IB Biology 2015

1. Essential idea: The structure of DNA is ideally suited to
its function
7.1 DNA structure and replication

2. Understandings
Statement Guidance
7.1 U.1 Nucleosomes help to supercoil the DNA.
7.1 U.2 DNA structure suggested a mechanism for DNA replication
7.1 U.3 DNA polymerases can only add nucleotides to the 3’ end of a
primer
7.1 U.4 DNA replication is continuous on the leading strand and
discontinuous on the lagging strand. [Details of DNA
replication differ between prokaryotes and eukaryotes. Only
the prokaryotic system is expected.]
7.1 U.5 DNA replication is carried out by a complex system of
enzymes. [The proteins and enzymes involved in DNA
replication should include helicase, DNA gyrase, single strand
binding proteins, DNA primase and DNA polymerases I and
III.]
7.1 U.6 Some regions of DNA do not code for proteins but have other
important functions. [The regions of DNA that do not code for
proteins should be limited to regulators of gene expression,
introns, telomeres and genes for tRNAs.]

3. Applications and Skills
Statement Utilization
7.1 A.1 Rosalind Franklin’s and Maurice Wilkins’ investigation of DNA
structure by X-ray diffraction
7.1 A.2 Use of nucleotides containing deoxyribonucleic acid to stop
DNA replication in preparation of samples for base
sequencing.
7.1 A.3 Tandem repeats are used in DNA profiling.
7.1 S.1 Analysis of results of the Hershey and Chase experiment
providing evidence that DNA is the genetic material.
7.1 S.2 Utilization of molecular visualization software to analyze the
association between protein and DNA within a nucleosome

4. 7.1 S.1 Analysis of results of the Hershey and Chase experiment
providing evidence that DNA is the genetic material.
Hershey and Chase Experiments (1952): Definitive proof that DNA
rather than Protein carries the hereditary information of life
E. Coli bacteriophage: A virus that infects bacteria.
Bacteriophages only contain a protein coat (capsid) and DNA.
They wanted to find out whether the protein or DNA carried the
genetic instructions to make more viruses.
They labeled either the viral proteins or DNA:
– Protein capsid: Labeled with radioactive sulfur (35S)
– DNA: Labeled with radioactive phosphorus (32P)
Radioactive labeled viruses were used to infect cells.

5. Either Bacteriophage DNA or Proteins Can be
Labeled with Radioactive Elements
7.1 S.1 Analysis of results of the Hershey and Chase experiment
providing evidence that DNA is the genetic material.

6. Hershey Chase Experiment: DNA is Genetic Material
7.1 S.1 Analysis of results of the Hershey and Chase experiment
providing evidence that DNA is the genetic material.

7. Hershey and Chase Experiments (1952):
Bacterial cells that were infected with
the two types of bacteriophage, were
then spun down into a pellet
(centrifuged), and examined.
Results:
1. Labeled viral proteins did not enter
infected bacteria (found in
supernatant).
2. Labeled viral DNA did enter bacteria
during viral infection (found in cell
pellet).
Conclusion:
Protein is not necessary to make new
viruses.
DNA is the molecule that carries the
genetic information to make new
viruses!!!!
7.1 S.1 Analysis of results of the Hershey and Chase experiment
providing evidence that DNA is the genetic material.

8. Rosalind Franklin (1950’s)
• Worked with Maurice Wilkins
• X-ray crystallography = images
of DNA
• Provided measurements on
chemistry of DNA
7.1 A.1 Rosalind Franklin’s and Maurice Wilkins’ investigation of DNA
structure by X-ray diffraction
James Watson & Francis Crick (1953)
• Discovered the double helix
by building models to
conform to Franklin’s X-ray
data and Chargaff’s Rules.

9. DNA Double Helix
Nitrogenous
Base (A,T,G or C)
“Rungs of ladder”
“Legs of ladder”
Phosphate &
Sugar Backbone
DNA
• Two strands coiled called
a double helix
• Sides made of a pentose
sugar Deoxyribose
bonded to phosphate
(PO4) groups by
phosphodiester bonds
• Center made of nitrogen
bases bonded together
by weak hydrogen bonds
7.1 U.2 DNA structure suggested a mechanism for DNA replication

10. DNA
• Stands for Deoxyribonucleic acid
• Made up of subunits called
nucleotides
• Nucleotide made of:
1. Phosphate group
2. 5-carbon sugar
3. Nitrogenous base
7.1 U.2 DNA structure suggested a mechanism for DNA replication

