Exam 2 Study Guide Chapters 8-14

Chapter 8: From Single-Celled Organisms to Kingdoms

Aristotle / (384-322 BCE) / Greek /
  • Two kingdom system: Plantae and Animalia; This classification lasted for more than 2000 years
  • His writings cover many subjects, including physics, metaphysics, poetry, theater, music, logic, rhetoric, linguistics, politics, government, ethics, biology, and zoology.
  • He was a student of Platoand a great mind of the time, but his legacy as an unquestioned authority held back scientific progress for centuries.
  • He made collections of creatures, did dissections of animals, recognized different kinds of organisms.
  • He noted the sequence of organ development by observing chicken eggs.
  • The world can be understood with observation and reason
  • a slow rate for geological change, undetectable in the lifetime of a human being
  • proclaimed that there was a hierarchical order of species from most imperfect to most perfect, a concept refined over the centuries as the "Great Chain of Being." Scala Naturae (Scale of Nature) which ranked things from the inorganic to humans to Gods.
  • believed species were immutable

Carl von Linné (Carolus Linnaeus) / (1707-1778) / Swedish /
  • 1735- three kingdom system: Plantae (L. planta, plant), Animalia(L. anima, breath, life), and Lapideum (L., lapedeus, stone)
  • Popularized the binomial nomenclature
  • The idea originated with Swiss Botanist Gaspard Bauhin in 1623 in his PinaxTheatriBotanici
  • Attempted to classify the material world as evidence of the power of the Christian God with SystemaNaturae (1753)

Three Kingdoms withProtistans /
  • John Hogg (1800-1869)
  • Sir Richard Owen (1804-1892)
  • Ernst Haeckel (1834-1919)

Richard Owen / (1804-1892) / British /
  • 19th Century Christian Catastrophist and anti-Darwinist comparative anatomist who never accepted Darwinism
  • important comparative anatomist and paleontologist who identified homologies to establish characteristic Platonic "archetypes,""ideal" body plans /bauplansfor higher taxa, especially vertebrates

Charles Darwin / (1809-1882) / English /
  • British naturalist, wrote On the Origin of Species (1859) which established that all species of life have descended over time from common ancestry, and proposed the scientific theory that this branching pattern of evolution resulted from a process that he called natural selection.
  • All true classification is genealogical
  • Grand analogy: Evolution is a branching tree and organisms change over time
  • Only after his theory was published did biological evolution become an acceptable alternative to earlier explanations

Ernst Haeckel / (1834-1919) / German /
  • 1866 – phylogenetic tree of life
  • Prominent biologist who popularized Charles Darwin’s work in Germany
  • Embryologist who developed recapitulation theory (ontogeny recapitulates phylogeny)
  • Three kingdom system: Plantae, Animalia, Protista
  • artist (Art Forms in Nature)
  • Coined the term “ecology”

Hans Christian Jachim Gram / (1853-1938) / Danish /
  • 1884- Developed the gram stain method

Edouard Chatton / (1883-1947) / French /
  • Defined the terms Prokaryota and Eukaryota (1925)
  • The terms had little impact on classification for decades

Herbert F. Copeland / (1902-1968) / American /
  • 1938- proposed a four kingdom classification, moving the two prokaryotic groups bacteria and “blue green algae” into the kingdom Monera
  • Copeland's Four Kingdoms:Monera (prokaryotes), Protista (primitive eukaryotes), Metaphyta (plants), Metazoa (animals)
  • wrote The Classification of LOWER ORGANISMS (1956)

Robert Harding Whittaker / (1920-1980) / American /
  • American plant ecologist
  • Elevated the fungi to their own Kingdom (1969)
  • proposed a five kingdom system with Monera(prokaryotes), Protista (primitive eukaryotes), Mycota(fungi), Metaphyta (plants)andMetazoa (animals)

Carl Woese / (1928-2012) / American /
  • microbiologist who wrote The Genetic Code (1967) that catalogued the presence and frequencies of various sequences in the 16S rRNA components of ribosomes in representatives of the 3 Domains
  • Determined that Archaebacteria should be placed in a separate domain-defined Archaea
  • proposed the three domain classification of life with Eubacteria, Archaea, and Eukaryawith 5-6 nested Kingdoms
  • Saltationist

Thomas Cavalier-Smith / (1942-present) / English /
  • 1981- divided the domain Eukaryota into 9 kingdoms
  • 1993- reduced Eukaryota kingdoms to 6
  • classified domains Eubacteria and Archaebacteria
  • Eight kingdom system: Plantae, Animalia, Protozoa, Fungi, Eubacteria, Archaebacteria, Chromista, and Archezoa
  • Rejects the three domain system ENTIRELY

Chapter 8: Concepts

~Based on microfossils there is a two billion year diversification period after cells were created by abiogenesis, ~4.0-3.5 Bya, descendants developed into the ancestor for the eukaryotic cells, 2.5-2.8 Bya.

