A.

Unit and diversity

1. Nucleic Acids
1.2.1 - 1.2.10
 A.1.2 Nucleic Acids
How does the structure of nucleic acids allow hereditary information to be stored?

All of the information encoded on a computer is ultimately based on

binary code-a code based on two options, O and 1. A computer byte is
8 binary digits. Figure 1 shows the letters converted to binary code.
How would the term "DNA" be represented in binary code? Because
each digit can have four values instead of two, DNA codons with three
symbols have 64 possible values, compared with a binary byte which
has 256 possibilities using eight symbols. For this reason, scientists
have worked to develop DNA computers.
Figure 1.
 A.1.2 Nucleic Acids
How does the structure of DNA facilitate accurate replication?

Cells divide for the purposes of maintenance, repair, growth and

reproduction. Why must dividing cells produce new DNA? The
structure of DNA is dependent on complementary base pairing-A is
always paired with T and C is always paired with G. Complementarity
guides accurate replication. Chromosomes are mainly composed of
DNA. These chromosomes (Figure 2) are seen during the early stages
of cell division. The double structure of each chromosome shows that
the DNA has replicated to form two identical strands, known as Figure 2. A coloured scanning
electron micrograph of two
chromatids. These strands are linked by a region called the human chromosomes

centromere.
 A.1.2.1 DNA as the genetic material of all living organisms

Genetic material is a store of information. If copied, it can be passed from cell to cell and also
from parent to offspring. Because genetic material is inherited it is sometimes called hereditary
information. All living organisms use DNA to store hereditary information.
The full name for DNA is deoxyribonucleic acid. The other type of nucleic acid is ribonucleic acid
or RNA. Nucleic acids were first discovered in the cell nucleus, hence the name. They are very
large molecules, made from subunits called nucleotides which link to form a polymer.
Some viruses use RNA as their genetic material, for example, coronaviruses and HIV. This
observation does not seem to fit the theory that genes are made of DNA in all living organisms.
Figure 3. The virus shown in the centre (black
However, reproduction is a fundamental property of living organisms and viruses cannot structure) uses DNA as its genetic material. The
virus has burst open and its
reproduce themselves. Instead, they rely on a host cell for this process so they are not considered
DNA has spilled out of the polyhedral head,
to be true living organisms. Therefore, they do not falsify the claim that all living organisms use where it is stored

DNA as their genetic material.

 A.1.2.2 Components of a nucleotide

Nucleotides consist of three parts: Figure 4 shows these parts and how they are linked together to
• A sugar, which has five carbon atoms so is a pentose form an RNA nucleotide. The base and the phosphate are both
sugar linked by covalent bonds to the pentose sugar. The five carbon
• A phosphate group, which is the acidic and atoms in the pentose sugar are numbered, with the base linked to
negatively charged part of nucleic acids Cl and the phosphate to C5.
• A base that contains nitrogen and has either one or Figure 5 shows a nucleotide in symbolic form, with a circle to
two rings of atoms in its structure. represent the phosphate, a pentagon for the pentose sugar and a
rectangle for the base.

Figure 5. Simple diagram of a nucleotide

Figure 4. Parts of a nucleotide

 A.1.2.3 Sugar-phosphate bonding and the sugar-phosphate "backbone" of DNA and RNA

To link nucleotides together into a chain or polymer, covalent bonds are formed
between the phosphate of one nucleotide and the pentose sugar of the next
nucleotide.
Whenever nucleic acids are produced by living organisms, the nucleotides are
always added the growing polypeptide in the same way: the phosphate of the
nucleotide being added is linked by a covalent bond to the pentose sugar of the
previous nucleotide. Linking together nucleotides in this way creates a series of
alternating sugar and phosphate groups, with a chain of carbon, oxygen and
phosphorus atoms covalently bonded together. This chain forms a strong sugar-
phosphate backbone in DNA and RNA molecules that helps to conserve the
Figure 6. The oxygen atom shown in red forms links
sequence of bases. between the phosphate of one nucleotide and the
pentose sugar of the next nucleotide
 A.1.2.4 Bases in each nucleic acid that form the basis of a code