11. DNA Nucleotide
O=P-O
O
Phosphate
Group
N
Nitrogenous base
(A, G, C, or T)
CH2
O
C1
C4
C3 C2
5
Sugar
(deoxyribose)
O
7.1 U.2 DNA structure suggested a mechanism for DNA replication

12. Pentose Sugar
• Carbons are numbered clockwise 1’ to 5’
CH2
O
C1
C4
C3 C2
5
Sugar
(deoxyribose)
7.1 U.2 DNA structure suggested a mechanism for DNA replication

13. 13
DNA
P
P
P
O
O
O
1
2
3
4
5
5
3
3
5
P
P
P
O
O
O
1
2 3
4
5
5
3
5
3
G C
T A

14. Antiparallel Strands
• One strand of DNA
goes from 5’ to 3’
(sugars)
• The other strand is
opposite in
direction going 3’
to 5’ (sugars)
7.1 U.2 DNA structure suggested a mechanism for DNA replication

15. Nitrogenous Bases
• Double ring PURINES
Adenine (A)
Guanine (G)
• Single ring PYRIMIDINES
Thymine (T)
Cytosine (C) T or C
A or G
7.1 U.2 DNA structure suggested a mechanism for DNA replication

16. Base-Pairings
• Purines only pair with Pyrimidines
• Three hydrogen bonds required to bond
Guanine & Cytosine
CG
3 H-bonds
7.1 U.2 DNA structure suggested a mechanism for DNA replication

17. T A
•Two hydrogen bonds are required to
bond Adenine & Thymine
7.1 U.2 DNA structure suggested a mechanism for DNA replication

18. DNA Replication
7.1 U.3 DNA polymerases can only add nucleotides to the 3’ end of a
primer

19. Synthesis Phase (S phase)
• S phase during interphase of the cell
cycle
• Nucleus of eukaryotes
Mitosis
-prophase
-metaphase
-anaphase
-telophase
G1 G2
S
phase
interphase
DNA replication takes
place in the S phase.
Mitosis
-prophase
-metaphase
-anaphase
-telophase
G1 G2
S
phase
interphase
DNA replication takes
place in the S phase.
7.1 U.3 DNA polymerases can only add nucleotides to the 3’ end of a
primer

20. • DNA replication is very specific to the
arrangements of base pairs
• In DNA replication, the strands separate
– Enzymes use each strand as a template to assemble
the new strands
DNA REPLICATION
Parental molecule
of DNA
Both parental strands serve
as templates
Two identical daughter
molecules of DNA
Nucleotides
A
7.1 U.3 DNA polymerases can only add nucleotides to the 3’ end of a
primer

21. • DNA replication begins at the different
origins in the 5’ to 3’ direction at
the replication fork.
• RNA primase attaches to the DNA
and adds a small RNA primer to
provide a free 3’ OH starting point
since DNA polymerases can only add
nucleotides to the 3’ end of a primer
• DNA polymerase
III adds free nucleotides in the 5’ to 3’
direction in the direction of the
replication fork.
7.1 U.3 DNA polymerases can only add nucleotides to the 3’ end of a
primer

22. • Begins at Origins of Replication
• Two strands open forming Replication Forks (Y-
shaped region)
• New strands grow at the forks
Replication
Fork
Parental DNA Molecule
3’
5’
3’
5’
7.1 U.3 DNA polymerases can only add nucleotides to the 3’ end of a
primer

23. DNA Replication
• As the 2 DNA strands open at the origin, Replication
Bubbles form
• Prokaryotes (bacteria) have a single bubble
• Eukaryotic chromosomes have MANY bubbles
Bubbles Bubbles
7.1 U.4 DNA replication is continuous on the leading strand and
discontinuous on the lagging strand. [Details of DNA replication differ
between prokaryotes and eukaryotes. Only the prokaryotic system is
expected.]

24. 7.1 U.4 DNA replication is continuous on the leading strand and discontinuous on the
lagging strand. [Details of DNA replication differ between prokaryotes and eukaryotes.
Only the prokaryotic system is expected.]
DNA replication creates two identical strands with each strand consisting of one new and
one old strand (semi-conservative).
DNA replication occurs at many different places on the DNA strand called the origins of
replication (represented by bubbles along the strand).

