The%20Origins%20of%20Life%20and%20Precambrian%20Evolution

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The Origins of Life and Precambrian Evolution

• Chapter 16

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Questions

• What was the first living thing?
• Where did it come from?
• What was the last common ancestor of todays
  organisms and when did it live?
• What is the shape of the tree of life?
• How did the last common ancestors descendants
  evolve into todays organisms?

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Cartoon of the tree of life (Fig. 16.1)
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What is alive?

• Living things have
• the ability to replicate or reproduce, together
  with the ability to store and transmit heritable
  information to have a genotype
• the ability to express that information to have
  a phenotype
• the ability to evolve to make changes in the
  heritable material and to have those changes
  tested in order to distinguish valuable ones
  from detrimental ones

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Molecules as living things

• In principle, a molecule could be alive by our
  definition
• If it had the ability to copy itself using raw
  materials in its environment, and if errors in
  copying led to differences in the speed of
  self-replication or in chemical stability
• In this case, the genotype is the chemical
  structure of the molecule, and the phenotype is
  the speed of self- replication or stability of
  the molecule

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Protein vs. nucleic acid

• Proteins possess the enzymatic function that
  would presumably be necessary for a
  self-replicating molecule but there is no
  evidence that proteins can propagate themselves
• Nucleic acids possess, in principle, the ability
  to direct their self-replication via
  complementary base-pairing but until about 20
  years ago were not known to possess any enzymatic
  function

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The RNA world hypothesis

• Catalytic RNA molecules were a transitional form
  between non-living matter and the earliest cells
• In the early 1980s it was discovered
  independently by Sidney Altman and Thomas Cech
  that some RNA molecules had enzymatic activity
  specifically, they could form and break the
  phosphoester bonds that link adjacent nucleotides
  in nucleic acids ribozymes
• This enzymatic function would be essential if
  nucleic acids were the first self-replicating
  things

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Ribozyme from Tetrahymena themophila a
self-splicing intron between adjacent rRNA
genes(Fig. 16.2 a)
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The catalysis performed by the Tetrahymena
ribozyme in vitro (Fig. 16.2 b)
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The case for an RNA-based system as an early life
form

• Existence of catalytic RNA
• RNA is a core component of the apparatus for
  translating genetic information into proteins
  rRNA a component of ribosomes (probably the
  component that actually catalyzes protein
  synthesis), and tRNA adapters also required for
  protein synthesis
• Ribonucleoside triphosphates (ATP, GTP) are the
  basic energy currency of all cells and are
  components of electron-transfer cofactors such as
  NAD (nicotinamide adenine dinucleotide) and FAD
  (flavin adenine dinucleotide)

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Can RNA evolve? experimental evolution of
RNA(Beaudry and Joyce 1992)

• Select for the ability of Tetrahymena ribozyme to
  catalye the cutting of a DNA oligonucleotide and
  attachment of a fragment to its 3 end

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Test tube evolution of RNA (Beaudry and Joyce
1992) (Fig. 16.4)
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Can RNA evolve? experimental evolution of
RNA(Beaudry and Joyce 1992)

• Experiment was seeded with a large population of
  randomly mutated ribozymes
• After 10 generations the catalytic ability of
  the average RNA in the population had improved by
  a factor of 30
• Most of the improvement in catalytic ability was
  attributable to mutations at 4 locations
• Many additional experiments with natural and
  synthetic RNA have produced ribozymes that can
  catalyze reactions such as phosphorylation,
  peptide bond formation, and carbon-carbon bond
  formation.
• BUT, a crucial piece is missing from the
  experiment that we have just described
  self-replication

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Genotypic changes in an evolving RNA population
(Beaudry and Joyce 1992) (Fig. 16.5b)
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Toward self-replicating RNA molecules

• So far, we do not have a self-replicating RNA
  molecule (or a self-replicating system of RNA
  molecules)
• If we can produce such a thing (perhaps by
  selective breeding experiments in the
  laboratory) then, by one definition at least, we
  will have succeeding in creating life (although
  obviously not complex cells)

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Laboratory evolution of the ability of catalyze
the joining of adjacent nucleotides (phosphoester
bond) (Bartel and Szostak 1993)

• Variable population of synthetic RNA molecules
  selected for ability to catalyze joining of
  nucleotides
• This is not self-replication, but a necessary
  function of a self-replicating RNA molecule
• Experiment still depends on the use of
  replicating enzymes to reproduce the
  successful RNA molecules after each generation

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Test-tube selection scheme for identifying
ribozymes that can link nucleotides (Bartel and
Szostak 1993) (Fig. 16.6 a,b)
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Test-tube selection scheme for identifying
ribozymes that can link nucleotides (Bartel and
Szostak 1993) (Fig. 16.6 c,d)
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Test-tube selection scheme for identifying
ribozymes that can link nucleotides (Bartel and
Szostak 1993) (Fig. 16.6 e)
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Evolution of catalytic ability in a laboratory
population of ribozymes (Bartel and Szostak 1993)
( Fig. 16.7)
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RNA world summary

• RNA molecules possess at least some of the
  necessary properties of living systems
• the sequence of nucleotides provides a heritable
  information storage mechanism ( genotype)
• Catalytic ability is a variable, heritable
  phenotype upon which selection can act
• Natural or synthetic ribozymes possess a variety
  of enzymatic activities, including the ability to
  join nucleotides together to make short (40 - 50
  bp) polynucleotide strands
• However, so far, no one has succeeded in
  producing an RNA molecule that can copy itself
• Even if that is achieved, it still leaves the
  question of how the first RNA molecules were made

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Pre-biotic synthesis of organic moleculesthe
Miller Urey experiments (1953)

• Water vapor methane ammonia hydrogen
  electric spark amino acids (glycine, alanine)
• Similar experiments by others have yielded other
  organic compounds, including nitrogenous bases
  (from ammonia and hydrogen cyanide) and ribose
  (from formaldehyde)

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The Oparin Haldane model (Fig. 16.12)the
prebiotic soup
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Criticisms of Miller Ureyand Oparin Haldane

• Earths early atmosphere may not have been
  composed of methane and ammonia, but rather
  carbon dioxide and nitrogen, which would not have
  been favorable for formation of the necessary
  organic molecules (although aldehydes could be
  formed from carbon dioxide)
• Formation and stabilization of polymers of basic
  buiding blocks (such as amino acids) in the
  aqueous prebiotic soup also appears to present
  difficulties (mineral scaffolding?)
• Still a long way from biological polymers to
  cells

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Extra-terrestrial origins?

