Structure and Function of Nucleic Acids

Chromosome theory of inheritance

DNA replication

Helicase
Topoisomerases
ssb protein 3’
5’
5’

Primase
New strands
Christine Carrington
2022
DNA polymerase I
3’
Chromosome theory of inheritance

The established theory that genes are

linked to chromosomes and that
chromosomes are the carriers of the
genetic material (DNA).
 Development of the chromosome
theory of inheritance
• Gregor Mendel
– Austrian priest and scientist
– Studied inheritance of traits in pea plants
– father of genetics

• 1860's: proposed that discrete inherited factors segregate and

assort independently during gamete formation
– https://www.nature.com/scitable/topicpage/gregor-mendel-and-the-principles-
of-inheritance-593/ Gregor Mendel
(1822 -1884)

• Worked out that “inherited factors”:

– are paired in organisms
– separate during gamete formation (gametes carry one of pair)
– fertilization restores the paired condition.
 Development of the chromosome theory of
inheritance
1875: mitosis (somatic
cell division) described

1890: meiosis (formation

of gametes) decribed
 Development of the chromosome
theory of inheritance
1900: Correns (Germany), von Seysenegg (Austria) and deVries
(Netherlands) independently rediscovered Mendel's principles of segregation
and independent assortment.
 Development of the chromosome
theory of inheritance

1902: Sutton, Boveri and others noticed parallels between

behaviour of Mendel's factors and behavior of chromosomes:
– Chromosomes and genes both paired in diploid cells.
– Homologous chromosomes separate and allele pairs segregate
during meiosis.
– Fertilization restores the paired condition of both chromosomes
and genes.
Theodor Boveri

Based upon these observations, biologists developed the

chromosome theory of inheritance:
– Mendelian factors or genes are located on chromosomes.
– It is the chromosomes that segregate and independently assort.

Walter Sutton
 Which component is the genetic material?

• Proteins or DNA?
• Protein initially favoured
• 1928 Griffith experiment
suggested protein not the genetic
material.
Frederick Oswald T.
• 1944 Avery and colleagues Avery
Griffith
(1920s) confirmed Griffith’s findings; (1940s)
showed that DNA was the
genetic material.
 The transforming principle
Griffith (1928)

Conclusion: (i) Molecules that can carry inheritable information are present in S strain
cells; (ii) the inheritable information is NOT denatured by heat treatment.
 Avery et al (1944)

http://biology.kenyon.edu/courses/biol114/KH_lecture_images/How_DNA_works/how_DNA-works.html
 Discovery of the structure of DNA
Rosalind Franklin
(25 July 1920 – 16 April 1958)
English chemist and X-
ray crystallographer
whose X-ray diffraction
images of DNA led to
discovery of DNA double
helix.

Photo 51
This X-ray diffraction
image of crystallized
DNA was critical
evidence in identifying
James Watson & Francis Crick are credited with the structure of DNA.
the discovery of the molecular structure of DNA in
1953. They received the Nobel Prize for this
discovery in 1962.
The genetic material in all cells is DNA

DNA is the most important

molecule of life
Responsible for maintaining the
integrity of cells and organisms
during their life-time and from one
generation to another.
Flow of genetic information
Flow of genetic information

Protein synthesis
 DNA replication occurs
during interphase prior to cell
division

Ref: http://www.accessexcellence.org/AB/GG/comparison.html
 DNA replication

Original
ds DNA
molecule

Original
strands

New
strands

Two identical
DNA molecules
 Enzymes and other proteins involved
in DNA replication*
• Helicase Also required are DNA
• Topoisomerase template and dNTPs
• Single strand binding
proteins
• Primase
• DNA polymerase III
• DNA polymerase I
• Ligase
• Telomerase * E. coli replication used as model; essentially the same
in other organisms
 Initiation of replication
Replication begins at the origin of replication (Ori)

circular DNA
with a single
Ori

linear DNA with several Ori

 Replication is bidirectional
Circular DNA (in bacteria)
Ori

Double
Original strands in black stranded Replication forks
New strands in red DNA

There are two replication forks because replication begins at

the Origin of replication (Ori) and proceeds in two directions as
shown by the blue arrows.
 Replication is bidirectional
Linear DNA (in eukaryotes)

5’ 3’
3’ 5’

With linear DNA molecules there are numerous origins of replication and at
each origin replication proceeds in two directions.

