Slides covering material from Topic 2.6 (and some AHL material from 7.1) of the updated IB Biology syllabus for 2016 exams

1. Structure of DNA & RNA (2.6 & 7.1 HL)
IB Diploma Biology
Essential Idea: The structure of
DNA allows efficient storage of
genetic information.

2. The human genome project which has decoded the case sequence
for the whole 6 feet of the human genome requires a data
warehouse (pictured) to store the information electronically.
Scientists have programmed nearly 500,000
DVD’s worth of data into 1 gram of DNA!

3. 2.6.1 The nucleic acids DNA and RNA are polymers of nucleotides.

4. 2.6.1 The nucleic acids DNA and RNA are polymers of nucleotides.
A Nucleotide: A single unit of a Nucleic Acid polymer
There are two types of Nucleic Acids: DNA and RNA.
Nucleic acids are very large
molecules that are constructed
by linking together nucleotides
to form a polymer.

5. 2.6.1 The nucleic acids DNA and RNA are polymers of nucleotides.
Covalent bond
Covalent bond
A Nucleotide: A single unit of a Nucleic Acid polymer
• Five carbon atoms = a pentose sugar
• If the sugar is Deoxyribose the polymer is
Deoxyribose Nucleic Acid (DNA)
• If the sugar Ribose the polymer is Ribose
Nucleic Acid (RNA)
• Acidic
• Negatively charged
• Contains nitrogen
• Has one or two rings in it’s
structure

6. 2.6.1 The nucleic acids DNA and RNA are polymers of nucleotides.
There are four nitrogen bases in DNA:
Adenine (A) Guanine (G) Thymine (T) Cytosine (C)
RNA shares the same bases except that Uracil (U) replaces Thymine
NOTE: When talking about bases always use
the full name on the first instance
• Adenine & Guanine are two-ringed bases called Purines
• Thymine & Cytosine are one-ringed based called Pyrimidines

7. 2.6.1 The nucleic acids DNA and RNA are polymers of nucleotides.
• Nucleotides a linked into a single
strand via a condensation reaction
• Bonds are formed between the
phosphate of one nucleotide and the
pentose sugar of the next
• The phosphate group (attached to the
5'-C of the sugar) joins with the
hydroxyl (OH) group attached to the 3'-
C of the sugar
• This results in a Phosphodiester bond
between the two nucleotides and the
formation of a water molecule
• Successive condensation reactions
between nucleotides results in the
formation of a long single strand

8. DNA RNA
Type of Pentose
Sugar
Number of
Strands
Two anti-parallel,
complementary strands
form a double helix
Single stranded, and
often, but not always,
linear in shape
Nitrogen Bases
Adenine (A)
Guanine (G)
Thymine (T)
Cytosine (C)
Adenine (A)
Guanine (G)
Uracil (U)
Cytosine (C)
2.6.2 DNA differs from RNA in the number of strands present, the base
composition and the type of pentose.

9. 2.6.2 DNA differs from RNA in the number of strands present, the base
composition and the type of pentose.

10. 2.6.3 DNA is a double helix made of two antiparallel strands of nucleotides linked
by hydrogen bonding between complementary base pairs.

11. 2.6.3 DNA is a double helix made of two antiparallel strands of nucleotides linked
by hydrogen bonding between complementary base pairs.

12. 2.6.3 DNA is a double helix made of two antiparallel strands of nucleotides linked
by hydrogen bonding between complementary base pairs.

13. 2.6.3 DNA is a double helix made of two antiparallel strands of nucleotides linked by
hydrogen bonding between complementary base pairs.
• Each polynucleotide chain (strand) consists of
a chain of nucleotides bonded covalently.
• Two polynucleotide chains of DNA are held
together by hydrogen bonds between
complementary base pairs:
Adenine pairs with Thymine (A=T) via two
hydrogen bonds
Guanine pairs with Cytosine (G=C) via three
hydrogen bonds
• In order for bases to be facing each other and
thus able to pair, the two strands must run in
opposite directions (i.e. they are anti-parallel)
• As the polynucleotide chain lengthens, the
atoms that make up the molecule will arrange
themselves in an optimal energy
configuration. This position of least resistance
results in the double-stranded DNA twisting
to form a double helix with approximately 10
- 15 bases per twist.
In Summary:

14. 2.6.5 Drawing simple diagrams of the structure of single nucleotides of DNA and RNA, using
circles, pentagons and rectangles to represent phosphates, pentoses and bases.
To make sure you have learn this skill you need to practice it repeatedly...
DNA: RNA:

15. 2.6.4 Crick and Watson’s elucidation of the structure of DNA using model making.
“We have discovered the secret of life!”
– Francis Crick (An English pub, 1953)
In early 1953, Linus Pauling, an American chemist proposed a
model for DNA with phosphate groups in the core of the
molecule and the nitrogen bases facing outward…
After this was disproved, three major groups, including
Pauling’s Cal Tech group, James Watson and Francis Crick at
Cambridge, and Maurice Wilkins and Rosalind Franklin at the
University of London, were competing to elucidate the
correct structure of the molecule…
Whilst others worked using an experimental basis Watson and
Crick used stick-and-ball models to test their ideas on the
possible structure of DNA. Building models allowed them to
visualize the molecule and to quickly see how well it fitted the
available evidence.
Watson and Crick ultimately won the race, publishing their
model of DNA in a 900 word paper later in 1953
http://www.hhmi.org/biointeractive/watson-constructing-base-pair-models

16. 2.6.4 Crick and Watson’s elucidation of the structure of DNA using model making.
It was not all easy going however. Their first model, a
triple helix, was rejected for several reasons:
• The ratio of Adenine to Thymine was not 1:1 (as discovered
by Erwin Chargaff)
• It required too much magnesium (identified by Franklin)
From their setbacks they realized:
• DNA must be a double helix.
• The relationship between the bases and base pairing
• The strands must be anti-parallel to allow base pairing to
happen
Because of the visual nature of their work the second
and the correct model quickly suggested:
• Possible mechanisms for replication
• Information was encoded in triplets of bases
Watson and Crick gained Nobel prizes for their discovery.
It should be remembered that their success was based
on the evidence they gained from the work of others. In
particular the work of Rosalind Franklin and Maurice
Wilkins, who were using X-ray diffraction was critical to
their success.

