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The Transition to

? Chemical Evolution Biological Evolution The Transition to Life

Interacting Chemicals Reproduction of Natural Selection

Based on Simplest Life Now: Update: Mimivirus

Need: • A very large was discovered in 2003 1. Nucleic Acids Replicable Information • Both RNA and DNA 2. Enzymes (Catalysts) • More DNA than some (> 1000 ) 3. Lipids Membranes (Enclosure) • Genes for , DNA repair enzymes 4. Carbohydrates Energy Storage • Leading to reevaluation of (Pigments) (Energy Conversion) • May be ancient lineages – Precursors to bacteria, or – Controversial Too much to ask of chemical evolution ⇒ Protolife?

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Protolife Image of Mimivirus 1. “Virus” Free living but equivalent in complexity + + Supply by Environment

Genetic Code

2. Protein Protolife Protein Self Replication?

3. Nucleic Acid Protolife RNA Self Catalysis?

4. Something Else Protein-Based Protolife Minerals 1. Proteinoid microspheres - Sidney Fox Amino Acids + Dry Heat Proteinoids Clay Layers (Hot Tidepool?) H2O (Tide) Mineral - Molecule Microspheres Pyrite Protolife? Bacteria Thioesters Can Add Proteinoid Grow Split Divide “Reproduce” Bud Bud Genetic Takeover Form Chains Form chains

? RNA DNA But “Reproduction” not exact Later incorporate Nucleic Acids Proteinoid Cells Genes

Problem: How to incorporate Nucleic acids?

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Nucleic Acid Based Protolife Picture of Proteinoid Microspheres RNA Genes Protein Cells Self-replicating RNA molecules Experiment by Sol Spiegelman

RNA from Qβ Virus - parasite on bacteria Injects RNA - Bacterium makes replicase Enzyme to Replicate RNA RNA multiplies, using activated nucleotides in bacterium to copy RNA and make new viruses

In Test Tube: Template RNA, Replicase, Manfred Eigen - further experiments with RNA Activated Nucleotides (ATP, CTP, GTP, UTP) in test tube: Mutant RNA strands compete ⇒ RNA copied without machinery of Degrade to smallest (~ 200 nucleotides) RNA that replicase could recognize Variation: No template RNA (Monster - Selfish RNA)

Replicase made RNA from nucleotides RNA can do self-catalysis in some cases Could this have led to self replication? Protein

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Eigen scenario 4. Complex interactions (hypercycles) 1. A replicating RNA molecule forms by chance (random replicator - not a ) 6. Use lipids to make protocells (catalyst, made of RNA) 6. Competition leads to biological evolution 2. Family of similar RNAʼs develops (quasispecies)

3. Connection to proteins (quasispecies specialize to make parts of protein)

Problems with Nucleic Acid First Scenario 1. Hard to get monomers 2. Unlikely to link correctly 3. Need existing proteins and lipids 4. Hypercycles subject to instabilities N = size of molecular population If N small If N large

Population Collapse Selfish RNA Short Circuit

A B

If B D Short Circuit D C ⇒ Only narrow range of sizes works

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The Origin of the Genetic Code

• We need more than either protein or RNA protolife • Need interaction via genetic code • Need translation • Letʼs recall what is needed for translation…

Shapiroʼs Fable The case for the “chicken” Protein first ⇒ replication problem “interpreters” aminoacyl tRNA synthetases tRNA Match tRNA & Amino acids Could an earlier version have copied proteins directly?

Proto-interpreter

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1. Early Evolution: Start with 4-6 4. Begin to copy RNA(Full Qβ replicase) types, gradually add more Natural selection leads to better ribosome enzymes increase in size and catalytic power

2. First use of phosphate as energy? (ATP) 5. Specialized, Short RNA aided attachment of or sugar-phosphate chains for construction amino acids to proteins; became tRNA (Teichoic acids in membranes of some bacteria) 6. Then mRNA - to align tRNAʼs (partial Qβ replicase) now a separate genetic system that evolves 3. Bases added for structure Support for protein synthesis ribosome 7. DNA developed from RNA

Support for the “chicken” Shapiro dates last step to prokaryote - split (different ways of storing DNA info) 1. 1988 discovery that interpreter does not use tRNA codon to recognize correct tRNA Tests: (in some cases) ~ 1/2 1. Synthesize in lab? Not possible yet. - instead a single base pair at the other end of tRNA simpler, older code 3. Molecular archaeology - vestigial ability of ⇒ second genetic code interpreters to recognize amino acids in proteins ⇒ connection of interpreter and tRNA more primitive than current code 3. Survivors of protein era? ?

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2. Dyson modeling of molecular “populations”

Transition from disorder to order (non-life) (life)

Finds number of monomer types likely to be 9 - 11 (ok if used ~ 1/2 of modern proteins) But nucleotides (only 4) - not enough

Favors protein first

The Egg Strikes Back Translation Other work shows some RNA can catalyze Non-RNA reactions

1. RNA in ribosome appears to be what catalyzes bond formation Noller, et al. 1992, Science, 256, 1416

2. RNA “ribozyme” catalyzes reactions between amino acids and tRNAs First “interpreter” may have been RNA Piccirilli, et al. 1992, Science, 256, 1420

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Origin of the Genetic Code For mRNA Genetic Code First Third RNA RNA Crucial step in any theory Base U C A G BASE

Phenylalanine Serine Tyrosine Cysteine U Phenylalanine Serine Tyrosine Cysteine C Allows communication U Leucine Serine Stop Stop A Leucine Serine Stop Tryptophan G Nucleic Acids Proteins Leucine Proline Histidine Arginine U Leucine Proline Histidine Arginine C C Leucine Proline Glutamine Arginine A Leucine Proline Glutamine Arginine G Early versions probably coded fewer amino Isoleucine Threonine Asparagine Serine U Isoleucine Threonine Asparagine Serine C acids - less specific A Isoleucine Threonine Lysine Arginine A Start/Methionine Threonine Lysine Arginine G Valine Alanine Aspartic Acid Glycine U Valine Alanine Aspartic Acid Glycine C G Valine Alanine Glutamic Acid Glycine A Valine Alanine Glutamic Acid Glycine G

Amino Acids

Purine Either Evolution of Genetic Code Some evidence for RNY and G - C more stable Gaining specificity Pyrimidine

⇒ 4 codons GGC glycine Common in If early tRNAs carried more than 1 kind of GCC alanine Miller-Urey amino acid GAC aspartic acid and Meteorites e.g. Glycine or alanine Glycine GUC valine tRNA Mutation

Others added later CGG CCG GCC GGC mRNA mRNA

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Evidence that code has evolved Freeland, et al. Tested 106 other codes Summary

Only one better at minimizing bad effects of • Transition to life is poorly understood mutations • Need to consider “protolife” ⇒ Natural Selection • Can we get by with only one polymer? – If so, protein or RNA Still Evolving – If so, how do we get genetic code going? Some organisms have slightly different codes in mitochondria or in nucleus

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