CELL STRUCTURE AND FUNCTION
Cell Structure and Function: Teacher’s notes
Structure and function of DNA
The genotype of a cell is determined by the sequence of bases in its DNA.
(a) Structure and replication of DNA
DNA is the molecule of inheritance and can direct its own repl ication.
(i)
Structure of DNA
Key concepts
1.
2.
3.
4.
5.
6.
7.
8.
9.
Scientific discovery takes place in the context of a community of
scientists, where the results of one team lay the foundations for the
work of others.
Scientific work is presented in different formats , including journal
papers, posters and conference presentations ; each of these has its own
merits.
DNA is the genetic material of living things.
DNA is composed of two polynucleotide chains.
Nucleotides consist of a sugar, phosphate and base .
Nucleotides bond to form a sugar–phosphate backbone.
The two polynucleotide chains run antiparallel , with a deoxyribose
sugar at the 3′ end and phosphate group at the 5′ end.
The nucleic acid bases are paired by hydrogen bonding in the centre to
form a double helix.
Base pairing is specific, with adenine pairing with thymine and cytosine
pairing with guanine.
Prerequisite knowledge
No previous Higher biology knowledge is needed but students require a
general science background for terms such as molecule, bond and so on. The
ability of each student will determine the depth of their research and therefore
the task will be differentiated by outcome.
Students should know that DNA is the genetic material.
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Background information
The elucidation of the genetic code by Watson and Crick in 1953 was the
culmination of years of scientific research by a range of scientists. The
research and events surrounding the discovery have been the topic of book s,
media stories and even a film. The story is not only one of scientific
discovery but also of personalities and intrigues, and lends itself well to
independent research and developing a conceptual u nderstanding of the
significance, structure and function of DNA, laying down the foundations for
Unit 1 of Higher Biology. An appreciation of how short a time there has been
since its discovery and the huge amount of research that has followed in the
field never fails to amaze and is also important when considering the moral,
ethical and social implications of this area of biological science.
Knowledge of the molecular structure of DNA was part of the content of the
old Higher exam, and so plenty of material showing its structure already
exists. Here are some good websites for information and resources:
The University of Utah
The University of Utah has two excellent sites with high -quality resources for
teaching and learning genetics. If you do not visit any other site, go to those
from The University of Utah:
http://learn.genetics.utah.edu/
http://teach.genetics.utah.edu/
The Nature Publishing Group
http://www.nature.com/scitable
The Wellcome Trust
The Wellcome Trust produces high-quality material with an emphasis on
human health. In particular, they produce a fun and scientifically rigorous
booklet called the Big Picture and their January 2010 copy focuses on genes,
genomes and health. Print copies can be ordered and a PDF is available. It is
very accessible and interesting for young people :
http://www.wellcome.ac.uk/Education-resources/Teaching-andeducation/index.htm
Nucleic acid problem set:
http://www.biology.arizona.edu/molecular_bio/problem_sets/nucleic_acids/nu
cleic_acids_1.html
A level biology revision site:
http://www.s-cool.co.uk/
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Further reading and other references
To find out more detail about each set of experiments a nd the story
surrounding the discovery of the structure of DNA you could refer to the
following references:
Websites
The Nature education site gives a detailed account of the story:
http://www.nature.com/scitable/topicpage/discovery -of-dna-structure-andfunction-watson-397
The interactive site for students in genetics produced at Cold Spring Harbour
in America – one of the tasks in Section 1 on the menu called ‘code’ is about
the elucidation of the structure of DNA and is written for students to work
through like a problem, giving information about what each of the scientists
in the puzzle discovered.
http://www.dnai.org/a/index.html
This website is dedicated to ‘The race for DNA’:
http://osulibrary.oregonstate.edu/specialcollections/coll/pauling/dna/index.ht
ml
Books
For a very readable book that describes the elucidation by Watson and Crick
from the viewpoint of Watson, and which is very accessible to students, the
following is highly recommended:
Watson, James (1968). The Double Helix: A Personal Account of the
Discovery of the Structure of DNA. Atheneum.
The discovery is also told from the viewpoint of Crick in:
Crick, Francis (1990) What Mad Pursuit: A Personal View of Scientific
Discovery, Basic Books.
…and Franklin:
Maddox, Brenda (2002). Rosalind Franklin: the Dark Lady of DNA.
HarperCollins.
…and Wilkins:
Wilkins, Maurice (2003). The Third Man of the Double Helix: The
Autobiography. Oxford University Press.
There is also a film produced for TV by Horizon in 1987 called Life Story.
This chronicles the story of Watson and Crick, who raced to find the structure
of DNA before Linus Pauling, Maurice Wilkins, or Rosalind Franklin. The
drama was directed by Mick Jackson and has been released under different
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titles: Race for the Double Helix and The Double Helix. It can be difficult to
get hold of but your local library might have a copy or a Google search will
help reveal sources and YouTube snippets. An extract of the drama would
serve as a good lesson starter.
Possible lesson starters
To encourage the class to start thinking about the structure of DNA, the
lesson could begin by examining the biological problem that scientists were
facing at the beginning of the century:
What is the genetic material of living things composed of? They knew that
living things somehow passed on information but didn’t know what did this
and how it was done.
In pairs, students could consider the criteria that this ‘material’ would have to
fulfil.
Answers:
 It must somehow store the information to allow an organism to develop
and reproduce.
 It would have to be able to replicate this information accurately.
 It must be able to be ‘passed on’ to offspring.
 It must be capable of change or difference to account for the variety of
living things that we see.
You could use an extract of the film Life Story (see above).
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Student activities
Poster
Use the Word document ‘Discovering the structure of DNA’. This activity
allows students to research the science behind the discovery of the structure
of DNA and produce a poster for presentation to the class.
