Early Earth and The Origin of Life

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• Chapter 26
• Early Earth and The Origin of Life

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Early history of life

• Solar system - 12 billion years ago (bya)
• Earth - 4.5 6.2 bya
• Life - 3.5 to 4.0 bya
• Prokaryotes - 3.5 to 2.0 bya stromatolites
• Oxygen accumulation - 2.7 bya photosynthetic
  cyanobacteria
• Eukaryotic life - 2.1 bya
• Muticelluar eukaryotes - 1.2 bya
• Animal diversity - 543 mya
• Land colonization - 500 mya

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The Origin of Life

• Spontaneous generation vs. biogenesis (Pasteur)
• The 4-stage Origin of life Hypothesis
• 1- Abiotic synthesis of organic monomers
• 2- Polymer formation
• 3- Origin of Self-replicating molecules
• 4- Molecule packaging (protobionts)

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Organic monomers/polymersynthesis

• Oparin (Rus.)/Haldane (G.B.) hypothesis
  (primitive earth) volcanic vapors (reducing
  atmosphere) with lightning UV radiation
  enhances complex molecule formation (no O2)
• Miller/Urey experiment
• water, hydrogen, methane, ammonia
• all 20 amino acids, nitrogen bases, ATP formed
• Fox proteinoid formation (abiotic polypeptides)
  from organic monomers dripped on hot sand, clay
  or rock
• Oparin (coacervates) protobionts (aggregate
  macromolecules abiotic) surrounded by a shell of
  H2O molecules coated by a protein membrane

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Abiotic genetic replication

• First genetic material
• Abiotic production of ribonucleotides
• Ribozymes (RNA catalysts)
• RNA cooperation
• Formation of short polypeptides (replication
  enzyme?)
• RNA-DNA template?
• Viruses?

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The Major Lineages of Life
Whitaker System
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Classification
Domain Kingdom Phylum Class Order Family Genus Spe
cies Scientific Name Genus species

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3 DOMAIN SYSTEM
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• Chapter 27
• Prokaryotes and the Origins of Metabolic Diversity

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Initially Archaea seem more similar to Eubacteria
than to Eukaryotes.   Archae and Eubacteria are
BOTH PROKARYOTIC organisms they both have
closed, circular DNA They both are
transcription and translation linked and they
both usually reproduce via binary fission.
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However, there are several differences between
Archae and Eubacteria.

1.  They utilize different metabolic pathways. 
2. They also differ in number of ribosomal proteins
   and in the  size and shape of their ribosomal S
   unit. 
3. The Eubacteria genome is almost two times larger
   and they contain more plasmids than Archae. 
4. Archaea are similar to Eukaryotes in that they
   have several kinds of RNA polymerase, have a
   great number of histone-like proteins, have DNA
   in the form of nucleosomes, and contain introns.

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Biochemical determination

• Archaebacteria are distinguished by cell walls
  with pseudopeptidoglycan or protein components,
  and cell membranes composed of branched
  hydrocarbons linked to glycerol molecules.

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ALL ABOUT ARCHAEBACTERIA

• Archaea are highly diverse organisms, both
  morphologically (form and structure) and
  physiologically (function). 
• The organisms' possible shapes include spherical,
  rod-shaped, spiral, lobed, plate-shaped,
  irregularly shaped, and pleomorphic. There are
  many different types of Archaea that live in
  extremely diverse environments. 
• Modern-day Archaebacteria are found in extreme
  environments, such as areas of intense heat or
  high salt concentration.

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EUBACTERIA
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EUBACTERIA
Within their domains, identification of microbes
begins with their physical appearance, followed
by biochemical and genetic tests.
SHAPE is/was the most commonly used physical
appearance for determination of species.
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Sex or conjugation Pili for the transfer of extrachromosomal DNA between donor and recipient.                              
 Attachment Pili or Fimbriae. There are many and are used for attachment to surfaces. Pili are virulence factors.                                

Pili Made of the protein pilin and project from
the cell surface. There are 2 types

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Gram positive bacteria
Gram negative bacteria
Have a thin layer of peptidoglycan in their cell
wall. AND have lipopolysaccharides with protein
channels in the cell membrane. This keeps dyes
(along with antibiotics) out!
Have an extra layer of peptidoglycan in their
cell wall, and retain dye.
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http//www.sirinet.net/jgjohnso/monerans.html
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A bacterial flagellum has 3 basic parts a
filament, a hook, and a basal body.

• 1) The filament is the rigid, helical structure
  that extends from the cell surface. It is
  composed of the protein flagellin arranged in
  helical chains so as to form a hollow core.
  During synthesis of the flagellar filament,
  flagellin molecules coming off of the ribosomes
  are thought to be transported through the hollow
  core of the filament where they attach to the
  growing tip of the filament causing it to
  lengthen.

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• 2) The hook is a flexible coupling between the
  filament and the basal body
• 3) The basal body consists of a rod and a series
  of rings that anchor the flagellum to the cell
  wall and the cytoplasmic membrane. Unlike
  eukaryotic flagella, the bacterial flagellum has
  no internal fibrils and does not flex. Instead,
  the basal body acts as a molecular motor,
  enabling the flagellum to rotate and propell the
  bacterium through the surrounding fluid. In fact,
  the flagellar motor rotates very rapidly. (The
  motor of E. coli rotates 270 revolutions per
  second!)

