Lecture 6: Genome Complexity Flashcards
How can mutations lead to phenotypic variation?
Can cause changes in gene expression or protein products
How can new genes be made?
From gene duplications and non-coding DNA
Mutations affecting what areas of DNA are likely to have an impact on gene expression?
promotor region, enhancers/silencers
What is beak shape diversity in Darwin’s finches an example of?
Regulatory evolution
What was examined from 6 of Darwin’s finches and what did they find?
expression patterns of growth factor genes in 6 of Darwin’s finches at different development stages. found expression pattern of Bmp4 correlates with beak depth and breadth. More Bmp4 means greater sized beak.
How can the protein products be changed?
AA subs/ deletions/ additions can change the coding frame and truncate the protein.
How can chromosomal rearrangements create new genes?
gene duplications, fusion/fission
Why are mutations in non-coding areas unlikely to be fixed in the population?
Unlikely to be kept as are unlikely to be beneficial in in non-coding region
What is likely after duplication?
For both copies to acquire further mutations
What are the three types of mutation likely to arise after duplication?
Non-functionalisation, subfunctionalisation, neofunctionalisation
What is non-functionalisation?
most of these are lost and degrade in a few million years which is the most common fate
What is subfunctionalisation?
Where both copies only partially fullfill the function of the original gene. is the most common route for maintaining two copies.
How does gene expression evolve?
Through changes on promoter/enhancer/silencer regions, acquisition of novel regulatory elements, mutations or expression changes in activator/repressor machinery, changes in chromatin structure.
What is neofunctionalisation?
one gene gets another function but is very rare.
Explain the gene duplication event behind dogs with long and short legs
ch18. Gene had a duplication event. A retrotransposon captures a mature RNA and copies it back into RNA. results in an extra copy of the gene with no introns and a very long poly-A tail. Most land at random points that are non-functional but this one has a strong effect on phenotype.
How do new functions replace other ones?
Some amino acids replace other ones, new genes are generated but others are lost. the overall amount of info stays stable.
How are eukaryotes more complex than prokaryotes?
Eukaryotes have cell compartmentalisation. Have 100s cell types and specialised organs.
What ways can we measure complexity?
Eg how much independence they have eg bacteria being parasitic, free living or symbiotic
Of parasitic, free living and symbiotic, what are the two that will have lost some genes and what is the order of increasing complexity and genome size?
parasitic and symbiotic as get some things from host. free living more than parasitic more than symbionts
What is the case in prokaryotes?
More complex organisms have larger genomes
What is genome size correlated with in prokaryotes?
Gene number
Which has the larger genome, eukaryotes or prokaryotes?
Eukaryotes
Name some differences between prokaryotic and eukaryotic genomes
1) Prokaryotes have a genome not in a nucleus whereas eukaryotes have so transcription and translation are separated
2) Prokaryotes have non condensed chromatin, eukaryotes do
3) Prokaryotes have single, circular DNA, eukaryotes have linear chromosomes
4) prokaryotes have a single replication origin, eukaryotes have multiple.
Why are eukaryotic cells able to divide faster?
have multiple origins of replication
What is the difference between eukaryotes and prokaryotes in genes?
Genome size and gene number are related to complexity in prokaryotes but not eukaryotes
Why is it difficult to sort eukaryotes on their level of complexity?
Not a link between higher complexity and bigger genomes as Homo Sapiens have an average genome size
What could we use to measure complexity?
Number of cell types as is easier to follow than functions
What does increased complexity not reflect?
Species success
What is the C-value paradox?
Mismatch between complexity and genome size.
How is the C-value paradox explained?
Variations in ploidy, accumulation of non-coding DNA. Genome size is determined by the amount of non-coding DNA such as transposons
What is the G value paradox?
Gene number doesn’t correlate with organism complexity.
What are the four genomic basis for increase in organism complexity?
1) regulation of transcription may be more complex at multiple levels eg promoter regions.
2) Gene content changes eg in number and gene family size variation derived from a single ancestor gene
3) Proteins produced interact with more proteins
4) More distinct transcripts are produced by alternative splicing
What is biological complexity associated with?
total and mean number of binding sites per proteosome and how many conformations a protein can have
Give a definition of alternative splicing
A common post-transcriptional process by which multiple distinct functional protein products are produced by a single gene by selectively cutting out segments of the coding regions in the mRNA molecule
What two things is alternative splicing probably correlated with?
Complexity and diversification of cell types
What has risen in some lineages?
the number of alternative splicing events
What is the problem with saying alternative splicing is correlated with complexity?
We would need to know if complex species would still have evolved without alternative splicing
What do some studies show?
more complex species have lower populations as it takes more energy to develop a more complex organism
What do vertebrates have?
A very low number of species
What is also considered important for complexity?
The acquisition of mitochondria and chloroplasts