Create your own DNA
The PowerPoint document ‘Create your own DNA!’ can be used by students
to construct the molecular structure of DNA. The images can be dragged and
dropped onto a new slide or can be printed so that students can cut out the
pieces and use them on a table top.
Make your own edible DNA
Make your own edible DNA double helix. Go to the University of Utah’s
excellent ‘Teach Genetics’ website:
http://teach.genetics.utah.edu/
Follow the Print-And-Go™ Lesson Plan Index, and you will find many
activities, including instructions on how to make a double helix out of sweets.
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(ii) Arrangement of DNA in chromosomes
Key concepts
1.
2.
3.
4.
DNA in eukaryotes is packaged into chromosomes.
The DNA in chromosomes has undergone four stages of packaging to
achieve the most condensed state seen during metaphase.
The level of packaging changes depending on the stage of the cell
cycle.
DNA combines with proteins to achieve its packaged state.
Prerequisite knowledge
Students should understand the following concepts before beginning this part
of the course:
 the cell cycle, including mitosis and meiosis
 the structure of DNA.
Background information
The level of organisation in the packaging of DNA is truly amazing. The
length of a DNA molecule, if held taut end to end, in just one of your
chromosomes would measure 4 cm. If that was not bewildering enough, given
that cells are not nearly that big, our cells are capable of packaging this
amount of DNA into chromosomes 1.2–2 µm in length. This means that end to
end you could fit 10,000 chromosomes along the length of a fingernail. If you
take this figure and the fact that we have 46 chromosomes in each cell we can
calculate a total length of DNA in one human c ell to be 1.84 m, or the height
of a 6-foot person. Considering the number of cells we have, we have so
much DNA that, if it were put end to end it would reach the moon and back.
The next section will examine how the DNA in eukaryotic chromosomes is
packaged to achieve this feat of organisation. There are four levels of
packaging seen within cells, the highest of which is only seen during
metaphase.
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Level 1: Nucleosomes
DNA in the form of a double helix is wound
around histone proteins, forming
nucleosomes or what is commonly called
‘beads on a string’. The histones are
positively charged and so bind tightly to the
negatively charged DNA. The lengths of DNA
between the nucleosomes are called linker
DNA. The length of linker DNA between
nucleosomes is constant within cells but can
vary between species and tissues.
This level of organisation is seen throughout
the cell cycle, with only transient separation
during replication.
The combination of proteins and DNA is
called chromatin, so the beads on a string
structure shown here is a chromatin fibre.
Level 2: Thick chromatin fibre
The length of nucleosomes then coils to form
a thicker chromatin fibre, about 30 nm wide,
due to interactions between the nucleosomes
and linker DNA.
This level of packaging can be seen during
interphase.
Level 3: Looped fibres
The thick chromatin fibre then folds along a
non-histone protein scaffold, producing fibres
that are now 300 nm thick.
This level of packaging can be seen during
prophase.
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Level 4: More folds to make the most compacted chromosome
The chromatin folded along the
protein scaffold then folds
further to produce the compacted
chromosomes that are seen
during metaphase. This is DNA
in its most compacted form.
Note that this image shows a
metaphase chromosome, which
consists of two chromatids
following replication.
Overview of the levels of packaging seen in a metaphase chromosome:
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Student activities
The packaging of DNA in eukaryotic chromosomes
This PowerPoint presentation shows the images of each level of chromosome
packaging, corresponding to the background notes above. These stages can be
talked through with the class whilst they take notes of each one.
Beads and string
The packaging of DNA into chromosomes can be conceptual ly difficult for
students, in particular the fact that packaging occurs at different levels
depending on the stage in the cell cycle. As a class or in groups physically
model the packaging levels using beads and string.
Sequencing activity, explaining the stages of packagin g of DNA in
eukaryotic chromosomes
The word document ‘The packaging of DNA in eukaryotic chromosomes’
shows the four images used in the background information and the
PowerPoint to show the different levels of chromosome packaging, but in the
wrong order. Students should either draw these in the correct order or cut
them out and stick them in the correct order. Students can then write a short
paragraph to explain what is happening at each stage.
Know your chromosomes from your chromatid and your chromatin
Not surprisingly, these terms are often confused. Students could look up their
definitions in the glossary of genetics at the link below, and share their
findings with a partner:
http://www.genome.gov/glossary
The opportunity could also be taken to look at other terms encountered when
looking at the packaging of DNA in chromosomes.
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(iii) Replication of DNA
Key concepts
1.
2.
3.
4.
5.
6.
7.
Prior to cell division, DNA polymerase replicates a DNA strand
precisely using DNA nucleotides.
DNA polymerase needs a primer to start replication.
DNA unwinds to form two template strands.
DNA polymerase adds complimentary nucleotides to the deoxyribose
(3′) end of a DNA strand.
This process occurs at several locations on a DNA molecule.
DNA polymerase can only add nucleotides in one direction , resulting in
one strand being replicated continuously and the other strand being
replicated in fragments.
Fragments of DNA are joined together by ligase.
Prerequisite knowledge
Students require knowledge of DNA structure and the process of mitosis.
New content areas
DNA requires a primer to start replication.
Background information
Every time a cell divides in our body, the DNA it contains must be replicated
exactly. For this to occur, an original strand of DNA, free DNA nucleotides
and DNA polymerase enzyme must be available. DNA unwinds to form two
template strands and DNA polymerase adds complimentary nucleoti des to the
deoxyribose (3′) end of a DNA strand. The DNA polymerase needs a primer
to start replication as it can only add nucleotides to existing DNA. In most
cases the primer is a short piece of RNA that is made in the nucleus for this
purpose. This process occurs at several locations on a DNA molecule. DNA
polymerase can only add nucleotides in one direction , resulting in one strand
being replicated continuously and the other strand being replicated in
fragments. These fragments of DNA are joined together by another enzyme
known as DNA ligase. DNA replication is described as being semi conservative, as each new double helix consists of one original and one new
strand.
