microbio 3.4

evolution

random dna changes and selection which causes change in gene frequency in populations and communities

isotope fractionation

light isotopes are incorporated over heavy isotopes, enzymes prefer light isotopes

hydrothermal vents

first life formed on bottom of ocean, more stable condition, had supply of energy in reduced inorganics, geochemistry supported abiotic production of molecules, mineral structures made compartments to conserve energy

RNA functions 

life began in rna, backbone of essential molecules, binds small molecules, catalyze biochemical reactions, template for own synthesis, regulate genes 

RNA to cellular life

proteins replaced rna as catalysts, dna became genome and template for rna, earliest life had rna, dna and protein

LUCA

last universal common ancestor, bacteria and archaea diverged

small subunit ribosomal rna

in prokaryotic cells as 16s rrna molecules, present in all cellular organisms, good record of evolution, are chronometers for evolution

the universal tree of life

shared genes for central cellular function, eukaryotic and archeal genes are similar, encode core transcription, translation and dna replication function

LECA

last eukaryotic common ancestor, 4000 genes, has characteristic features of eukaryotic cells, 70 percent of genes in only eukaryotes, rest shared with bacteria and archaea

endosymbiotic origin of eukaryotes

chloroplasts and mitochondria same size as bacteria, independently replicate, both contain own genomes of bacterial genes and ribosomes, are circular, sensitive to antibiotics

ancestor of mitochondria

alphaproteobacteria

ancestor of chloroplast

cyanobacteria

systematics

study of diversity of organism and relationship, links phylogeny and taxonomy

polyphasic approach

uses phenotypic, genotypic, and phylogenetic analysis

homologs

sequences inherited from common ancestor

ortholog

sequence with same function and originate from a single ancestral gene in a common ancestor

paralogs

sequence evolved to have different functions resulting from gene duplication

evolution details

change in allele frequencies over time, increase of genetic diversity, flow of genetic info from old to new species

gene deletions in microbial genomes 

when many bacteria live together, one bacteria will make one specific amino acid for all bacteria so they delete other genes that are unnecessary

horizontal gene transfer

impacts microbial evolution, allows transfer of dna between distant branches of evolutionary tree, through transformation, transduction, and conjugation, unidirectional, asymmetrical, not constrained by species

core genome

genes shared by all strains of a species

pan genome

core genome plus genes not shared by all strains

building the phylogenetic tree

requires inheritance from common ancestor, sequences are homologous and similar

microbial systematics

names and classifies microorganisms, describe traits, investigate histories

nomenclature

following binomial system in which species are given descriptive genus names and species epithets

taxonomy 

classifies organisms into groups based on similarity 

taxonomic hierarchy (broad to narrow)

domain, phylum, class, order, family, genus, species

species

a taxonomic category that defines a population of individuals that descended from common ancestor, genomically and phenotypically coherent, can be clearly differentiated

ANI

average nucleotide identity method, used to measure how genetically similar two prokaryote genomes are

phenotypic analysis

observable characteristics provide differentiable traits, can depend on growth conditions and differ between lab and environment

description of new species

new strain has to be compared to see if it is different to be described as a new taxon, new taxa has to follow prokaryotic code, molecular and genomic techniques can characterize phenotypic and genotypic characteristics

Bergey’s Manual of Systematics of Archaea and Bacteria

most widely accepted classification

THE Prokaryotes

a second source to classify