Properties and attributes of selfassembly:

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MOLECULAR EVOLUTION MB437 and ADVANCES IN
MOLECULAR EVOLUTION MB537 Marcie McClure, Ph.D.
,mars_at_parvati.msu.montana.edu, 994-7370 Fall,
2006, Tu/Th 1100-1215 Cooley-B2 Lecture 1
8/29/06 Organization Introduction What is
molecular evolution? Lecture 2 8/31/06
The BIG BANG and formation of the elements
necessary for life. Lecture 3 9/5/06
Biogenesis I The primitive earth and the
prebiotic soup. Lecture 4 9/7/06
Biogenesis II Self-assembly, Energetics
and Bioinformational Molecules. Lecture 5
9/12/06 Biogenesis III Protein
or Nucleic Acids first? RNA or DNA? Lecture 6
9/14/06 The RNA world the
three Domains of life and LUCA. Lecture 7
9/19/06 Origin of the Genetic Code and more
on LUCA Lecture 8 9/21/06
Genomes Content and Architecture. Lecture 9
9/26/06 Mutation nucleotide
substitutions and amino acid replacements. Lecture
10 9/28/06 Methods Analyzing sequences
rates/patterns. Lecture 11 10/3/06
open discussion Lecture 12 10/5/06
Molecular Phylogeny I History, terms,
definitions, and limits. Lecture 13 10/10/06.
Molecular Phylogeny II How to determine a
phylogenetic tree. Lecture 14 10/12/06
Molecular Phylogeny III Improvements and
Extensions to Genome Trees. Lecture 15 10/17/06
NEW? Bayesian and HMM Approaches to
plylogenetic reconstruction Lecture 16 10/19/06
Deviation from Tree-like behavior
horizontal transmission of information Lecture 17
10/24/06 open discussion Lecture 18
10/26/06 Convergent Evolution the
antifreeze story. Lecture 19 10/31/06
Evolution of Viruses Lecture 20 11/2/06
Retroid Agents eukaryotic hosts and disease
states. Lecture 21 11/7/06 UNIVERSITY HOLIDAY
Lecture 22 11/9/06 Bioethics of the
Human Genome Project/ Introduction to
Bioinformatics. Lecture 23 11/14/06
Examples of in silico research I the RNA
polymerase story. Lecture 24 11/16/06
Examples of in silico research II the Genome
Parsing Suite finds Retroid Agents. Lecture 25
11/21/06 Protein Disorder predictions
Measles the elegance of in silico and wet
experiments 11/22-24/06 THANKSGIVING
HOLIDAY Lecture 26 11/28/06 Lecture 27
12/30/06 Lecture 28 12/5/06 Lecture 29
12/7/06
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The Next Three Lectures Will Cover

• 1) Speculation and research on the origin of
  life.
• Structure of the arguments
• There are two approaches to the study of the
  origin of life
• From small to large--chemical approach
• From the complex to simple--biological approach
• Geological approach--most recent data
• We will cover five stages
• The early earth environment
• Prebiotic chemistry
• Energetics
• Self-assembly processes
• Bioinformational molecules

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Properties and attributes of self-assembly

• Hydrogen bonds as participants in self-assembly
• assemble small clusters of molecules
• in complementary of double-stranded nucleic acids
• in protein the alpha helix and beta pleated
  sheets

2) Chirality as a product of self-assembly, all
life forms exhibit chirality or handedness
3) Non-polar forces stabilize supramolecular
assembly phase separation
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What is chirality?
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Three Possible Ways Chirality Arose
1) In 1957, Wald suggested that the prebiotic
atmosphere was such that the UV polarized
component of sunlight degraded D-amino acid
isomers, leaving a concentrated solution of L
isomers.
2) An alternative explanation of Walds was that
minerals could have had a chiral nature, thereby
selecting one form over the other.
3) In 1984, Joyce demonstrated chiral selectivity
using RNA templates and activated monomers. It
is more likely that the chiral selectivity
occurred as a function of the self-assembly
processes. System activated guanosine
mononucleotides self-assemble on poly-C RNA
templates monomers polymerize to oligos. Assay
addition of racemeric mixture of L and D
guanosine substantially inhibited
polymerization. Control the correct isomeric
form D-guanosine produced polymers up to 20
nucleotides long. Suggestion a prebiotic system
could have existed in which optical specificity
was very high, such a system would gave a big
advantage.
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Lisa Kirks View

• Variation in the earths magnetic field does
  occur but there is no data going back
• to the Hadean period. This field is thought to be
  generated by differential thermal
• convection in the earths inner and outer cores.
  Such changes probably have occurred
• many times the early accretion process and
  formation of the planet.
• 2) The earths magnetic field does under go
  reversal. When this happens data suggest
• that the intensity of the filed drops
  significantly.
• 3) Under these conditions the earth would no
  longer be shield from
• solar and cosmic radiation.
• Therefore, it may be that during these time
  periods of geomagnetic
• reversal that isomer selection occurred, rather
  that positing an
• extraterrestrial origin of molecules of one
  chirality or another.

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Models of self-assembly. Three different
perspectives.
lipid/membrane/protocell David Deamer and
colleagues
metabolic Gunter
Wachtershauser
nucleic acid/proteins 3 different views Nielson
and Miller Eschenmoser Du Duve
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Features of Protocells
Protocells are postulated to have contained a
minimal set of basic cellular functions 1)
energy and nutrient capture from environment 2)
growth via catalysis of components 3)
replication of storage molecules Summary of
necessary events for self-assembly of
protocells 1) self-assembly of lipid-like
compounds into membranous structures,
forming enclosed microenvironments 2) ability of
said structures to make energy (e.g., ion
gradients) and perform inward transport of
nutrients 3) aggregation, breakage and resealing
allows the possibility of growth and
division 4) inclusion of catalytic polymers and
genetic storage systems
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Retroid Agents
Retroviruses, retrotransposons,
pararetroviruses, retroposons, retroplasmids,
retrointrons, and retrons
reverse transcriptase mediated replication or
transposition
RNA viruses e.g., Ebola, rabies, influenza, polio
All cellular systems most DNA Viruses
RNA
DNA
transcription
Replication by DNA-dependent DNA polymerase
Replication by RNA-dependent RNA Polymerase
translation
snRNAs, ribozymes, tRNA, rRNA
PROTEIN SYNTHESIS
McClure, 2000
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Possible Ways Bioinformational Molecules Arose

• Early functional proteins replicated directly.
  They invented nucleic acids and were ultimately
  enslaved by them.
• Early nucleic acids or related molecules
  replicated directly. They invented protein
  synthesis. Uncoded polypeptides may or may not
  have been involved in the earliest precoding
  replication mechanism.
• Nucleic acid replication and genetic code of
  proteins coevolved.
• The first form of life on earth was based on some
  inorganic or organic system unrelated to proteins
  or nucleic acids.