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.