Again this was covered in detail in the old Higher courses and so there is a
wealth of information available.
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Further reading and other resources
http://www.sumanasinc.com/webcontent/animations/content/meselson.html
http://highered.mcgrawhill.com/olcweb/cgi/pluginpop.cgi?it=swf::535::535::/sites/dl/free/007243731
6/120076/bio22.swf::Meselson%20and%20Stahl%20Experiment
http://www.learnerstv.com/animation/animation.php?ani=20&cat=biology
http://www.dnalc.org/view/15331-Proposed-models-of-DNA-replicationMatthew-Meselson-.html
http://www.dnalc.org/view/15880-Models-of-DNA-replication.html
http://www.dnalc.org/view/15879-Semi-conservative-replication.html
These sites all provide information on the discovery of the semi -conservative
model of DNA replication.
Student activities
Case study: How does DNA replicate?
This case study allows students to investigate the experimental data that led
to the discovery of this process and identify the method for themselves. Once
students have completed this task it would be beneficial to show an animation
of DNA replication in action, for example, see:
http://highered.mcgrawhill.com/olcweb/cgi/pluginpop.cgi?it=swf::535::535::/sites/dl/free/007243731
6/120076/micro04.swf::DNA%20Replication%20Fork.
Although this is more complex than required it is reasonably easy to follow
and shows the differences in replication of the leading and lagging strands.
The final task involves students creating an educational resource to teach
DNA replication. This could be peer assessed using the six questions in the
instructions as success criteria.
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(b)
Gene expression through protein synthesis
The phenotype is determined by the proteins produced as the result of gene
expression, influenced by intra- and extracellular environmental factors. Only
a fraction of the genes in a cell are expressed. Gene expression is controlled
by the regulation of both transcription and translation. mRNA is transcribed
from DNA in the nucleus and translated into proteins by ribosomes in the
cytoplasm.
(i)
Structure and function of RNA
Key concepts
1.
2.
3.
4.
The structural differences between RNA and DNA.
mRNA carries a copy of the DNA code from the nucleus to the
ribosome.
RNA
DNA
Single stranded
Double stranded
Uracil
Thymine
Ribose sugar
Deoxyribose sugar
rRNA and proteins form the ribosome.
Each tRNA carries a specific amino acid.
Prerequisite knowledge
Students should have covered the structure of DNA earlier in the course.
Knowledge of the ultrastructure of eukaryotic cells is also necessary and
some time may be required to cover this.
New content areas
Structure of ribosomes – rRNA and proteins form the ribosome.
Background information
RNA stands for ribonucleic acid. There are three main differences between
RNA and DNA. RNA is single stranded, a uracil base has replaced thymine
and the nucleotide contains a ribose sugar instead of deoxyribose s ugar.
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These molecular structures are
for the teacher’s benefit only as
the students do not have to know
the molecular structure of each
of the sugars.
Phosphate
group
Base
Ribose
sugar
adenine
guanine
cytosine
uracil
There are two forms of RNA involved in protein synthesis: messenger RNA
(mRNA) and transfer RNA (tRNA). mRNA is formed inside the nucleus from
free nucleotides and carries a copy of the DNA code from the nucleus t o the
ribosome to direct the synthesis of proteins.
The ribosomes are found in the cytoplasm, either floating freely or attached
to the rough endoplasmic reticulum (ER). The ultrastructure of the cell may
not have previously been covered and, if so, some time should be spent
teaching this. Ribosomes floating freely are used to synthesis e proteins for
use within the cell; those attached to the ER synthesise proteins for export or
inclusion in the membrane. Ribosomes are formed from proteins and a third
type of RNA known as ribosomal RNA (rRNA). Each tRNA carries a specific
amino acid to the ribosome for attachment to the peptide chain.
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Student activities
Protein synthesis role play
There is a Word document and PowerPoint outlining a protein synthesis role
play. Students act out the steps of protein synthesis to gain an understanding
of the processes involved. This can be carried out as an introduction to the
topic of protein synthesis. Each of the steps can then be studied in more
detail.
Production of ID cards
This PowerPoint presentation involves production of ID cards for each of the
molecules involved in protein synthesis using information cards provided in
The protein synthesis role play or other classroom resources.
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(ii) Transcription of DNA into an RNA molecule
Key concepts
1.
2.
3.
4.
RNA polymerase moves along DNA, unwinding the double helix.
Primary transcript of RNA is synthesised from RNA nucleotides by
complimentary base pairing.
Genes have introns (non-coding regions of genes) and exons (coding
regions of genes).
The introns of the primary transcript of mRNA are removed in RNA
splicing.
Prerequisite knowledge
Students require knowledge DNA structure and location from previous areas
of the course.
New content areas
Eykaryotic genes have introns (non-coding regions of genes) and exons
(coding regions of genes). The introns of the primary transcript of mRNA are
removed in RNA splicing.
Background information
Transcription copies the information in DNA into an RNA molecule. This
occurs in the nucleus. RNA polymerase enzyme attaches to a sequence of
DNA known as the promoter. It then moves along the DNA, unwinding the
double helix and breaking the hydrogen bonds holding the base pairs together
to create a transcription bubble. This first stage is known as initiation. This is
followed by elongation, where free RNA nucleotides enter the transcription
bubble and align with the complementary base pairs on the DNA . During this
the RNA polymerase moves from the 3’ to 5’on the DNA molecule with
nucleotides being added to the 3’ end of the nascent RNA molecule . The RNA
nucleotides are held in place by hydrogen bonding while strong covalent
bonds form between the phosphate of one nucleotide and the ribose sugar of
the adjacent nucleotide. The final stage is termination, when the transcription
termination sequence is recognised on the DNA and the RNA polymerase
enzyme is released. The RNA that has been produced at this stage is known as
the primary transcript.