25. 1. Helicase: unwinds DNA at origins of replication
2. Initiation proteins separate 2 strands  forms replication
bubble
3. Single-Strand Binding Proteins attach and keep the 2 DNA
strands separated and untwisted
4. Primase: puts down RNA primer to start replication
5. DNA polymerase III: adds complimentary bases to leading
strand (new DNA is made 5’  3’)
6. Lagging strand grows in 3’5’ direction by the addition of
Okazaki fragments
7. DNA polymerase I: replaces RNA primers with DNA
8. DNA ligase: seals fragments together
7.1 U.5 DNA replication is carried out by a complex system of enzymes.
[The proteins and enzymes involved in DNA replication should include
helicase, DNA gyrase, single strand binding proteins, DNA primase and
DNA polymerases I and III.]

26. 7.1 U.5 DNA replication is carried out by a complex system of enzymes.
[The proteins and enzymes involved in DNA replication should include
helicase, DNA gyrase, single strand binding proteins, DNA primase and
DNA polymerases I and III.]

27. DNA Replication
• DNA polymerase can only add nucleotides to the 3’ end of the
DNA
• This causes the NEW strand to be built in a 5’ to 3’ direction
RNA
PrimerDNA Polymerase
Nucleotide
5’
5’ 3’
Direction of Replication
7.1 U.5 DNA replication is carried out by a complex system of enzymes.
[The proteins and enzymes involved in DNA replication should include
helicase, DNA gyrase, single strand binding proteins, DNA primase and
DNA polymerases I and III.]

28. Remember HOW the Carbons Are Numbered!
O
O=P-O
O
Phosphate
Group
N
Nitrogenous base
(A, G, C, or T)
CH2
O
C1
C4
C3 C2
5
Sugar
(deoxyribose)
7.1 U.5 DNA replication is carried out by a complex system of enzymes. [The proteins
and enzymes involved in DNA replication should include helicase, DNA gyrase, single
strand binding proteins, DNA primase and DNA polymerases I and III.]

29. 29
Remember the Strands are Antiparallel
P
P
P
O
O
O
1
2
3
4
5
5
3
3
5
P
P
P
O
O
O
1
2 3
4
5
5
3
5
3
G C
T A

30. Synthesis of the New DNA Strands
• The Leading Strand is synthesized as a single
strand from the point of origin toward the
opening replication fork
RNA
PrimerDNA PolymeraseNucleotides
3’5’
5’
7.1 U.5 DNA replication is carried out by a complex system of enzymes.
[The proteins and enzymes involved in DNA replication should include
helicase, DNA gyrase, single strand binding proteins, DNA primase and
DNA polymerases I and III.]

31. Synthesis of the New DNA Strands
• The Lagging Strand is synthesized discontinuously against overall
direction of replication
• This strand is made in MANY short segments It is replicated from
the replication fork toward the origin
RNA Primer
Leading Strand
DNA Polymerase
5’
5’
3’
3’
Lagging Strand
5’
5’
3’
3’

32. Lagging Strand Segments
• Okazaki Fragments - series of short segments
on the lagging strand
• Must be joined together by an enzyme
Lagging Strand
RNA
Primer
DNA
Polymerase
3’
3’
5’
5’
Okazaki Fragment
7.1 U.5 DNA replication is carried out by a complex system of enzymes. [The proteins
and enzymes involved in DNA replication should include helicase, DNA gyrase, single
strand binding proteins, DNA primase and DNA polymerases I and III.]

33. Joining of Okazaki Fragments
• The enzyme Ligase joins the Okazaki
fragments together to make one strand
Lagging Strand
Okazaki Fragment 2
DNA ligase
Okazaki Fragment 1
5’
5’
3’
3’
7.1 U.5 DNA replication is carried out by a complex system of enzymes. [The proteins
and enzymes involved in DNA replication should include helicase, DNA gyrase, single
strand binding proteins, DNA primase and DNA polymerases I and III.]

34. Conservation of base sequence
The DNA base sequence is usually read down one side of the
molecule or the other. The sequence is usually read with reference
to the bases and their corresponding identifying letter.
e.g. (1) ATG CTC ATT TTA GGG CCC ATA CTC
= 24 bases thus we can write the complementary sequence of the other helix
as:
(2) TAC GAG TAA AAT CCC GGG TAT GAG
In DNA replication
(1)will act as the template for a new complementary sequence of
bases
copy 1: (1)ATG CTC ATT TTA GGG CCC ATA CTC
(2)TAC GAG TAA AAT CCC GGG TAT GAG

