Using Genome Projects (A Level Only)
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教育者の方へ： Using Genome Projects (A Level Only)（Biology、AQA）向けのすぐ使えるレッスンスライド, 復習ノート — レッスンで使うか、学習者がライブゲームとして遊ぶインタラクティブなクラス活動としてトピックを実施できます。
レッスンノート
Genome Sequencing Projects
- A genome is all of the genes within an organism.
- Genome sequencing projects collect DNA samples from many individuals of a species, sequence them and compare them to create a reference genome.
- More than one individual is used because one organism may have anomalies or mutations in its DNA sequence that are atypical of the species.
- Advances in technology have allowed scientists to map and sequence the genes within an organism's genome; sequencing projects have read the genomes of a wide range of organisms, from flatworms to humans.
- Genome sequencing can aid in the understanding of gene function and interaction.
The Human Genome Project
- The Human Genome Project (HGP) began in 1990 as an international, collaborative research programme.
- It was publicly funded so that there would be no commercial interests or influence, and the results would be made publicly available.
- As a result, the data can be shared rapidly between researchers and can be used by any researcher, maximising human benefit.
- DNA samples were taken from multiple people around the world, sequenced and used to create a reference genome.
- By 2003 the human genome had been sequenced to 99.9% accuracy.
- The finished genome was over 3 billion base pairs long but contained only about 25,000 genes — much less than expected.
- Following the success of sequencing the human genome, scientists have now moved onto sequencing the human proteome and epigenome.
The Proteome and Epigenome
- The proteome is all of the proteins that can be produced by a cell.
- Although there are roughly 25,000 genes within the genome, there are many more proteins within the proteome; this may be due to processes such as alternative splicing and post-translational modification.
- The epigenome is the inherited changes in DNA that do not involve a change in DNA base sequence.
- The proteome is not the same in all cells, and it changes over time based on conditions and signals.
Determining Protein Sequences
- The genome of simpler organisms can be used to obtain the proteome of the organism.
- Large databases are created containing information about an organism's gene sequences and amino acid/protein sequences.
- Once the genome is known, scientists can use bioinformatics to identify genes, predict the amino acid sequences of proteins, and study which proteins are actively expressed in different conditions.
- This information can be used for a range of applications, for example identifying potential antigens for use in vaccine production.
- Simpler organisms like bacteria and viruses are used because they have smaller genomes, no introns (especially in prokaryotes), and less complex gene regulation.
- This makes the genomes of simpler organisms easier to sequence and interpret than those of eukaryotes.
Vaccine Production
- Knowing the proteome of pathogens (like bacteria or viruses) enables scientists to identify antigens — the proteins on the surface of the pathogen that trigger an immune response.
- This can be carried out by sequencing the genome of the pathogen, then using computational tools to predict the proteome (which proteins are made).
- Proteins are identified that are found on the surface of the pathogen, are unique to the pathogen (not found in humans), and can stimulate an immune response.
- These proteins are then used as antigens in vaccines.
The Malaria Vaccine
- Plasmodium falciparum is a species of parasite that causes severe forms of malaria.
- Thousands of these parasites have been used for genome sequencing.
- Scientists have been searching for differences between their DNA sequences to identify the genes that display the highest level of variation between individuals.
- A high level of variation suggests that those genes are under strong selective pressure; these genes could code for the antigen proteins found on the parasites.
- Once the antigenic genes are identified, the antigen they code for can be used in vaccine production.
- RTS,S (Mosquirix) is the first malaria vaccine approved for human use; it targets a surface protein of Plasmodium falciparum, and this antigen was identified using genomic and proteomic data from the parasite.
Non-Coding DNA & Regulatory Genes
- It can be highly difficult to translate the genome of complex organisms into their proteome.
- Proteins are made from the coding regions of the genome, via transcription and translation.
- Determining the proteome of humans is difficult as large amounts of non-coding DNA are present in human genomes; the full genome includes introns and repetitive sequences.
