Classification and Taxonomy

• Classification organizes organisms based on shared characteristics.
• Carolus Linnaeus developed the Linnaean system of taxonomy.
• This system names living organisms by genus and species.
• Taxonomy is classifying and naming organisms based on structure and function.
• Animals may shift classifications as new discoveries are made.

Naming System

• Binomial nomenclature is a 2-name system created by Linnaeus, where names are in Latin and written in italics.
  • Example: Tyto alba (Barn owl)
• Genus (1st name):
• Includes one or more similar species.
• Always capitalized.
• Species (2nd name):
• Most specific taxon.
• Always lowercase and follows the genus name.
• Taxonomy uses "nested" levels, with each group called a taxon that gets more specific.
• Naming can be based on location, physical features, and more.
• Scientific names prevent confusion from different common names for the same species. Examples:
  • Puma concoloris can be called a puma, cougar, etc.
• Modern classification relies on genetic similarities.
• Phylogeny represents the evolutionary history of a group of species.
• Cladistics classifies organisms based on evolutionary relationships, represented by a cladogram.

Classification History

• New discoveries lead to changes in classification.
• Until 1866, there were only 2 kingdoms: Animalia and Plantae.
• In 1866, single-celled organisms were moved to kingdom Protista.
• Protista is a group for all organisms not Animalia/Plantae
• In 1938, all prokaryotes were moved to kingdom Monera.
• In 1959, fungi moved to its own kingdom
• In 1977, kingdom Monera split into kingdoms Bacteria and Archaea due to DNA differences.

Domains

• Domains were created after realizing the differences between Bacteria and Archaea
• Domain Bacteria includes prokaryotes and has only 1 kingdom, called Kingdom Bacteria or Eubacteria.
• Domain Archaea includes prokaryotes and only 1 kingdom, called Kingdom Archaea or Archaebacteria.
• Archaea have metabolic pathways similar to Eukaryotes and can survive in extreme conditions (extremophiles).
• Domain Eukarya includes all eukaryotes.
• Kingdom Protista consists of mostly unicellular organisms with diverse features.
• Also includes Kingdom Plantae, Kingdom Fungi, and Kingdom Animalia.

Viruses

• Viruses require a host cell to reproduce and are considered infectious obligate intracellular parasites.

Viral structure

• Genetic material (DNA or RNA)
• Protein shell (capsid)
• Many have a lipid envelope
• Spike proteins act as keys to match with cell receptors.
• Lipid envelope facilitates entry into the cell.
• DNA viruses have mechanisms to correct copy errors, unlike RNA viruses, which mutate more.
• DNA viruses include adenovirus, herpesvirus, smallpox virus, papillomavirus (HPV).
• RNA viruses include the common cold, influenza, dengue, polio, measles, rabies, hepatitis C, coronavirus, HIV.

Viral Infection Life Cycle

• For regular viruses:
• Attachment to the cell membrane.
• Entry where the capsid comes apart.
• Replication and gene expression to create copies of the genome and viral proteins via host ribosomes.
• If viral DNA is replicated:
• Viral DNA is transcripted into RNA and translated into proteins by ribosomes.
• If viral RNA is created:
• Process occurs in the cytoplasm
• Assembly of new viruses (caploids form).
• Release from the cell, often killing it.
• HIV (retrovirus) infection cycle:
• Attachment and entry.
• Reverse transcription: RNA is transcribed into DNA using an enzyme.
• Integration: viral DNA is inserted into host cell DNA.
• Replication: viral DNA is replicated and transcribed along with host DNA.
• Assembly.
• Release without necessarily killing the cell.
• Viruses typically target specific cell types.
• Cytopathic effects: Negative effects on cells due to viruses which can cause cells to become sick or break after the virus replicates inside them.

