TuTh

1
Fall 2009 MB437/537 3credits Molecular
EvolutionADVANCES IN Molecular Evolution
What ARE THE latest theories on the Origins of
life? What are genome Sequencing
projects Teaching us about evolutionary
Complexity? What are the Bioethical implications
of Your Future Research?
LUCA
From the Big Bang to Bioinformatics and Beyond

• Tu/Th
• 1100 AM - 1215 PM
• LEWIS HALL 110

Teach Evolution! Learn Science!
Professor Marcie McClure marsmcclure_at_gmail.com
2
MOLECULAR EVOLUTION MB437
ADVANCES IN MOLECULAR EVOLUTION
MB537   SYLLABUS   Lecture 1 9/1/09
Comments. Organization Introduction Lecture 2
9/3/09 Evolution the Big Picture Lecture
3 9/8/09 The BIG BANG and formation of the
elements necessary for life. Lecture 4
9/10/09 Biogenesis I The primitive earth and
the prebiotic soup. Lecture 5 9/15/09
Biogenesis II Self-assembly, Energetics and the
Protocell. Lecture 6 917/09 Biogenesis III
More on protocelluar formation. Lecture 7
9/22/09 Biogenesis IV Protein or Nucleic Acids
first? RNA or DNA? Lecture 8 9/24/09
The RNA world the three Domains of life and
LUCA or LUCC. Lecture 9
9/29/09 Origin of the Genetic Code and more
on LUCC Lecture 10 10/01/09 Last Day of LUCA
Genomes Content and Architecture
Chap 8 Lecture 11 10/6/09 open
discussion Lecture 12 10/8/09 Mutation
nucleotide substitutions and amino acid
replacements. Chap 1 3 Lecture 13
10/13/09 Methods Analyzing sequences
rates/patterns. Chap 1,
3-4 Lecture 14 10/15/09 Molecular Phylogeny I
History, terms, definitions, and limits.
Chap 5 Lecture 15 10/20/09 Molecular
Phylogeny II How to determine a phylogenetic
tree. Lecture 16 10/22/09 Molecular
Phylogeny III Improvements and Extensions to
Genome Trees. Lecture 17 10/27/09 WHATS NEW?
Bayesian and HMM Approaches to phylogenetic
reconstruction. Lecture 18 10/29/09 Deviation
from Tree-like behavior horizontal transmission
of information. Lecture 19 11/3/09
EXAM Lecture 20 11/5/09 Convergent Evolution
the antifreeze story. Lecture 21
11/10/09 Evolution of Viruses. Lecture 22
11/12/09 Retroid Agents eukaryotic hosts
and disease states. Lecture 23 11/17/09 Do
viral RNA polymerases share ancestry? Lecture 24
11/19/09 Bioethics of the Human Genome Project/
Introduction to Bioinformatics. Lecture 25
11/24/09 open discussion 11/25-27/09 THANKSGIV
ING HOLIDAY Lecture 26 12/1/09 Lecture 27
12/3/09 Lecture 28 12/8/09 Lecture 29
12/9/09
BIG BANG PRIMORDIAL SOUP LUCA BASIC
MOLECULAR EVOLUTION ANALYSIS SPECIAL
TOPICS BIOETHICS
3
We learned that two types of energy are required
at four different levels for biogenesis.
We learned a supra-molecular system is an
aggregate of simpler compounds that have
self-assembled on its way to a living system.
We dont know how the chiral forms were selected
but life on earth uses only
L-amino acids
D-carbohydrates
D-nucleotides
concentrate
synthesize
We learned that proto cells must
grow/decay
external energy
internal energy
Dave Deamer and colleagues
4
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.
5
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
6
(No Transcript)
7
First Life The Surface Metabolists
Original theory, 1988 by Günter Wächtershäuser
The Iron-Sulfur World
8
Features of the Early Organisms, Known as
Autotrophic Surface Metabolists
Acellular, lack a mechanism for division, yet
they grow. Possess no enzymes, yet they
metabolize (autocatalytically). Have no nucleic
acids (or any other template), yet they have
inheritance and selection.
9
Growth w/o division?

• Not cellular.
• Surface metabolists.
• Thus, growth occurs by spreading to vacant
  surfaces.