This primary transcript now has to be modified. The primary transcript of
RNA is composed of introns and exons. The introns are non-coding regions of
genes and so do not appear in the mRNA in eukaryotic cells. The exons are
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coding regions of genes and so do appear in the mRNA. The introns of the
primary transcript of mRNA are removed in RNA splicing.
In RNA splicing the primary transcript is cut at the boundaries between the
introns and exons. The introns are removed and the exons are joined together.
The mRNA can then leave the nucleus via a nuclear pore and enter the
cytoplasm.
Areas of difficulty
Students often get the terms transcription and translation muddled up. They
also often find it difficult to explain the process in a step -by-step manner. It
may therefore be of benefit to teach the basic steps involved in transcription
and translation first to ensure a firm understanding. Introns, exons and
splicing can then be covered, followed by the additional modifications
covered in Section B: One gene, many proteins.
Further reading and other references
The website below is a good step-by-step animation of transcription, which
could be used before the introduction of splicing.
http://wwwclass.unl.edu/biochem/gp2/m_biology/animation/gene/gene_a2.html
Student activities
Word document ‘Protein synthesis diagram’
A summary diagram of protein synthesis that can be completed using
information cards from the protein synthesis role play or other classroom
resources. Box 2 can be missed out and completed later if splicing is being
taught at a later date.
Word document ‘Production of ID cards’
This activity involves production of ID cards for each of the molecules
involved in protein synthesis using information cards provide d in the protein
synthesis role play (if not carried out in previous lesson).
The Word document ‘Introns and exons’ is a simple activity that can be used
to allow students to visualise the concept of introns and exons using simple
sentences.
The PowerPoint ‘Splicing’can be used to introduce the concept of splicing.
This information can then be used to complete box 2 of the student’s protein
synthesis diagram.
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(iii) Translation of mRNA into a polypeptide
Key concepts
1.
2.
3.
4.
5.
6.
tRNA folds due to base pairing to form a triplet anticodon site and the
attachment site for a specific amino acid.
Triplet codons and anticodons of the genetic code.
The function of start and stop codons.
Codon recognition of incoming tRNA.
A peptide bond forms between adjacent amino ac ids.
tRNA exits from the ribosome as polypeptide is formed.
Prerequisite knowledge
Students should have an understanding of the structure of RNA and the
process of transcription. Some consolidation may be required of the
codon/amino acid relationship.
New content areas
Start and stop codons.
Background information
Translation is the process in which a polypeptide is synthesised from an
mRNA template.
Complementary base pairing occurs between residues within the strand of
tRNA, producing tRNA’s distinctive structure. This structure exposes a triplet
anticodon site and the attachment site for a specific amino acid. The triplet
anticodon site is complementary to the triplet codon site on the mRNA. Each
codon codes for a particular amino acid. Students must be able to identify the
correct amino acid from an mRNA codon, DNA codon or tRNA anticodon.
Most tables of the genetic code will give the mRNA codons for each amino
acid.
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Often the SQA will show mRNA codons in the following form:
C
First base
A
G
C
Ser
Ser
Ser
Ser
Pro
Pro
Pro
Pro
Thr
Thr
Thr
Thr
Ala
Ala
Ala
Ala
A
Tyr
Tyr
Stop
Stop
His
His
Gln
Gln
Asn
Asn
Lys
Lys
Asp
Asp
Glu
Glu
G
Cys
Cys
Stop
Trp
Arg
Arg
Arg
Arg
Ser
Ser
Arg
Arg
Gly
Gly
Gly
Gly
U
C
A
G
U
C
A
G
U
C
A
G
U
C
A
G
Third base
U
Second base
U
Phe
Phe
Leu
Leu
Leu
Leu
Leu
Leu
Ile
Ile
Ile
Start/Met
Val
Val
Val
Val
The genetic code is described as being ‘redundant’ as there are far more
possible codons than amino acids. There are 64 (4 3 ) possible combinations of
the four bases but only 20 amino acids occurring in nature. This has led to
more than one codon coding for an amino acid. There are three codons that do
not code for amino acids: UGA, UAA and UAG. The occurrence of these
codons in the genetic code terminates translation and they are therefore
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known as stop codons. The genetic code also includes start codons, where
translation begins. In eukaryotes this is almost always AUG, which also codes
for the amino acid methionine. In prokaryotes other codons may occasionally
be used.
During translation the mRNA passes through the ribosome. The codons are
recognised by tRNA, each carrying a particular amino acid. The appropriate
tRNA brings its amino acid to the ribosome as it moves along the mRNA.
Adjacent amino acids then join with a peptide bond. The tRNA then leaves
the ribosome. This process continues until a stop codon is reached and the
polypeptide is released.
Areas of difficulty
Students often get confused between codons and anticodons when being asked
to identify amino acids from the genetic code. The importance of reading the
question carefully should be emphasised.
Further reading and other references
The Nobel Prize site has information on transcription and translation ,
including a couple of animations.
http://nobelprize.org/educational/medicine/dna/intro.html
The Wellcome Trust site has an animation showing transcription and
translation.
http://www.wellcome.ac.uk/Education-resources/Teaching-andeducation/Animations/DNA/WTX057748.htm
The University of Utah site allows students to use an edible model of DNA to
investigate transcription and translation. The usual considerations of
laboratory health and safety should be made before carrying out this activity.
http://teach.genetics.utah.edu/content/begin /dna/reading_DNA.html
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Student activities
Production of ID cards
This activity involves production of ID cards for each of the molecules
involved in protein synthesis using the information cards provided in The
protein synthesis role play (if not carried out in a previous lesson).
The genetic code quiz
This is a quick quiz to allow students to practice working with the genetic
code.
