Download Biology 4974/5974, Evolution

The First Cells II
Evolution
Biology 4974/5974
D. F. Tomback
Biology 4974/5974
Evolution
The First Cells II
Figures and tables from M.W. Strickberger (2000) Evolution, 3 rd ed, Jones and Bartlett.
Learning goals: know and understand
• The key arguments for the “RNA World,” or RNA
first hypothesis.
• The genetic code: its triplet codon form, why it is
universal, and why it is redundant.
• Steps in the origin of anaerobic metabolism and
early ‘photosynthesis.’
• The merger of photosystems I and II and release of
molecular oxygen, followed by the evolution of
aerobic metabolism.
• The origin of eukaryotic cells through
endosymbiosis and supporting evidence.
• The oldest fossil cells.
Early biochemical pathways
Central dogma:
Replication (DNA to DNA) 
Transcription (DNA to
RNA)  Translation (RNA
to protein)
• Which came first: proteins
or nucleic acids and which
nucleic acids?
• How did metabolic
pathways arise?
From: de Duve (1995)
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The First Cells II
Evolution
Biology 4974/5974
D. F. Tomback
Properties of RNA: “RNA First” and the “RNA world”
RNA as both template and catalyst
•
RNA can catalyze its own replication
without protein enzymes; can bind ATP
for energy.
• RNA can make peptide bonds.
• Introns in m-RNA and nuclear RNA are
self-splicing.
• RNA can cleave t-RNA precursors at the
proper bond.
• “Ribozymes” cleave phosphoester bonds
of RNA.
• RNA can catalyze the cleavage of an
amide bond.
• RNA silencing, through double-stranded
RNA.
• Self-cleaving ribozymes may regulate the
expression of some genes.
• RNA fragments join with coenzymes in
many metabolic reactions(e.g., NAD,
FAD).
Basic argument: only a self-replicating
molecule can build a functional unit.
The universal genetic code
• All organisms essentially
share the same genetic
code.
• The genetic code is
redundant.
• What does that mean?
• How did the code evolve?
• Triplet code initially
involved fewer amino
acids?
• The first two positions
specify which amino acid.
• The number of codons per
amino acid is proportional
to the frequency of the
amino acid in proteins.
Why is the genetic code universal?
To code for 20 amino acids + stop code, at least 1,070
possibilities using 64 codons. Why this code?
Proposed explanations (hypotheses):
1. Stereochemical affinity between either a codon or
an anticodon and an amino acid: no evidence.
2. Amino acid-codon association arose by chance and
perhaps several times. In a successful group of
protocells, any major change would produce nonfunctional proteins. Thus, one code was favored
and changes then were limited: frozen accident
viewpoint.
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The First Cells II
Evolution
Biology 4974/5974
D. F. Tomback
The evolution of metabolism
See Endboxes to Chapter 8
ATP (Adenosine Triphosphate): early breakthrough as
an energy carrier.
Anaerobic glycolysis
Embden-Myerhoff glycolytic pathway. First metabolic
pathway? (End Box 8.2)
• Converts glucose (C6 H12O6) to 2 pyruvic acids, with
a net yield of 2 ATPs
• C6H12O6 + 2 ADP + 2 Pi + 2 NAD+ 
2 C3H4O3 + 2 ATP + 2 NADH +2 H+ + 2 H2O
Note: Retrograde evolution--Metabolic pathways
evolved with depletion in the environment of
required molecules. This exerts selection for
synthesis of that molecule from a precursor. The
pathway then gets longer and longer over time.
Photosynthesis End Box 8.1
Cyclic photosynthesis (came first)
• Yields 1 ATP for each round.
• Nearly all photosynthesis systems
depend on chlorophyll.
• Bound to membrane of protocell.
• This system could reduce CO2 to
produce a carbon source.
• Leads to the first autotrophs.
Calvin Cycle
• Synthesizes glucose from CO2 using
energy.
• Advantage: freed organisms from
external carbon sources.
• Anaerobic autotrophs
Which came first: autotrophs or
heterotrophs? (Hint: use the parsimony
principle –Occam’s razor)
Oxygen and aerobic metabolism
Photosystems I and II
merger
• Likely that non-cyclic
photosystems I and II merged
together (from lateral gene
transfer).
• Found only in cyanobacteria
and chloroplasts of
eukaryotes.
