The Origin of Life: A Dual Origin Hypothesis

Heather E. JordanBryant Lab, 232 S. Frear

The Pennsylvania State UniversityUniversity Park, PA 16802

MICRB 497-B3/25/2004

http://www.best3dart.com/3d_space_004.jpg

Where did I come from?• Cells? Our genes? What

did we descend from?• Stardust• The first life form on

Earth– Progenote– Cenancestor(s)– LUCA

• Are we alone?• Nobody knows for sure

(but there may be clues!)

http://www.sternwarte-ehingen.de/Galerie/SpaceArt.htm

Past Attempts to Answer the Question

• Pagan Folklore

http://www.bcimall.org/calendar/JC2000/image/queen_of_heaven_mother_of_earth.jpg

Past Attempts to Answer the Question

• Pagan Folklore• Religion

http://www.fredleavitt.com/DayTwo.html

Past Attempts to Answer the Question

• Pagan Folklore• Religion• Spontaneous

Generation (Pasteur)

Totora, G., Funke, B. and Case, C.. Microbiology: An Introduction. Pg 8. Redwood City: The Benjamin/Cummings Publishing Company. 1995.

Past Attempts to Answer the Question

• Pagan Folklore• Religion• Spontaneous

Generation (Pasteur)• Directed Panspermia

(Crick)

http://homepage.hispeed.ch/Final-Frontier/Erde.html

Vital Force or Vital Farce?• Wöhler (1828) accidentally

synthesized urea while trying to make Ammonium cyanate (evaporated instead of allowing crystalization @ room temp.)

• Letter to Berzelius: "I can no longer, so to speak, hold my chemical water and must tell you that I can make urea without needing a kidney, whether of man or dog; the ammonium salt of cyanic acid is urea".

• AgCNO + NH4Cl AgCl + NH4CNO

(Minard, PSARC Presentation)

The Miller-Urey Experiment• Original:

– H2

– H2O– NH3

– CH4

• Modified • Experiments:

– CO– CO2

– CH2=CH2

– HC=CH– N2

– HCNhttp://ircamera.as.arizona.edu/NatSci102/lectures/lifeform.htm

Energy Sources: PhotochemicalShock wavesHeatElectrical

Products:Amino AcidsNitrogenous BasesAldehydesAlcoholsHydrocarbonsAmines3-6 C SugarsEstersCarboxylic AcidsAmidesKetonesEthersHCN, CO, CO2, H2O2, H2CO3, NH2CONHCONH2, etc.

The Biochemistry of Titan (Maybe?)

– Protection of Organic Polymers:

• Thick Atmosphere

– Saturn’s Cosmic Rays & e-s + Solar UV: N2 + CH4 free radicals

– Yield: Hydrocarbons, Acetylene, HCN (& polymers)» Drifts down to the lunar surface

• Extreme Cold (-178oC)

– Liquid H2O could result transiently from:

» Volcanic Activity

» Impacts

– Heat could also be provided for reactions this way

– NH3 is an antifreeze for H2O (pooled on surface)

(Lunine, http://www.astrobio.net/news/modules.php?op=modload&name=News&file=article&sid=183)

The Biochemistry of Titan (Maybe?)

– Protection of Organic Polymers:

(Lunine, http://www.astrobio.net/news/modules.php?op=modload&name=News&file=article&sid=183)

• O from liquid H2O is donated to hydrocarbon chains on surface

• Heat Dissipates

• Organics are deep-frozen & preserved

•Additional shielding from atmosphere

http://www.arcadiastreet.com/cgvistas/saturn_050a.htm

Strecker Synthesis• The methane and nitrogen in the atmosphere reacted to form hydrogen &

hydrogen cyanide

CH4 + N2 2 HCN + 3H2

• The hydrogen cyanide in turn, reacted with the formaldehyde

HCN + HCHO H2N-CH2OH

• Other products resulted from this

H2N-CH2OH HN=CH2 + H2O

HN=CH2 + HCN H2NCH2CN

H2NCH2CN + H2O H2NCH2COOH + NH3

HCN + NH3 Adenine

– Successive wetting & freeze-drying under UV– Clusters of HCN formed 5-member ring

Incredible HCN!• Other purines & pyrimidines produced

in smaller amounts

• Strecker Synthesis also forms Gly

• HCN spontaneously polymerizes

– xHCN HCNx

– 2 Forms: (Polymerization?)

