BIOL 25 Lecture 3 (Themes- Classification)

Kingdom Animalia `

- Eukaryotes - heterotrophic - multicellular - no cell wall - found in all environments - capable of movement - some microscopic - greatest diversity of form - of concern as agents of transmission and as parasites - differentiation of cells - mobile

Kingdom Protista

- Eukaryotic cells (most complex) - unicellular, colonial, a few multicellular - specialization vs complexity - includes both autotrophs (algae) and heterotrophs (protozoans) - not closely related to groups: a "junk" kingdom aka fruit salad - ancestors to multicellular kingdoms: fungi, plants and animals

Classification Hierarchy

- Kingdom - Phylum - Class - Order - Family - Genus - Species

How does Evolutionary Tree/Cladograms differ from Linneaus' view

- Linneaus believed in 2 kingdom system with plantae (autotrophic and cell walls) and animalia (heterotrophic and no cell walls) - now use phylogeny (relatedness) to show organisms' evolutionary history - evolutionary trees/cladograms don't attempt to rank organisms

Evolutionary Trees/Cladograms

- comparateive genomics and biochemistry: amino acid (cytochrom c, bwlow) or DNA sequencing or metabolic diversitity and other clinical distinctions - considers phylogeny (relatedness) over time based on homology (how related)

Kingdom Fungi

- eukaryotes - heterotrophic - absorb food from environment - cell walls of chitin - mainly terrestrial - some microscopic - cytoplasmic continuity, a different brand of multicellularity - important in decomposition - includes yeasts and molds - differentiation of cells - no motility

Kingdom Plantae

- eukaryotic cells - multicellular - autotrophic (photosynthetic: can make energy themselves through photosynthesis (don't tend to be parasitic bc can get own nutrients)) - cell walls of cellulose - terrestrial and aquatic environments - of little interest to clinicians other than as fomites (things that carry infection like clothes and furniture) - differentiation of cells - no motility

archaebacteria

- extremophiles and live in extreme environments - sequence different between the two so branched monera out

What was Linnaeus' legacy to science?

- laid down the basic rules for taxonomic categories - realized that a system for recognizing and defining the properties of living things would prevent chaos in science by providing a unique name and slot to catalog it and would serve as a future identifier of that same organism - the binomial system in which you give each species two names: Genus and species - categorized organisms using the scala natura= God's divine order to rank species: species at top= closest to god - 2 kingdom system (plantae= autotrophic with cell walls; animalia= heterotrophic with no cell walls)

eukaryotic cells

- larger - more complex - membrane bound organelles (like nuclei, mitochondria) - includes protists, fungi, plants and animals (Eu= true= true nucleus)

what types of characteristics are used to classify organisms? which are most useful when trying to identify or classify microorganisms

- morphology (complexity and structure) - physiology (fxn) - genetics (inheritance) - phylogeny - quantitative systematics= best for microorganisms because Woese proved that when you isolate ribosomal sequences (present in all living things), unicellular organisms are more different genetically than morphologically

Viruses

- not in a kingdom - not alive - obligate intracellular parasites (can be maintained only inside living cells as a host to hijack its cellular machinery) - viruses do not eat, grow, metabolize, make proteins, or reproduce by themselves (but they do evolve) - consist of a small amount of genetic material encased in a bit of protect protein - viruses have either DNA or RNA, not both

Two kinds of Cells

- prokaryotic- simple - eukaryotic- complex

Taxonomy during the Transition Period - Carrolus Linnaeus (1707-1778)

- proposed the binomial system in which you give each species 2 names: Genus and Species - The scala natura- God's Divine order: - plantae= autotrophic, cell walls - animalia= heterotrophic, no cell walls (taxonomy: identify organisms, name them and then put into groups)

prokaryotic cells

- small - simple - no internal membrane-bound organelles - includes the bacteria (pro= pre; karyotic- nuclei; before nuclei; have ribosomes bc no membrane= site where proteins are made; have DNA organized more simply)

