Genome projects

Question 1

How do you create a complete map of all the genetic material in an organism?

Answer 1

• projects to determine the entire DNA nucleotide base sequence of a wide range of organisms, including humans, have taken place over the past few decades
• the idea has been to map the DNA base sequences that make up the genes of the organism and then to map these genes on the individual chromosomes of that organism
• in those way a complete map of all the genetic material in an organism (the genome) is obtained

Question 2

What are sequencing genomes?

Answer 2

• when you consider that the human genome consists of over 3 billion base pairs organised into around 20000 genes, sequencing every one of those bases is a mammoth task and yet it took just 13 years to complete
• this would have been impossible without the use of bioinformatics
• bioinformatics is the science of collecting and analysing complex biological data such as genetic codes
• it uses computers to read, store and organise biological data at a much faster rate than previously
• it also utilises algorithms (mathematical formulae) to analyse and interpret biological data

Question 3

What is DNA sequencing?

Answer 3

• determining the complete DNA base sequence of an organism uses the technique of whole-genome shotgun (WGS) sequencing
• this involves researchers cutting the DNA into many small, easily sequenced sections and then using computer algorithms to align overlapping segments to assemble the entire genome
• sequencing methods such as these are continuously updated which along with the increased automation of the process involved, have led to extremely rapid sequencing of whole genomes
• the medical advances that have been made as a result of sequencing the human genome are many
• for example over 1.4million single nucleotide polymorphisms (SNPs) have been found in the human genome
• SNPs are single-base variations in the genome that are associated with disease and other disorders
• medical screening of individuals has allowed quick identification of a potential medical problems and for early intervention to treat them
• sequencing of DNA of different organisms has also made it possible to establish the evolutionary links between species

Question 4

What is the proteome?

Answer 4

• of greater practical importance to humans is not the genes themselves, but the nature of the proteins these genes code for
• these proteins are known as the proteome
• a general definition of the proteome is all the proteins produced by the genome
• however as a protein is only produced by the genome
• however as a protein is only produced when a gene is switched on and genes are not switched on all the time a more specific definition is all the proteins produced in a given type of cell (cellular proteome) or organism (complete proteome) at a given time under specified conditions
• there are differences in the ease with which we can determine the genomes and proteomes of simple and complex organisms

Question 5

How do you determine the genome and proteome of similar organisms?

Answer 5

• the first bacterium to have its genome fully sequenced was haemophilus influenza in 1995 H. influenza contains 1700 genes compromising 1.8 million celled eukaryotic organisms are currently being sequenced as part of the human microbiome project
• it is hoped that the information gained will help cure disease and provide knowledge of genes that can be usefully exploited
• for example, ones from organisms that can withstand extreme or toxic environmental conditions and so have potential uses in cleaning up pollutants or in manufacturing biofuels
• knowledge of the proteome organisms like bacteria has a number of applications
• of particular interest is the identification of those proteins that act as antigens on the surfaces of human pathogens
• these antigens can be used in vaccines against diseases caused by these pathogens
• in the case of vaccines against disease caused by these pathogens
• in the case of vaccines, the antigens can be manufactured and then administered to people in appropriate doses
• in response to the antigen, memory cells are produced which trigger a secondary response when the antigen is encountered on a second occasions
• one example is sequencing of the DNA of plasmodium falciparum which causes malaria
• all 5300 genes on plasmodium’s 14 chromosomes have been sequenced giving us an insight into its metabolism and knowledge of the proteins it produces
• all this will be invaluable in helping us to develop the elusive vaccine against this globally important disease

Question 6

Why is it easy to determine the proteome of prokaryotic organisms like bacteria?

Answer 6

• the vast majority of prokaryotes have just one, circular piece of DNA that is not associated with histones
• there are non of the non-coding portions of DNA which are typical of eukaryotic cells

Question 7

How do you determine the genome and proteome of complex organisms?

Answer 7

• the success in mapping the human genome in 2003 is a testimony to what can be achieved in mapping DNA sequences of complex organisms
• there are around 20000 genes in the human genome although this number is constantly being revised down as our techniques for identifying genes improves
• the problem in complex organisms is translating knowledge of the genome into the proteome
• this is because the genome of complex organisms contains many non-coding genes as well as others that have a role in regulating other genes
• in humans, it is thought that as few as 1.5% of genes may code for proteins
• these is a human proteome project currently underway to identify all the proteins produced by humans
• there is also the question of whose DNA is used for mapping
• all individuals, except identical twins have different base sequences on their DNA
• the DNA mapped will differ, if only slightly, form everyone else DNA