Properties and attributes of selfassembly:

1
Teach Evolution! Learn Science!
Molecular Evolution MB437 and Advances in
Molecular Evolution MB537
From the Big Bang to Bioinformatics From the
primordial soup to Bioethics
Fall, 2008, Tu/Th 11-1215 Lewis Hall 110
Who Professor Marcie McClure
mars_at_parvati.msu.montana.edu 994-7370
Text Fundamentals of Molecular Evolution by Li
and Grauer
2
Universe 16bya
Planets/Sun 4.6bya
Life 3.6-3.9bya
Hadean
Archean
O2
Impact Frustration of life
3
MOLECULAR EVOLUTION MB437 and ADVANCES IN
MOLECULAR EVOLUTION MB537 SYLLABUS Lecture 1
8/28/07 Comments. Organization
Introduction Lecture 2 8/30/07
Evolution the Big Picture Lecture 3 9/4/07
The BIG BANG and formation of the elements
necessary for life. Lecture 4 9/6/07
Biogenesis I The primitive earth and the
prebiotic soup. Lecture 5 9/11/07
Biogenesis II Self-assembly, Energetics and
Bioinformational Molecules. Lecture 6 9/13/07
Biogenesis III Protein or Nucleic Acids first?
RNA or DNA? Lecture 7 9/18/07
open discussion Lecture 8 9/20/07 The RNA
world the three Domains of life and LUCA or
LUCC. Lecture 9 9/25/07 Origin of the
Genetic Code and more on LUCC Lecture 10
9/27/07 Genomes Content and Architecture Lectur
e 11 10/2/07 Mutation nucleotide substitutions
and amino acid replacements. Lecture 12 10/4/07
Methods Analyzing sequences rates/patterns. Lect
ure 13 10/09/07 mid-term I????? Lecture 14
10/11/07 open discussion Lecture 15 10/16/07
Molecular Phylogeny I History, terms,
definitions, and limits. Lecture 16 10/18/07
Molecular Phylogeny II How to determine a
phylogenetic tree. Lecture 17 10/23/07
Molecular Phylogeny III Improvements and
Extensions to Genome Trees. Lecture 18 10/25/07
WHATS NEW? Bayesian and HMM Approaches to
phylogenetic reconstruction. Lecture 19 10/30/07
Deviation from Tree-like behavior horizontal
transmission of information. Lecture 20 11/1/07
mid-term II????? Lecture 21 11/6/07
Convergent Evolution the antifreeze
story. Lecture 22 11/8/07 Evolution of
Viruses. Lecture 23 11/13/07 Retroid
Agents eukaryotic hosts and disease
states. Lecture 24 11/15/07 Do viral RNA
polymerases share ancestry? Lecture 25 11/20/07
Bioethics of the Human Genome Project/
Introduction to Bioinformatics. 11/21-23/07 THA
NKSGIVING HOLIDAY Lecture 26 11/27/07 Lecture
27 11/29/07 Lecture 28 12/4/07 Lecture 29
12/6/07
4
Levels of Evolution
Particulate
Galactic
Stellar
Planetary
Chemical
Biological
5
Necessary and sufficient components for
biogenesis
1) nitrogen, hydrogen, carbon, and a little oxygen
2) reasonable temperature range
3) some energy
4) a marine environment
6
Todays Lecture

• 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

7
(No Transcript)
8
(No Transcript)
9
What occurred to transform a prebiological system
of molecules to for life to begin?
1) Gather precursors
2) Maintain assembly
3) Grow
4) Reproduce
What is such a system called?
A supra-molecular system is an aggregate of
simpler compounds that self-assemble and interact
10
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
11
What is chirality?
12
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.
13
(No Transcript)
14
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.

15
most scientists carrying out research on the
origin of life belong to one of two opposing
camps they are either metabolists or
geneticists.

Leslie Orgel
The Metabolists think that life originated
without the use of a template for replication
and this life was two dimensional in the
beginning. The Geneticists think that an
original template(s) was necessary and That life
began in a prebiotic broth.
16
Features of Protocells
Protocells must have 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
BUT IS THIS ENOUGH TO BE CONSIDERED ALIVE?
A faithful code for replicative fidelity of
information.
Replication of a genetic code
Generation of cellular products according to a
faithful code.
Transcription and Translation
Material continuity that records changes over
time.
EVOLUTION
17
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
18
Models of self-assemblydifferent perspectives
lipid/membrane/protocell David Deamer and
colleagues
metabolic/membrane/protocell Gunter
Wachtershauser W. Martin and M
Russell Y. Koga
nucleic acid/proteins 3 different views Nielson
and Miller Eschenmoser Du Duve
19
Central Question in Origins of Life Research.
How were the initial microenvironments
established?
What do we all already know?

• Modern fluid lipid bilayers are a permeable
  barrier,
• interrupted by various transmembrane proteins
  that confer different fcns.
• 2) it is plausible to thin k that some type of
  primitive bilayer existed to
• bound the first microenvironments

20
(No Transcript)
21
David Deamer and colleagues are responsible for
some of the earliest and most consistent work
on membrane biogenesis
22
FROM the Murchison Meteorite
Self -assembly of pure nonanoic acid
23
(No Transcript)
24
(No Transcript)
25
(No Transcript)
26
(No Transcript)