Protein synthesis storyboard
This activity allows students to show their understanding of the processes
involved in protein synthesis. Alternatively it could be used after the
introduction of splicing. It provides an opportunity for peer, self- or teacher
assessment. If peer or self-assessment is being used, students can be given the
steps of protein synthesis so that they can compare them to their own
descriptions. Alternatively the class can come up with a group position on
what should be included.
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(iv) One gene, many proteins
Key concepts
1.
2.
3.
4.
5.
6.
A variety of proteins can be expressed from the same gene .
Different mRNA molecules are produced from the same primary
transcript depending on which RNA segments are treated as exons and
introns.
Alternative RNA splicing treats different sections of RNA as introns
and exons.
Post-translational modification allows proteins to be altered covalently.
Proteins can have their protein chains cut and combined .
Proteins can have a phosphate or carbohydrate added .
Prerequisite knowledge
Students require an understanding of protein synthesis and the process of
RNA splicing.
New content areas
Different mRNA molecules are produced from the same primary transcript
depending on which RNA segments are treated as exons and introns.
Background information
There are 20,000–25,000 genes in the human genome but over 100,000
proteins in the human body. One gene can produce a variety of proteins as a
result of alternative RNA splicing and post -translational modification.
Different mRNA molecules are produced from the same primary transcript
depending on which RNA segments are treated as exons and intro ns. This is
called alternative RNA splicing. The exons can be combined in different ways
through a variety of methods. The most common is exon skipping, where an
exon may be removed or included. Other methods are:
 mutually exclusive exons, where one of two exons may be included in the
mRNA molecule but not both
 alternative donor sites, which change the exon boundary before an intron
 alternative acceptor sites, which changes the exon boundary of the
following exon
 intron retention, where an intron, or part of an intron, is not spliced out.
There is a good diagram to illustrate this on Wikipedia
http://en.wikipedia.org/wiki/Alternative_splicing
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Once translation is complete the protein can be modified in order to alter its
function, for example by addition of a phosphate or carbohydrate group.
Many proteins have a carbohydrate added to their structure , which is usually
added to asparagine, serine or threonine. These carbohydrate-modified
proteins are known as glycoproteins and are formed through the process of
glycosylation. Glycoproteins can perform a variety of roles and are often
found as integral membrane proteins aiding cell –cell interactions, including
antibody action and white blood cell recognition processes. Other examples
are antifreeze proteins in cold water fish, certain hormones and proteins in
mucus.
Proteins can also become phosphorylated, a process which involves the
addition of a phosphate group by a kinase enzyme. This is an important
mechanism in controlling the activity of many enzymes an d receptors. The
addition of a phosphate group causes a conformational change in the protein
structure, switching its biological activity on or off. This is often reversible,
the phosphate group being removed by one of many phosphatise enzymes.
Examples of this process include the phosphorylation of Na + /K + -ATPase,
which is involved in transporting sodium and potassium across the cell
membrane.
The structure of a protein can also be modified by cutting and combining
polypeptide chains. For example, the hormone insulin, which increases the
uptake of glucose by cells, consists of two polypeptide chains , which
originate as one chain. Disulphide bridges form between cysteine residues in
the original polypeptide chain, the latter known as pro-insulin. A protease
enzyme (an enzyme that cuts protein at a peptide bond) cuts the polypeptide
chain in two places. The middle section of the protein is then removed . The
resulting insulin molecule therefore consists of two polypeptide chains.
A second example is the enzyme trypsin. This is produced in an inactive form
called chymotrypsin and is only activated when a section of the polypeptide
chain is removed.
Student activities
The ‘One gene, many proteins’ worksheet involves students extracting
information from a passage and using it to complete a flow diagram.
An article on alternative splicing can be downloaded from the Bioscience
Explained website in PDF form. It is advanced but could be used as an
extension activity for more able students. It contains some questions for
students to consider.
www.bioscience-explained.org
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(c)
Genes and proteins in health and disease
(i)
Proteins
Key concepts
1.
2.
3.
4.
Proteins have a large variety of structures and shapes , resulting in a
wide range of functions.
Amino acids are linked to peptide bonds to form polypeptides.
Polypeptide chains fold to form the three -dimensional shape of a
protein.
Chains are held together by hydrogen bonds and other interactions
between individual amino acids.
Prerequisite knowledge
Students should have an understanding of the importance of protein synthesis
to the resulting phenotype of a cell.
Background information
Proteins have a wide variety of structures and shapes, resulting in a wide
range of functions. The primary structure of all proteins is the sequence of
amino acids from which they are made. These amino acids are joined together
by peptide bonds to form polypeptides. The peptide bond is formed when the
carboxyl group of one amino acid reacts with the amino group of another,
releasing a water molecule. Hydrogen bonds then form between amino acid
residues, causing the polypeptide to form its secondary structure and making
the protein more stable.
The main groups of the secondary structure are α helices and β sheets. α
helices form when hydrogen bonds joins amino acids several residues apart. β
sheets are produced when hydrogen bonds form between chains of
polypeptides that lie adjacent to one another, forming a flat sheet. The
secondary structure then folds together to form the protein’s tertiary
structure. This folding is based on the hydrophobic nature of some amino acid
side chains, which must be buried within the protein to avoid contact with
water. The tertiary structure is held in place by interactions between amino
acids, including the hydrogen bonds and disulphide bonds that form between
two cysteine residues. When more than one polypeptide chain combines, a
quaternary structure is formed, with each polypeptide chain being known as a
sub-unit. This structure is held together by the same types of interactions as
found in the tertiary structure. Some proteins also have prosthetic groups
(non-protein) incorporated into them, eg haemoglobin contains iron ions.