• Orange (water soluble)

• Black (water insoluble)

– Acid hydrolysis

• 20%+ amino acids• Mostly Gly• Trace Ala, Asp, Glu, Ser, β-

Ala & α-amino isobutyric acid.• Urea, Adenine & more!

Base

Catalyst

(Minard, HCN Photos)

Great but, how else can they be protected from degradation?

0

0.5

1

1.5

2

2.5

3

3.5

4

Miller-Urey Murchison HCNx

Gly

Val

Pro

Ala

Asp

Glu

Urea

Adenine

Uracil

Other AA

• Preserved by absorption into minerals (meteorites!)

• Amino Acids Diversity:– Miller-Urey (30+ in original, 90+ in variations)– Murchison (69+)– HCNx (7)

Biological Triad• 3 elements are required by

life: 1) Water

2) Energy

3) Atmosphere

• Which planets/moons in our solar system have these elements?– Titan

• 2/3 (very little water)

– Mars, Ganymede, Europa, Callisto

• Have complete triadhttp://solarsystem.dlr.de/polarlander/msss/mars_relay/mars2earth/

Biological Triad• Ganymede

– Light Atmosphere: H, O2, CO2 & traces– H corona– Embedded in Jupiter’s magnetosphere (intense

radiation & charged particles)– Ozone at the poles (e-s travel along field lines & hit

polar ice)

• Europa– Light Atmosphere: H, O2, CO2 & traces– Significant O2 levels in atmosphere (HST emission

measurements)– Embedded in Jupiter’s magnetosphere (intense

radiation & charged particles)

• Callisto– Light Atmosphere: H, O2, CO2 & traces– H corona– Embedded in Jupiter’s magnetosphere (intense

radiation & charged particles)http://ffden-2.phys.uaf.edu/211_fall2002.web.dir/Melissa_Smith/Moons.htmhttp://www.astrobio.net/news/modules.php?op=modload&name=News&file=article&sid=713

Planetary Atmospheres• Venus

– CO2 96.0%– N2 3.5%– H2O trace

• Mars– CO2 95.0%– N2 3.0%– O2/H2O trace

• Earth Signature of Life?

– N2 78.1%– O2 21.0%– Ar 0.9%– H2O 0.1-3.0%– CO2 0.03%

http://lithops.as.arizona.edu/~jill/EPO/Posters/VenusEarthMars/VEM.jpg

The Parsimonious Conclusion• Currently, most think that

early Earth’s atmosphere was composed primarily of CO2 & N2

• "This type of atmosphere is "This type of atmosphere is neutral for oxidation and neutral for oxidation and reduction reactions and does reduction reactions and does not allow an easy and direct not allow an easy and direct formation of long chains of formation of long chains of organic molecules,“ organic molecules,“ (Jonathan I. Lunine, University of Arizona planetary sciences Professor).

http://ircamera.as.arizona.edu/NatSci102/lectures/lifeform.htm*http://ucsu.colorado.edu/~sbrooks/impacts.html

The Parsimonious Conclusion• Large moons of giant, Jovian planets

are likely to have thick atmospheres

• Proximity of moons to giants provides a source for various gasses

• Simulations of KBO impacts demonstrate why Titan was the only large moon to retain a thick atmosphere in our solar system*

• Escape Velocities:– Titan-Saturn: 35.489 km/s – Ganymede-Jupiter: 2.74 km/s– Europa-Jupiter: 2.02 km/s– Callisto-Jupiter: 2.45 km/s

*http://ucsu.colorado.edu/~sbrooks/impacts.htmlhttp://www.croastro.com/halloffame/halloffame.htm

The Parsimonious Conclusion• The “Miller-Urey”

atmosphere did not exist on Earth (not enough CH4 to make the organic precursors)

• Earth was seeded with organics from space (asteroids & comets)

• Must have been many small impacts of organic-rich material (and 1 really big one?)

• What types of molecules could have fallen here?

http://ircamera.as.arizona.edu/NatSci102/lectures/lifeform.htm

The Origin of Organic Molecules

• Starting Materials:– Methane– Nitrogen– Formaldehyde– Water

http://nolswf.bbc.net.uk/science/space/life/looking/titan.shtml

From a moon or planet with a reducing atmosphere: A dead solar system (?)

