chapter 21 part 2 Flashcards
Bioinformatics
the development of the software and computing tools needed to organise and analyse raw biological data, including the development of algorithms, mathematical models, and statistical tests that help us to make sense of the enormous quantities of data being generated
Computational biology
after bioinformatics has been used, CB then uses this data to build theoretical models of biological systems, which can be used to predict what will happen in different circumstances.
Computational biology is the study of biology using computational techniques, especially in the analysis of huge amounts of biodata.
Computational biology uses
it is important in the analysis of the data from sequencing the billions of base pairs in DNA, for working out the 3D structures of proteins, and for understanding molecular pathways such as gene regulation.
It helps us to use the information from DNA sequencing - for example in identifying genes linked to specific diseases in populations and in determining the evolutionary relationships between organisms.
genomics
The field of genetics that applies DNA sequencing methods and computational biology to analyse the structure and function of genomes
Analysing the human genome: part 1
Since the first complete draft of the human genome was published in 2003, tens of thousands of human genomes have been sequenced as part of research projects such as the 10000 Genomes Project UK10K, and most recently the 100000 Genomes Project.
Computers can analyse and compare the genomes of many individuals, revealing patterns in the DNA we inherit and the diseases to which we are vulnerable.
Analysing the human genome: part 2
This has enormous implications for health management and the field of medicine in the future.
Genomics is changing the face of epidemiology.
However, scientists increasingly recognise, with the exception of a few relatively rare genetic diseases caused by changes in a single gene, that our genes work together with the environment to affect our physical characteristics, our physiology, and our likelihood of developing certain diseases.
advantages of the increased speed and affordability in sequencing the genomes of pathogens, including bacteria, viruses, fungi, and protoctista:
Doctors to find out the source of an infection, for example bird flu or MRSA in hospitals.
Doctors to identify antibiotic-resistant strains of bacteria, ensuring antibiotics are only used when they will be effective and helping prevent the spread of antibiotic resistance.
For example, the bacteria that cause tuberculosis (TB) are difficult to culture, slow growing, and some strains are resistant to most antibiotics. Whole genome analysis makes it easier to track the spread of transmission and to plan suitable treatment options.
This has enormous implications for successful treatment of this potentially fatal disease, especially as TB is spreading fast around the world again, linked to the spread of HIV/AIDS.
Scientists to track the progress of an outbreak of a potentially serious disease and monitor potential epidemics, for example flu cach winter, Ebola virus in 2014/15.
Scientists to identify regions in the genome of pathogens that may be useful targets in the development of new drugs and to identify genetic markers for use in vaccines.
Identifying species (DNA barcoding):
why ssing traditional methods of observation can be very difficult
difficult to determine which species an organism belongs to or if a new species has been discovered.
Genome analysis provides scientists with another tool to aid in species identification, by comparison to a standard sequence for the species.
The challenge for scientists is to produce stock sequences for all the different species.
DNA Barcoding Technique:
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
In the International Barcode of Life (iBOL) project, scientists identify species using relatively short sections of DNA from a conserved region of the genome… for animals…
in plants…
For animals, the region chosen is a 648 base-pair section of the mitochondrial DNA in the gene cytochrome c oxidase, that codes for an enzyme involved in cellular respiration.
This section is small enough to be sequenced quickly and cheaply, yet varies enough to give clear differences between species.
In land plants, that region of the DNA does not evolve quickly enough to show clear differences between species, but two regions in the DNA of the chloroplasts have been identified that can be used in a similar way to identify species.
The barcoding system is not perfect - so far scientists have not come up with suitable regions for fungi and bacteria, and they may not be able to do so - but DNA sequencing is nevertheless having a big impact on classification.
why DNA sequences of different organisms can be compared
because the basic mutation rate of DNA can be calculated scientists can calculate how long ago two species diverged from a common ancestor.
DNA sequencing enables scientists to build up evolutionary trees with an accuracy they have never had before.
Spliceosomes: part 1
The mRNA transcribed from the DNA in the nucleus includes both the exons and introns.
Before it lines up on the ribosomes to be translated, this ‘pre-mRNA’ is modified in a number of ways.
The introns are removed, and in some cases, some of the exons are removed as well.
Spliceosomes: part 2
Then the exons to be translated are joined together by enzyme complexes known as spliceosomes to give the mature functional mRNA.
The spliceosomes may join the same exons in a variety of ways.
As a result, a single gene may produce several versions of functional mRNA, which in turn would code for different arrangements of amino acids, giving different proteins and resulting in several different phenotypes.
Proteomics
the study and amino acid sequencing of an organism’s entire protein complement.
The DNA sequence of the genome should, in theory, enable you to predict the sequence of the amino acids in all of the proteins it produces.
The evidence is that the sequence of the amino acids is not always what would be predicted from the genome sequence alone.
Some genes can code for many different proteins.
Protein modification:
Some proteins are modified by other proteins after they are synthesised.
A protein that is coded for by a gene may remain intact or it may be shortened or lengthened to give a variety of other proteins.
The study of proteomics is constantly giving us increasing knowledge of the extremely complex relationship between the genotype and the phenotype.
