Using DNA sequencing

Computational biology and bioinformatics

• Bioinformatics = development of software and computing tools to organise and analyse raw biological data 
• Computational biology = uses the data from bioinformatics to build theoretical models of biological systems to predict what will happen in certain circumstances (study of biology using computational techniques --> work out 3D structures of proteins or understanding molecular pathways like gene regulation)

Genome-wide comparisons

• Genomics = field of genetics that applies DNA sequencing methods and computational biology to analyse the structure and function of genomes

Analysing the human genome

• Computers can analyse and compare the genomes of many individuals, revealing patterns of DNA we inherit and the diseases to which we are vulnerable
• ^ enormous implications for health management and the field of medicine
• But scientists keep in mind that with the exception of a few genetic diseases, the interaction of our genes and the environment are what influence our physiology 

Analysing the genomes of pathogens

• Enables doctors to find out the source of an infection
• Lets doctors identify antibiotic-resistant strains of bacteria so antibiotics will only be used when they'll be effective --> stops spread of antibiotic resistance
• Scientists can track the progress of an outbreak of a potentially serious disease or manage epidemics
• Identify regions of the genome of pathogens that could be useful targets in the development of new drugs & identify gene markers to use in vaccines

Identifying species (DNA barcoding)

• Genome analysis provides another way to identify species --> compare a sample against a standard sample for the species
• One useful technique is to identify particular sections of the genome that are common to all species but vary between them so comparisons can be made <-- DNA barcoding
• For animals, they use 648 base-pairs from mitochondrial DNA in the gene for enzymes involved in cellular respiration
• ^ section is small enough to be sequenced quickly and cheaply yet varies between different species
• In plants, two regions of the DNA of the chloroplasts are used instead
• Barcoding system isn't perfect - scientists have not come up with suitable DNA regions to use for fungi or bacteria

Searching for evolutionary relationships

• DNA sequences of different organisms can be compared and the basic mutation rate can be calculated to see how long ago the species diverged from their common ancestor

Genomics and proteomics

• Proteomics = study of amino acid sequencing of an organism's entire protein complement
• Has revealed that some genes can code for many different proteins because the expected phenotype of an organism based on its sequenced genome is different to the actual phenotype

      Spliceosomes

• Spliceosomes = enzyme complexes that join the exons to be translated together
• They may join some exons in a variety of ways therefore a single gene may produce several versions of mature mRNA which all code for different arrangements of amino acids giving different proteins and therefore different phenotypes

      Protein modificiation

• A protein coded for by a gene may remain intact or it may be shortened or lengthened to give a variety of other proteins

Synthetic biology

• Synthetic biology = the design and construction of novel biological pathways, organisms or devices, or the redesign of existing natural biological systems
• Different techniques:
  • Genetic engineering --> may involve a single change in a biological pathway or relatively major genetic modification of an entire organisms
  • Use of biological systems or parts of biological systems in industrial complexes (fixed or immobilised enzymes)
  • The synthesis of new genes to replace faulty genes (cystic fibrosis) 
  • The synthesis of an entire new organism