Unit 1: DNA and the Genome - duncanrig.s-lanark.sch.uk · Unit 1: DNA and the Genome Sub-topic 1.1 The Organisation and Structure of DNA Sub-topic 1.2 The Replication of DNA . Higher

Higher Biology Pupil Course Notes

Duncanrig Secondary MHC 2014 Page 1 of 17

Unit 1: DNA and the Genome

Sub-topic 1.1 The Organisation and Structure of DNA

Sub-topic 1.2 The Replication of DNA



On completion of these sub-topics I will be able to:

State what is meant by prokaryote and eukaryote

State that prokaryotes contain a circular chromosome

State that eukaryotes contain linear chromosomes

State that eukaryotic DNA is packaged with proteins in the nucleus

State that mitochondria and chloroplasts also contain circular DNA molecules

Describe a plasmid and state that plasmids are found in yeast and bacteria

Describe the structure of a nucleotide

Number the carbons on the sugar in a nucleotide

State that DNA is a double stranded helix with antiparallel strands

Describe how covalent bonds are involved in producing DNA strands

State the complementary base pairing found in DNA

State that DNA is replicated by semi-conservative replication

State the 5 requirements for DNA replication

Describe the roles of the enzymes DNA polymerase and ligase in DNA

replication

Describe the process of replication of DNA

Explain why leading and lagging strands form during DNA replication

State that the Polymerase Chain Reaction (PCR) produces many copies of a

specific section of DNA

Describe the cycle in PCR

Explain the importance of primers in PCR

Explain the use of positive and negative controls in PCR

Describe a practical application of PCR



Prior Learning:

Unit 1 Cell Biology:

1.1 Cell structure:

Cells differ in structure as to whether they are animal, plant, fungi or bacterial

cells.

The detail of the organelles inside living cells is known as the ultrastructure.

Nucleus, cell membrane, cytoplasm, mitochondrion and ribosome are

organelles found in both animal and plant cells.

Nucleus contains genetic information and controls all cell activities.

Ribosome is the site of protein synthesis.

Chloroplast is the site of photosynthesis.

A bacterium and a fungus, such as yeast, are unicellular organisms.

Plasmid is a structure found in a bacterium.

Bacterium has a cell wall, and the chromosomal material is not in a nucleus.

Fungus has a cell wall and has a nucleus.

1.4 DNA and the production of proteins:

Chromosomes contain genetic information that gives rise to an organism’s

characteristics.

Chromosomes are made from a chemical called deoxyribonucleic acid (DNA).

DNA is a double stranded helix.

Each strand of DNA is made up of subunits which have DNA bases as part of

their structure.

The two DNA strands are held together by complementary base pairs.

The four bases found in DNA are called Adenine (A), Thymine (T), Cytosine (C)

and Guanine (G).



1.1 (a) Structure and Arrangement of DNA

All living cells contain genetic material, at least at some stage of their lives.

In some cells, known as eukaryotes (e.g. plant and animal cells), genetic material

is stored mainly in the nucleus of the cell. It consists of molecules of a chemical

called DNA (deoxyribonucleic acid) and is arranged in linear structures known

as chromosomes. However, some DNA can be found as small circles inside

mitochondria and the chloroplasts of green plants.

In other cells, known as prokaryotes (e.g. bacterial cells), the genetic material is

found as a large circular chromosome as well as smaller rings known as

plasmids. There are no linear chromosomes.

Linear chromosomes, circular chromosomes and plasmids are all made of DNA.

Prokaryotic Cell e.g. bacterial cell Eukaryotic Cell e.g. plant cell

Complete the table below to show the differences between prokaryotic and

eukaryotic cells. Eukaryotic organisms contain membrane-bound organelles.

Prokaryotic organisms DO NOT contain membrane-bound organelles.

Characteristic of Cell Prokaryote Eukaryote Nucleus

Shape of most chromosomes

Plasmids present in cytoplasm

Circular DNA present in some organelles

Cell wall

Cell membrane

Chloroplast

Cytoplasm

l Vacuole

Nucleus



The Arrangement of DNA in Linear Chromosomes

Strands of DNA are very long molecules. In order to fit them into the nucleus of a

eukaryotic cell and prevent them tangling, the molecules must be organised in a

particular way.

Molecules of DNA are tightly coiled and wrapped around protein bundles. They are

able to unwind when required to do so and then wind up again.

1.1 (b) The Structure of DNA

A molecule of DNA consists of two strands. Each strand is made up of repeating sub-

units known as nucleotides.

Each DNA nucleotide consists of three components:

A deoxyribose sugar

A phosphate group

An organic base.

Bundle of protein

DNA



Deoxyribose sugar

This is a 5 carbon sugar. It is represented diagrammatically as a pentagon.

The carbons are always numbered in a particular way as shown below.