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The overall structure of proteins falls into two main structural groups:
 fibrous structures, where secondary structures lie along side one another,
and are mainly structural proteins, eg keratin, collagen and elastin
 globular structures, which are generally spherical and play a wide variety
of roles, including as enzymes, messengers (eg the hormone insulin),
transporters of molecules through membranes or as regulators eg
regulating enzyme activity.
Further reading and other references
‘Biomodel 3’ allows students to work through the four stages of protein
structure. A java applet may need to be installed on school computers to allow
this program to run. This should be checked ahead of time.
http://biomodel.uah.es/en/model3/index.htm
‘Protopedia’ provides information and images for a wide variety of proteins.
Click on the table of contents for an easy-to-navigate list.
http://proteopedia.org/wiki/index.php/
‘RasMol’ or ‘Protein Explorer ’ software allows investigation of the shape and
structure of fibrous and globular proteins (see links in protein structure and
function activity). An online guide in PDF format and tutorial for
investigating proteins can also be downloaded from:
http:// www.bioscience-explained.org/ENvol2_2/index.html
Practicals
Gel electrophoresis – students could try separation and identification of fish
proteins by agarose gel electrophoresis, but this may be difficult to deliver
due to cost and time considerations.
http://www.ncbe.reading.ac.uk/NCBE/PROTOCOLS/protein.html
Paper chromatography – an alternative to gel electrophoresis is separation
and identification of amino acids using paper chromatography.
Student activities
Protein structure and function activity
This activity involves investigating a variety of proteins using RasMol
modelling software. This worksheet is intended to be used alongside Raswin
2.6, which is available to download for free from:
http://www.umass.edu/microbio/rasmol/getras.htm#raswin
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The molecules required for this activity can be downloaded from the Protein
Data Base (PDB) using their PDB codes. See:
http://www.pdb.org/pdb/home/home.do
Once downloaded they can be saved for use by students.
Protein
Glucagon
Myoglobin
Dihydrofolate reductase
Insulin
Aspartate transcarbamoylase
Green flourescent protein
Collagen
Haemoglobin D
Amylase
PDB code
1GCN
1L2K
1DRF
3I40
3E2P
3I19
1BKV
1A3N
1SMD
Investigating proteins
This involves researching individual proteins to create a class display.
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(ii) Mutations and genetic disorders
Key concepts
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
Genetic disorders are caused by changes to genes or chromosomes that
result in the proteins not being expressed or the proteins expressed not
functioning correctly.
Single-gene mutations involve the alteration of a DNA nucleotide
sequence as a result of the substitution, insertion or deletion of
nucleotides.
Single nucleotide substitutions include missense, nonsense and splice
site mutations.
Missense mutations replace one amino acid codon with another.
Nonsense mutations replace an amino acid codon with a stop codon.
Splice site mutations create or destroy the codons for exon –intron
splicing.
Nucleotide insertions or deletions result in a frameshift mutation or an
expansion of a nucleotide sequence repeat.
Mutations affect the structure of the protein and its function and this
has an effect on individuals.
The structure of chromosomes can be altere d by deletion, duplication or
translocation.
Chromosome mutations are often lethal.
Prerequisite knowledge
An understanding of the processes of protein synthesis, meiosis and splicing
are required. In addition, students must be aware of t he role of the genetic
code and stop codons and the link between a protein’s structure and function.
New content areas
Although mutations were covered in the previous Human Biology course ,
splice site mutations are new, as are the connection between mutations and
the structure of the protein, its function and the effect on mutations on
individuals.
Background information
Single-gene mutations involve the alteration of a DNA nucleotide sequence as
a result of the substitution, insertion or deletion of nucleotides. This in turn
can result in a wide array of conditions. Single nucleotide substitutions
include missense, nonsense and splice site mutations.
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Missense mutations
Missense mutations occur when one amino acid codon is replaced with
another. Conditions resulting from this mutation include sickle cell disease
and phenylketonuria (PKU).
Sickle cell disease
Sickle cell disease is caused by a mutation of the HBB gene on chromosome
11. This gene codes for haemoglobin beta, a protein that forms two of the
four subunits of haemoglobin in our red blood cells. The most common
mutation is when residue 6, glutamic acid (GAG) changes to valine (GTG).
This causes the two haemoglobin beta chains to clump together and create a
blood cell with a sickle shape. These misshapen red blood cells find it
difficult to pass through narrow blood vessels.
PKU
Several different mutations, the majority of which are missense, can occur in
the PAH gene on chromosome 12. This gene codes for the enzyme
phenylalanine hydroxylase, which converts phenylalanine to tyrosine. The
mutations reduce the activity of the enzyme or remove it completely, causing
a build up of phenylalanine in the blood. This leads to brain damage.
Nonsense mutations
Nonsense mutations replace an amino acid codon with a stop codon.
Conditions resulting from this mutation include Duchenne muscular
dystrophy (DMD).
DMD
The DMD gene on the X chromosome codes for the protein dystrophin , which
stabilises and protects muscle fibres. The production of a stop codon in this
gene results in no dystrophin being produced, leading to progressive muscle
weakness and wasting.
Splice site mutations destroy or create codons for exon –intron splicing and
lead to conditions such as beta thalassemia.
Beta thalassemia
As in sickle cell disease, it is the HBB gene on chromosome 11 that is
mutated in beta thalassemia. This time, the mutation results in a reduced
production of haemoglobin beta. This means that the red blood cells do not
develop normally, leading to a shortage of mature cells to carr y oxygen. This
leads to sufferers developing anaemia.
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Nucleotide insertions and deletions
Nucleotide insertions and deletions result in frameshift mutations (Tay –Sachs
syndrome or cystic fibrosis) or an expansion of a nucleotide sequence repeat
(fragile X syndrome or Huntington’s disease).
