ASTR/GEOL-2040: Search for life
in the Universe: Lecture 7
• Metabolism first vs
replication first
• RNS world & LUCA
On Thursday (Feb 9)
• Lecture 3:30 – 4:10
– Giving out HW3, review, Q/A
• Quiz 4:15 – 4:45
• Special accommodations
– I have emailed everybody if you
contacted me
– Not everybody contacted me, so make
sure you do
2
Today
•
•
•
•
Metabolism first?
RNA world
LUCA
Reading:
– RGS pp. 30-40
– Lon pp. 193-195
– BS pp. 172-176, 206-208
3
Primitive cells
• Lipid bilayers
• Protein droplets (Oparin 1924)
• Dehydration – rehydration (S Fox 1958)
4
Properties of protocells
• Confinement of organics
within cells is advantageous:
– Facilitates chemical reactions.
– Cooperative relationships evolve.
• Membrane-like spheres easily made in
lab experiments!
– Cooled amino acids solutions.
– Lipids in water.
• First “cell” may
have been RNA
replicating within
simple membrane.
Role of minerals
• Support
– Amino acids polymerize on surfaces
• Selection
– Different crystal faces select left/right
– Both possible  natural selection chose one
• Catalysis
– N2 to N3H via metalic surfaces
– Suitable in hydrothermal vents
6
Minerals as Templates?
• How could first RNA “genetic” strands arise?
• Lab experiments: clays + water + organics  complex
organics, including RNA strands.
• Repeating chemical structure of minerals may facilitate
assembly of complex organics!
clay (microscopic image)
pyrite
Role of minerals
• Support
– Amino acids polymerize on surfaces
• Selection
– Different crystal faces select left/right
– Both possible  natural selection chose one
• Catalysis
– N2 to N3H via metalic surfaces
8
Metabolism
• How to make a living (Longstaff 193)
• Use of catalysts
– Speeds up reaction
– Regardless of direction (!)
• Two types
– Proteins
– RNA catalysts (=ribozyme)
9
Three requirements
• Source of carbon (CO2 or CH2O)
• Source of energy
– To reduce inorganic to org macromolecule
– Electron donor (e.g. H2)
• An oxidant
– To harness chemical potential energy
– Electron acceptor (e.g. O2)
10
“Food” in Greek?
RGS 36, Lon 195, BS 174
11
Troph (Greek) = food
• auto – hetero
• photo – chemo
• litho – organo
•
•
•
•
Photoautotroph
Chemoautotroph
Photoheterotroph
Chemoheterotroph
RGS 36, Lon 195, BS 174
12
Range of possibilities
• e.g.: Chemolithoheterotroph
• Altogether 8 possibilities!
13
Thiobacillus denitrificans
• Discovered 1904
– 0.5x1x3 mm3
• Soil & mud
– Oxidize U(IV)U(VI)
• Chemolithoautotroph
or chemoautotroph
– H2S+CO2CH2O+2S
14
Gray bacterium in rock spaces
Always found to be growing
Excreting CO2
Rocks mineral structure depleted in Fe
A.
B.
C.
D.
Chemoautotroph
Lithoautotroph
Photoautotroph
Lithoheterotroph
15
Blue-green in petri dish
Cells grow when exposed to sunlight
Excrete O2
Grow and produce O2 as long as in sunlight
A.
B.
C.
D.
Chemoautotroph
Lithoautotroph
Photoautotroph
Lithoheterotroph
16
Metabolism/replication first?
• Organism needs 2 things
– Replication (otherwise not self-sustaining)
• Turn disorder to ordered chem reactions to
extract energy from surroundings
 metabolism, needed to control flow of energy
17
DNA transcription
• DNA  messenger RNA (mRNA, transient)
• mRNA read out by ribosome (rRNA)
– Ribosomes contain their own type of RNA
– Amino acids + RNA (tRNA, small)
• Ribosome synthesizes proteins (incoming tRNA)
– Forges peptide bonds between amino acids
– tRNA liberated, captures new amino acids
– 10-20 amino acids/second
18
Walter Gilbert
(1986, Nature 319, 618)
The RNA world
• Central dogma of chemistry of life
– DNA  RNA  protein
store messenger
enzyme
• RNA world: only RNA
– RNA acts as enzyme, messenger, and store for itself!