- Thick atmosphere of NH3, CH4 & N2

- Covered in tar and formaldehyde

*CRASH!!!*

• Frozen organic planet (Mars-sized?) crashes into Earth 4.5 bya• Earth crust melts on impact but much debris is scattered in

space (some of which forms the moon)• Earth cools & crust re-forms• Atmosphere restored via geothermal processes

http://www.donaldedavis.com/2002_addons/MOONFORM.jpghttp://nai.arc.nasa.gov/news_stories/news_detail.cfm?ID=111

*CRASH!!!*

• Many asteroids fall to Earth, carrying organics from the invading body

• Organics are concentrated at the surface but protected from degradation until erosion releases them from the rocks.

http://nai.arc.nasa.gov/news_stories/news_detail.cfm?ID=111

• Any planets orbiting α-Centauri A or B; 4.35 ly away may have Any planets orbiting α-Centauri A or B; 4.35 ly away may have worked their way into the Oort cloud surrounding that systemworked their way into the Oort cloud surrounding that system– Both stars are ~ 5-6 billion years oldBoth stars are ~ 5-6 billion years old

• All 3 stars of the triad are older than our sun and 1 of them All 3 stars of the triad are older than our sun and 1 of them (closest) is a brown dwarf (Proxima)(closest) is a brown dwarf (Proxima)

• Proxima is spectral type M5Proxima is spectral type M5\\

– This star has a MS lifespan of 2 x 10This star has a MS lifespan of 2 x 101212 years ( years (11stst generation! generation!))– Stars in any given region of the galaxy tend to be about the same Stars in any given region of the galaxy tend to be about the same

age so… where are Proxima’s solar siblings? age so… where are Proxima’s solar siblings? – Is the material in our solar system Is the material in our solar system (including pre-biotic organics)(including pre-biotic organics)

leftover from the event that created α-Centauri A & B?leftover from the event that created α-Centauri A & B?

http://homepage.sunrise.ch/homepage/schatzer/Alpha-Centauri.htmlhttp://www.wncc.cc.ne.us/courses/aveh/lecture/lecevol.htm#Appendix

How plausible is this?

• Pluto, Quaoar (kwa-whar) & Sedna

– Sedna is 0.014 ly from sun

– Oort cloud extends 3 ly from sun

• Oort clouds of other stars can perturb it.

– Captured from another solar system?

http://science.nasa.gov/headlines/y2004/16mar_sedna.htm?list799130

Precious Cargo

– Body exposed to a supernova shockwave Propulsion!– May not have traveled far…– May have been in our own cosmic backyard!

http://www.aetheronline.com/mario/AIG/1999+2000/Tantalis.htm

The Chirality Riddle

• More L-amino acids in Murchison & Murray meteorites

– Extraterrestrial cause

• Neutron star synchrotron radiation from supernova

– Circularly polarized radiation (Counterclockwise from the star's northern hemisphere and clockwise from the southchiral radiation!)

– Polarization too low

http://pauillac.inria.fr/algo/vandenbogaert/Proteins/

The Chirality Riddle• High circular polarizations in

star-forming regions of reflection nebulae– Orion OMC1 (a region in the Orion

nebula M42) – NGC 6334.

http://www.ast.cam.ac.uk/AAO/local/www/jab/astrobiology/chirality.html/

http://www.sternwarte-ehingen.de/Galerie/SpaceArt.htm

The Chirality Riddle• High circular polarizations in

star-forming regions of reflection nebulae– Orion OMC1 (a region in the Orion

nebula M42) – NGC 6334.

• Prediction: “Circular polarization should also be present at the UV wavelengths needed for asymmetric photolysis of molecules such as amino acids.”

• Our own solar system may have formed in a region of high circular polarization

http://www.ast.cam.ac.uk/AAO/local/www/jab/astrobiology/chirality.html/

Anglo-Australian Telescope IR ImageHighest circular polarization in white

More stuff!

