BIO-31: E.4 P.R quiz. Ch.10

Phylogenetic Relationships

• Taxonomy classifies organisms, showing their similarities and differences using Taxon/Taxa categories
• Systematics, is the study of an organism's evolutionary background.
• A taxonomic hierarchy shows the evolutionary relationships among organisms.

History of Classification

• 1735: Linnaeus proposed the kingdoms Plantae and Animalia
• 1800's: Bacteria, fungi, and other microorganisms were placed in the kingdom Plantae by Nageli. Haeckel proposed Kingdom Protista for them.
• 1937: Prokaryote definition was introduced to distinguish cells without nuclei
• 1968: Murray proposed Kingdom Prokaryotae
• 1969: Whittaker introduced the five-kingdom system
• 1978: Two prokaryotic cell types were discovered, prokaryotic relationships were then determined by rRNA sequencing
• 2001-2025: A complete inventory of all species occurred

Three Domains

• Woese proposed the three domains in 1978. This was based on sequences of nucleotides in rRNA
• The three domains: Eukarya (animals, plants, fungi), Bacteria, and Archaea (methanogens, extreme halophiles, hyperthermophiles)

Key Concepts

• Organisms evolved from cells over 3 billion years ago
• Conserved DNA is passed on from ancestors
• Domain Eukarya includes kingdoms Fungi, Plantae, Animalia, and protists
• Domains Bacteria and Archaea are prokaryotes

Characteristics of Domains

• Archaea are prokaryotic and have a variable cell wall composition that lacks peptidoglycan

• Composed of branched carbon chains attached to glycerol by ether linkage

• The first amino acid in protein synthesis is Methionine

• Not sensitive to antibiotics and lacks rRNA loop and common arm to tRNA

• Bacteria are prokaryotic and have peptidoglycan

• Consist of straight carbon chains attached to glycerol by ester linkage

• The first amino acid in protein synthesis is Formylmethionine

• Sensitive to antibiotics and have rRNA loop and common arm to tRNA

• Eukarya are eukaryotic and have cell walls that vary and contain carbohydrates

• Composed of straight carbon chains attached to glycerol by ester linkage

• The first amino acid in protein synthesis is Methionine

• Not sensitive to antibiotics and lacks rRNA loop but has common arm in tRNA

Prokaryotic vs Eukaryotic

• Prokaryotic DNA is circular, some containing two circular forms, or linear, while Eukaryotics have Linear DNA
• Histones are present in Archaea and absent in Eukaryotic organelles
• The first amino acid in protein synthesis is Formylmethionine for bacteria and archaea; Methionine otherwise
• Ribosomes are 70S and binary fission facilitates growth
• Eukaryotic cells have an 80S ribosome and Mitosis facilitates growth

Origins

• Eukaryotes came from infoldings of prokaryotic plasma membranes
• Endosymbiotic bacteria adapted into organelles

Phylogenetic Tree

• Grouping organisms according to common properties: Fossils and Genomes
• Groups of organisms evolved from a common ancestor
• Each species retains some of its ancestor's characteristics

Scientific Nomenclature

• Common names differ when affected by language and geography
• Binomial nomenclature is the worldwide, consistent, and accurate naming system
• Binomial nomenclature contains Genus and specific epithet (species)

Naming Examples

• Salmonella enterica: named in honor of Daniel Salmon who was a public health microbiologist; enterica refers to the intestines
• Streptococcus pyogenes: named for cells appearing in chains (strepto-) and forming pus (pyo-)
• Saccharomyces cerevisiae: fungi that uses sugar (saccharo-) to make beer (cerevisia)
• Penicillium chrysogenum: named for its paintbrush appearance (penicill-) under a microscope and produces a yellow pigment (chryso-)
• Trypanosoma cruzi: is named for its corkscrew shape (trypano-) and honors Oswaldo Cruz

Taxonomic Hierarchy

• A series of subdivisions, with Linnaeus’ hierarchy classifying plants and animals
• Similar species into a genus, genera into a family, families into an order, orders into a class, classes into a phylum, phyla into a kingdom and kingdoms into a domain

Prokaryotic Classification

• Prokaryotic species: population of cells with similar traits
• Culture: bacteria grown in a laboratory
• Clone: population of cells derived from one parent cell
• Strain: genetically different cells within a clone

