidine:
too
narrow
Purine + pyrimidine: width
consistent with X-ray data
Structure of DNA
DNA = double helix


“Backbone” = sugar +
phosphate
“Rungs” = nitrogenous
bases
By the 1950s, it was already
known that DNA is a
polymer of nucleotides,
each consisting of a
nitrogenous base, a sugar,
and a phosphate group
Structure of DNA
Nitrogenous Bases





Adenine (A)
Guanine (G)
Thymine (T)
Cytosine (C)
purine
pyrimidine
Pairing:



purine + pyrimidine
A=T
GΞC
Structure of DNA
Hydrogen bonds between base pairs of the two strands
hold the molecule together like a zipper.
Covalent bonds connect the nucleotide components
together
Structure of DNA
Antiparallel: one strand (5’ 3’), other strand runs in
opposite, upside-down direction (3’  5’)
DNA Comparison
Prokaryotic DNA






Double-stranded
Circular
One chromosome
In cytoplasm
No histones
Supercoiled DNA
Eukaryotic DNA






Double-stranded
Linear
Usually 1+ chromosomes
In nucleus
DNA wrapped around
histones (proteins)
Forms chromatin
Problem:
How does DNA replicate?
Replication: Making DNA from existing DNA
3 alternative
models of DNA
replication
Meselson & Stahl
Meselson & Stahl
Replication is semiconservative –
“daughter” DNA molecules consist of one original
parental strand and one new strand
DNA Replication Video
http://www.youtube.com/watch?v=4jtmOZaIvS0
&feature=related
Major Steps of Replication:
1. Helicase: unwinds DNA at origins of replication
a. Initiation proteins separate 2 strands  forms replication bubble
2. Primase: puts down RNA primer to start replication
3. DNA polymerase III: adds complimentary bases to leading
strand (new DNA is made 5’  3’)
4. Lagging strand grows in 3’5’ direction by the addition of
Okazaki fragments
5. DNA polymerase I: replaces RNA primers with DNA
6. DNA ligase: seals fragments together
1. Helicase unwinds DNA at origins of replication
and creates replication forks
Getting Started: Origins of Replication




Replication begins at special sites called origins of
replication, where the two DNA strands are separated
by helicase, 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
At the end of each replication bubble is a replication
fork, a Y-shaped region where new DNA strands are
elongating
2. Primase adds RNA primer
Priming DNA Synthesis



DNA polymerases cannot initiate synthesis of a
polynucleotide; they can only add nucleotides to the 3
end
The initial nucleotide strand is a short one called an
RNA or DNA primer
An enzyme called primase can start an RNA chain
from scratch
3. DNA polymerase III adds nucleotides in 5’3’
direction on leading strand
Elongating a New DNA Strand



Enzymes called DNA polymerase III catalyze the
elongation of new DNA at a replication fork
Each nucleotide that is added to a growing DNA
strand is a nucleoside triphosphate
The rate of elongation is about 500 nucleotides per
second in bacteria and 50 per second in human cells
Replication on leading strand
Leading strand vs. Lagging strand
4. DNA polymerase III adds nucleotides in 3’5’
direction on lagging strand