Treatment of Viral Infections

• Antiviral drugs help people recover and fight against viruses
• They are not widely available
• Vaccines introduce the immune system to a pathogen beforehand.
• White blood cells recognize spike proteins and fight against them.
• Memory T cells are created for future encounters with the same antigens.
• Vaccines inject weakened, dead or parts of the whole virus.

Bacteriophages

• Viruses that infect only bacterial cells by injecting RNA or DNA through the membrane.
• Lytic infections:
• Attachment
• Entry
• DNA replication and synthesis
• Assembly
• Lysis
• Lysogenic infections:
• Attachment
• Entry
• Integration
• Cell division, duplicating viral DNA
• Prophage is triggered and all cells will enter the lytic cycle

Prokaryotes

• Prokaryotes: Bacteria and Archaea
• Antonie van Leeuwenhoek discovered prokaryotes in 1677.
• Prokaryotes can be classified by their need for oxygen:
• Obligate aerobes need oxygen; obligate anaerobes are poisoned by oxygen.
• Facultative anaerobes can live with or without oxygen.
• Classified by shape:
• Bacillus (rod-shaped); Coccus (spherical); Spirilla (spiral).
• Classified by arrangement: Staph (group like grapes); Strep (group like a chain).
• Prokaryotes share a similar cell structure:
• Circular DNA and plasmids distinct from chromosomal DNA, plasma membrane, and ribosomes.
• Reproduce asexually via binary fission and exchange genes via conjugation.
• Exchange genes during conjugation (random chance?)
  • Plasmids can go between bacteria through conjugation bridges
• Transformation occurs when a bacteria finds a piece of DNA and picks it up.
• Transduction: viruses take up DNA from one bacterium and infect another.

Differences Between Bacteria, Archaea, and Eukarya

• Archaea: recently discovered (1977), many extremophiles, found in almost every habitat, no obvious pathogens.
• Bacteria: pathogenesis (how a disease develops, progresses, and is resolved).
• Can survive harsh conditions by forming an endospore.
• Methods of causing disease:
• invading tissue
• making toxins.
• Antibiotics are the primary treatment, but can lead to antibiotic resistance.

Protista

• The most diverse of all kingdoms and can be animal-like, plant-like, or fungus-like.
• Protist characteristics: mostly single-celled and microscopic, all eukaryotes, difficult to classify.
• Animal-like protists (protozoans) are heterotrophs, single-celled, and can move
• Protozoans use a flagellum to swim
• Pseudopods (false feet) or amoeboid movement
• Ciliates help capture food
• Plant-like protists (algae) are photosynthetic, single-celled, colonial, or multicellular, and lack roots, stems, or leaves (kelp).
• Euglena: photosynthetic, have an "eye", one or two flagella.
• Dinoflagellates: two flagella, may be bioluminescent, can cause red tide.
• Diatoms: hard shells made of silica, produce oxygen, found in water or dirt.

Fungus-like Protists

• Decompose dead organisms, heterotrophs, can move (like animals), single celled (but can form multicellular structures)
• Slime molds:
• Plasmodial slime molds act multicellular
• Slime molds move by changing chemical shape
• Cellular slime molds -Cells start to bunch together to form pseudoplasmodium
• Water molds are parasites of plants or fish and caused the Irish potato famine.
• Pathogenic protists: Malaria (caused by Plasmodium parasite, transmitted by Anopheles mosquito).

Fungi

• Fungi vs plants:
• Fungi: cell walls of chitin, no chlorophyll, heterotrophs.
• Plants: cell walls of cellulose, contain chlorophyll, autotrophs.
• Mycorrhizal relationship: symbiosis between fungi and plant roots.
• Plants provide fungi carbohydrates; fungi provide water, minerals, and nutrients.
• Most fungi are multicellular (except yeast).

Basic Structure Fungi

• Hyphae
• Mycelium
• Fruiting Body
• Spores
• 3 types of fungi:
• Sac Fungi
• Bread molds
• Spore-producing structures called sporangia
• Club Fungi