• Ammonia (imported) + water vapor (native) hydroxyl acids• H2S gas (UV absorbing gas) + lightning cysteine• Possibly over 90 other amino acids (imported)• Same processes that synthesized also degraded them

– Aldehydes & cyanides continued to react http://www.arcadiastreet.com/cgvistas/venus_030a.htm

More organics form…

• Rocks which preserved imported organics (meteorites) eroded and released them into environment

• Formaldehyde combined with organics to form sugars and amidinium carbodiimide– Catalyzes formation of peptide bonds at 70oC in dilute

solutions

http://bizpresenter.corbis.com/search/detail.asp?imageid=11517922

High Tide

• Tides created by the gravitational pull of the moon• Cool water rushes in and suspends dried, polymerized

organicshttp://www.sternwarte-ehingen.de/Galerie/spaceart/Space-Art_007.jpg

The Moon

• Washed organics onto rocks (mostly iron with some zinc, etc.) like pyrite – Bound there & aligned by charge– Zn facilitated polymerization– Most fell apart but a few didn’t

• Baked under UV during the day http://ircamera.as.arizona.edu/NatSci102/lectures/lifeform.htm

Sunscreen for Pre-biotic Molecules?!• Evolution:

– 5 classes of chlorophyll-protein complexes share a common ancestor

– Derived from a large pigment-carrying protein with more than 10 transmembrane spans

– Complex protects (cell?) against UV light

– Dissipative chemistry photosynthesis

http://www.hsv.k12.al.us/schools/middle/wtms/student/cell/cell_energy.htmlMulkidjanian, A.Y. & Junge, W. (1997) On the origin of photosynthesis as inferred from sequence analysis. Photosynthesis Research 51:27-42.

The UV-Protector Hypothesis

• Hypothesis: Monomers of reaction centers were pigment-carrying antenna proteins

• Evidence: sequence alignments revealed clustered UV-absorbing residues

• With each other

• With chlorophyll & cofactor ligands

– Clusters most highly conserved in RC1

• Most ancient (Baymann et al., 2001)

Baymann, F., Brugna M., Muhlenhoff, U. & Nitschke, W. (2001) Review: Daddy Where Did PSI Come From? Biochimica et Biophysica Acta 1507: 291-310.

Advantages of Clustering

• ↓ Liklihood of photocleavage by:

• ↓ Lifetime of the excited state, which then:

• ↑ Photostability

• Then:

– Excitation pigments (rapid internal conversion to lowest excited singlet state)

– Thermal energy release & dissipation

http://bio.winona.msus.edu/bates/Bio241/images/figure-08-12-2.jpg

UV Trapping• 3 layers

– Each α-helix helps pack residues with pigments

– Increases absorption cross section of the membrane

• Arrangement helped dissipate energy

Does this make sense?• Glycine + Acetate Protoporphyrin IX

– Precursors were available to make this

– Intermediate in heme biosythesis

• Elasticity of α-helices (where porphyrins are attached)

• Chlorophyll favored due to lower energy singlet state production (in comparison)

– Natural selection crucial component in photosynthesis later

http://www.indstate.edu/thcme/mwking/heme-porphyrin.html

Lots of chemistry going on it’s all still inanimate… what’s missing?

• Chemistry needs a container!

– Brings reagents together

• The ocean is too dilute... puddles are too risky… what the heck are all these bubbles? All those white flakes can’t be soap!

– Polymerization of washed up organics, dried on the shore are reclaimed by the tide & voila!

http://ajt.iki.fi/travel/lsm/page4.htmlhttp://www.todayinsci.com/cgi-bin/indexpage.pl?http://www.todayinsci.com/3/3_24.htm

The First “Container”?

• Spontaneously form proteinoid microspheres (electrostatic interactions)– Able to take up molecules & have electrical potentials across

“membranes”– Respond to changes in osmotic pressure

• High Tide = Dinner time!!http://www.biologie.uni-hamburg.de/b-online/e41/3.htm

Microsphere Meals

• Phosphate also taken up (some already contained A & sugars) AMP ATP

• Contained up to 250 amino acids

• Wide variety of proteins & enzymes produced

– Proteolytic

– Michaelis-Menten kinetics

– pH optimum

– ATPase activity

http://tycho.bgsu.edu/~laird/ast305/class/IVC-5.html

Elusive Phosphorus

• Most P trapped in insoluble minerals• Heat from volcanic activity released it into oceans• Combined with amino acids acyl phosphates (in

vivo) + phosphoramidates (in vitro)• Phosphoric acid more efficiently catalyzes

formation of peptide bonds @ 70oChttp://www.kao.re.kr/~neopat/ne07-1.htm

What a Little Phosphate Can Do

• Phosphates + Glycerol + Fatty Acids

Phospholipids

• Clumped together

Phospholipid Bilayers

Liposomes• Acquired many different

solutes while drying

• Nucleotides!