~The first successful protocells would have been heterotrophs. It is assumed that after raw materials in the “organic soup” early oceans became short in supply some of these cells become photosynthetic autotrophs, cyanobacteria.

~Methane concentrations in ancient rocks suggest that some of the early cells produced methane as a byproduct from their metabolic pathways.

~Stromatolites(cyanobacterialcolonies) on the coast of Australia support the theory that life had diversified 3.4 Bya and existed in structured, biological ecosystems.

~All organisms are bound by four essential facts: 1) they share a common inheritance; 2) their past has been long enough for inherited changes to accumulate; 3) the discoverable relationships among organisms are the result of evolution; 4) discoverable biological processes explain how organisms arose and how they were modified through time by the process of evolution.

~The first two kingdoms recognized were Plantae, plants, and Animalia, animals. This later changed to account the unicellular forms as another kingdom, the Protista.

~In 1938 a proposed kingdom for bacteria and the blue-green algae was called Kingdom Monera, collecting all prokaryotes without nuclei or membrane-bound organelles.

~In 1969 the fungi, formerly classified as plants, were elevated into their own kingdom, Kingdom Fungi.

~ Carl Woese, having performed genetic comparisons on different cell species, was able to define three domains for the living world. The Eubacteria, which include the prokaryotic bacteria and cyanobacteria; theArchaea, cells that have cell walls made of different molecules from those found in bacteria and cells which often live under more rigorous conditions, and the Eukarya, which included slime molds, protistans, and the multicellular kingdoms of the Plantea, Animalia, and Fungi.

~Archaebacterial traits distinguishable from Eubacteria are the different cell wall chemistry, membrane lipid chemistry, major nutrient metabolic pathways, ribosomes and RNA polymerase and DNA associated with histones, like Eukaryotes.

Five Kingdoms Became Three Domains

Carl Woese's Three Domains:

  • Eubacteria (Bacteria) - prokaryote (lacking a nucleus or other membrane-bound organelles) unicellular organisms with cell walls which include peptidoglycan and may be distinguished by the Gram stain (positive, negative, or variable); most are heterotrophic and some are photosynthetic, a minority are chemotrophic. Most are either coccal (spherical), rods, or spiral forms
  • Archaea (Archaebacteria) - prokaryote (lacking a nucleus or other membrane-bound organelles) unicellular organisms with cell walls which lack peptidoglycan and are not easily distinguished by the Gram stain; they may be heterotrophic, photosynthetic, or chemotrophic. Some live in extreme environments. They are the sister group to Eukarya because they use histone proteins in their DNA supercoiling. Archaea is a Domain that is sometimes also referred to as a Kingdom.
  • Eukarya (Eukaryota): DNA organized as linear chromosomes. Many cytoplasmic membrane-bound organelles. Eukaryotic cytoskeleton and ribosomes. Presence of external cell wall variable . Sexual reproduction predominates, various means of gene recombination. Unicellular or multicellular.

Five Kingdoms become Six

  • Thomas Cavalier-Smith (1942- ) published extensively on the classification of protists, wrote Predation and Eukaryote Cell Origins: A Coevolutionary Perspective (2008).

-Has been tinkering with the classification for more than a decade and his taxa remain controversial--he rejects the three-domain system entirely.

-Divided the domain Eukaryota into nine kingdoms. (1981)

-Reduced the total number of eukaryote kingdoms to six. (1993)

-Later classified the domains Eubacteria and Archaebacteria as kingdoms, adding up to a total of eight kingdoms of life (Plantae, Animalia, Protozoa, Fungi, Eubacteria, Archaebacteria, Chromista, and Archezoa)

-His classification treats the archaebacteria as part of a subkingdom of the Kingdom Bacteria (2004)

Cavalier-Smith's Six Kingdoms (2004):

  • Bacteria
  • Protozoa
  • Chromista
  • Plantae
  • Fungi
  • Animalia

~The Last Universal Common Ancestor of all organisms today had DNA as the hereditary material, DNA replication with helicase and RNA Primase and DNA synthetases, ribosome-based protein synthesis, several common metabolic pathways, ATP, phospholipid bilayer fluid-mosaic model cell membrane, and active transport across membranes.

~Cyanobacteria fossils are the oldest fossils found in Western Australia from about 3.5 Bya making it surprising due to the fact that the earliest rocks are only dated back to 3.8 Bya.

