LBC01 Flashcards
How can comparative genomics be used in conjunction with bioinformatics to find drug targets?
- Isolate human DNA sequence
- Translate DNA sequence into amino acids
- Obtain a model of the protein structure by finding homologous proteins found on model organisms with known structure
- Find drugs that can bind to this homologous protein and attempt to see if they can be used to interact with this protein
What is a karyotype?
Karyotypes are images of all the chromosomes that can be found in a person’s cell and is usually isolated from white blood cells and visualised using specific stains.
Briefly outline the procedures for cloning (assume human cloning)
- Obtain an oocyte and strip of its genetic content
- Obtain another cell with a complete genome
- Inject this complete genome into the oocyte
- Develop the embryo in a laboratory before inserting into a surrogate mother
- New offspring is a clone of the DNA donor
Name 2 ethical concerns with human cloning
- Gene/protein modifications may occur from non-specific modification that causes side effects
- Essential genes may be disrupted leading to production of a deformed mutant baby
What are the two methods for silencing genes?
- Morpholino oligo antisense RNA
Morpholine is a synthetic chemical compound that can be utilised to form artificial DNA sequences that target mRNA and prevent it from being translated. It also tags mRNA for destruction. - Hairpin siRNA/shRNA
Hairpin siRNA is processed by DICER and forms RNA-induced silencing complex RISC that targets and degrades target mRNA
Briefly outline how CRISPR-Cas9 system works in genome editing
- Introduce CRISPR and guide RNA by encoding them onto a plasmid into a mammalian cell
- Guide RNA and CRISPR forms an active complex
- Guide RNA recognizes target DNA site while CRISPR protein unwinds and cleaves the target DNA to induce a double strand break
- A gene sequence that is homologous to the target site can then be introduced to allow homologous recombination to occur (can be used to knock genes out completely)
Why do we use animal models? (State 2 reasons)
- Human testing is ethically impossible
- Animal models share physiological similarity with humans and can be used to study similar physiological functions.
- Some model organisms also share similar syntenic groups with humans
- We can use animal models to study specific gene sequences that are unique to humans
What is synteny?
Synteny is the physical colocalization of genes on the chromosome and can be used to compare between different organisms to see conservation of the order of genes.
What are introns?
Introns are intervening sequences of nucleotides found between the expressed sequence of a gene (exons). They are spliced out (excised) during mRNA processing
What are some speculated benefits for having introns? (Name 2)
- Introns elongate the genome and as such, lowers the chance that random mutations may end up in exons that may be detrimental to gene function (something like genome dilution)
- Introns elongate the genome and this increases the propensity of chromosomal rearrangements
- Introns encode miRNA that allows greater control of protein expression
- Introns elongate the genome and allows gene expression to be controlled by structural changes in the genome (longer genome can adopt more complex 3d structures than shorter genomes)
The fugu fish is an excellent model to study what aspect of the genome?
Fugu fish has very short introns in the genome although it encodes largely the same proteins as humans
Briefly state what are the unique factors of transposable elements (TEs) found in the Fugu fish (state at least 2)
- They are extremely active
- The transposable elements in Fugu fish are extremely diverse (>40 families of TEs)
- Almost every class of TE found in eukaryotes can be found in the Fugu fish
The fugu fish has comparable number of genes and introns as humans but yet has a much smaller genome. How does the fugu fish accomplish this?
- Fugu fish has smaller introns on average (75% of introns in fugu are <429bp whereas in humans it is 2609bp)
- Fugu fish has many more short introns (modal value of intron length is 79bp whereas in humans it is 87bp)
If the fugu genome is so compact with short introns, is it still able to manage genes with long introns?
Yes, the Musashi homolog shows that the Fugu fish has retained 1 gene with extraordinarily long intron length as compared to humans and yet they still possess the genetic machinery to process such a gene.
How does the Musashi homolog gene show that Fugu fish likely inherited genes with long introns but managed to downsize the introns off over time?
The fugu fish has short introns in general but yet is still able to process genes with large introns. This suggests that it likely used to process genes with large introns but evolved to have shorter introns while still retaining the ability to process genes with large introns.