www.bio.davidson.edu/Courses/Molbio/MolStudents/.../Favorite_Molecular_Tool.html

Fatty Acids

• Many different chain lengths• 14-C chain had special properties:

– No large proteins could pass– Small enzymes & nucleotides enter but can’t exit!

http://animalscience.unl.edu/pomplab/metabolome.htm

Creation of Protocells

• Microspheres picked up everything… even liposomes• ATP + nucleotides oligonucleotides (inside ingested

liposome)

– Began to base pair with itself RNA?

– Ribose: 21-51 linkage

• Liposomes + hollow proteins “membrane” pores– Now oligonucleotides can leavehttp://www.stc.uniroma2.it/cfmacro/cfmacroindex.htm

A Pre-RNA World?

• RNA is simpler than DNA but still complex

• Possible RNA precursors:

– PNA

– pNA

– TNA

• Best candidate

http://nai.arc.nasa.gov/news_stories/news_detail.cfm?ID=189

A Pre-RNA World?• PNA

– Peptide/Polyamide Nucleic Acid

– L-arabinopyranosyl-(4121) oligonucleotides

• Strongest base-pairing system of pentopyranosyl family

– An HCN Polymer

– Hybridizes to cDNA, RNA * PNA oligomers

– Can cause steric hindrance of RT, Telomerase & the Ribosome

– Uncharged (neither repelled by – charged cell walls nor by high inside – membrane potential

– Promising for anti-microbial drug development

(Dr. B. Minard, PSARC Presentation)

Cherny, D.Y., et al., 1993, Proc. Natl. Acad. Sci. USA 90, 1667-70; Wittung, P. et al., 1994, Nature, 368, 561-63.

PNA: A self-complimentary Sequence!

A PNA World• ‘T’s attached to

aminoethylglycine backbone

• Bind selectively to ‘A’s of oligos & double-stranded DNA– Strand displacement:

PNAA-strand & T-strand (single) excluded

(Dr. B. Minard, PSARC Presentation)Cherny, D.Y., et al., 1992, Proc. Natl. Acad. Sci. USA 90, 1667-70;

A PNA World• ‘T’s attached to

aminoethylglycine backbone

• Bind selectively to ‘A’s of oligos & double-stranded DNA– Strand displacement:

PNAA-strand & T-strand (single) excluded

• Binding to closed, circular DNAunwinding of double-helix (1 turn/10bp)

• DNA.PNA complex:– Forms @ low [salt]– Kinetically stable & cannot

be dissociated by ↑ [salt] up to 500 nM.

Arrow = unwound DNA by PNA

Cherny, D.Y., et al., 1992, Proc. Natl. Acad. Sci. USA 90, 1667-70;

↑↑

↓↓

A TNA World?• (L)-α–threofuranosyl-(3121)

oligonucleotide– Threose is the sugar

• Simplest nucleic acid alternative– Possible ancestor of RNA– Possible protector/regulator of

RNA (binds to it)

• Forms base pairs– G=C & T/U=A – Informational in anti-parallel– Cross-pairs with RNA & DNA

• A & T nucleobase analogs:– 2’-amino-(2’-NH2 TNA)– 3’-amino-(3’-NH2 TNA)

• Bst PolI, bacteriophage T7 DNA Pol (exo-) & MMLV-RT

Chaput, J.C., Ichida, J.K & Szostak, J.W. (2002) DNA Polymerase-Mediated DNA Synthesis on a TNA Template. J. AM. CHEM. SOC. 125, 856-857.

A TNA World?• Easily forms hairpins• much more stable to

hydrolytic cleavage than are RNAs and may be as stable as DNAs

• TNA strands can be synthesized by template-controlled ligation with either complementary TNA or RNA strands as templates

• corresponding formation of RNA sequences by ligation on a TNA template does also occur, although with less efficiency

http://www.scripps.edu/research/sr2001/chm03.html

RNA Replication• Sequence that

allowed it to copy itself

• Not advantageous in itself unless– the sequence copied has some advantageous parts in it.