Tay–Sachs syndrome
The HEXA gene on chromosome 15 codes for the A subunit of the beta
hexosaminidase enzyme. This enzyme catalyses the breakdown of a fatty
substance called GM2 ganglioside. Mutations in this gene prevent the enzyme
functioning and so GM2 ganglioside builds up to toxic levels, destroying
nerve cells in the brain and spinal cord.
Cystic fibrosis
Cystic fibrosis is caused by a mutation in the cystic fibrosis transmembrane
conductance regulator (CFTR) gene on chromosome 7. This gene codes for a
chloride channel protein. The most common mutation is the deletion of bases ,
as shown below:
ATC
Ile
TTT
Phe
GGT
Gly
ATT
Ile
GGT
Gly
This leads to an abnormality in cells that produce sweat and mucus.
Fragile X syndrome
The FMR1 (fragile X mental retardation 1) gene on the X chromosome
normally has 30 repeats of CGG at the start of the gene. Genes with the full
mutation have more than 200 of these repeats. This causes the cell to
methylate a regulatory region of the gene, switching it off.
Huntington’s disease
The HTT gene on chromosome 4 codes for the protein huntingtin. The
function of this protein is unknown but it is thought to be important in nerve
cells. In the normal gene, CAG is repeated 10–35 times but in the mutated
gene the repeat is 36–120 times. The abnormally long protein is cut into small
toxic segments that accumulate in neurones , causing uncontrolled movements,
emotional problems and loss of cognition.
Chromosome structure changes
The structure of chromosomes can also be altered. Deletion is the loss of a
segment of chromosome, duplication is the repeat of a segment of
chromosome and translocation is the rearrangement of chromosomal material
involving two or more chromosomes. These mutations are often lethal.
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Cri-du-chat syndrome
Cri-du-chat syndrome is caused by deletion of part of the short arm of
chromosome 5 and results in mental retardation. Infants with this condition
characteristically have a high-pitched cry due to abnormal larynx
development, hence the name, which means ‘cry of the cat’ in French.
Chronic myeloid leukemia
Chronic myeloid leukemia is due to the reciprocal transloction of a gene from
chromosome 22 fused with a gene in chromosome 9. The ends of
chromosomes 9 and 22 detach and switch places. This disrupts the ABL gene
on chromosome 9 and the BCR gene on chromosome 22. An abnormal fused
gene is produced, which is called Bcr-Abl, and the resulting protein functions
abnormally, reducing the growth and survival of the cell.
Down’s syndrome
Five per cent of cases of Down’s syndrome are inherited from a parent with
Robertsonian translocations, where the majority of chromosome 21 is
translocated to chromosome 14. These Down’s syndrome individuals have 46
chromosomes but, due to the extra information from chromosome 21 located
on chromosome 14, they exhibit the standard symptoms for Down’s
syndrome.
Further reading and other resources
PowerPoint covering genetic mutations
This can be seen at:
http://ghr.nlm.nih.gov/handbook/illustrations/chromosomechanges?show=bala
ncedtranslocation
The vast majority of the slides are pitched just at the right level for an
introduction to chromosome mutations, although there are one or two bits that
show that there are other types of mutations. However, these are
straightforward and should not cause any confusion.
Ken Miller Human Chromosome 2 Genome
The 3.5-minute video clip ‘Ken Miller Human Chromosome 2 Genome’ gives
an interesting and easy-to-follow account of chromosomal translocation in
terms of human evolution. The clips can be converted into mp4 format using
the Zamzar website.
http://www.youtube.com/watch?v=8FGYzZOZxMw
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Your genes, your health
The ‘Your genes, your health’ website contains a lot of good information on
genetic disease.
http://www.ygyh.org
Home page for gene gateway
This is a site for exploring genes and genetic disorders, and contains a lot of
useful information on individual conditions.
http://www.ornl.gov/sci/techresources/Human_Genome/posters/chromosome/i
ndex.shtml
University of Utah
This site also has a lot of information on genetic disorders.
http://learn.genetics.utah.edu/content/disorders/whataregd/
Student activities
Point mutations
This Word worksheet allows students to visualise the effect of point
mutations using sentences.
Chromosome structure mutations
This Word worksheet allows students to identify the different types of
chromosome structure mutations.
Research project
Students can research diseases caused by different types of mutations and use
the information to create a spider diagram. This activity could be taken
further and an in-depth study of a particular condition could be undertaken. If
students are struggling they can be pointed in the direction of the descriptions
of the diseases in the background information above.
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(d) Human genomics
(i)
Sequencing DNA
Key concepts
1.
2.
3.
4.
5.
6.
7.
8.
The sequence of bases can be determined for individual genes and
entire genomes.
Bioinformatics uses computer technology to analyse and share data .
Bioinformatics identifies coding sequences similar to known genes,
start sequences or sequences lacking stop codons.
Bioinfomatics is used to identify base sequences that correspond to the
amino acid sequence of a protein.
Systematic comparison of genomes of different species provides
information on evolutionary relationships and origins .
Analysis of an individual’s genome may lead to personalised medicine.
It is important to distinguish between neutral and harmful mutations .
Genome information is used in the choice of effective drugs
(pharmacogenetics).
Prerequisite knowledge
The concepts of sequencing DNA, bioinformatics, systematics and
personalised medicine are all new to the Higher Human Biology course.
Background information
In 2003, after 13 years of research, the human genome project came to an
end. Scientists from around the world had successfully sequenced the entire
human genome. Research still continues to identify all of the 20,000 –25,000
genes which form the human genome.
Bioinformatics has allowed the analysis and sharing of the huge amount of
data created by this project as well as data created by other teams focused on
different organisms. Computer technology can be used to analyse gene
sequences by looking for coding sequences similar to known genes, start
sequences or sequences lacking stop codons. They can also be used to
identify base sequences that correspond to the amino aci d sequence of a
protein. Without the use of bioinformatics this project would have proved
very difficult.