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EUKARYOTIC FLAGELLA

• Cell Locomotion via Cilia and FlagellaCilia and
  flagella, which extend from the plasma membrane,
  are composed of microtubules, coated with plasma
  membrane material. Eukaryotic cilia and flagella
  have an arrangement of microtubules, known as the
  9 2 arrangement (9 pairs of microtubules
  (doublets) around the circumference plus 2
  central microtubules). "Spokes" radiate from the
  microtubules towards the central microtubules to
  help maintain the structure of the cilium or
  flagellum.
• Each of the microtubule doublets have motor
  molecule "arms", the dynein arms, which can grip
  and pull an adjacent microtubule to generate the
  sliding motion. (The protein of this motor
  molecule is dynein.)

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Prokaryote flagella function

• Flagella are the organelles of locomotion for
  most of the bacteria that are capable of
  motility. Two proteins in the flagellar motor,
  called MotA and MotB, form a proton channel
  through the cytoplasmic membrane and rotation of
  the flagellum is driven by a proton gradient.
  This driving proton motive force (def) occurs as
  protons accumulating in the space between the
  cytoplasmic membrane and the cell wall as a
  result of the electron transport system travel
  through the channel back into the bacterium's
  cytoplasm.

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Under environmental stress (lack of water, nutrients etc.) some vegetative cells produce endospores e.g. Clostridium and Bacillus. Spores can be dormant for many years. They can survive extreme heat, desiccation, radiation and toxic chemicals. However, when conditions become favorable they revert to a vegetative state. Spore germination is activated by heat in the presence of moistures but the endospore must degrade the layers around the spore.
ENDOSPORES
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PROKARYOTIC CELL DIVISION

• Binary Fission
• cell elongates, duplicates its chromosome

Allocation of chromosomes to daughter cells
depends on MESOSOME an extension of the cell
membrane
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A diagram of the attachment of bacterial
chromosomes, indicating the possible role of the
mesosome.

• It ensures the distribution of the "chromosomes"
  in a dividing cell.
• Upon attachment to the plasma membrane, the DNA
  replicates and reattaches at separate points.
• Continued growth, to about twice the size of the
  cell, gradually separates the chromosomes.

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BACTERIA
VIRUS
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What is an antibiotic?

• Chemical substances that INHIBIT the growth of
  bacteria or KILL it.
• HOW
• Prevent cell wall from forming properly
• Prevent protein synthesis
• Interfere with chromosome replication
• Disrupt plasma / outer membrane
• Interference with metabolism

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Alexander Fleming discovers the first antibiotic
(1928)

• Sir Alexander Fleming discovers the drug
  penicillin, which counteracts harmful bacteria.
  Fleming makes the discovery by accidentally
  contaminating a bacteria culture with a
  "Penicillium notatum" mold.

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• He noticed that the non-toxic mold halts the
  bacteria's growth, and later conducts experiments
  to show penicillin's effectiveness in combating a
  wide spectrum of harmful bacteria

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ZONE OF INHIBITION
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What is antibiotic resistance?

• The ability of a bacterial cell to resist the
  harmful effect of an antibiotic. This could be
  incorporated into the chromosome or plasmid.
• System to prevent entry?
• To destroy the antibiotic if into cell
• To block action of antibiotic
• A pump system to move antibiotic out

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How is antibiotic resistance acquired?

• Consistent exposure to antibiotics
• Long-term therapy
• Farm animals
• Indiscriminate usage of antibiotics
• For example for a cold/flu
• Non-therapeutic use
• For animals to gain weight

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Transfer of antibiotic resistance genes by
conjugation
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CAN BACTERIA BE GOOD FOR YOU?

• The majority is not only helpful but necessary!
• Occupy and compete for limited nutrients
• Tough for bad bacteria to get a foothold
• Antibiotics kill both good AND bad bacteria
• Thus, good are killed and some could become
  antibiotic resistant. Since theres no good
  bacteria to stop them -
• Bad strain increases in number

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• Chapter 28
• The Origins of Eukaryotic Diversity

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Protists

• Ingestive (animal-like) protozoa
• Absorptive (fungus-like)
• Photosynthetic (plant-like) alga

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The Endosymbionic Theory

• Mitochondria and chloroplasts were formerly from
  small prokaryotes living within larger cells
  (Margulis)

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Protist Systematics Phylogeny, I

• 1- Groups lacking mitochondria early eukaryotic
  link Giardia (human intestinal parasite severe
  diarrhea) Trichomonas (human vaginal
  infection)
• 2- Euglenoids autotrophic heterotrophic
  flagellates Trypanosoma (African sleeping
  sickness tsetse fly)

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Protist Systematics Phylogeny, II

• Alveolata membrane-bound cavities (alveoli)
  under cell surfaces dinoflagellates
  (phytoplankton) Plasmodium (malaria)
  ciliates (Paramecium)

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Protist Systematics Phylogeny, III

• Stamenophila water molds/mildews and heterokont
  (2 types of flagella) algae numerous hair-like
  projections on the flagella most molds are
  decomposers and mildews are parasites algae
  include diatoms, golden, and brown forms

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Protist Systematics Phylogeny, IV

• Rhodophyta red algae no flagellated stages
  phycobilin (red) pigment
• Chlorophyta green algae chloroplasts gave rise
  to land plants volvox, ulva

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Protist Systematics Phylogeny, V

• Affinity uncertain
• Rhizopods unicellular with pseudopodia amoebas
• Actinopods ray foot (slender pseudopodia
  heliozoans, radiolarians

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Protist Systematics Phylogeny, VI

• Mycetozoa slime molds (not true fungi) use
  pseudopodia for locomotion and feeding
  plasmodial and cellular slime molds