• More protocells with L-amino acids than R so more D-sugars were used

http://www.esb.utexas.edu/jdudley/bio330/quicktime%20and%20avi%20files.htm

The Protonucleus

• Did not originally divide

– Streamed through pores, filled up cell & inhibited metabolism– Clogged pores breakdown of liposome/protonucleus

http://www.botany.hawaii.edu/faculty/webb/BOT410/anatweb/pages/ORNuc-4.htm

The Protonucleus

• Ribozymes

– Excised fragments of RNA (introns?)

– Crowded protonucleus burst

• 2 tangles of folded RNA (replicated)

• Intron scraps

http://ndbserver.rutgers.edu/NDB/NDBATLAS/P/pr0005/pr0005_1_gif.html

U1A SPLICEOSOMAL PROTEIN/HEPATITIS DELTA VIRUS GENOMIC RIBOZYME COMPLEX

Protonuclear Division

• Liposome phospholipids attracted to each other but pushed apart by tangles of RNA

– Reform encircling RNA (some mistakes, i.e., picking up introns or nothing)

– RNA folding ensured that everything stuck together (daughter cell received 1 copy)

http://www.biologiateorica.it/organiccodes/cap5/p124.htm

Primitive Protocell Metabolism

• Precursors needed to maintain “membranes”

– Proteins, lipids & carbohydrates

– First chemoorganotroph (popular; simple metabolism)

– Protocells died when starved, became toxic, got too big or in wrong environment

– Some grew faster than others, made products that facilitated growth, etc.

http://www.funhousefilms.com/sciencpg.htm

Fortunate mistakes• RNA has a high error rate

• Enough nucleic acid precursors?

– Multi-protonuclei

– Less nutrients coming in & available (volume increased faster than surface area)

– Few cells acquired a mutation that provided the protocell with a cytoskeleton

• Contracted along equatorial plane in response to diminished nutrient levels

• Cleaved cell & split up protonuclei

http://image.bloodline.net/stories/storyReader$1349

So… what is it?

• Self-replicating, Gram negative chemoorganotroph with ability to pass on genetic information to progeny

• Competition:– Food– Advantageous mutations Zn-containing polymerases (from

washing on rocks & still used today)http://www.bact.wisc.edu/bact330/lecturestaph

A Cenancestor?• Retention of favorable

mutations required higher fidelity

– DNA (with deoxyribose, now have 51-31 linkage)

– But RNA not completely out of the picture (just in different niches as it diversified)

– Ribosomes from protonucleus?

– Viruses still have the protein coats (lost genes?)• Genome shortened as it took up residence in larger

protocells faster replication top priority

http://www.braum.de/2001/thomas/hintergrundbilder/1024/Virus.jpg

But… there is one other possibility!

• The first life form may have been photosynthetic! You’re kidding, right?

http://www.bact.wisc.edu/bact330/lecturestaph

What is agreed upon• Anaerobic

environment

• 1st photosynthesizers used H2 or H2S as substrates

• Microbes still do this (H2SH2 + S)

– Purple & green sulfur bacteria

– PSI has 11 transmembrane domains

http://bio.winona.msus.edu/bates/Bio241/images/figure-08-12-2.jpg

UV-Protector Energy Producer

• Mutations that prevented chlorophyll binding

– Cavity exposed charges of ligands

– Attracted cofactors (FeS complexes/quinones)

• Re-stabilized the polypeptide

•↑ UV absorbance & dissipation

• Mutations:

– Gene fission

– Loss of α-helical domains (1o e- binding site)

Exhibit A: Careful! It’s 3.5 billion years old!

• 3.5 billion year-old cyanobacteria-like fossils

– Already photosynthesizing

– Pigment-carrying antenna protein may have evolved concurrently with life

– 200 million-year window from the solidification of Earth’s crust & this fossil!

• Much of this time, too warm for the right chemistry so…

http://www.ucmp.berkeley.edu/historyoflife/mysteries/mystery9/mystery9.html

Acknowledgements

Dr. Bob Minard

Dr. Greg Ferry

Dr. John Golbeck

Sabrina Zimmerman

??Questions??