Download Genomic sequencing

From your notebook and/or glossary select 5 key
terms from KA 1.7 and write each one on a study
card.
On the reverse write a meaning or explanation of
each key term.
Key Area 1.8
Genomics and genomic sequencing
 Explain the term ‘genomic sequencing’.
 Describe what ‘bioinformatics’ is why it is used.
 Define the term ‘phylogenetics ’.
 Describe what a molecular clock is.
 Describe how evidence is used to determine the main
sequence of events in evolution.
 Explain how the sequence of events can be determined using
sequence data and fossil evidence.
 Name the three domains and describe how the comparison of
sequences provides evidence of these domains.
What is a
genome?
 Genomics: the study of genomes
 Genomic sequencing: determining the sequence of
the nucleotide base molecules all the way along an
organism's DNA and then relating the information
about the genes to their functions.
 Bioinformatics: the fusion of molecular biology,
statistical analysis and computer technology. Has
allowed genomics to make major scientific
advances.
From Darwin & Mendel to the Human Genome Project:
How can their genomes
be sequenced?
TED: How to sequence the human genome
Using the CfE Higher Biology text
book page 94 – 95:
Research the different approaches
to genomic sequencing.
Read the pages individually
2. With a partner note down key
information on a show me board
3. Share and compare your
information with another pair.
1.
1.
Use of restriction endonucleases.
2. Genome shotgun approach.
3. Sequencing DNA with fluorescent
dyes.
Write a brief note to describe each process
 Use of restriction endonuclease: a type
of enzyme that recognises a specific
short sequence of DNA nucleotides
called a restriction site on a DNA
strand.
 It ‘cuts’ the DNA at this exact site all
the way along the DNA strand.
Genome shotgun approach
1. Use of restriction endonucleases to cut up
the same extract of DNA, since each
recognise different restriction sites on the
DNA they cut it at different points.
2. Take each fragment produced and sequence
it to establish the order of its bases. Many
of the fragments may overlap.
Fluorescent tagging
is used when a portion of DNA with an unknown base sequence has
been chosen to be sequenced. Many copies of this template DNA
are made
Modified nucleotides are tagged with a different fluorescent dye
and halt the synthesis of the complementary strand of DNA being
made.
Electrophoresis is used to separate DNA fragments according to
size and an automated sequence analyser processes and displays
the DNA sample as a complete sequence.
 2003: Completion of the human genome.
 DNA from several human donors – the
reference genome.
 Since then the following organisms have
been sequenced:
 many pathogenic viruses and bacteria
 pest species, e.g. mosquito
 model organisms which aid the
understanding of the malfunctioning of
genes, and possible new treatment.
Comparing the sequenced genomes of:
 Members of different disease causing
micro-organisms – do they have important
genetic sequences in common?
 Member s of the same species, e.g.
harmless strain of E. coli vs the stain that
causes food poisoning - which genetic
sequence causes illness?
 Cancerous vs normal cells – what is the
specific sequence that causes a healthy cell to
become cancerous?
Similarities in Genome
 Genomes can also reveal similarities, indicating
a high level of conservation (very similar DNA
sequences are present in the genomes).
 For example humans and whales are very
distant relatives! The base sequences of many
of their genes are very similar (apart from 4
point mutations), even though their
evolutionary paths diverged about 100 million
years ago.
 This is the study of evolutionary relatedness
among different organisms.
 Uses information found from comparison of
genome sequence data to deduce sequences of
events involved in the group’s evolution.
 Over time a group of closely related living things
acquires its own set of mutations (such as
nucleotide substitutions) which gradually alter its
genome.
 This group may give rise to two groups that
become more and more different from one
another and eventually diverge.
 The more different the base sequences of two
genomes are found to be, the more distantly
related the two groups to which they belong and
vice versa.
 The evolutionary distance between the two
groups can be found by counting the number
of differences per unit length of DNA
sequence between the two genomes.
 These distances can then be used to construct
a phylogenetic tree.
 This shows the probable evolution of related
groups of organisms and their phylogenetic
patterns of divergence.
1.
Answer two KA 1.7 extended response
questions of your choice from the h/w booklet
in your animal jotter – 10 minutes.
2. From your notebook select 2 key terms from
KA 1.8 and write each one on a separate study
card.
3. Have your phylogenetic tree h/w task ready to
share.
Think up
Pair up
Square up
 Explain the term ‘genomic sequencing’.
 Describe what ‘bioinformatics’ is why it is used.
 Define the term ‘phylogenetics’.
 Describe what a molecular clock is.
 Describe how evidence is used to determine the main
sequence of events in evolution.
 Explain how the sequence of events can be determined
using sequence data and fossil evidence.
 Name the three domains and describe how the comparison
of sequences provides evidence of these domains.