As the genome of more and more organisms are sequenced, comparisons
allow evolutionary relationships and origins to be ascertained. This area of
biology is called systematics. Essentially, the greater the similarities in the
genomes of organisms the more recently they have evolved into different
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species. Conversely, the greater the differences, the longer they have been
independent species. It is important to note that systematics is not taxonomy:
the latter purely deals with the identification and naming of organisms and
does not consider their evolutionary pathway.
The information gained from DNA studies can provide information on the
structure of genes and proteins involved in disease. This in turn allows
researchers to develop specific drugs that will attach to these proteins or
prevent their synthesis by binding to a specific piece of DNA or mRNA. As
this technology develops it is hoped that medi cine will become more and
more personalised. The knowledge of where mutations have occurred and
which of these mutations are harmful will allow doctors to understand the
risk of disease and make an informed choice when prescribing drugs.
Further reading and other resources
Bioinformatics fact sheet
This is a fact sheet providing a very readable introduction to bioinformatics.
http://www.ncbi.nlm.nih.gov/About/primer/bioinformatics.h tml
Oak Ridge National Laboratory
This website has very good information on pharmacogenetics and the possible
future uses of the technology.
http://www.ornl.gov/sci/techresources/Human_Genome/medicine/pharma.sht
ml#status
Nuffield
The Nuffield website has a summary of a paper discussing the ethical issues
involved in pharmacogenetics.
http://www.nuffieldbioethics.org/sites/default/files/pharm_short_version%20
FINAL%20-%20updated%202006.pdf
Wellcome Trust
This is the issue of the Wellcome Trust’s ‘Big Picture’ series that deals with
the genome. There is a lot of useful information.
http://www.wellcome.ac.uk/Education-resources/Teaching-and-education/BigPicture/All-issues/Genes-Genomes-and-Health/index.htm
University of Utah
This site has a range of ready-to-go lesson plans on pharmacogenomics.
http://teach.genetics.utah.edu/content/
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Student activities
Genomics
This Word information sheet, with associated questions, provides an
introduction to the topic of genomics. The activity looks at what genomics is
and some of the possibilities it may lead to. There are also some websites
listed, which students can look at to gain a more in-depth understanding.
Personal genomics summary questions
This Word document is a straightforward information card and set of
summary questions dealing with the area of personal genomics and
pharmacogenetics in more detail.
Personal genomics diamond 9
This Word document outlines an activity aiming to facilitate group discussion
and allow students to delve into some of the issues surrounding the area of
pharmacogenetics.
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(ii) Amplification and detection of DNA sequences
Key concepts
1.
2.
3.
4.
5.
6.
7.
8.
9.
The polymerase chain reaction (PCR) is a technique for amplifying
DNA in vitro.
Primers are complementary to the target sequence at each end of the
DNA to be amplified.
DNA is heated to separate strands and cooled to allow binding of
primers.
DNA polymerase replicates DNA.
DNA probes are used to detect the presence of specific sequences in
samples of DNA.
Probes are short single-stranded fragments of DNA complementary to a
specific sequence.
Fluorescent labelling allows detection.
Screening for the presence or absence of a sequence allows a diagnos is
of disease status or risk of disease onset .
DNA profiling allows the identification of individuals through
comparison of regions of the genome with highly variable numbers of
repetitive sequences of DNA.
Prerequisite knowledge
An understanding of DNA structure and compl ementary base pairing is
required. Students should also understand the link between genes and health.
New content areas
PCR, DNA probes and their medical and forensic applications are all new to
the Higher Human Biology course.
Background information
Before DNA can be analysed it often has to be amplified to increase the
quantity of DNA available to work with. This is done using the polymerase
chain reaction (PCR), which involved heating and cooling DNA in a thermal
cycler along with primers, DNA nucleotides and DNA polymerase. More
information on this technique can be found in the case study on PCR.
Once DNA has been amplified, DNA probes can be used to detect the
presence of specific sequences. Each probe is a short, single-stranded
fragment of DNA that is complementary to a specific sequence. If these
probes have a fluorescent label attached to them they can be detected when
attached to the DNA of interest. These probes can be used to detect single-
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gene mutations. Genotype microarrays are devices displaying hundreds, or
even thousands, of specific oligonucleotide probes. These probes can be used
to search an individual’s DNA for multiple genetic markers simultaneously.
Gene expression microarrays can be manufactured from RNA transcripts and
can help determine the levels of expression of particular genes in certain
conditions. For example, in drug design they could be used to measure the
levels of toxicity.
By combining PCR and DNA probes, a patient’s genome can be analysed to
look for the presence or absence of a particular sequence. This can then
provide information about the individual’s disease status or risk of
developing a disease. These two techniques have also proved vital in forensic
applications. Small samples of DNA can be amplified and regions containing
highly variable numbers of repetitive sequences compared to identify an
individual.
Further reading and other resources
DNA Learning Center
For further information about PCR refer to the following website:
http://www.dnalc.org/resources/animations/pcr.html
McGraw-Hill
This website contains a good animation about DNA probes.
http://highered.mcgrawhill.com/sites/0072556781/student_view0/chapter14/animation_quiz_4.html
And for something a little more creative…
A PCR song:
http://www.youtube.com/watch?v=x5yPkxCLads
and a PCR rap:
http://www.youtube.com/watch?v=oCRJ4r0RDC4&feature=related
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Student activities
PCR case study
This case study allows students to investigate PCR in a real-life scientific
context. There is a Word document and a PowerPoint presentation.
Applications of PCR
This activity allows students to discuss some of the different situations in
which PCR may be employed. Students should work in groups to discuss the
different applications, each of which is described on a different card. They
can then produce a simple spider diagram summarising the applications. This
activity provides an excellent opportunity for co-operative learning. However,
the diagram could easily be produced by individuals and peer assessed.
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