Therefore deoxyribose sugar molecules have a 3’ end and a 5’ end.

Phosphate group

This is usually represented diagrammatically as a small circle.

Organic base

There are 4 types of base found in DNA nucleotides. Each is a different shape and is

complimentary to one other.

They are

Adenine (A)

Thymine (T)

Guanine (G)

Cytosine (C)

They are represented by 4 different shapes as shown.

Colour thymine yellow Colour adenine purple

Colour guanine pink Colour cytosine green

1’

2’ 3’

4’

5’

T A

G C



These three basic components join together in a particular arrangement, known as a

nucleotide.

As there are 4 different types of bases, there are therefore 4 different types of

nucleotides.

Using the individual shapes for the four different bases (see previous page), draw

the four types of nucleotides that can be made in the space below.

Shade each of the bases with the appropriate colour and label them with their

names.

Phosphate

Deoxyribose sugar

Base



Forming a DNA Strand

To form each strand of DNA, a strong chemical covalent bond forms between the

phosphate group of one nucleotide and the 3’ carbon of the next nucleotide. As each

nucleotide joins in a similar fashion, a long strand of nucleotides forms, each linked

by their sugar and phosphate. This forms the sugar phosphate backbone of the

DNA strand.

Label the three parts of the nucleotide and the type of bond indicated in the

following diagram.

Base Pairing

Two strands of nucleotides join together to make a molecule of DNA. The strands

join with each other by forming weak hydrogen bonds between the bases.

Due to the shape of the bases and the type of bonding which occurs, only certain

base pairing is possible.

Adenine always pairs with Thymine

and

Cytosine always pairs with Guanine

-----------------------

Bond

3’

5’

3’

5’



On the diagram below, label where a hydrogen bond would be found.

The hydrogen bonds hold the two strands together and forms a ladder-like structure.

The whole thing is twisted like a spiral staircase and is known as a double helix.

In order to fit together one of the strands needs to be ‘upside-down’ compared to

the other. They are known as antiparallel strands. To lengthen a strand of DNA,

nucleotides can only be added to the 3’ end of the molecule. Therefore one strand

has its growing end at the bottom of the chain, while the other strand ‘grows’ from

the top.



On the following diagram, mark the 3’ end and the 5’ end of each DNA strand.

DNA arrangement and structure – What do I know?

Answer the questions (in sentences) from Page 14 ‘Higher Biology’ by Torrance.

Check your answers.

Two strands twisted into

a coil (double helix)

Pairs of bases linking

strands



1.2 (a) The Replication of DNA

DNA has the capability of replicating itself. This is necessary during the division of a

cell in order to ensure that the chromosome complement of each of the two new

cells is identical to the original cell.

Process of Replication

The process begins with the double helix unwinding and as it does, the weak

hydrogen bonds (which held the base pairs of the two strands together) break. This

allows the two strands to separate and is sometimes referred to as ‘unzipping’.

It means that the individual bases on the nucleotides become exposed and the DNA

molecule forms a Y-shape. This area of separation is called a replication fork.

As with all complex biological reactions, replication requires specific enzymes. An

enzyme called DNA polymerase is responsible for the sugar-phosphate bonding of

nucleotides. However, this enzyme can only add new nucleotides to a chain which

has already been started. In order for DNA polymerase to add any nucleotides, a

primer must be present. A primer is a short strand of joined up nucleotides formed

at the 3’ end of the DNA to be copied.

Replication fork

a: template

b: leading strand

c: lagging strand

d: replication fork

e: primer.

e



Each strand on the parental DNA acts as a template against which another strand

can be built up from free DNA nucleotides present in the nucleus.

Weak hydrogen bonds form between the bases of the DNA nucleotides and the

bases of the parental DNA, following the base-pairing rule.

DNA polymerase then forms a sugar-phosphate bond between the primer and the

first adjacent nucleotide and then between subsequent nucleotides as they link into

place.

Replication of the parental strand is continuous and forms what is known as the

leading strand in DNA replication.

Lagging strand in DNA replication

Due to the fact that DNA polymerase is only able to add nucleotides to the 3’ end of

a DNA molecule, the parental strand which has the 5’ end has to carry out

replication in short fragments. Each of the fragments needs a primer to bind to the

3’ end to start the process and allow DNA polymerase to carry out its function. Once

the replication of a fragment is completed, the primer is replaced with DNA. Next

another enzyme, called ligase, joins the fragments together.

This strand is known as the lagging strand.

If a chromosome is very long, there may be several replication forks at various

stages along its length. This speeds up the copying process.



There are therefore 5 requirements for the replication of DNA. These are:

DNA (to act as a template)

Primers

DNA nucleotides (4 different types)

Enzymes (including DNA polymerase and ligase)

ATP (a chemical which supplies energy for the process to occur)

When copying is completed, the two new DNA molecules each form a separate

double helix. Each DNA molecule is know as being semi-conservative, as each

contains one strand from the original parent and one newly synthesised strand.