- It can be very hard to identify these sections of DNA from the coding DNA; simply knowing the sequence doesn't tell you which regions are coding or expressed.
- Regulatory genes control the expression of other genes; they do not code for proteins directly, but they influence which genes are transcribed and translated.
- The presence of regulatory genes and the process of alternative splicing in human genomes also affect gene expression and the synthesis of proteins.
- The proteome is larger than the genome due to alternative splicing and post-translational modification of proteins — the modification of the protein molecule after translation, which often takes place in the Golgi apparatus or endoplasmic reticulum.
Sequencing Methods
- DNA sequencing is the process of determining the exact order of nucleotide bases (A, T, C, G) in a DNA molecule.
- DNA sequencing allows for the base sequence of an organism's genetic material to be identified and recorded.
- Sequencing methods are continuously evolving and becoming faster; advances in technology have allowed scientists to rapidly sequence the genomes of organisms.
- Most sequencing methods used are now automated.
- The data obtained from sequencing can be entered into computers with specialised programmes that compare the base sequences of different organisms.
DNA Sequencing and Chain Termination
- All methods of DNA sequencing use dideoxyribose nucleotides.
- A dideoxyribose molecule is very similar in structure to ribose molecules and deoxyribose molecules; it has one less oxygen atom than a deoxyribose molecule and two fewer oxygen atoms than a ribose molecule.
- Dideoxyribose can form nucleotides in the same way that ribose and deoxyribose molecules do, by binding to a phosphate molecule and an organic base.
- Dideoxyribose nucleotides can pair with deoxyribose nucleotides on the template strand during DNA replication; they will pair with nucleotides that have a complementary base.
- When DNA polymerase encounters a dideoxyribose nucleotide on the developing strand, it stops replicating — this is the chain-termination technique used for DNA sequencing.
- In DNA sequencing, it's the new (test) strand that is sequenced, not the original template strand; because DNA bases pair specifically (A with T, C with G), you can work out the template strand by applying base-pairing rules.
Automated DNA Sequencing
- Sequencing methods are continuously updated and have become automated.
- Automated DNA sequencing makes use of the chain-termination technique.
- An automated DNA sequencing machine can read roughly 100 different DNA sequences within 2 hours.
- The process is extremely accurate and can detect fragments differing by just one base.
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練習問題
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1.Which of the following best defines the term genome?
Easy- AAll of the genes within an organism
- BAll of the proteins that can be produced by a cell
- CThe non-coding sections of DNA only
- DThe total number of chromosomes in a cell
2.Which of the following best defines the term proteome?
Easy- AAll of the proteins that can be produced by a cell
- BAll of the genes within an organism
- CAll of the non-coding DNA in a cell
- DThe complete set of chromosomes in a cell
3.The Human Genome Project was publicly funded so that there would be no commercial interests or influence, and the results would be made publicly available.
EasyTrue or false?
4.The human genome contains approximately 25,000 genes and is over 3 billion base pairs long.
EasyTrue or false?
5.Which enzyme is used in the chain-termination method of DNA sequencing to synthesise the new DNA strand?
Easy- ADNA polymerase
- BDNA ligase
- CRestriction endonuclease
- DRNA polymerase
6.What is the role of primers in DNA sequencing?
Easy- AThey provide a starting point for DNA polymerase to begin synthesis
- BThey terminate the DNA chain by lacking a 3'-OH group
- CThey separate DNA fragments by size during electrophoresis
- DThey join together Okazaki fragments on the lagging strand
7.Which process is used to separate DNA fragments by size after chain-termination sequencing?
Medium- AGel electrophoresis
- BCentrifugation
- CChromatography
- DFiltration
8.Why is it necessary to sequence the DNA of several individuals of the same species to create a reference genome?
Medium- AOne individual may have anomalies or mutations that are atypical of the species
- BSequencing one individual is too expensive
- CDifferent individuals have completely different genes
- DThe genome of one individual is too large to sequence
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