35. 7.1 U.1 Nucleosomes help to supercoil the DNA
• A nucleosome consists of DNA wrapped
around 8 histone proteins.
• The DNA wraps twice around the histone
protein core.
• Another histone protein is attached to the
outside of the DNA strand. It helps maintain
the colloidal structure of the nucleosome.
• DNA, because of its negative charge is
attracted to the positive charge on the amino
acids of the histone proteins.
• Tails of neighboring histones, link up during
chromosomal condensation, causing the
nucleosomes to pull closer together.
• This is part of the supercoiling process that
occurs during mitosis and meiosis
• Supercoiling in general helps regulate
transcription because only certain areas of
the DNA are accessible for the production of
mRNA by transcription. This regulates the
production of a polypeptide. http://pbil.univlyon1.fr/members/sagot/htdocs/tea
m/projects/chromo_net/images/epi.jpg

36. 7.1 U.6 Some regions of DNA do not code for proteins but have other important
functions. [The regions of DNA that do not code for proteins should be limited to
regulators of gene expression, introns, telomeres and genes for tRNAs.]
• Regulators such as enhancers are short DNA sequences that regulate protein
production or to activate transcription. Regulators such as silencers prevent
transcription. The figure below shows how an enhancer might affect gene
transcription by bringing distal DNA close to the promoter using coiling or
uncoiling with nucleosomes.
http://employees.csbsju.edu/hjakubowski/classes/ch331/bind/olbindtransciption.html

37. 7.1 U.6 Some regions of DNA do not code for proteins but have other important
functions. [The regions of DNA that do not code for proteins should be limited to
regulators of gene expression, introns, telomeres and genes for tRNAs.]
• There are many areas of DNA
containing repetitive sequences,
especially in eukaryotic DNA, in
humans it makes up between 24-37%
of our genome. These repetitive
areas usually occurs near the ends of
chromosomes.
• These non-coded regions are called
introns, they must be removed
before leaving the nucleus for protein
synthesis to take place.
• Spliceosome are constructed from
RNA and are used in eukaryotic cell
to remove these introns.
http://www.phschool.com/science/biology_place/bio
coach/images/transcription/eusplice.gif

38. 7.1 U.6 Some regions of DNA do not code for proteins but have other important
functions. [The regions of DNA that do not code for proteins should be limited to
regulators of gene expression, introns, telomeres and genes for tRNAs.]
• These repetitive sequences
called telomeres, protect the
DNA during replication. Since
enzymes can’t replicate all the
way to the end of the
chromosome, the parts that
aren’t copied are part of the
telomeres. This prevents the loss
of genes near the end of the
chromosomes.
Telomeres stained green and red at
the ends of the chromosomes
http://www.newswise.com/images/uplo
ads/2010/09/28/karlsederhr.jpg

39. • Dideoxyribonucleotides inhibit DNA
polymerase during replication, thereby stopping
replication from continuing.
• Dideoxyribonucleotides with fluorescent markers,
is incorporated into sequences of DNA, to stop
replication at the point at which they are added.
• This creates different sized fragments with
fluorescent markers that can be separated by gel
electrophoresis and analyzed by comparing the
color of the fluorescence with the fragment
length.
7.1 A.2 Use of nucleotides containing deoxyribonucleic acid to stop
DNA replication in preparation of samples for base sequencing

40. 7.1 A.3 Tandem repeats are used in DNA profiling.
• Short tandem repeats (STRs), also known as variable tandem repeats (VNTRs) are regions of
noncoding DNA that contain repeats of the same nucleotide sequence. These short repeats
show variations between individuals in terms of the number of times the sequences is
repeated.
• For example, CATACATACATACATACATACATACATA is a STR where the nucleotide sequence
CATA is repeated 7 times for one individual. However, in another individual, this tandem
repeat could occur only 11 times CATACATACATA CATACATACATACATACATACATACATACATA.
These variable tandem repeats are the basis for DNA profiling used in crime scene
investigations and genealogical tests (paternity tests). The diagram below shows how the
different number of these alleles are used to create a DNA fingerprint of an individual.
http://www.intechopen.com/source/html/16506/media/image2.jpg

41. 7.1 S.2 Utilization of molecular visualization software to analyze the association between protein and
DNA within a nucleosome
Use the RCSB Protein Bank to read about
nucleosomes and examine Jmol images of
them.
Article on nucleosomes:
http://www.rcsb.org/pdb/101/motm.do?mo
mID=7
Jmol visualisation of a nucleosome:
http://www.rcsb.org/pdb/explore/jmol.do?s
tructureId=1AOI&bionumber=1
Identify the two copies of each histone
protein. This can be done by locating
the ‘tail of each protein’. The tails of the
proteins are involved in regulating gene
expression.
Suggest how the positive charges help
to form the nucleosome with the
negatively charged DNA molecule.