There are four different bases in DNA and in RNA. Three bases are the same
but the fourth one differs. All of the bases contain nitrogen this is why they are
often referred to as nitrogenous bases.
Each nucleotide contains one base so there are four types of nucleotide in DNA
and in RNA. Any two nucleotides can be linked to each other, because the
phosphate and sugar used to make the bond are the same. Any base sequence is
therefore possible along a DNA or RNA molecule and the number of possible
sequences is almost infinite.
Table 1.
The sequence of bases is how information is stored. The information is stored
in a coded form -this is the universal genetic code that is shared by all
organisms.
 Data-based questions: Bases in DNA

Look at the molecular models in Figure 7 and answer the following questions:
1. State one difference between adenine and the other bases. [1]
2. Each of the bases has a nitrogen atom bonded to a hydrogen atom in a similar position (shown lower left). Deduce
how this nitrogen is used when a nucleotide is being assembled from its subunits. [2]
3. Identify three similarities between adenine and guanine. [3]
4. Compare the structure of cytosine and thymine. [4]
5. Although the bases have some shared features, each one has a distinctive chemical structure and shape.
Remembering the function of DNA, explain why it is important for each base to be distinctive. [5]
 Communication skills: Interpreting and evaluating information presented in different forms
Figure 7 in the data-based questions shows three different representations of each base. The first is a
structural formula, the second is a ball and stick model and the third is a space filling model. The command
term "evaluate" means to make an appraisal by weighing up strengths and limitations.
Evaluate each tvpe of representation. Which was most useful in answering the data-based questions?
 A.1.2.5 RNA as a polymer formed by condensation of nucleotide monomers

RNA is a single, unbranched polymer of nucleotides. The nucleotides are subunits of a

polymer, so they are monomers. The number of nucleotides in a molecule of RNA is
unlimited, but they are always linked in the same way, by a condensation reaction.
In a condensation reaction, two molecules are combined to form a single molecule and
water is eliminated. Hydroxyl groups (OH) on the phosphate of one nucleotide and on
the pentose sugar of another nucleotide are used. One of the OH groups is removed
entirely. It is combined with the hydrogen from the other OH, producing water. The
remaining oxygen forms a new covalent bond, linking the two nucleotides. This is
shown in Figure 9. Figure 8. RNA polymers can be represented
using circles, pentagons and rectangles
A.1.2.5 RNA as a polymer formed by condensation of nucleotide monomers

Figure 9. Condensation reaction between two nucleotides

 A.1.2.6 DNA as a double helix made of two antiparallel strands of nucleotides with the two strands
linked by hydrogen bonding between complementary base pairs

DNA is composed of strands or polymers of nucleotides. The pentose sugar in

each nucleotide is deoxyribose and the bases are adenine, cytosine, guanine and
thymine.
A DNA molecule consists of two strands of nucleotides linked to each other by
their bases. The links between the bases are hydrogen bonds. Adenine (A) only
forms hydrogen bonds with thymine (T). Guanine (G) only forms hydrogen bonds
with cytosine (C). This results in complementary base pairing. A and T
complement each other by forming base pairs and similarly G and C complement
each other by forming pairs.

Figure 10. The double helix

 A.1.2.6 DNA as a double helix made of two antiparallel strands of nucleotides with the two strands
linked by hydrogen bonding between complementary base pairs

The two strands of nucleotides are parallel to each other. However, they run
in opposite directions so they are said to be antiparallel. For this reason, one
strand ends with the phosphate group of the terminal nucleotide while the
other strand ends with a deoxyribose. If the two strands were oriented in the
same direction, the bases would not be able to form hydrogen bonds with
each other.
DNA molecules usually adopt a helical shape. A helix is a coiled structure
that has a constant diameter of 2 nanometres (2 nm). Because of the two
strands, DNA is a double helix. Figure 10 shows its features. Figure 11. Complementary base pairing between the
antiparallel strands of DNA
Drawings of the structure of DNA on paper cannot show all features of the
three-dimensional structure of the molecule. Figure 11 shows how the
structure of DNA can be represented simply in a diagram.
 A.1.2.7 Differences between DNA and RNA