Phylogenetic Tree Chat!
In your group chat about:
1. the phylogenetic tree that you identified at
home
2. using your examples in the group, can you
form a connection between the number of
differences between 2 groups and the time
since divergence took place?
 The use of molecular information to determine
evolutionary relationships and can be illustrated using a
phylogenetic tree.
 Useful when comparing groups that are structurally
similar or identical.
 Two groups may share a common ancestor if the base
sequences for a selection of genes only differ by a few
bases, i.e. they diverged fairly recently.
 The greater the number of differences, the longer
the time since the point of divergence.
This phylogenetic
tree shows 5 related
species of carnivore.
 Which two species
are most closely
related?
 Which species is the
most distantly
related to the
others?
All species exist at the present time
Common ancestor of all
species
 Explain the term ‘genomic sequencing’.
 Describe what ‘bioinformatics’ is why it is used.
 Define the term ‘phylogenetics’.
 Describe what a molecular clock is.
 Describe how evidence is used to determine the main
sequence of events in evolution.
 Explain how the sequence of events can be determined
using sequence data and fossil evidence.
 Name the three domains and describe how the comparison
of sequences provides evidence of these domains.
 Sequence divergence can be used as a molecular
clock to estimate the time since lineages diverged.
 Sequence divergence can be used to create a
molecular clock graph, by plotting a number of
molecular differences it has evolved against a time
scale based on fossil records (e.g. for haemoglobin,
P36 How To Pass).
 These graphs assume that the mutation rate of
genes leading to amino acid differences in proteins
is constant through time.
 Therefore a molecule of nucleic acid (or a protein
coded for by the nucleic acid) can be regarded as a
molecular clock.
 Molecular clocks are used as tools to date the
origins of groups of living things and to determine
the sequence in which they evolved.
 What does this graph tell you about the common
ancestor of the human and kangaroo compared to
that of the sheep and goat?
1. Fossils
2. Combined Evidence
 Conversion of bone,
 Scientists have used
teeth or shells into
rock.
 Age of fossils is
determined by
estimating the age of
the rock it is made of.
 The older the rock,
the less radioactivity
it emits.
combination of genome
sequence data and
fossil evidence to work
out the sequence in
which key events have
taken place.
 Evidence supports that living things have undergone a
millions of years ago
series of modifications from the first emergence of
life to the present day, gradually becoming more and
more complex as evolution has progressed.
475 
evolution of land plants
540
evolution of vertebrates animals
600 
evolution of animals
1000 
evolution of multicellular organisms
2000 
evolution of eukaryotic cells
3400 
evolution of first organisms to use photosynthesis
3500 
evolution of last universal ancestor (prokaryote)
3600 
evolution of cells resembling prokaryotes
4500-3600  evolution of life on Earth
This evidence supports the
idea that living things are
made up of three domains.
1. the bacteria (prokaryotes)
2. the archaea (mostly
prokaryotes that inhabit
extreme environments such
as hot springs and salt
lakes)
3. the eukaryotes (fungi,
plants and animals)
What does this diagram
indicate about the
divergence between the
three domains?
 Personal genomics is the branch of genomics
involved in sequencing an individual's genome and
analysing it using bioinformatics tools.
 Analysis of an individual’s genome could lead to
personalised medicine through increased
information on the likelihood of a treatment being
successful for a specific person.
 In the near future it may be possible to sequence
an individual’s entire genome early in life and store
that information for future consultation by doctors
when required.
 Variations are mostly due to mutations, which
range from missing or extra chromosomes to just
a change in a single nucleotide.
 Not all mutations are harmful, i.e. lead to the
failure to code for an essential protein. Some
may be neutral (have no negative effect). It is
often difficult to distinguish between harmful and
neutral mutations.
 If scientists can establish a link between a
particular mutation and a specific genetic disease
(or disorder) is said to be molecularly
characterised.
 This has been achieved for 2200 genetic disorders
and diseases in humans. However, most medical
disorders depend on genetic and environmental
factors so it is not always simple to produce
treatments for these disorders.
In future……
 it may be possible to prescribe the most suitable drug
and the correct dosage as indicated by personal
genomic sequencing, reducing side effect and the
increasing the effectiveness of the drug.
 it may also be possible to scan an individual's genome
and predict a risk early enough to allow suitable action
to be taken (for example, through appropriate drug
treatment combined with a healthy lifestyle).
 Complete a short report on personalised medicine.
 You can include advantages and disadvantages.
 Examples of personalised medicine.
 Details of the process.
 The names or backgrounds of companies who
specialise in this.
 Evidence for or against its use.
 Read ‘Ethical Issues’ on pg. 105
 Make a note of what your views are on this.
 Your teacher will lead a class discussion.