Rimicaris shrimp at NW Eifuku (Pacific Rim of Fire)
Shrimp ( Cypridina hilgendorfii ) uses bioluminescent vomit to avoid preda6on
41 st Saas‐Fee course from Planets to Life 3‐9 April 2011 Lecture 5 ‐ Origin of Life and its Early Evolu6on on Earth
Abbreviated history of origin of life ideas: metabolism versus replica6on • Darwin’s warm liKle pond (LeKer to Joseph Hooker, 1 Feb. 1871) • Oparin‐Haldane ‐ Life started in a prebio6c soup • RNA world (Gilbert, 1986) • RNA catalysis preceded and led to metabolism (Eigen, Orgel etc, 1980’s) • Dyson (1985) ‐ ATP produced and consumed by protein‐based organisms led to RNA from accumulated AMP; Kauffman, 1998 broadened Dyson’s idea so as to include other polymers and metabolites (autocataly6c sets) • Metabolic reac6ons catalyzed by pyrites under hydrothermal vent condi6ons (Wächtershäuser, 1988); Experimental evidence provided by Cody and others (2001‐2004); Eschemosser (2006), autocataly6c metabolic systems may be possible.
Outline • BoKom‐up approach to the origin of life – Sources of organic compounds – Chemical reac6ons to make biologically relevant organic compounds • Replicator first – RNA as both the “Chicken and egg” • Metabolism‐first – “sparseness” of organic compounds favor metabolism – Metabolism needed to synthesize RNA
DNA life Genetic code and protein synthesis From Shen & Buick 2005 RNA world Metabolic circuits CO 2 , CO Encapsulation? Organic precursors (multiple sources) Top Down Approaches Bottom Up Approaches (Infer from extant life) a) Settings for the origin of life b) Ancient physiologies (T°C, ± O 2 etc) c) “Ancient” metabolisms (autotrophy vs heterotrophy) d) Ribozymes and the RNA world and models for the origin of the code e) Early replicators: ribozymes, ancient viruses, minerals, etc f) Origin of catalytic proteins
The pathway leading to life (Earth) 1. Forma6on and concentra6on of organic precursor Linked? compounds and organic catalysts 2. Condensa6on and polymeriza6on 3. ??? RNA, protein, protometabolism A living en>ty? 4. ??? The gene6c code, ribosomes etc 5. “Unity of biochemistry”: selec6on of the fiKest genes, biochemistry etc before the separa6on of the three domains of life 6. Transi6on from RNA to DNA 7. The three domains of life The origin of eukaryotes – Loca>on, loca>on, loca>on
BoKom‐up approaches to origin of life studies: Five broad topics 1) Sources or organic precursors to life and chirality selection of d- and l-isomers 2) Synthesis of biopolymers 3) Metabolism versus “replicator” as the first step leading to cells 4) The origin of nucleic acids, the genetic code, and the evolution of the “central dogma” and the first evolving entity 5) Settings for the different steps (still unknown) in the origin of life and how settings can affect the outcomes in 1, 2 and 3
SOURCES OF ORGANIC CARBON ON THE PREBIOTIC EARTH ‐ Includes many of the organic building blocks of life SPACE ATMOSPHERE UV CATALYSIS IDP’S, COMETS, METEORITES, LIGHTNING SHOCK SYNTHESIS PHOTOREDUCTION OF OCEAN CARBON HYDROTHERMAL ORGANIC SYNTHESIS REDUCED INORGANIC SPECIES CRUST Peridotite-hosted hydrothermal vent magma
The Building Blocks – The first experiment Urey, Miller 1953 – from Schopf, 2002 & Smith, Szathmary,1995 From Schopf,2002
Organic Chemistry of Carbonaceous Meteorites COMPOUNDS CM OCCURRENCE BIOLOGY Biochemical Building Blocks Amino acids + Proteins Fatty acids + Glycerol + Membranes Phosphate + Purines + Pyrimidines + Nucleic acids Ribose ‐ + Phosphate Others Alcohols + Aldehydes + Amides + Amines + Carboxylic acids + Hydrocarbons + Ketones + Phosphonic acids + Sulfonic acids + Sulfides +
Synthe6c organic reac6ons poten6ally occurring on the early Earth • Gas phase reac6ons – Reduced gases (H 2 , CH 4 , NH 3 , H 2 ) + energy (heat, electric discharge, UV etc) → Cyanide (HCN) and formaldehyde • Reac6ons producing water‐soluble products – HCN → purines (e.g. adenine) – HCHO → simple sugars (glyceraldehyde, glucose) – HCN + HCHO → amino acids (Strecker synthesis) • Reac6ons producing water insoluble products (hydrocarbon deriva6ve s) – CO, H 2 + heat, iron catalyst → hydrocarbons and amphiphiles (long‐chain faKy acids, alcohols) (Fisher‐Tropsch reac6ons) • Polymeriza6on reac6ons (least undestood) – Amino acids + dry heat → pep6de bonds (protein‐like polymers) – Glyceraldehyde → polyglyceric acid – Purines, pyrimidines, sugar, phosphate → nucleic acids