Only one primer is needed to synthesize the leading
strand, but for the lagging strand each Okazaki
fragment must be primed separately
LE 16-15_1
Primase joins RNA
nucleotides into a primer.
3
5
5
3
Step 1:
Primase
joins RNA
nucleotides
into a
primer
Template
strand
Overall direction of replication
LE 16-15_2
3
Primase joins RNA
nucleotides into a primer.
5
5
Template
strand
3
3
DNA pol III adds
DNA nucleotides to
the primer, forming
an Okazaki fragment.
RNA primer
5
Overall direction of replication
3
5
Step 2:
DNA pol IIl
adds
DNA
nucleotides to
the primer,
forming
an Okazaki
fragment
LE 16-15_3
Primase joins RNA
nucleotides into a primer.
3
5
5
Template
strand
3
3
DNA pol III adds
DNA nucleotides to
the primer, forming
an Okazaki fragment.
RNA primer
3
5
5
After reaching the
next RNA primer (not
shown), DNA pol III
falls off.
Okazaki
fragment
3
3
5
5
Overall direction of replication
Step 3:
After
reaching the
next RNA
primer (not
shown), DNA
pol III
falls off.
LE 16-15_4
Primase joins RNA
nucleotides into a primer.
3
5
5
Template
strand
3
3
DNA pol III adds
DNA nucleotides to
the primer, forming
an Okazaki fragment.
RNA primer
3
5
5
After reaching the
next RNA primer (not
shown), DNA pol III
falls off.
Okazaki
fragment
3
3
5
5
After the second fragment is
primed, DNA pol III adds DNA
nucleotides until it reaches the
first primer and falls off.
5
3
3
5
Overall direction of replication
Step 4:
After the
second
fragment is
primed, DNA pol
III adds DNA
nucleotides
until it reaches
the
first primer and
falls off.
LE 16-15_5
Primase joins RNA
nucleotides into a primer.
3
5
5
3
Template
strand
3
DNA pol III adds
DNA nucleotides to
the primer, forming
an Okazaki fragment.
RNA primer
3
5
5
After reaching the
next RNA primer (not
shown), DNA pol III
falls off.
Okazaki
fragment
3
3
5
5
After the second fragment is
primed, DNA pol III adds DNA
nucleotides until it reaches the
first primer and falls off.
5
3
3
5
5
3
DNA pol I replaces
the RNA with DNA,
adding to the 3 end
of fragment 2.
3
5
Overall direction of replication
Step 5:
DNA pol I
replaces
the RNA with
DNA,
adding to the 3
end
of fragment 2.
LE 16-15_6
Primase joins RNA
nucleotides into a primer.
3
5
5
3
Template
strand
3
DNA pol III adds
DNA nucleotides to
the primer, forming
an Okazaki fragment.
RNA primer
3
5
5
After reaching the
next RNA primer (not
shown), DNA pol III
falls off.
Okazaki
fragment
3
3
5
5
After the second fragment is
primed, DNA pol III adds DNA
nucleotides until it reaches the
first primer and falls off.
5
Step 6:
DNA ligase
forms a
bond between
the newest
DNA and the
adjacent DNA
of fragment 1.
3
3
5
5
3
Step 7:
DNA pol I replaces
the RNA with DNA,
adding to the 3 end
of fragment 2.
3
5
DNA ligase forms a
bond between the newest
DNA and the adjacent DNA
of fragment 1.
The lagging
strand in the region
is now complete.
5
3
3
5
Overall direction of replication
The lagging
strand in the
region
is now
complete.
Okazaki Fragments:
Short segments of DNA
that grow 5’3’ that are
added onto the Lagging
Strand
DNA Ligase: seals
together fragments
Proteins That Assist DNA Replication



Helicase untwists the double helix and separates the
template DNA strands at the replication fork
Single-strand binding protein binds to and stabilizes
single-stranded DNA until it can be used as a template
Topoisomerase corrects “overwinding” ahead of
replication forks by breaking, swiveling, and rejoining
DNA strands
Proteins That Assist DNA Replication




Primase synthesizes an RNA primer at the 5 ends
of the leading strand and the Okazaki fragments
DNA pol III continuously synthesizes the leading
strand and elongates Okazaki fragments
DNA pol I removes primer from the 5 ends of the
leading strand and Okazaki fragments, replacing
primer with DNA and adding to adjacent 3 ends
DNA ligase joins the 3 end of the DNA that
replaces the primer to the rest of the leading strand
and also joins the lagging strand fragments
Concept Check
1.
2.
3.
4.
5.
Which of the following best describes the arrangement of the sides of the DNA
molecule?
A. twisted
B. antiparallel
C. bonded
D. alternating
If a DNA molecule is found to be composed of 40% thymine, what percentage of
guanine would be expected.
A. 10%
B. 20%
C. 40%
D. 80%
The enzymes that break hydrogen bonds and unwind DNA are:
A. primers B. forks
C. helicases
D. polymerases
During replication, what enzyme adds complimentary bases?
A. helicase
B.synthesase C. replicase
D. polymerase
6. The base pair rules states that:
A. Replication is semiconservative
B. A pairs with T, G pairs with C
C. DNA is a double helix held together by hydrogen bonds
D. A pairs with G, T pairs with C
Proofreading and Repair



DNA polymerases proofread as bases added
Mismatch repair: special enzymes fix incorrect
pairings
Nucleotide excision repair:
 Nucleases
cut damaged DNA
 DNA poly and ligase fill in gaps
Nucleotide Excision Repair
Errors:
 Pairing
errors: 1 in 100,000
nucleotides
 Complete DNA: 1 in 10 billion
nucleotides
Problem at the 5’ End



DNA poly only adds
nucleotides to 3’ end
No way to complete 5’
ends of daughter strands
Over many replications,
DNA strands will grow
shorter and shorter
Telomeres: repeated units of short nucleotide sequences
(TTAGGG) at ends of DNA


Telomeres “cap” ends of DNA to postpone erosion of genes
at ends (TTAGGG)
Telomerase: enzyme that adds to telomeres
 catalyzes the lengthening of telomeres in eukaryotic germ
cells
Telomeres stained
orange at the ends of
mouse chromosomes
Telomeres & Telomerase
BioFlix: DNA Replication
http://media.pearsoncmg.com/bc/bc_0media_b
io/bioflix/bioflix.htm?8apdnarep