1. 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.

2. Key Area 1.8 Genomics and genomic sequencing

3. 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.

4. What is a genome?

5. 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.

6. From Darwin & Mendel to the Human Genome Project:

7. How can their genomes be sequenced? TED: How to sequence the human genome

8. Using the CfE Higher Biology text book page 94 – 95: Research the different approaches to genomic sequencing. 1. 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.

9. 1. Use of restriction endonucleases. 2. Genome shotgun approach. 3. Sequencing DNA with fluorescent dyes. brief note Write a brief note to describe each process

10. 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.

11. 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.

13. 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.

14. 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.

15. 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?

16. 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.

17. 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.

18. 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.

19. 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.

20. 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.

21. Think up Pair up Square up

22. 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.

23. 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?

24. 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.

25. 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?

26. Common ancestor of all species All species exist at the present time

27. 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.

28. 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.

29. 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.

30. What does this graph tell you about the common ancestor of the human and kangaroo compared to that of the sheep and goat?

31. 1. Fossils Conversion of bone, 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. 2. Combined Evidence Scientists have used combination of genome sequence data and fossil evidence to work out the sequence in which key events have taken place.

32. Evidence supports that living things have undergone a 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 millions of years ago

33. 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?

36. 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.

37. 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.

38. 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.

39. 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).

40. 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.

41. Read ‘Ethical Issues’ on pg. 105 Make a note of what your views are on this. Your teacher will lead a class discussion.