1.2 (b) Polymerase Chain Reaction (PCR)

The purpose of the polymerase chain reaction is to increase or amplify DNA so that

many copies of it can be made from even a very small amount. This could then be

used for a number of purposes, including forensic testing such as DNA

fingerprinting. This process happens outside the body of an organism (known as in

vitro).

It is a process which mimics the natural replication of DNA.

Firstly, the DNA to be amplified is heated to 95oC to break the hydrogen

bonds between the bases, therefore separating the two strands.

The DNA strands are then cooled to about 55oC.

Primers which have been made to be complementary to a specific target

sequence at the 3’ end are applied and bind to their target sequence at this

temperature.

It is then heated again to approximately 72oC.

A special heat tolerant form of DNA polymerase is then able to add

nucleotides to the primers at the 3’ end of the original DNA strand.

The first cycle of replication produces two identical molecules of DNA. The cycle is

run again, using both the original and the new copies of the DNA. Continual

repetition of the cycle means that millions of copies can be produced in about 3

hours.



Control Experiments

Whatever technique is being carried out, it is essential to have an experimental set

up that will allow you to verify that you are measuring what you intended. To do

this, you must set up the appropriate control experiment(s).

The Use of Positive and Negative Controls in PCR

1. A positive control contains a template of DNA with a known sequence to

which the primers are complementary. This means that if it is unsuccessful,

you know that there is something wrong with the set-up, e.g. problems with

the primers or the conditions.

2. A negative control would have a template which is not complementary to the

primers or might have no DNA template. This means that if there is

amplification, there must have been some contamination.



Below is an example of a practical application of PCR.

Forensic Testing

A sample of DNA which has been left at a crime scene is amplified. It is then cut into

fragments and separated out using gel electrophoresis. This produces a banding

pattern. This is repeated for a DNA sample taken from a suspect and the two sets of

banding are compared to each other to see if they match. Due to the amplification

of the DNA sample from the crime scene, this can be repeated many times without

running out of DNA.

In the example shown below, a suspect for several crimes has given a DNA sample

to the police. The suspect’s DNA profile was compared with DNA evidence collected

from the crime scenes. In some cases, the evidence contained more than one

person’s DNA.

In which crime(s) was the suspect involved?

PCR can be used to amplify DNA from a variety of sources including blood, semen or

tissue cells from a crime scene, or embryonic cells for prenatal diagnosis of inherited

disorders. Plant DNA can also be amplified and used in investigations into plant

evolution.



Other uses of PCR include:

Research – A large stock of DNA can be built up from a small initial quantity

and then used for research teams to work on.

Medical uses – Amplification of Viral DNA can be carried out when only a

few cells of a patient are infected, rather than waiting until there is a greater

number of infected cells, causing distress to the patient.

Phylogenetics – Small samples taken from e.g. mummified remains or

fossils can be amplified and used to examine differences in DNA through

mutations. This allows evolutionary maps to be constructed.

Replication of DNA and the Polymerase Chain Reaction – What do I know?

Answer the questions (in sentences) from Page 24 ‘Higher Biology’ by Torrance.

Check your answers.



Sub-topic 1.1 The Organisation and Structure of DNA

Sub-topic 1.2 The Replication of DNA

How well do you rate your knowledge and understanding?

On completion of these topics, I can

1 2 3

State what is meant by prokaryote and eukaryote

State that prokaryotes contain a circular chromosome

State that eukaryotes contain linear chromosomes

State that eukaryotic DNA is packaged with proteins in the nucleus

State that mitochondria and chloroplasts also contain circular DNA molecules

Describe a plasmid and state that plasmids are found in yeast and bacteria

Describe the structure of a nucleotide

Number the carbons on the sugar in a nucleotide

State that DNA is a double stranded helix with antiparallel strands

Describe how covalent bonds are involved in producing DNA strands

State the complementary base pairing found in DNA

State that DNA is replicated by semi-conservative replication

State the 5 requirements for DNA replication

Describe the roles of the enzymes DNA polymerase and ligase in DNA replication

Describe the process of replication of DNA

Explain why leading and lagging strands form during DNA replication

State that the Polymerase Chain Reaction produces many copies of a specific section of DNA

Describe the cycle in PCR

Explain the importance of primers in PCR

Explain the use of positive and negative controls in PCR

Describe a practical application of PCR

Complete:

Row 1 before your Unit assessment

Row 2 before your Prelim

Row 3 before your May exam

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Unit 1: DNA and the Genome - duncanrig.s-lanark.sch.uk · Unit 1: DNA and the Genome Sub-topic 1.1 The Organisation and Structure of DNA Sub-topic 1.2 The Replication of DNA . Higher