Newly synthesized DNA

 dsDNA  ssDNA
Helicase
unwinds DNA
Single strand binding
protein stabilises single
stranded DNA

Topoisomerases relieve
supercoiling ahead of
replication fork
Topoisomerase I
relieves supercoiling
by nicking DNA
then resealing after
rotation

ntri.tamuk.edu/cell/ topoisomerase.gif
 Enzymes and other proteins at replication fork

Replication fork moving this way

Helicase
Consider the Topoisomerases
ssb protein 3’
events occurring at
one of the 5’
replication forks in
5’
a replication
bubble
Primase
New strands DNA polymerase III

DNA polymerase I
3’
 Synthesis of new strands
• Synthesis of polynucleotides by polymerases always occurs in a 5’ to 3’
direction (nucleotides are always added to the 3’ end of a growing chain)

No!!!
X 5’ 3’ 5’ 3’

Yes!
Step 1: 5’ 3’
Yes!
Step 2: 5’ 3’

Step 3: 5’ 3’
 Primase synthesises a PRIMER

Direction of
NTP added to
synthesis G
3’ end U
RNA primer C
5’ 3’ C
A
U A GG
A T C C AG G A T C C AG G
3’ 5’
Single strand DNA template
Note complimentary base pairing
The enzyme PRIMASE is a DNA dependent
RNA polymerase
DNA polymerase III extends the primer by
adding dNTPs

A C
Direction of
synthesis G
T
C
New DNA
RNA primer
3’ dNTPs added
5’ to 3’ end
U A GG UC C T A G G T C
A T C C AG G A T C C AG G
3’ 5’
DNA template
Note complimentary base pairing
DNA polymerase III extends the primer by
adding dNTPs

A C
Direction of
synthesis G
T
C
New DNA
RNA primer
3’ dNTPs added
5’ to 3’ end
U A GG UC C T A G G T C
A T C C AG G A T C C AG G
3’ 5’
DNA template
Note complimentary base pairing
 Enzymatic activity of DNA polymerase III

DNA dependent DNA polymerase

• 5’ to 3’ polymerase activity
• Processivity =~1000 nucleotides
• Speed = ~1000 nucleotides/second
• Also has 3’ to 5’ exonuclease activity
 DNA pol III uses its 3’ to 5’ exonuclease activity to
remove errors

Direction of
synthesis
1. Mismatch!!! No
5’ 3’ hydrogen bond
formation.
U A GG UC C T A G G T C G
A T C C AG G A T C C AG G

3’ 5’
DNA template G
3’
2. DNA pol III uses
exonuclease activity to G T C
remove mismatched C
nucleotide C AG G 3. Correct nucleotide
added
 Leading and Lagging strands

Helicase and topoisomerase

5’ separate strands
3’
3’
5’

5’
Primase makes primers in 5’ 3’
3’ direction

DNA pol III can extend primer on upper strand because it has
available 3’ end.
 Leading and Lagging strands con’t

3’ As the unzipping of strands

continues, the enzymes advance.
5’ 3’

DNA pol III can extend primer on

3’ lower strand but cannot work on
5’ end of upper strand.

New primer is laid down on the

Primase upper strand which
5’ is then extended by DNA pol III.
DNA pol III
 Leading and Lagging strands con’t

3’ Primase

Upper (lagging strand)

is synthesised in short
fragments known as
Okasaki fragments
3’

DNA pol III Lower (leading strand) is

synthesized continuously
5’
Enzymic activity of DNA polymerase I

• DNA dependent DNA polymerase

• 5’ to 3’ polymerase activity
– Processivity =~20 nucleotides
– Speed =~10 nucleotides/sec
• 3’ to 5’ exonuclease activity to correct errors
• Also has 5’ to 3 exonuclease activity to remove
RNA primers
 DNA polymerase I removes primer
DNA pol I
DNA pol III
3’ Primase
5’ 3’

3’

DNA pol I uses its 5’ 3’

exonuclease activity to
5’
remove primers
DNA polymerase I fills gaps and edits errors
DNA pol I
DNA pol III
3’ Primase
5’
3’

3’ DNA pol I uses its 5’

to 3’ polymerase
activity to fill gaps,
and it’s 3’to 5’
exonuclease activity
5’ to edit any errors.
 Ligase joins fragments

3’
5’ 3’
5’ Ligase forms a phosphodiester
bond between the 5’ phosphate
and 3’ hydroxyl groups on
adjacent Okasaki fragments

5’
Synthesis of leading and lagging strands
Synthesis of leading and lagging strands
Leading and lagging strands in a
replication bubble

homepages.ius.edu/ GKIRCHNE/DNA.htm
 Replication of circular DNA
When this primer is
removed the gap
created is filled by
5’ 3’ DNA pol I using the
free 3’OH on the
lagging strand

When this primer

Replication forks removed, gap created
filled by DNA pol I
Leading 5’ using the free 3’OH
strand
3’ on the leading strand

One newly created dsDNA molecule

 Linear DNA: removal of primer by DNA pol I leaves gaps at the ends of
lagging strands that cannot be filled by DNA pol I since there is no free 3’OH
group available. These gaps are filled by the enzyme TELOMERASE

Linear DNA
Newly synthesized DNA

5’ 3’

5’
3’

Gaps left at these ends when

primers are removed are filled by
TELOMERASE
 Telomerase fills overlapping ends of lagging strands at ends of
linear DNA molecules. The following is one possible mechanism
by which it works
If a primer is 3’
removed and
there is no free
3’ end for DNA
5’
pol I to work
with. 3’ 3. Ligase joins these ends

4. Loop is cut open 3’ 5’

2. Polymerase fills gap

1.Telomerase creates a primer