1. What is an organism's genome ?
Answer
It is all the genes in an organism.
2. Explain why scientists have spent time determining the genome of simpler organisms.
Answer
It allows scientists to understand the proteome of an organism.
3. What is an organism's proteome ?
Answer
All of the proteins that a cell is able to produce.
4. Reverse vaccinology is a procedure used to produce vaccines. Scientists study the genome of a pathogen to identify genes coding for suitable proteins that might be good targets for a vaccine. Suggest what key characteristics scientists are looking for when looking for "suitable proteins" for a vaccine from a pathogen's genome. Explain why.
Answer
Scientists look for proteins located on the pathogen's cell surface membrane, since these are the most likely to trigger an immune response and are the first proteins encountered by helper T cells and B cells. They also focus on proteins encoded by highly conserved genes, because this reduces the chance that the pathogen will mutate and become resistant to the vaccine.
5. Scientists isolated 600 possible genes that coded for potential antigens that might prove to be useful in a vaccine. These were then tested through in vivo gene cloning with E. coli. Describe the process by which scientists were able to obtain antigens through this method.
Answer
Scientists use restriction enzymes to cut out the gene of interest from the pathogen's DNA. The same restriction enzyme is then used to cut open the plasmid in E. coli, creating complementary sticky ends through base pairing. DNA ligase is added to join the gene into the plasmid by forming phosphodiester bonds. The recombinant plasmid is introduced into E. coli, which then expresses the gene and produces the antigen. These antigens can be harvested and tested for their suitability in vaccine development.
6. Suggest why producing vaccines against proteins that are similar to human proteins is undesirable.
Answer
If an immune response is initiated, antibodies may attach to self-antigens, leading to tissue damage in the body. Alternatively, if the pathogen's antigens are too similar to self-antigens, no immune response will occur. This means memory B cells will not be produced, so a secondary immune response would not be possible, and the person would not develop immunity.
7. Another aspect of reverse vaccinology that was advantageous over traditional vaccinology is that the least variable antigens were able to be identified. Suggest why this was beneficial to the scientists.
Answer
If antigens are highly variable, it becomes difficult to develop a long-lasting vaccine. This is because if the antigen changes shape, the antibodies produced will no longer be complementary to it. As a result, the person would not remain immune, and no effective secondary immune response could occur.
8. This type of vaccine development has its limitations in that it is unable to be used to develop vaccines that contain glycolipids or glycoproteins. Explain why.
Answer
Genome provides information for proteins coded for by pathogen. Glycolipids are not encoded in an organism's genome. Glycoproteins are processed in the Golgi apparatus and only the protein portion will have a gene connected to it.
9. From knowledge gained from the Human Genome Project, scientists are now learning that we inherit the ways our bodies respond to medication. It is hoped that this knowledge can be used to predict which medication should be given to a particular individual, minimising the risk of side effects and also the drug not working. Suggest why a particular drug may not be equally effective in every person.
Answer
Different people carry different alleles, which means they produce different proteins. As a result, drugs may interact more or less effectively with these proteins, leading to variations in their effects.
10. Thiopurine drugs break down inside the body to produce toxic compounds that are able to kill certain immune system cells. Thiopurine S-methyltransferase (TPMT) is an enzyme made by humans that hydrolyses the toxic compounds. Some people have TPMT deficiency. People with TPMT deficiency produce a faulty enzyme that is unable to break down thiopurine drugs. Suggest the effect having TPMT deficiency would have on taking this drug.
Answer
The enzyme is no longer functional because its tertiary structure and active site have changed. As a result, the toxic drug remains in the body for longer and may accumulate, which can lead to excessive damage to immune system cells.
11. The inheritance of TPMT is described as being autosomal co-dominant. Suggest how this might affect treatment outcomes with the drug thiopurine.
Answer
Autosomal co-dominance means that both alleles, if present, contribute to and are expressed in the phenotype. Individuals with two alleles for functioning TPMT receive the maximum benefit from the drug. Those with two alleles for non-functioning TPMT cannot break down thiopurine and therefore gain no benefit from the drug. Individuals with one functioning and one non-functioning allele can break down some of the drug, but not all, so they do not receive the maximum benefit.
12. Explain how the Human Genome Project will help prevent this negative reaction to this drug.
Answer
Difference in allele bases sequence can be detected. Those with the allele causing TPMT deficiency will not be given the drug and therefore will not have a build-up of toxic compounds in the body.