There are three important differences between the two types of nucleic acid:
1. There are usually two polymers of nucleotides in DNA, whereas there is only one
in RNA. The polymers are often referred to as strands, so DNA is double-stranded
and RNA is single-stranded.
2. The four bases in DNA are adenine, cytosine, guanine and thymine. The four
bases in RNA are adenine, cytosine, guanine and uracil, so uracil is present instead
of thymine in RNA.
3. The pentose sugar within DNA is deoxyribose, whereas the sugar in RNA is
ribose. Figure 12 shows that deoxyribose has one fewer oxygen atom than ribose.
The full names of DNA and RNA are based on the type of sugar in them -
Figure 12. Ribose has an OH group and an H atom
deoxyribonucleic acid and ribonucleic acid. attached to carbon 2, whereas deoxyribose has two H
atoms
 A.1.2.8 Role of complementary base pairing in allowing genetic information to be replicated and
expressed

In DNA, adenine can only pair with thymine and cytosine can only pair with guanine. This is complementary base
pairing. It allows an exact copy of a DNA molecule to be made in a process called replication. In DNA replication,
the two strands of the double helix separate. Each of the original strands serves as a guide, or template, for the
creation of a new strand. The new strands are formed by adding nucleotides one by one and linking them together.
Each nucleotide that is added must be carrying the base that is complementary to the next base on the template strand.
This means the newly synthesized strand on each of the two template strands should have exactly the same base
sequence as the other template strand. Replication changes one original DNA molecule into two identical DNA
molecules, each with one strand from the original molecule and one new strand. This is called semi-conservative
replication. Genetic information consists of sections of DNA called genes.
 A.1.2.8 Role of complementary base pairing in allowing genetic information to be replicated and
expressed

Each gene contains information needed for a particular purpose. When the information in a
gene has an effect on the cell, this is called gene expression. The first stage in expressing a
gene is the copying of its base sequence, but the copy is made of RNA rather than DNA.
Only one of the two DNA strands is used as a template for this. The rules of complementary
base pairing are followed but adenine on the template strand pairs with uracil on the new
strand of RNA, rather than thymine. This process of making an RNA copy of the base
sequence of DNA is called transcription.
RNA that is produced by transcription may have a regulatory or structural role in the cell, or
it may be used in protein synthesis. To synthesize a protein, the base sequence of the RNA
molecule is translated into the amino acid sequence of a protein. Again, complementary base
pairing is involved. Both transcription and translation are more fully described in Topic D1.2.

Figure 13. Semi-conservative replication of DNA

 A.1.2.9 Diversity of possible DNA base sequences and the limitless capacity of DNA for storing
information

Genetic information is stored in the base sequence of one of the two strands of a DNA molecule. Any sequence of
bases is possible.
• There are four possibilities for each base in the sequence-A, C, G or T.
• There are 42 or 16 possibilities for a sequence of two bases-AA, AC, AG and so on.
• There are 43 or 64 possibilities for a sequence of three bases-AAA, AAC, AAG and so on.
• With n bases, there are 4" possible sequences. As n increases, the number of possibilities becomes immense. With
a sequence of just 10 bases, there are over a million possibilities.
DNA molecules can be any length, adding to the potential diversity of base sequences. The range of possible
sequences is effectively limitless, which is an ideal feature for an information storage system.
 A.1.2.9 Diversity of possible DNA base sequences and the limitless capacity of DNA for storing
information

The diameter of a DNA molecule is just 2 nanometres, so

immense lengths of DNA can be stored in a very small
volume. Compared with data-storage systems devised by
humans, DNA is very economical, both in terms of the
space it takes up and the amount of material used to make
it.

Figure 14. A sperm is a DNA delivery system. These human sperm cells
each contain 3.3 picograms of DNA, with a total length of about 2 metres
and over 3 billion base pairs in total. The microscope image has a grid of
lines 50 micrometres apart. How long is each sperm and how wide is the
head where the DNA is stored?
 Data-based questions: DNA lengths

1. In Homo sapiens, the smallest chromosome land therefore the shortest DNA molecule) is the Y chromosome
which has 57,227,415 base pairs. Assuming that the human genome has 3.08 billion base pairs in total, what
percentage of this does the Y chromosome contain? [1]
2. The bacterium Carsonella ruddi has just 173,904 base pairs in its genome, with an estimate of 224 genes. Of these,
194 code for proteins. A surprisingly low 7.3% of the bases are guanine. Calculate the percentage of bases that are
adenine, cytosine and thymine. [3]
3. Canine circovirus has a genome of 2,063 bases with two protein-coding genes. This type of virus has a protein
coat that is only 17 nanometres in diameter. Its genetic material is single-stranded DNA. Suggest one advantage and
one disadvantage of this DNA being single-stranded. [2]
 Data-based questions: DNA lengths