Themes Part 2: an overview of microbial diversity- taxonomy and systematics

- the cell theory - prokaryotic and eukaryotic cell structure - taxonomy, classification, and systematics - an overview of 5 kingdoms (+ viruses) - more current taxonomic frameworks

Cellular organization of living things

- unicellular organisms: one celled - colonial: many cells but little division of labor (differentiation) - true multicellularity: many cells and highly differentiated (have cells that all have same DNA but do diff fxns), specialization with division of labor, interdependence (cells dependent on each other)

Basic Concepts of Microbiology: The Cell Theory

1. the cell is the simplest form of life 2. all living things are composed of one or more cells 3. all cells come from pre-existing cells - 1600s- Hook= original cell theory with 1st two - 1839- Schleiden and Schwann added #3

The Scientific Revolution

2 Kingdom System (Linnaeus, mid 1700) (Plantae= autotrophic, cell walls and Animalia= heterotrophic, no cell walls) --> Darwin 1859 Theory of Evolution (all species originate from pre-existing species; closely related organisms have similar features bc they evolved from common ancestral forms) --> 5 Kingdom system and Systematics

Kingdom Monera

= PROKARYOTES/PROKARYOTIC - includes both heterotrophs (bacteria) and autotrophs (cyanobacteria) - very simple cells - have no nucleus or complex organelles - reproduce asexually - most closely resemble the earliest ancestral cells from 3.7 BYA - ecologically and clinically important ex: E. coli

Eukaryotic Kingdoms

Kingdoms= Protista, Fungi, Animalia, Plantae - have nuclei with DNA inside - complex organelles - derived from ancestral Monera - capable of sexual reproduction - the great evolutionary leap forward

Systematics

Taxonomy and classification based upon phylogeny (similarities of characteristics) - each kingdom is further subdivided according to a hierarchy

What is the difference between systematics and taxonomy? give an example of the levels of the taxonomic hierarchy

Taxonomy= classification (organize organisms into groups that indicate evol history and relationships- Domain, kingdom, phylum, class, order, family, genus, species), nomenclature (assigning names- genus and species), identification (using specific characteristics and capabilities of an organism to determine its exact identity and placement in taxonomy) ; considers structure and complexity as well as other characteristics including metabolic strategies= 5 kingdom system (comparative morphology) Systematics= taxonomy and classification based upon phylogeny (similarity of characteristics) - uses comparative biochemistry and genomics (e.g. AA (cytochrome, DNA sequencing) to group organisms by similarity of sequence - uses cladograms - evolutionary basis

5 Kingdom system

a system that considers structure and complexity as well as other characteristics including metabolic strategies - Robert Whittaker, 1969 (used systematics and morphology)

The 5 Kingdom System:

living organisms - prokaryotic= MONERA - eukaryotic - eukaryotic= * simple multicells or unicells= PROTISTA * multicellular - multicellular= * autotrophic= PLANTAE *heterotrophic - heterotrophic= need to get nutrients through consumption * absorptive nutrition/can't move= FUNGI * ingestive nutrition/motile= ANIMALIA

Alternative Views of the K. Monera

may be split into two separate kingdoms= eubacteria and archaebacteria= Carl Woese

Taxonomy during the Transition Period

nature and superstition were closely aligned - miasmas and disease - the concept of spontaneous generation (abiogenesis) - Carrolus Linnaeus (1707-1778)

Carl Woese, 1976

the 3 domain system= more accurately aligned in terms of genetics and biochemistry - another way of classifying things is using domains (above kingdoms) 1. archaea (the archaebacteria) 2. eubacteria (all other bacteria and cyanobacteria) 3. eukarya (all other living things) - gene common to all living things that they use to classify: RNA confined to ribosomes (place where proteins are made so need ribosome to make other things happen); Woese sequenced RNA (using quantitative systematics) - unicellular organisms (prokaryotes) less related to each other compared tp how related animals are to plants (even tho in multicellular organisms) in terms of biochemical and chemical reactions; makes us understand that morphology doesn't solely determine relatedness - protista ribosomal sequences so different so branched out so put in different kingdoms (7-12 kingdoms) while animals, fungi and plants stayed same