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Who developed binomial nomenclature?
How does binomial nomenclature work?
- 2 names:
- Generic name (genus)
- Specific name (species)
How are the names chosen?
- Most names are descriptive and derived from Latin or Greek
- Some derived from the name of the discoverer
What are the taxonomic categories?
What does phenetic mean?
What does phylogeneic mean?
How old is the Earth?
about 4.5 billion years
When is the first evidene of microbial life?
about 3.86 billion years
What are stromatolites?
Microbial mats consisting of layers of filamentous prokaryotes, sediments, and extracellular matrix
Which bacteria formed ancient stromatolites?
Anoxygenic phototrophic filamentous bacteria
Which bacteria form modern stromatolites?
Oxygenic phototrophic cyanobacteria
What was early Earth like?
- Much hotter than today
What is the surface origin hyothesis?
- The 1st membrane-enclosed, self-replicating cells arose out of primordial soup rich in organic and inorganic compounds in ponds on Earth's surface
- Dramatic temperature fluctuations (day/night) and mixing from metero impacts, dust clouds, and storms argue against this hypothesis
What is the subsurface origin hypothesis?
- Life originating at hydrothermal springs on ocean floor
- Conditions would have been more stable
- Steady and abundant supply of energy (ex - H2, H2S) may have been available at these sites
First self-replicating systems may have been ___-based
Why does RNA world theory exist?
- RNA can bind small molecules (ATP, other nucleotides)
- RNA has catalytic activity; may have catalyzed its own synthesis
Why would DNA eventually become the genetic repository?
More stable molecule
What are other important steps in emergence of cellular life?
- Buildup of lipids
- Synthesis of phospholipid membrane vesicles
- Vesicle synthesis is catalyzed by the clay of the mound
What is LUCA?
- Last universl common ancestor
- Population of early cells from which cellular life may have diverged into ancestors of modern-day Bacteria and Archaea
Primitive cells must have been ____ and ____ due to the conditions on early Earth
What was the carbon source for primitive organisms?
What is mutation?
Changes in the nucleotide sequence of an organism genome (nucleotide change, insertion, deletion)
Why do evolutionary pressures select or discard mutation?
- Adaptive mutations improve fitness of an organism, increasing its survival in its environment
- Silent mutation may be beneficial in other environment allowing the microorganism to colonize new niches
How can we detect phenetic similarities?
- GC ratios
- DNA-DNA hybridization
How can we detect phylogenic similarities?
- Fossil record
- Ribosomal RNA sequences
- Multi-locus sequences typing
- Whole genome sequencing
What is the traditional method for the classification of prokaryotes?
- Introduced 200 years ago by Michael Adanson
- All characteristics should be considered to be of equal importance (unbiased)
- Classification should be based on as many features as possible
- Organisms should be grouped on the basis of overall similarity
What is the similarity coefficient?
- (S) also known as the Jaccard coefficient (SJ)
- A large number of characteristics were determined for each organism and the similarities between pairs of microorganisms were then calculated and expressed as the similarity coefficient
What is a dendrogram?
A tree diagram showing taxonomic relationships
What is a phenon?
A group of organisms that have characters in common
How do you calculate (S) the similarity coefficient?
S = (Number shared)/(Total number tested)
How do you calculate (SJ) the Jaccard coefficient?
SJ = (number shared)/((total number tested)-(number negative for both))
What is the GC ratio?
- Percentage of guanine-cytosine base pairs in the genome
- If the GC ratio of two organisms differs by more than about 5% they cannot be closely related
- Organisms with similar or even identical GC ratios may be unrelated (like homo sapiens 42, and b. subtilis 43)
How do you calculate the GC ratio?
What is DNA-DNA hybridization?
- Genomes of 2 organisms are hybridized to examine proportion of similarities in their gene sequences
- Usful for differentiating very similar organisms, very sensitive methods
How do you interpret hybridization values?
- 70% or higher suggest strains belong to the same species
- 25% or higher suggest same genus
Who established the presence of the 3 domains of life (bacteria, archaea, eukarya)? When?
Carl Woese, 1970s
What is Carl Woese famous for?
- Sequencing of the small subunit rRNA (SSU rRNA):
- 16S rRNA in prokaryotes, 18S rRNA in eukaryotes
- Establishing the 3 domains of life
- Providing a unified phylogenetic framework for bacteria
What does the routine procedure of comparitive rRNA sequencing involve?
- Amplification of the gene encoding SSU rRNA
- Sequencing of the amplified gene
- Analysis of sequence in reference to other sequences
What is rRNA sequencing used to infer?
The phylogeny of prokaryotes and other microorganisms
How does the phylogenetic tree work?
- It is a graphic illustration of the relationships among sequences
- Branches define the order of descent and ancestry of the nodes
- Branch length represents the number of changes that have occured along that branch (usually a scale is included)
What do nodes indicate on a phylogenetic tree?
Nodes mean a putative common ancestor
What does unrooted mean in reference to a phylogenetic tree?
- Relationship between organisms (sequence similarity)
What does rooted mean in reference to a phylogenetic tree?
- Relationship and evolutionary path
What is the endosymbiosis theory?
- A well supported hypothesis for the origin of eukaryotic cells
- Contends that mitochondria and chloroplasts arose from symbiotic association of prokaryotes within another type of cell
What does it mean that the eukaryotic cell is chimeric?
- Eukaryotes have similar lipids and energy metabolisms to bacteria
- Eukaryotes have transcription and translational machinery most similar to archaea
What are the 2 hypotheses that exist to explain the formation of the eukaryotic cell?
- 1. Eukaryotes began as nucleus-bearing lineage that later acquired mitochondria and chloroplasts by endosymbiosis
- 2. Eukaryotic cells arose from intracellular association between O2-consuming bacterium (the symbiont), which gave rise to mitochondria, and an archaeal host. The archaeal host later developed a nucleus.
What is meta-analysis?
- Use next-generation sequencing (massively parallel sequencing)
- Sequence up to 100 Gb in 2 days
What does metagenomic mean?
Determine the physiological potential of a population (DNA)
What does metatranscriptomic mean?
Determine the function performed by a population (RNA)
What are the 3 methods to the polyphasic approach to bacterial taxonomy?
- 1. Phenotypic analysis
- 2. Genotypic analysis
- 3. Phylogenetic analysis (16S rRNA)
What is a drawback to bacterial taxonomy?
Need to classify different strains of the same species
What is multilocus sequence typing (MLST)?
- Method in which several different "housekeeping genes" from an organism are sequenced
- Has sufficient resolving power to distinguish between very closely related strains
What does identification of an unknown microorganism depend on?
- The comparison of its properties with those of organisms that have already been classified and name:
- -Biochemical properties
- -GC content
- -16S rRNA sequencing
What do dichotomous keys help with?
Morphology and phenoype
What other things help with identification of organisms?
- Characterization of the fatty acids in the membrane
- Sequencing DNA encoding rRNA
What does FAME stand for?
fatty acid methyl ester
What does fatty acid analysis depend on?
Relies on variation in type and proportion of fatty acids present in membrane lipids for specific prokaryotic groups
What does fatty acid analysis require?
Rigid standardization because FAME profiles can vary as a function of temperature, growth phase, and growth medium
What is ribotyping?
- Method of identifying microbes from analysis of DNA fragments generated from restriction enzyme digestion of genes encoding SSU rRNA
- Highly specific and rapid
What is ribotyping used for?
Used in bacterial identification in clinical diagnostics and microbial analyses of food, water, and beverage
How do you sequence DNA encoding ribosomal RNA?
- Compare sequence to database
- Standard procedure for classification of new species