View
228
Download
0
Category
Preview:
Citation preview
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
Higher Biology Pupil Course Notes
Duncanrig Secondary MHC 2014 Page 2 of 17
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
Higher Biology Pupil Course Notes
Duncanrig Secondary MHC 2014 Page 3 of 17
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).
Higher Biology Pupil Course Notes
Duncanrig Secondary MHC 2014 Page 4 of 17
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
Higher Biology Pupil Course Notes
Duncanrig Secondary MHC 2014 Page 5 of 17
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
Higher Biology Pupil Course Notes
Duncanrig Secondary MHC 2014 Page 6 of 17
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
Higher Biology Pupil Course Notes
Duncanrig Secondary MHC 2014 Page 7 of 17
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
Higher Biology Pupil Course Notes
Duncanrig Secondary MHC 2014 Page 8 of 17
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’
Higher Biology Pupil Course Notes
Duncanrig Secondary MHC 2014 Page 9 of 17
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.
Higher Biology Pupil Course Notes
Duncanrig Secondary MHC 2014 Page 10 of 17
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
Higher Biology Pupil Course Notes
Duncanrig Secondary MHC 2014 Page 11 of 17
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
Higher Biology Pupil Course Notes
Duncanrig Secondary MHC 2014 Page 12 of 17
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.
Higher Biology Pupil Course Notes
Duncanrig Secondary MHC 2014 Page 13 of 17
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.
Higher Biology Pupil Course Notes
Duncanrig Secondary MHC 2014 Page 14 of 17
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.
Higher Biology Pupil Course Notes
Duncanrig Secondary MHC 2014 Page 15 of 17
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.
Higher Biology Pupil Course Notes
Duncanrig Secondary MHC 2014 Page 16 of 17
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.
Higher Biology Pupil Course Notes
Duncanrig Secondary MHC 2014 Page 17 of 17
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
Recommended