1. Unit 1 1.8- Genomic sequencing
Higher Biology
Unit 1
1.8- Genomic sequencing

2. Genomics Genomics is the study of the genome
It involves determining the sequence of nucleotide bases all the way along an organism’s DNA
This allows scientists to relate the genetic information about genes to their functions

3. Genomic Sequencing
To sequence a genome it needs cut into smaller pieces using an enzyme called restriction endonuclease
Restriction endonuclease recognises a specific short sequence of DNA nucleotides called a restriction strand
The DNA strand will be cut at this restriction site all along the strand

4. Genome shotgun
One copy of the genome will be cut up using a restriction endonuclease
Another copy of the genome will be cut up using a different restriction endonuclease
Each genome is cut at different points as the enzymes recognise different restriction sites

5. Each DNA fragment is then sequenced to determine the order of bases on it
This information is entered into a computer which works out the sequence of fragments
The computer will recognise where there is an overlap in the sequence of bases and determine that the end of one fragment is the start of another
The computer will work this out for all fragments and will compile a complete genome
This allows the sequencing of individual genes as well as entire genomes

6. Importance
The nucleotide sequence of the genome of different species has been determined
In 2003 the DNA sequence of the human genome was successfully sequenced
Other organisms whose genomes have been sequenced include:
viruses, bacteria, pest species and model organisms used for research

7. Comparative genomics
Comparative genomics compares the sequenced genomes of member of different species, members of the same species and allows comparison between cancerous cells and healthy cells in an individual.
Comparing genomes can determine the sequences of DNA that cause illness

8. Differences in genome
One way that the genome of 2 individuals of the same species can be found to differ is a single base pair
This is knows as a single nucleotide polymorphism (SNP)
By mapping and cataloguing SNPS scientists believe they will be able to identify and understand how genes affect disease

9. Genomic similarities
Sequencing of the genome also shows important similarities
Different genomes may show a high level of conservation, where similar or the same DNA sequences are present in the genome. Among the most highly conserved genetic sequences are those that code for the active sites of essential enzymes

10. Highly conserved DNA sequences can be used to compare the genomes of two organisms to find out closely or distantly related they are
The greater the number of conserved DNA sequences in common the more closely related the organisms are

12. Phylogenetics
Phylogenetics is the study of evolutionary relatedness among different groups of organisms
Sequences of events involved in the evolution of a species (known as phylogenies) can be worked out using comparisons of genomes
Diagrams can then be constructed to show evolutionary relationships (phylogenetic tree)

13. This representation of evolution is wrong
This representation of evolution is wrong. Monkeys, apes and humans evolved from a common ancestor as populations split off and adapted to their environment.

14. Common ancestors
This is the correct representation of evolution. Each “branch” splitting off shows a common ancestor that a group of organisms evolved from.
In the above example humans share a common ancestor with gibbons, orang-utans, gorillas and chimpanzees.
The distance between organisms represents how closely related they are. For example humans are more closely related to chimpanzees than they are to gibbons.

15. Divergence
The genome of groups of closely related organisms will change over time due to mutations
If this results in 2 or more distinct groups that become increasingly different from each other we call this divergence
Looking at molecular information to establish evolutionary relationships is called molecular phylogenetics
This is a much more conclusive way of assessing relatedness than comparing physical structures

16. Molecular clocks
By comparing the equivalent genetic sequences of 2 organisms the length of time since the 2 groups diverged can be measured
A molecule of nucleic acid (or protein coded for by it) can therefore be regarded as a molecular clock
The number of molecular difference can then be compared to fossil records
This can be used to try to date the origin of groups of living things and the sequence in which they evolved

17. The graph shown is produced using molecular clock information.
A limitation of molecular clock use is that it works on the assumption that mutations occur at a relatively constant rate. This is less reliable for use in dating the origins of distantly related groups.

18. Domains
Sequences of DNA and RNA have been used to trace the evolutionary lineage of all living things
This has been largely based on ribosomal RNA (rRNA) from different organisms
The genes that code for rRNA are ancient, have suffered little or no horizontal gene transfer and are present in all living things, making them useful as molecular clocks
Using this information we can divide living things into 3 domains:
Bacteria (prokaryotes)
Achaea (prokaryotes that inhabit extreme environments)
Eukaryotes (fungi, plants and animals)

19. 3 domains