• Meteorites are sources of amino acids, at least
  some of which survive impact
• The Panspermia hypothesis
• Life originated elsewhere in the solar system and
  was carried here on meteorites that originated
  from other planets or moons, or possibly life
  originated outside the solar system
• McKay et al. (1996) meteroite from Mars
  contained globules of carbonate magnetite, iron
  sulfide, and polycyclic aromatic hydrocarbons
  and a suggestion of microfossils that resemble
  bacteria
• Many (most?) are not convinced that the Martian
  rock provides evidence of life the compounds
  that were present can also be formed by abiotic
  processes
• In any event, the Panspermia hypotheis merely
  shifts the problem of the origin of life to
  somewhere else at some other time

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When was life first present on Earth?

• Radiometric dating of meteorites suggests that
  the solar system, including Earth, is about 4.5
  to 4.6 billion years old
• Sedimentary rocks from Greenland, and dated at
  3.7 billion years, contain microscopic graphite
  globules that have a 12C/13C isotopic ratio that
  is characteristic of molecules produced by
  biological processes
• This may be about the oldest evidence of life
  that we are likely to find, because conditions
  much before that might have been unsuitable for
  life, or would have obliterated earlier origins
  of life

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The history of large impacts on Earth and Moon
(Sleep et al. 1989) (Fig. 16.11)
Red boxes represent lunar impacts blue boxes
terrestrial impacts (some of which are
hypothetical. Dashed line represents impact
energy sufficient to vaporize the global
ocean. A Archaean spherule beds V
Vredevort S Sudbury M Manicougan K/T
Cretaceous-Tertiary impact crater (Yucatan)
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What was the most recent common ancestor of all
extant organisms?

• Regardless of the origin of organic molecules,
  and whether or not an RNA world was an
  intermediate step in the evolution of life, the
  evidence that all present day life forms share a
  common ancestor is compelling
• All life forms (except some viruses) use DNA and
  proteins, and all use them in the same way (same
  20 amino acids, same genetic code)
• The oldest cellular fossils (which resemble
  bacteria) are 3.4 billion years old

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The phylogeny of everything

• Carl Woese (and others)
• We need a highly conserved molecule that has
  recognizable similarities across all life forms
• Small subunit ribosomal RNA
• all organisms have ribosomes
• all use ribosomes in the same way (translation)
• all ribosomes are composed of RNA protein
• all ribosomes have similar structure, being
  composed of small and large subunits

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Small-subunit rRNA phylogeny (Woese 1996) (Fig.
16.18)Three-domain classification
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The tree of life old style (Fig.
16.17)five-kingdom classification
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Three-domain classification systemBacteria,
Archaea, Eucarya

• Archaea (archaebacteria) more closely related to
  eukaryotes than they are to true Bacteria
• Archaea composed of two (or three) kingdoms
• Protista must be abandoned as a kingdom
  (paraphyletic) or must include animals, plants,
  and fungi.
• Animals, plants, and fungi do appear as natural,
  monophyletic groups (with removal of slime molds
  from fungi)

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What was the most recent common ancestor like?

• Highly evolved and biologically sophisticated
  perhaps similar to modern bacteria
• All living organisms store genetic information as
  DNA and have similar transcription and
  translation machinery
• DNA polymerases are relatively similar across
  domains
• All organisms have DNA-dependent RNA polymerases
  that show strong similarities across all domains

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Different genes give different universal
phylogenies 1 (Fig. 16.22 a,b)
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Different genes give different universal
phylogenies 2 (Fig. 16.22 c,d)
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Horizontal gene transfer

• Inconsistencies among genes for the universal
  phylogeny have led to the suggestion that taxa
  have exchanged genes horizontally
• Bacteria are known to be able to take up DNA from
  their environment and to incorporate that DNA
  into their genomes (transformation, etc.)
• 18 of E. coli genes estimated to have arrived by
  horizontal gene transfer in last 100 million
  years (Lawrence and Ochman 1998)

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Evidence for horizontal gene transfer of the
HMGCoA reductase gene into an archaean (Doolittle
and Lodgson 1998) (Fig. 16.23)
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The cenancestor was not a single species, but a
community (Fig. 16.26)
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The latest possible date for the root of the tree
of life

• Oldest known probable eukaryotic fossils (algae)
  are 1.85 2.1 billion years old
• Fossil cyanobacteria also suggest that the root
  is more than 2 billion years old
• The most recent date for the root of the tree of
  all living organisms is between 3.4 and 2 billion
  years ago

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The origin of mitochondria and chloroplasts

• The mitochondria and chloroplasts of eukaryotic
  cell have their own genomes
• Analysis of small-subunit rRNA genes suggests
  that both organelles are derived from bacteria
  which have become obligate endosymbionts

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Placement of mitochondria and chloroplasts on the
universal tree based on small-subunit rRNA
genes(Giovannoni et al. 1988) (Fig. 16.30)