4. Bacteria can store genetic information in small circular DNA molecules called plasmids. A plasmid with 1,440
base pairs has been found in the bacterium Acetobacter pasteurianus. The main chromosome of this bacterium has
3.155 Mb (Mb = megabase pairs).What is the ratio between the length of the plasmid and the length of the main
chromosome? [2]
5. Can you find examples of DNA molecules from animals, bacteria, viruses or plasmids that are shorter than the
examples given here? Can you find an example of DNA with less than 7.3% guanine? [2]
 A.1.2.10 Conservation of the genetic code across all life forms as evidence of universal common
ancestry

The sequence of bases in DNA or RNA contains information in a coded form. The information is decoded during
protein synthesis. Groups of three bases are called codons and have meanings in the code. There are 64 different
codons, because each base in a codon can be any of four, so there are 4 × 4 × 4 combinations. Each of the 64 codons
has a meaning:
• Most codons specify one particular amino acid.
• One codon signals that protein synthesis should start.
• Three codons signal that protein synthesis should stop.
Details of the genetic code are described in Topic D1.2.
It is an extraordinary fact that-with a few minor exceptions-all living organisms and all viruses use the same genetic
code. It represents a sort of genetic language.
 A.1.2.10 Conservation of the genetic code across all life forms as evidence of universal common
ancestry

Humans use many different spoken languages, each of which is an effective form of communication. Many different
versions of a genetic code could be devised and they would probably function perfectly well, but all life forms use
essentially the same version. For this reason, it is called the universal genetic code.
The minor exceptions to the universal genetic code found in some organisms are changes to the meaning of one of
the 64 codons. In most cases, one of the three stop codons has changed to code for a specific amino acid instead.
Life has been diversifying by evolution over billions of years so it is not surprising that there have been a few very
small changes to the genetic code in some organisms. It is noteworthy that the code has changed so little and that all
forms of life still speak essentially the same genetic language.
 Communication skills: Evaluating the role of emotions and attitudes in science

The words below were spoken by Marshall Nirenberg, who was awarded the Nobel Prize in Physiology or
Medicine in 1968 for his work on the genetic code.
The finding that the code is universal had a terrific philosophical effect on me. I knew everything about
evolution at the time, but these findings were so immediate and so profound, because l understood that
most or all forms of life on this planet use the same genetic instructions and so we are all related.
We're related to all living things and when I came in the garden and saw the plants, the squirrels and some
of the birds, it really had a profound effect on me, which lasts to this day. I think that the feeling of being
one with nature is very real and in fact is very true: we all use the same genetic language.
 Communication skills: Evaluating the role of emotions and attitudes in science

1. Why did the universality of the genetic code have such a profound effect on Marshall Nirenberg and
others at the time?
2. What are the implications of the recognition of the unity of life, to scientists and to other people?
3. Are there other examples of scientific discoveries causing a profound change in attitudes?
4. To what extent do emotional responses such as the one described here support or run counter to
stereotypical representations of scientists?
 Communication skills: Evaluating the role of languages in science

A language is a code which ascribes agreed meanings to symbols.

1. What are the benefits of sharing a common language?
2. For scientists, why is the standardization of terminology viewed as essential?
3. Esperanto is (see Figure 15) an international language created by Ludwik
Zamenhof in 1887. He hoped that a universal second language would promote
world peace and understanding. What are the difficulties in creating a new
language? Why does Esperanto not persist widely today?
4. In what ways is language diversification and extinction analogous to speciation?

Figure 15. Colours in Esperanto

 TOK TIME

Phoebus Levene made significant contributions to the development

of our understanding of nucleic acids. He established the existence of
the sugar-phosphate backbone in nucleic acids; he identified
deoxyribose as the sugar in DNA; and he coined the name nucleotide.
He also incorrectly stated that DNA was made up of repeating units
of the four DNA nucleotides stacked together. This was known as the
tetranucleotide hypothesis. This hypothesis led Levene to state that
DNA could not be the hereditary material, because the
tetranucleotides were not sufficiently variable to be the basis of the
code for the tremendous diversity of life that exists. This idea was
widely accepted. Instead, proteins were thought to form the
Figure 1. A tetranucleotide molecule
hereditary material, because they were known to have great variety of
structure.
 TOK TIME