The BIG gap • We know how to synthesize many of the organic compounds required by life but we know liKle about how to incorporate these compounds into “useful” macromolecules • While it is generally believed that RNA preceded DNA, we don’t know if it can be synthesized under “environmental condi6ons” in contrast to how we synthesize in a laboratory
The two compe6ng models for the origin of life: “Replicator first”, “Metabolism first” Both models involve encapsula6on into small cell like structures usually formed by lipids
Shapiro favors a “metabolism first” model; his model also starts in an organic soup except that organic compounds are incorporated into compartments that have a beKer chance of developing into a network of autocataly6c The Shapiro builds on an idea first discussed by cycles and eventually into an Freeman Dyson (1999) and summarized in one of his informa6on macromolecule. famous quotes: “Life began with liKle bags, the precursors of the cell, enclosing small volumes of dirty water containing miscellaneous garbage.” (From Shapiro, 2007)
The “Replicator first” model predicts that RNA preceded DNA, protein and metabolism The “Central Dogma” (left) and the RNA world (right). The transition from the RNA world to the DNA world is thought to have required “reverse transcription”. There are reverse transcriptase enzymes in some RNA viruses including the AID’s virus (Figure from De Duve, 1995)
The RNA world – a compelling model • RNA ‐ The all purpose molecule – Templates in chemical systems – Informa6on storage and retrieval – Catalysis • Self‐splicing • Self‐reproducing (self‐cleaving) • Pep6de forma6on • RNA combines genotype and phenotype: self‐ replica>on permits Darwinian evolu>on • The goal is to understand how a protein‐free RNA world became established on the primi6ve Earth ‐ led to the “Molecular Biologists Dream”
RNA and DNA The Ribosome: brown is RNA and blue is proteins. The ribosome contains 4 RNA molecules >50 proteins. The ribosome is the site where mRNA’s RNA with its nitrogenase bases to code is translated so as to form specific proteins the llen and DNA with its nitrogenase bases to the right
Some progress on the RNA world RNA molecule that can make copies of RNA from an RNA template Requires an RNA template and RNA primer (like in the PCR reac>on) and a mixture of the 4 nucleo>des. It can make an RNA molecule that is only 14 bases long ‐ more A ribozyme that func6ons as an RNA‐dependent work on this is needed RNA polymerase
Recent research results on the RNA world • Ribose and nucleo>des have been synthesized abio>cally (in some cases under unrealis>c early earth condi>ons) • Polymeriza>on of nucleo>des (oligonucleo>des 20‐50 mers) – Clays (Huang and Ferris 2006) – Eutec6c phase of water‐ice (Monnard et al., 2003) – Lipid‐bilayer lapces (Rajamani et al., 2007) • S>ll needed: – RNA polymerase ribozyme capable of self replica6on – Insight on the emergence of the RNA code (not dependent on the RNA polymerase ribozyme) – The origin and evolu6on of the ribosome – Linking metabolism and replica6on in a “compartment” (the emergence of a “cell”)
The “Molecular Biologists Dream” ‐ a scenario for the origin of the RNA world (from Orgel, no date) The Scenario: First, forma>on of precursors to nucleic acids on Earth or elsewhere and accumula>on on Earth Next, nucleo6des were formed from prebio6c bases, sugars and phosphates and accumulated in some “special” environment. Next, a mineral catalyst such as a mineral like clays then catalyzed the forma>on of long single‐stranded polynucleo>des some of which were converted to complementary double strands by template‐directed synthesis ‐ this resulted in a “library” of double‐stranded RNA on the primi>ve Earth Next, among the double‐stranded RNAs there is at least one that on mel6ng yields a single‐stranded ribozyme capable of copying itself and its complementary RNA ‐ this would eventually lead to an exponen6ally growing popula6on subjected to Darwinian evolu6on
Summary of outstanding problems with the RNA world • Sources (source reac6ons) of the precursors to RNA (nucleo6des, ribose* and phosphate) • Abio6c synthesis of RNA from precursors • The transi6on RNA to self‐replica6ng RNA (RNA catalysis) • The transi6on from a self‐replica6ng RNA to the “gene6c code”, transla6on and transcrip6on • The origin of the ribosome • The transi6on from RNA to DNA * Ribose demonstrated to be synthesized in the presence of boron minerals (Ricardo et al., Science 2004)
Encapsula6on and the emergence of “cell‐ like” structures
( From Deamer 2007)
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