17. 2.6.4 Crick and Watson’s elucidation of the structure of DNA using model making.
Nucleosomes
• DNA in eukaryotes is associated with
proteins called histones.
• The octamer & DNA combination is attached
to an H1 histone, forming a nucleosome.
• The nucleosome serves to protect the DNA
from damage and to allow long lengths of
DNA to be supercoiled
Supercoiling
• Supercoiling allows the chromosomes to be
mobile in mitosis & meiosis.
• Supercoiled DNA cannot be transcribed for
protein synthesis. Allows genes to be
switched ON and OFF.

18. 7.1.11 Utilize molecular visualization software to analyze the association between protein and
DNA within a nucleosome.
Visit:
http://www.rcsb.org/pdb/101/motm.do?momID=7
and
http://www.rcsb.org/pdb/explore/jmol.do?structur
eId=1AOI&bionumber=1
Explore:
• Find the two copies of each histone
protein by locating their “tails” (H2A,
H2B, H3, and H4)
• Visualize the positively charged amino
acids on the nucleosome core. How do
they play a role in the association of
the protein core with the negatively
charged DNA?

19. 7.1.6 Some regions of DNA do not code for proteins but have other important functions.

20. 7.1.6 Some regions of DNA do not code for proteins but have other important functions.

21. 7.1.6 Some regions of DNA do not code for proteins but have other important functions.
Functions of Non-Coding, Highly-
Repetitive DNA Sequences (Introns)
Production
of RNA
Some regions on DNA function to
produce tRNA and rRNA
Gene
Expression
Non-coding regions can have an role in
regulating the expression of genes by
promoting (enhancers) or inhibiting
(silencers).
Telomeres
Telomeres are located on the ends of
eukaryote chromosomes, they have a
protective function because DNA
cannot be replicated all the way to the
ends, so telomeres prevent loss of
important genes.

22. 7.1.7 Discuss Rosalind Franklin’s and Maurice Wilkins’ investigation of DNA structure by X-ray
diffraction.
• Rosalind Franklin worked at King’s College in London as a
technician doing X-ray crystallography.
• She improved the resolution of the cameras used in order
to obtain the most detailed images yet of X-ray diffraction
of DNA. These detailed images allowed her to make very
exact measurements related to the structure of DNA.
• Her work was shared with James Watson without her
permission.
• Watson and Crick used her measurements to show that
the phosphate groups were on the outside of the DNA
double helix, and that the nitrogenous bases were more
hydrophobic and thus on the inside.
• Watson & Crick published the structure of DNA first,
without crediting Franklin. They were awarded the Nobel
prize. Franklin died of ovarian cancer she developed as a
result of her work.

23. 7.1.7 Discuss Rosalind Franklin’s and Maurice Wilkins’ investigation of DNA structure by X-ray
diffraction.
X-Ray Crystallography:
• When X-rays pass through a substance, they diffract.
• Crystals have a regularly repeating pattern, causing X-
rays to diffract in a regular pattern.
• These patterns allow for measurements & calculations
to be made about the structure of molecules.
Franklin’s X-Ray “Photo 51” Showed…
• X pattern: DNA is a helix
• Angle of X: Calculate the steepness of the helix
• Distance between horizontal bars: Distance between
bases is 3.4nm.
• Distance between center of X and top of image:
0.34nm vertically between the repeating units (bases)
in the molecule- so 10 bases per turn of the helix.

24. 7.1.10 Analysis of results of the Hershey and Chase experiment providing evidence that DNA is
the genetic material.
• Until the Hershey-Chase experiment, it was widely
assumed that protein was the genetic material that
made up chromosomes because it had great variety in
structures (20 Amino Acids would allow for greater
range of coding than just 4 nucleotides…)
• Hershey & Chase took advantage of the fact that DNA
contains phosphorus, but not sulfur, & protein
contains sulfur, but not phosphorus. Viruses have
protein coats surrounding DNA.
• They grew two types of viruses: Type 1 with radioactive
phosphorus and Type 2 with radioactive sulfur.
• They had these viruses infect cells (which involved the
injection of viral genetic material into the cell) and then
checked for the radioactive labels.
• Cells infected by the Phosphorus-labeled viruses
contained the radioactive labels. Cells infected by the
Sulfur labeled viruses did not…

25. 7.1.10 Analysis of results of the Hershey and Chase experiment providing evidence that DNA is
the genetic material.
http://highered.mheducation.com/olcweb/cgi/pluginpop.cgi?it=swf::535::535::/sites/dl/free
/0072437316/120076/bio21.swf::Hershey%20and%20Chase%20Experiment

26. THE END…

27. Bibliography / Acknowledgments
Jason de Nys
Chris Paine