Evolution of Genomes

Nuclear genome evolution: Mutation, Gene duplication and loss, exon shuffling, repetitive DNA (transposable elements), Horizontal gene transfer (endosymbiosis).

Fate of duplicated genes: Paralogues from WGD obtain disabling mutations becoming pseudogenes and are lost.

Multigene families: formed from several WGD events.

Simple gene families: all members have identical or nearly identical sequences.

Complex gene families: Members have similar sequences but different enough to code for gene products with different properties.

Neofunctionalization: gain of new function, can be regulatory or coding.

subfunctionalization: partial loss of function. 

redundancy: results from duplication of genes, only one gene needed, leads to neofunctionalisation, pseudogenisation, or subfunctionalization due to changes in regulatory or coding regions.

Orthologues: Speciation of organisms results in the same gene in different species being orthologs.

Paralogues: result from gene duplication and divergence of genes, in the same organism.

isozymes: enzymes that catalyze the same biochemical reaction but in different tissue or at different times or with different properties.

Polypeptide domain shuffling: combines existing domains into novel gene architectures, increases gene architecture complexity.

Functional domain: part of the protein that codes for the active site.

Structural Domain: part of the protein that inserts into a membrane

Endosymbiosis: A symbiotic relationship where one organism lives inside the other 

Origin of the nucleus: an archaeal cell entered a Eubacterial cell and evolved into a nucleus

Origin of mitochondria:  alpha-proteobacteria became symbionts with a nucleus, through gene transfer and gene loss became mitochondria.

Origin of chloroplasts: cyanobacteria became symbionts with mitochondria protists.

Product specificity corollary: Nuclear-encoded gene products are retargeted to the organelle from whose genome they originated .

Product specificity corollary of the endosymbiotic theory is NOT supported.

Calvin cycle: CO2 fixation pathway in plant chloroplasts.

Endosymbiont genes transferred to host cell nucleus to: isolate genes from sites where mutagenic radiacals are formed, Have genes in a sexual population instead of an asexual population.

Hydrophobicity Hypothesis (HH): Some gene products are too hydrophobic to be imported into organelles. 

Code Disparity Hypothesis (CDH): Genetic code used in organelles and nucleus differ, which would lead to incorrectly translated proteins. 

Co-location for Redox Regulation (CORR): Proximity of genes to their products’ sites of activity allows a rapid response in gene expression to changes in metabolism.

•NUMTs – nuclear mitochondrial DNAs 

•NUPTs – nuclear plastid DNAs

 DNA transfer between intracellular compartments: Lysis of organelles and release of DNA, Fusion of organelles (lateral gene transfer), Physical contact between organelles, Plastids form stromules with other organelles.

DNA integration into genome : NHEJ  uses DSB repair mechanism that requires no homology between ends.

Horizontal (lateral) Gene transfer: transmission of genetic material between the genomes of two individuals by nonvertical inheritance.

•know the endosymbiotic theory of the origin of the nuclear, chloroplast and mitochondrial genomes, including the proposed ancestral genomes of each. 

•be able to explain the product specificity corollary of the endosymbiotic theory, and examples supporting/refuting it. 

•be able to explain the current hypotheses for why many endosymbiont genes were transferred to the host cell nucleus and why some have been retained in the organelles (including examples supporting and refuting each). 

•be able to explain NUMTs and NUPTs and how they are believed to remodel nuclear genomes. 

•be able to describe how DNA is thought to be transferred between intracellular compartments.

 •be able to explain the mechanism that facilitates the integration of organelle DNA into the nuclear genome. 

•be able to define horizontal gene transfer and give an example