ptys 214 – spring 2019 announcements · dna, rna • replication • transcription •...
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PTYS 214 – Fall 2019
Teaching Teams Program!
Change Th office hours to 1:30 – 2:30?
Away next week!
9/17: Energy!•9/19: No Class!
Midterm #2 9/24!
Announcements
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DNA, RNA• Replication• Transcription• Translation
Cells• Prokaryotes• Eukaryotes
Earliest biology -- top-down approach● RNA world● Metabolism-first
Last Time
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Exo-Ocean discovered? Not really!
K2-18b• 8 Earth masses• M-dwarf host star• In “habitable zone”
•
Atmosphere detected• Consistent w/ water vapor, but not conclusive!• If true, may suggest presence of ocean!
Tsiaris et al. Nature Astronomy; Sept 2019
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Bottom-Up Approach: Primordial Soup Theory
Life began in a warm pond/ocean from a
combination of basic building blocks of life (organic
molecules) into ever more complex organic molecules,
such as amino acids, proteins, and some early
version of RNA
Where did the building blocks of life come from?
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Building Blocks of Life: Atmosphere Carbon that comes out of volcanoes is in the form of CO2
Almost all organic carbon that we observe today is produced biologically (via photosynthesis):
CO2 + H2O CH2O + O2 (CH2O – any organic matter)
CO2 gas mixture does not produce organic molecules on its own
Where did organics come from •before there was life?
inorganicorganic
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CH4
NH3
H2O
C
H
N
O
HCN (cyanide)
H2CO (fomaldehyde)
Amino acids
Other simple organics
Spark discharge breaks the chemical bonds in CH4,
NH3, H2O
C, H, N, O atoms can recombine into various organic molecules that
eventually end up in the ocean
Urey-Miller Experiment “A
ncie
nt”
atm
osph
ere
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Problems of organic synthesis via Urey-Miller experiment
Debate over the presence of large amounts of NH3 and CH4 in the early (pre-biotic) atmosphere
In a CO2-rich atmosphere organic production by spark discharge is not very efficient
If CH4/CO2 < 0.1 essentially no organic production
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Why?
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CONONO2
H2O
O >> C,N,HCO2 >> CH4, NH3
In an atmosphere dominated by CO2 the most abundantradical after spark discharge or photolysis is O
CO2-Dominated Atmosphere
The dominant species after recombination are inorganic molecules!
Current Research: organic production in CO2-N2-H2 mixtures
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Organic synthesis in Hydrothermal Vents
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Plate tectonics: Mid-ocean ridges
Mantle circulation produces stresses on the Earth’s crust
Spreading centers form on the ocean floor, where the crust is thinnest -- mid-ocean ridges
Old material is subducted back into the mantle at continental margins
Mid-ocean ridges combine water, high temperatures, silicate minerals - hydrothermal vents
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Organic synthesis in Hydrothermal Vents
Hydrothermal vents were likely to be present in the pre-biotic environment
Organic synthesis requires only CO2, H2O and silicate rocks (and heat!)
Example: Serpentinization:
Spinel polymerization:
Olivine + Serpentine + Magnetite(spinel group)
Seawater & dissolved CO2
Hematite
Ethane
Methane
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Organic synthesis in Hydrothermal Vents
Actually, the story is likely more complicated:
McDermott et al., PNAS 112; May 2015
➔ Some organics formed through processes other than serpentinization
However:
Large organic molecules are unstable at high temperatures!
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Can you think of any other source of organic matter?
Both atmosphere and hydrothermal vents have problems producing complex organics
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Can you think of any other source of organic matter?
Both atmosphere and hydrothermal vents have problems producing complex organics
Space!
Extraterrestrial origin – organic material was synthesized in space and was brought to Earth somehow
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~150 interstellar and circumstellar molecules
H2
CH4
C6H6
NH3
Glycine
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Giant molecular cloud
Star/planet formation 16
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Do we have examples of extraterrestrial material on Earth?
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Do we have examples of extraterrestrial material on Earth?
Meteorites!
Murchison (1969, Australia)
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MeteoritesNatural objects originating in outer space that
survive an impact with the Earth's surface without being destroyed
Achondrites – 8%
Irons/Stony irons – 6%
Chondrites – 86% (oldest rocks in the solar system)
5% are Carbonaceous Chondrites:
- amino acids
- hydrocarbons
- fullerenes
- etc..