10
Autocatalytic Metabolism

• Hydrogen sulfide and ferrous ions
• Reduction for CO2 and CO. Here is the reaction
• FeS H2S(aq) CO2(aq) ? FeS2 H2O HCOOH
  ?G0 -12 kJ mol-1
• This reaction is driven in part by the
  insolubility of the pyrite product.
• Thus pyrite formation reduces CO2 and at the same
  time provides new surfaces for growth.

11
Evolution w/o Templates

• Reproduce by reproducing autocatalytic
  coenzymes as they spread to new surfaces.
• They evolve by the environmentally induced
  ignition of new autocatalytic cycles.
• Higher complexity arises from surface metabolism.

12
Basically

• Surface metabolism favors the formation of large
  molecular structures from less highly activated
  functional groups.
• Persisting surface metabolisms display continual
  turnover. New constituents come in and old ones
  go out. This constitutes a self-sorting process
  that functions as negative selection.
• Question How is it selective?

13
Negative Surface Selection

• Detachment
• Weak bonds vs. strong bonds
• Larger polyanionic structures are favored

14
membrane phospholipids
Archaea
isoprenoid ethers
sn-glycerol-1-phosphate (G1P)
G1PDH
Eubacterial and Eukaryal
fatty acid esters
sn-glycerol-3-phosphate (G3P)
G3PDH
15
What about Membrane Formation

• Isopreniod lipids
• 1) Formation is nearly universal mechanism.
• isopentenyl pyrophosphate --? isoprene
• 2) Major constituent of archaeal membranes.
• 3) Many the -P2O6-3 moieties tend to be
• surface bonding

16
Hypothetical

• Shown at left is a hypothetical surface mechanism
  that yields PMP.

17
These lipids got bigger And accumulated
18
Formation on a Surface

• a bilayer membrane with a greater thick-ness in
  the lipophilic zone arises.

?FLUID
?CRYSTAL
19
This is the first instance of individuation.

• Hydrophilic domains are holes in the surface
  membrane.
• Put a lid on it!
• Thus, semicellular structures are born.

20
The Third Stage Cells

• Finally, through other processes and further
  evolution, true cellular structures emerge,
  leaving forever their pyrite birthplace.

21
Cellular EvolutionThe Iron Swiss Cheese Model

• Martin W. and Russell M.

22
Iron Sulfide Deposits

• Formed when superheated water rushes up through
  the earths crust and becomes infused with
  hydrogen, sulfur, and iron.
• Honeycomb structure of holes a few hundredths of
  a millimeter across.

Russell Hall 1997, Geol. Soc. London 154, 377
23
Iron Sulfide Compartments

• Acted as semi-permeable cell walls
• Allowed hydrothermal fluids rich in hydrogen,
  cyanide, sulfides, and carbon monoxide to enter
• Prevented chemicals from diffusing away into the
  ocean
• Created a closed environment for chemical
  reactions to take place

24
Membrane Formation

• Biological processes produced and deposited fatty
  molecules along the inner surfaces of the iron
  sulfide cavities
• Eventually, these fats formed into cohesive
  membranes that fully enclosed the biological
  activity inside
• Once a lipid membrane formed, cells became
  free-living and floated out into the ocean

25

• The cells that survived were the ones who
  developed the proteins associated with redox
  chemistry, allowing them to feed on inorganic
  chemicals for energy
• Cells developed the precursors to RNA and DNA and
  could replicate themselves
• Within the confines differentiation of lineages
  was possible

26
(No Transcript)
27

• Explains why cells have the same genetic code,
  and genetic material.

• Why bacteria and archaea differ.
• Branches of bacteria and archaea split within
  compartments.
• Bacteria made one kind of lipid membrane, archaea
  another.

Russell, M. 1996Ore Geol. Rev.10, 199-214.
28
Martin and Russell, 2003, Trans. Roy. Soc.
London, 358B, 27-85 (Fig. 5)
29
Carbon and Hydrogen Rich gases Combine in FeS
Acetic acid forms and CO is added
Amino acids form and link into proteins
Pyruvic acid forms and combines with ammonia
Formaldehyde forms sugars and Cyanide forms bases
Genetic precursors to RNA and DNA could arise
30
Temperature Concern

• Pyruvic acid is extremely heat sensitive
• Amino acids, RNA, etc also break down in high
  temps
• Vent temperatures typically range between
  70-350C

31
(No Transcript)