~Cyanobacteria dominated the globe for 2 billion years, with some forms still existing today. They produced large quantities of oxygen by photosynthesis which would slowly eliminate the reducing atmosphere of early earth. First, the released oxygen had to oxidize all the surface minerals of the earth’s crust.

~Eukaryotic cells probably arose through a combination ofendosymbiosis and incorporation (e.g. chloroplast, mitochondria); and organelle formation by outer cell membrane enfolding.

~Horizontal Gene Transfer, HGT, may be achieved by a virus (transduction) or a small, circular DNA particle known as a plasmid (conjugation) that contains a foreign gene and as much as one-third of some prokaryotic genome has been acquired through HGT or by absorbing and incorporating naked DNA from the environment (transformation); it may also be achieved during endosymbiosis; it also occurs in eukaryotes by various mechanisms, especially hybridization/introgression – sexual reproduction between members of different species.

~Less than ten-percent of eukaryotes acquired one or two protein families through HGT.

~The three main ways of prokaryote HGT are

1) Transformation, the up-take of naked DNA from the external environmentand incorporating it into the cell’s DNA

2) Conjugationis an HGT process by which one bacterium transfers genetic material to another through direct contact. During conjugation, one bacterium serves as the donor of the genetic material, and the other serves as the recipient. They do not have to belong to the same species. The donor bacterium carries a DNA sequence called the fertility factor, or F-factor. The F-factor allows the donor to produce a thin, tubelike structure called a “sex” pilus or conjugation tube, which the donor uses to contact the recipient. The pilus or conjugation tube then draws the two bacteria together, at which time the donor bacterium transfers genetic material to the recipient bacterium. Typically, the genetic material is in the form of a plasmid, or a small, circular piece of DNA of plasmid DNA, though in some circumstances, it might be a part or all of the main bacterial "chromosome" or main circular DNA genome.[Conjugation is also the term for sexual reproduction in ciliate protistans.]

3) Transduction, or transfer via viral infection.

~prokaryoticHGTmaybe a beneficial process since they reproduce asexually, but with HGT a cell can acquire a allele that confers survival or a novel characteristic which enables them to thrive in harmful conditions or to utilize a new metabolite. It is through this process that resistance to antibiotics can be transferred from one bacterial cell to another.

~Another classic example for HGT is the origins of Mitochondria and Chloroplasts from endosymbiosis which would have occurred more than 2.8 to 2.5 billion years ago during the origin of eukaryotes.

~Archaebacteriaprobably acquired organelles by endosymbiosis.

~Early Eukaryotes has cell walls, were aerobic heterotrophs or phototrophs, and eventually developed sexual reproduction, which would lead to the decline of HGT among Eukaryotic lineages likely to the alternative sexual recombination.

Chapter 9: Eukaryotic Cells and
Multicellular Organisms

Lynn Margulis / (1938- ) / American /
  • Biologist who proposed endosymbiosis, a hypothesis used to explain the origin of mitochondria and chloroplasts

Thomas Cavalier-Smith / (1942-present) / English /
  • Evolutionary Biologist who divided the domain Eukaryota into 9 kingdoms (1981)
  • 1993- reduced Eukaryota kingdoms to 6
  • proposed the taxon of Rhizaria in 2002
  • classified domains Eubacteria and Archaebacteria
  • Eight kingdom system: Plantae, Animalia, Protozoa, Fungi, Eubacteria, Archaebacteria, Chromista, and Archezoa
  • Rejects the three domain system ENTIRELY

Sharma Barnabas / ? / Indian /
  • Along with fellow co-workers produced a tree of life that took into account the nucleotide sequences from 5s rRNA and amino sequences (1982)
  • This phylogeny provided strong support for the Symbiotic theory of organelle function

Concepts:

Evolution of Eukaryotes

  • As early as 1.5 Bya eukaryotic cells appear as fossils, though the arose earlier
  • Early eukaryotes were single-celled organisms or simple colonial clusters or filaments
  • Today, many eukaryotic organisms are multicellular and all contain a nuclear membrane and organelles, some membrane bound organelles
  • Kingdom Protista: all unicellular eukaryotes. Probably not monophyletic
  • Endosymbiotic events provided mitochondria, chloroplasts, possibly flagella/cilia and the nucleus
  • Microtubules drive the nuclear chromosomal division (mitosis)

