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

1

DNA, RNA• Replication• Transcription• Translation

Cells• Prokaryotes• Eukaryotes

Earliest biology -- top-down approach● RNA world● Metabolism-first

Last Time

2

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

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?

4

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

5

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

6

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

7

Why?

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

8

Organic synthesis in Hydrothermal Vents

9

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

10

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

11

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!

12

Can you think of any other source of organic matter?

Both atmosphere and hydrothermal vents have problems producing complex organics

13

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

14

~150 interstellar and circumstellar molecules

H2

CH4

C6H6

NH3

Glycine

15

Giant molecular cloud

Star/planet formation 16

Do we have examples of extraterrestrial material on Earth?

17

Do we have examples of extraterrestrial material on Earth?

Meteorites!

Murchison (1969, Australia)‏

18

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..

19

Some of the amino acids synthesized in the Miller-Urey experiment and also found in the Murchison meteorite

20

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

21

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)

22

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

23

Why do we care about phosphorus?

24

Without Phosphorous there would be no:

Nucleic acids (DNA,RNA)‏ ...

ATP ...

... or Phospholipids

25

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

26

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

27

However, phosphates might be incorporated into organic molecules under certain conditions!

Fernandez-Garcia et al. (2017) Life 7(3), p.31

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

28

Bottom-Up Approach - Synopsis 2. Subunits of RNA

Phosphates: rock (meteorite?) weathering

Ribose: 5 CH2O + H2O → C5H

10O

5

Bases: 5 HCN + NH3 → Adenine

(formaldehyde from U-M)

(and similar reactions for the other 3 RNA bases)

(hydrogen cyanide from U-M)

29

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

3030

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

3131

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

3232

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

3333

Monolayer

Bilayer Bilayer vesicle

Micelles

Cell Membrane

3434

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)

35

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

36

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

37

Central problem for the origin of life:

Simple organic

moleculesRNA world

Metabolism first?Replication first (RNA world)‏?

+Dilution problem

38

Origin of Life on EARTH: Summary

Bada & Lazcano (Science, 2002)‏ 39

?

Homework #5 available shortly on the web site

Homework

40