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Flashcards in lecture 3 - comparative genomics Deck (11):

How is genetic analysis carried out in E.coli?

1) Make random mutations & screen for interesting phenotypes (like a nutritional requirement)
2) Map the mutation, identify the gene that is disrupted and study the function of the gene
The functions of 2000 E. coli genes were discovered and characterised in this way
Problem: the genome sequence of E.coli reveals ~4300 genes


What is the explanation for some genes not being detectable by their mutant phenotype and the function of these genes is unknown? (forward genetic analysis)

Possible explanations:
The mutagenesis screen was incomplete?
Are more extensive screens required?
More screens might identify more mutations?
Might some mutations may be lethal?
Most probably explanation:
The phenotype of some mutants was not revealed, or was not detectable in the conditions of the screen (the experiment was not conducted in the natural environment of E. coli), or in environments that would reveal all possible phenotypes


What is reverse genetic analysis?

The sequence of the E. coli genome is complete and we can predict where all the genes are located
Make library of strains each containing a deletion of a single gene
About 3500 mutants have been made in this way and some genes have been found to be essential for growth
Screen this library of mutants for phenotypes that have not previously been detected and identify a function for that gene


What did comparative genomics show about the endosymbiotic theory?

Comparative genomics provided proof of the endosymbiotic theory and revealed much about the origins of chloroplasts & mitochondria
Plant cells contain at least three genomes (nuclear, mitochondrial & chloroplast)
Organelles (mitochondrial & chloroplast) have retained fragments of their original genomes


How dynamic are eukaryotic genomes?

Chloroplast DNA is most closely related to the DNA from prokaryote cyanobacteria
4300 A. thaliana genes have a prokaryotic origin
3000 genes are not required in the chloroplast - 1300 genes are required in the chloroplast
plastid DNA is more closely related to the DNA from cyanobacteria than from the nucleus of the same cell
endosymbiosis lead to a massive reduction in genome size relative to that of the genome of cycanobacteria
gene loss and transfer to the nucleus
not just one event, both primary and secondary endosymbiosis


Why did we sequence the human genome?

To establish functional categories for all human genes
To analyse genetic variations between humans, including the identification of single-nucleotide polymorphisms (SNPs)
To map and sequence the genomes of several model organisms
To develop new sequencing technologies, high-throughput computer automated systems for genome analysis
To disseminate genome information among scientists and the general public


What are transcriptional activators?

are proteins that have a positive effect on the transcription of a subset of genes


How do transcriptional activator families compare in eukaryotes?

In some cases, humans have more transcriptional activators than other model organisms
But these transcriptional activators can still be divided into the same groups
Most regulatory gene networks are controlled by the same families of transcriptional regulators in all eukaryotes


What are the important conclusions of comparative genomics?

there are similarities in gene content, position & order
The relative positions of genes are often the same and several segment blocks in these chromosomes appear the same
Some have been inverted or relocated during evolution
The conservation of gene order in this way is known as synteny


How can comparative genomics and synteny be used to locate human disease genes?

model organisms can be used to understand the genetic basis of human diseases by identifying an equivalent gene in a model organism
if the equivalent gene has been characterised in the model organism, then the biochemical role of the human gene can be better understood
if the equivalent gene has not been characterised - research can be directed at the newly identified equivalent gene in a model system
The mouse is often used as a model to study human diseases, but it is also possible to use yeast


How is yeast used as a model organism for human diseases?

In these experiments the equivalent yeast gene to the human disease gene has been identified and characterised
This has helped determine the function of the gene in yeast, which could not be determined from just the sequence of the human gene
The biochemical basis of Bloom’s syndrome & Werner’s syndrome was not understood - they are both human growth disorders
The equivalent gene was identified and characterised in yeast
Yeast sgs1 mutants live for shorter periods than wild-type yeast & show an accelerated onset of ageing
This is a physiological similarity between gene activity in yeast & humans. Human disease patients suffer similar symptoms
The yeast gene SGS1 codes for one of a pair of related DNA helicases required for the transcription of rRNA genes & for DNA replication
This has identified a potential biochemical basis of the human disease