Figure 2 shows the results of an experiment carried out in 1928 by

Griffiths involving viruses. Injecting mice with the rough strain of a
virus did not cause the death of the mice. The smooth strain did cause
the death of the mice. The heat-killed version of the smooth strain did
not cause death. However, mixing the heat-killed smooth version with
the living version of the non-deadly rough version did cause death.
Somehow the genetic material of theheat-killed version was able to
transform the living non-virulent version to the virulent version. In
1944, Avery, McCarty and McCleod took the experiment further. From
Griffith's experiment, they were aware that dead virulent strains of
Figure 2. Avery, McCleod and McCarty were aware
bacteria could transform living strains to make them.virulent. that heat-killed virulent bacteria contained a
chemical that could transform non-virulent bacteria.
They worked to identify the transforming chemical
was
 TOK TIME

In different experiments, they attempted to establish what the transforming material was by adding enzymes that
would break down different chemicals to determine if they could interfere with the transformation process. They
added RNAase, proteinase and DNAase. The DNAase was able to interfere with the transformation process. This
established that the hereditary material was DNA.
In 1950, Erwin Chargaff analysed the nucleotide composition of cells from a number of different species. He found
that the amount of adenine (A) was not equal to the amount of guanine (G), and the amount of thymine (T) was not
equal to the amount of cytosine (C). This was sufficient evidence to establish that the tetranucleotide hypothesis was
incorrect. The weight of evidence was beginning to support the theory that DNA was the genetic material. The
Hershey and Chase experiment in 1952 showed convincingly that DNA was the genetic material. The combination
of the three experiments was enough to establish that the new knowledge was an improvement upon past knowledge.
 End of chapter questions
.

1. Table 1 compares the physical properties of water and air.

a. Specific heat refers to the amount of energy it takes to change the temperature of one gram of substance by 1°C.
i. Identify which substance (air or water) is more resistant to changes in temperature. [1]
ii. Identify the habitat that would have a more stable thermal environment and discuss the implications of this. [3]
 End of chapter questions
.

b. Thermal conductivity is a measure of the degree to which the medium is a conductor of heat.
i. Calculate the factor by which the thermal conductivity of water exceeds the thermal conductivity of air. [2]
ii. Identify the medium in which it would be more difficult for organisms to sustain their internal temperatures
above that of the surrounding medium. [1]

c. Buoyancy is a measure of the upward force provided by a medium to counteract gravity. It is a function of the
density of the medium and the volume of the object.
i. Which organism would have to expend more energy to counteract the effects of gravity: a swimming seal or a
bird in flight? [1]
ii. Suggest a possible relationship between fish having air bladders and buoyancy. [2]
 End of chapter questions

d. Viscosity is the force per unit area resisting flow.

i. Calculate the factor by which the viscosity of water exceeds
the viscosity of air. [2]
ii. Identify the medium that offers the greater resistance to
movement. [1]
e. Construct a visual representation that compares the advantages
and disadvantages of air and water as a habitat for a flying bird
and a swimming seal. [4]
 End of chapter questions

2. Most intertidal animals are adapted to a marine

existence. However, during exposure to air at low tide, they
are subjected to the heat stress that is characteristic of the
terrestrial environment. This can affect the ability of
intertidal organisms to survive and reproduce.
The limpet Lottia giganted is an important food source for
shore birds and for subsistence human harvesters. A study
was carried out to model thermal stress. Some of the results
are shown in Figure 2.
 End of chapter questions
.

a. Compare and contrast the temperature variations over time between air (graph C) and water (graph D). [2]
b. Identify the temperature that is viewed as being lethal to limpets (graph A and graph B).
c. Graph A and Graph B represent the temperature over time in two areas: 0.5 m above the average low level water line
and 1.5 m above the average low level water line.
i. Deduce, with a reason, which graph represents which position. [2]
ii. Deduce which location results in a higher mortality rate due to thermal stress. [1]

3. Analysis of the base composition of the polio virus shows that it is adenine 30.4%, guanine 25.4%, cytosine 19.5%
and thymine 0.0%
a. From this data, what is the evidence that the polio virus is
i. an RNA virus. [1]
ii. Single-stranded. [1]