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Some of the amino acids synthesized in the Miller-Urey experiment and also found in the Murchison meteorite
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Comet 67P/Churyumov-Gerasimenko
Philae lander found 16 organic compounds
4 had never been seen before in comets
Goesmann et al. Science 349; July 2015
Target of ESA's Rosetta/Philae mission
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Problems with Extraterrestrial Organic Delivery (and other options)
Simple organics only – no large macromolecules
It is hard to accumulate necessary mass of carbon for the “concentrated” pre-biotic soup (dilution problem)
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The Phosphorus Problem
Cosmic
H 2.8 × 106
O 1400
C 680
N 230
S 43
P 1
Phosphorus is a relatively rare element in the universe
In terrestrial rocks it is found as insoluble phosphate minerals
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Why do we care about phosphorus?
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Without Phosphorous there would be no:
Nucleic acids (DNA,RNA) ...
ATP ...
... or Phospholipids
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Extraterrestrial P
Two forms:– Phosphate
Ca5(PO4)3(OH,F)
like typical phosphates on Earth
– Schreibersite
(Fe,Ni)3P
NOT a naturally-occurring crustal mineral
Seymchan meteorite (pallasite) 20 cm
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Phosphorus on the Earth’s surface Phosphates are not soluble in water at normal terrestrial
conditions
Schreibersite rusts in presence of water to form soluble and reactive P
Meteorites may be an important source of P for the origin of life
Pasek (2008) PNAS 105(3), p.853
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However, phosphates might be incorporated into organic molecules under certain conditions!
Fernandez-Garcia et al. (2017) Life 7(3), p.31
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Bottom-Up Approach - Synopsis1. Small organic molecules
Small organic carbon molecules could have come from three sources in the pre-biotic world:
• Synthesis in the atmosphere• Synthesis in the hydrothermal vents• Synthesis in space and delivery via meteorites
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Bottom-Up Approach - Synopsis 2. Subunits of RNA
Phosphates: rock (meteorite?) weathering
Ribose: 5 CH2O + H2O → C5H
10O
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Bases: 5 HCN + NH3 → Adenine
(formaldehyde from U-M)
(and similar reactions for the other 3 RNA bases)
(hydrogen cyanide from U-M)
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Formation of longer molecules from simple organic molecules
Dehydration reaction: two simpler organic molecules are bonded through the loss of water
Bottom-Up Approach - Synopsis
3. Polymerization
H2O
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Minerals can help polymerization
Minerals (like clay and pyrite) can provide a repeating pattern to act as a template for polymerization
Small organic molecules could have stuck to the mineral surface (organic film)
Kaolinite
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Primordial soup was probably too dilute in simple monomers to form very long molecules
Possible concentration mechanisms: Tidal pools (evaporation) Freezing water Mineral catalysts (clays)
All of them are quite inefficient compared to enzymes and cells
The Dilution Problem
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Lipids have hydrophilic head and hydrophobic tail
In solution these lipids can form monolayers, bilayers and bilayer vesicles spontaneously → proto-cells
Bottom-Up Approach - Synopsis
4. Formation of the cell membrane= water-loving
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Monolayer
Bilayer Bilayer vesicle
Micelles
Cell Membrane
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Bottom-Up Approach: Summary
1. There are 3 sources of small organic carbon molecules (up to amino acids, sugars) in the pre-biotic world
2. Small organic molecules must combine to form the basic sub-units of RNA
3. Polymerization allows for the formation of organic macromolecules
Dilution Problem The primordial soup was probably too dilute in simple
monomers to form very long molecules(a concentration mechanism is required)
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The RNA-first World Short strands of RNA-like molecules were produced
spontaneously (with some help, e.g. minerals)
Eventually some of the RNA-like molecules were able to catalyze their own replication
Copying errors introduced mutations and therefore Darwinian-like evolution
CCU G
GGA C U GGA C UCCU G A
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First DNA-based LifeThrough natural selection life figured
out that:
● DNA is a better way to store the hereditary information:
● more stable (better protected)
● Fewer replication errors
● Less susceptible to certain mutations
● Proteins are more efficient catalysts than RNA
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Central problem for the origin of life:
Simple organic
moleculesRNA world
Metabolism first?Replication first (RNA world)?
+Dilution problem
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Origin of Life on EARTH: Summary
Bada & Lazcano (Science, 2002) 39
?
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Homework #5 available shortly on the web site
Homework
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