• Photosystem II dissociates
water into electrons, protons,
and releases oxygen
• 2H2O 4e- + 4H+ + O2
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The First Cells II
Evolution
Biology 4974/5974
D. F. Tomback
Oxygen
• Fossil prokaryotes, 3 to
3.5 billion years of age
appear photosynthetic.
• First trace of O2 about
2 - 2.3 billion years ago,
shown by S isotopes.
• O2 levels remained
low (~1%) until about
2 billion years ago.
• Upsurge in
photosynthesis?
• Low O2 in deep oceans
until 580 mya.
• Current O2 levels bout
21%.
Des Marais (2000)
Oxygen increase
Increase in atmospheric oxygen rapidly
about 2 billion years ago
Evidence
• Deposition of banded iron in oceans--sedimentary deposits of iron, possibly
formed biologically (Fe2O3).
• Remained low in deep ocean.
Consequences
• Oxidizing atmosphere.
• Ozone layer—reduced energy.
• Harmful to many organisms: extinctions?
• Door opened for aerobic metabolism.
Aerobic metabolism
Higher oxygen levels paved the way for more efficient
metabolism—aerobic:
Krebs Cycle (citric acid cycle).
• Initially anaerobic metabolism and two pathways.
• Uses pyruvate from glycolysis, produces ATP,
electrons, and H+.
Electron transport system or oxidative phosphorylation
• Passes electrons from the KC down respiratory chain.
• Ultimately, O2 is reduced to 2 H2O.
• Glycolysis + Krebs cycle + OP generates 38 ATPs—
highly efficient.
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The First Cells II
Evolution
Biology 4974/5974
D. F. Tomback
Krebs cycle
and electron transport chain
Fig. EB3.1
Endosymbiosis theory
First eukaryote from a symbiosis between
an archaebacterium and a eubacterium,
which produced a nuclear membrane.
• Ancestral “eukaryote”: anaerobic with
flexible cell walls.
• Internal cytoskeleton with microtubules
and actin filaments.
• Allowed cells to change shape.
• Could “prey” on prokaryotes.
Steps in primary endosymbiosis:
• Aerobic prokaryote became
mitochondrion.
• Cyanobacterium became a chloroplast,
leading to photosynthesis.
• Spirochete, became a flagellum
• These symbionts over time became
organelles.
Secondary endosymbiosis:
• Some eukaryotes acquired chloroplasts
from other eukaryotes.
Fig. 9.4 Paramecium bursaria with symbiotic algae.
Evidence for endosymbiosis
• Mitochondria and chloroplasts
have their own DNA and
ribosomes like prokaryotes.
• The primitive amoeba Pelomyxa
and other species have bacterial
symbionts.
• Mitochondrial genome of the
freshwater protozoan
Reclinomonas americana contains
more genes than found in any
mtDNA (Lang et al. 1997);
symbiont is a rickettsia-like
bacterium; other members of this
group lack mitochondria.
• Eventually, genes are transferred
from the symbionts to the nucleus
or are lost.
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The First Cells II
Evolution
Biology 4974/5974
D. F. Tomback
Horizontal gene transfer
The incorporation of one organism’s genes into the nuclear
DNA of another organism.
•
•
•
•
•
•
Now known to be widespread.
Between prokaryotes.
Prokaryotes to eukaryotes.
Between some eukaryotes.
Continues today.
10% of genome of most single cells; one-third of genome
of prokaryotes from HGT.
• Mechanisms: via plasmids, intracellular symbionts, or
parasites.
The oldest fossil cells
Fig. 8.3A: Stromatolites composed of calcium carbonate secreted by cyanobacteria are the
oldest organisms known (3.5 By old) and the longest lasting.
Fig. 8.2 Filamentous unicellular fossil found in stromatolite chert in the3.5 By-old
Warrawoona formation in Western Australia.
Study guide
• What arguments support RNA evolving first?
• What are explanations for why the genetic code is
universal? What is meant by redundancy of the
code?
• Explain why heterotrophs probably evolved before
autotrophs?
• What were probably the main energy metabolic
pathways of the a) first heterotrophs, b) first
autotrophs?
• What new metabolic pathway led to the rise in
atmospheric oxygen? What pathways could then
evolve? How did that affect energy metabolism?
• What different forms of evidence support the
endosymbiosis hypothesis?
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