Kingdom Eukaryotes

• Eukaryotic species are similar organisms that breed among themselves
• Protista: a variety of autotrophic/heterotrophic organisms grouped into clades based on rRNA
• Fungi: chemoheterotrophic organisms; unicellular or multicellular and have cell walls of chitin.
• Plantae: multicellular organisms with cellulose cell walls; undergo photosynthesis
• Animalia: multicellular organisms; no cell walls; chemoheterotrophic

Viral Classification

• Viruses are not within any domain, are not cells, and require a host
• Viral species are viruses with similar traits that fill a certain ecological niche

Classifying Microorganisms

• Classification puts organisms in related groups
• Lists of characteristics of known organisms
• Identification matches the characteristics of the unknown organism to known organisms
• Clinical lab identification

Classifying Entities

• Bergey's Manual of Determinative Bacteriology provides identification schemes to identify bacteria and archaea (morphology, differential staining, biochemical tests)
• Bergey’s Manual of Systematic Bacteriology provides bacteria and archaea phylogenetic information (based on rRNA sequencing)
• Approved Lists of Bacterial Names lists species of known classification

Identifying Organisms

• Morphological features: Beneficial for categorizing eukaryotes and can infer limited phylogenetic relationships.
• Differential staining: Useful for bacterial differentiation, but not useful for bacteria without cell walls
• Biochemical tests can determine presence of bacterial enzymes

Biochemical Tests

• Rapid identification methods perform several biochemical tests simultaneously.
• Results are recorded, and assigned a number.

Tools for Identifying Organisms

• Dichotomous keys Identification keys with successive questions
• Cladograms Maps show evolutionary relationships among organisms; based on rRNA sequences

Serology

• Serology is the study of serum and immune responses in serum
• Microbes are antigenic: They cause the body to make antibodies in the serum
• Microbes reaction with specific antibodies
• Antiserum is a solution of antibodies tested against an unknown bacterium

Serological Reactions

• Serological testing can differentiate between species and strains within species
• Slide agglutination tests combine bacteria and antibodies, causing agglutination

ELISA

• (Enzyme-linked immunosorbent assay) Known antibodies and an unknown type of bacterium are added to a well and if the reaction occurs between them then the bacteria have been identified.

Classifying with Western Blotting

• Western blotting identifies serum antibodies as confirmation of HIV infection

Phage Typing

• Phage typing is used to identify bacteria by which phages are susceptible
• On a plate, clearings called plaques can appear when phages infect and lyse bacterial cells

Flow Cytometry and FACS

• Flow Cytometry measures electrical conductivity between species or fluorescence
• Fluoresence-Activated Cell Sorter (FACS) uses fluorescent dye antibodies

DNA Base Composition

• DNA base composition checks for guanine+cytosine percentage
• Closely related organisms will have similar ratios; If there is >10% difference they are not related

DNA Fingerprinting

• DNA fingerprint checks fragment sizes, made by restriction enzyme digests, to find genetic similarities.
• Electrophoresis is used to determine those DNA fragments for genetic comparison

Nucleic Acid Amplification Tests (NAATs)

• PCR (Polymerase chain reaction) is used to amplify DNA of unknown microorganisms that cannot be cultured
• Specific primer for known microorganism
• Amplified DNA after PCR and specific primer confirms the unknown microorganism

Nucleic Acid Hybridization

• A test for the ability of DNA strands from one organism to hybridize with DNA strands of another
• A greater degree of hybridization means a greater degree of relatedness
• Single strands of DNA or RNA from related organisms can hydrogen-bond to form a double-stranded molecule

Southern Blotting

• Southern blotting is nucleic acid hybridization that identifies unknown microorganisms using DNA probes

Characterizing with DNA Chips

• (Also called microarray) A DNA chip is a collection of DNA probes that can identify pathogens through hybridization
• Detected by fluorescence

Ribotyping

• Ribotyping is rRNA sequencing
• Fluorescent in situ hybridization (FISH) uses fluorescent DNA or RNA probes to stain a microorganisms being targeted- these enter live cells to determine their identity, abundance, and activity. It can then be tested for any biological environmental sample.