Five Eukaryotic Supergroups

  • Plantae (Archaeplastida): Charophyta (stem group), red algae, green algae, and all land plants
  • Excavata:
  • Various Protistans
  • many with parasitic lifestyles
  • Giardia, Trichomonas, Trypanosoma
  • Chromalveolata:
  • first proposed by Thomas Cavalier-Smith
  • algae, heterotrophic ciliates, water molds, dinoflagellates, diatoms
  • protistan parasites
  • Plasmodium falciparum, etc.
  • Rhizaria: advocated for by Cavalier-Smith.
  • Heterotrophic protistans
  • Foraminiferans, radiolarians
  • Unikonta:
  • Parasitic Protistans, choanoflagellates, fungi, animals, and Amebozoans (slime molds), amoeba

The two popular theories to explain the origin of the membrane bound organelles

  • Endosymbiosis - a well supported hypothesis which explains the origin of chloroplasts and mitochondria and their double membranes; This concept postulates that chloroplasts and mitochondria are the result of many years of evolution initiated by the endocytosis of aerobic bacteria and cyanobacteria/blue-green algae. According to this concept, cyanobacteria/blue green algae and bacteria were phagocytized but not digested; they became symbiotic instead and subsequently co-evolved with considerable horizontal gene transfer between the nuclear and organelle genomes. Other data supports an endosymbiotic origin for the eukaryotic nucleus and the eukaryotic flagella/cilia from spirochetes.
  • Invagination – the plasma membrane was enfolded or invaginated to form the endomembrane system (ER, Golgi, etc.).

Along with the theories above, were two models explaining the origin of the Eukaryotes, the Nucleus First-Mitochondria Later Model and the Mitochondria-Nucleus Co-origin model.

Origin of Eukaryotes

  • Endosymbiosis: When ancient anaerobic eukaryotic cells engulfed prokaryotic organisms and established a symbiotic relationship with the prokaryote. The prokaryotes were retained as cellular organelles – mitochondria and chloroplast – providing eukaryotes with additional sources of DNA for HGT.
  • Free-living aerobic bacteria developed mutually beneficial relationships within a host prokaryotic cell; these aerobic bacteria developed into mitochondria
  • Cyanobacteria developed into chloroplasts

Organelle DNA differs from Nuclear DNA

  • Location: organelle vs. nucleus
  • Organization: major singular circular and smaller circular plasmids vs. multiple linear strands = chromosomes
  • Function: Which proteins coded for and how regulated
  • Mode: of replication and inheritance

Mitochondrial DNA

  • Circular double-stranded DNA molecules
  • Many mitochondria in each cell
  • Similar to prokaryotic DNA because no histones or proteins, and no introns

Chloroplast DNA

  • double-stranded circular DNA molecules
  • inherited uniparentally from the maternal (seed) parent
  • 1/4th of DNA of cell

Origin of Various Photosynthetic Eukaryotes

  • The origin of early eukaryotic ancestors leading to the lineages of animals and fungi was probably an independent event from that of the origin of plants

Transfer of Genes Between Organelles and Nucleus

  • Many genes transferred back and forth so that the two genomes are interdependent. E.g., genes for amino acid synthesis
  • Improves efficiency and reduces damage mutations
  • Genes transferred to and from the eukaryotic nucleus and the mitochondria and chloroplasts are a form of Horizontal Gene Transfer
  • Complicates the establishment of phylogenies

The Molecular Clock: uses mutation rates to estimate evolutionary time of divergence of different taxa, calibrated with fossil evidence when available.

  • Mutations at a given locus occur at a relatively constant rate per locus in related species
  • This mutation rate is the ticking of the molecular clock
  • As more time passes there will be more mutations at a relatively constant rate
  • Each DNA sequence or polypeptide product will exhibit its own "clock" speed because mutation rates vary and selection forces acting on phenotypes controlled by different loci are of different strengths
  • Mutation rates are estimated by linking molecular data and real time history from the fossil record to calibrate the clock with the fossil record
  • Loci with higher rates are better for closely related species/taxa
  • Loci with lower rates are better for distantly related species/taxa

Organelle DNA as a Molecular Clock

  • The Molecular Clock is a powerful tool for estimating the dates of lineage-splitting events

Mitochondrial DNA and Ribosomal RNA

  • Different nucleic acid molecules or gene loci have different mutation rates
  • Ribosomal RNA used to study distantly related species
  • Lower mutation rates that most DNA loci
  • Mitochondrial DNA is used to study closely related species
  • 10 x faster mutation rates than nuclear DNA
  • Passed down from mother to offspring, so it is not subject to recombination, making it easier to trace.

Using DNA as a Molecular Clock

  • Easy to use DNA from living species to draw conclusions about phylogeny and times of divergence
  • Harder to use DNA from fossils and museums because such samples are probably contaminated by other DNA and only have small amounts of undamaged/undeterioratedDNA

Eukaryote Characteristics