– Ribonucleic acid enzyme = Ribozyme (mRNA, etc)
19
RNA itself acts as enzyme
– in addition to proteins!
20
RNA itself as enzyme
21
RNA world before DNA/protein
•
•
•
•
Nucleotides in RNA easier made
RNA evolved to DNA (greater stability)
No scenario for protein replication w/o RNA
Natural selection outcompeted DNA+protein
22
RNA world evolution
• RNA might produce small
proteins (polypeptides), which
aid RNA replication!
• Best-replicating RNA
“survive” and dominate.
• Mutations promote RNA
“genetic” variety.
• RNA role in making proteins is
consistent with an early RNA
world.
• More efficient DNA evolved
later.
Similarity with viruses
• Replicates only inside cell (all domains of life)
– RNA or DNA + protein (+lipid) coat
• Edge of life: have genes, evol nat selection
–
–
–
–
–
But no metabolism
20-300 nm size
Double-stranded: dsDNA, dsRNA
Single-stranded: ssDNA, ssRNA  retrovirus
High mutation rate
24
Evidence for RNA world
•
•
•
•
Ribozymes have been synthesized
E.g. polymerase
Catalyzed synthesis of 95 nucleotides
Itself able to manufacture another ribosome
25
Advantage of RNA over DNA?
A. Simpler, easier to synthesize?
B. Less stable?
C. Melting temperature lower?
D. All of the above.
E. Both A and B.
26
Phylogenetic Tree
• Based on physical & genetic differences
– Taxa: group of populations
• Darwin (1857): the time would come “when
we shall have very fairly true genealogical
trees of each great kingdom of nature.”
– RGS: life does not reject what evolution has
created, but simply builds on what has gone
before.
27
Phylogenetic Tree
• RGS: life does not reject what evolution has
created, but simply builds on what has gone
before.
– Biological record of continuous
additions/modifications in genetic material
• Tree construction:
– Similar molecules in different creatures
– Similar parts inherited from common ancestor
28
Position in classification scheme
bacteria
bacteria
deinococcus-thermus
proteobacteria
deinococcales
enterobacteriales
deinococcaaceae
enterobacteriaceae
deinococcus
escherichia
radiodurans
coli
29
Modern tree building
• Uses ribosomal RNA (rRNA)
– Branch length = difference in rRNA
• Three clear “domains”
– Bacteria, archea, eukarya
• Root on tree  LUCA
– Last universal common ancestor
• Closest to tree: thermophiles, hyperthermophiles
– Evolution from hot  cold
– chemotrophs
30
Rooted Tree
Unrooted Tree
Modern tree building
• Uses ribosomal RNA (rRNA)
– Branch length = difference in rRNA
• Three clear “domains”
– Bacteria, archea, eukarya
• Root on tree  LUCA
– Last universal common ancestor
• What types of organisms closest to the root?
33
Modern tree building
34
Thermus, thermofilum, methanopyrus,...
Deinococcus thermus
35
Closest to the root?
• ………..
• ……………….
36
Closest to the root?
• thermophiles, hyperthermophiles
– Evolution from hot  cold
• Chemotrophs
– Deep biosphere rather than surface
37
Cold organisms first?
•
•
•
•
…..
………
…………….
…………………
38
Cold organisms first?
•
•
•
•
Yes, also possible:
Hydrothermal vent first
Then ocean-sterilizing impact
Only thermophiles survives
39
Origin of Life: Summary
1.
2.
3.
4.
5.
“Organic soup” vs. dilute solution.
Complex organics developed (mineral templates?).
“Pre-cells” enclosed complex organics.
Natural selection increased RNA complexity.
DNA developed within some successful cell(s).
A reasonable scenario, though many details are missing!
On Thursday (Feb 9)
• Lecture 3:30 – 4:10
– Giving out HW3, review, Q/A
• Quiz 4:15 – 4:45
• Special accommodations
– I have emailed everybody if you
contacted me
– Not everybody contacted me, so make
sure you do
41
Next
•
•
•
•
Summary
Habitable zone
Origin of life on Earth
Chapter 2 of RGS pp 43-59