http://www.geocities.com/CapeCanaveral/Lab/2948/orgel.html
Leslie E. Orgel
When the earth formed some 4.6 billion years ago,
it was a lifeless, inhospitable place.
A billion years later it was teeming with organisms
resembling blue-green algae.
How did they get there?
How, in short, did life begin?
… in the mid-19th century two important scientific advances
set the stage for modern discussions of the origin of life.
In one advance Louis Pasteur
discredited the concept of spontaneous generation.
He offered proof that even bacteria and other
microorganisms arise from parents resembling themselves.
He thereby highlighted an intriguing question:
How did the first generation of each species come into existence?
http://www.geocities.com/CapeCanaveral/Lab/2948/orgel.html
The second advance, the theory of natural selection,
suggested an answer. According to this proposal, set forth by
Charles Darwin
and
Alfred Russell Wallace,
… individuals bearing traits that provide the best adaptation to the … environment
meet with the greatest reproductive success. …
… some of the differences between individuals in a population are heritable.
In other words, environmental pressures select adaptive traits for perpetuation.
Repeated generation after generation, natural selection
could thus lead to the evolution of complex organisms from simple ones.
The theory therefore implied that
all current life-forms could have evolved from a single, simple progenitor an organism now referred to as life's last common ancestor.
http://www.geocities.com/CapeCanaveral/Lab/2948/orgel.html
Darwin …posited in the final paragraph of The Origin of Species that
"the Creator" originally breathed life "into a few forms or into one."
Then evolution took over: "From so simple a beginning
endless forms most beautiful and most wonderful
have been, and are being evolved."
In private correspondence …
he suggested life could have arisen through chemistry,
"in some warm little pond, with all sorts of ammonia and
phosphoric salts, light, heat, electricity, etc. present."
For much of the 20th century,
origin-of-life research has aimed to flesh out Darwin's private hypothesis to elucidate how, without supernatural intervention, spontaneous interaction of
the relatively simple molecules dissolved in the lakes
or oceans of the prebiotic world could have yielded life's last common ancestor.
… it had to possess genetic information - heritable instructions …
and the means to replicate and carry out those instructions.
Otherwise it would have left no descendants.
Also, … its genetic material had to allow for some random variation in the
heritable characteristics of the offspring so that new traits could be selected …
http://www.geocities.com/CapeCanaveral/Lab/2948/orgel.html
… One can safely infer that
intricate features present in all modern varieties of life
also appeared in that common ancestor. …
… all living things consist of similar organic (carbon-rich) compounds.
… the proteins … are fashioned from one set of 20 standard amino acids. …
… carry their genetic information in nucleic acids - RNA and DNA and use essentially the same genetic code.
This code specifies the amino acid sequences of all the proteins …
… we can infer that our last common ancestor stored genetic information in
nucleic acids that specified the composition of all needed proteins.
… relied on proteins to direct … the reactions required for self-perpetuation.
Hence, the central problem of origin-of-life research can be refined to ask,
By what series of chemical reactions
did this interdependent system of nucleic acids and proteins
come into being?
http://www.geocities.com/CapeCanaveral/Lab/2948/orgel.html
… a paradox.
Nowadays nucleic acids are synthesized only with the help of proteins,
and proteins are synthesized only if their … nucleotide sequence is present.
In the late 1960s Carl R. Woese … Francis Crick … and I … independently …
proposed that RNA might well have come first and established what is now called
the RNA world a world in which RNA catalyzed all the reactions necessary
for a precursor of life's last common ancestor to survive and replicate.
… ribonucleotides in RNA are more readily synthesized
than are the deoxyribonucleotides in DNA.
C&R Fig 26.11
C&R Fig 26.13
Moreover, it was easy to envision ways that DNA could evolve from RNA
and then, being more stable, take over RNA's role as the guardian of heredity.
We suspected that RNA came before proteins … we had difficulty composing any
scenario in which proteins could replicate in the absence of nucleic acids.
{similarities}
{differences}
http://www.geocities.com/CapeCanaveral/Lab/2948/orgel.html
… there is good reason to think the RNA world did exist
and that RNA invented protein synthesis.
If this conclusion is correct,
the main task … explaining how the RNA world came into being.
The answer to this …
requires knowing something about … the prebiotic soup:
the aqueous solution of organic molecules in which life originated.
Fortunately, even before the RNA-world hypothesis was proposed,
investigators had gained useful insights into that chemistry.
By the 1930s
Alexander I. Oparin in Russia and J.B.S. Haldane in England
had pointed out that the organic compounds needed for life
could not have formed on the earth if the atmosphere
was as rich in oxygen (oxidizing) as it is today.
Oparin and Haldane proposed … that the atmosphere of the young earth,
like that of the outer planets, was reducing: it contained very little oxygen
and was rich in hydrogen (H2) … methane (CH4) and ammonia (NH3).
J.B.S. Haldane was approached by a distinguished theologian to ask
what inferences could drawn about the nature of the Creator from the study of His Creation.
Haldane replied with his usual terseness: "That He has an inordinate fondness for beetles.“
- approximately one-fifth of all known species are beetles--350,000 and growing.
http://www.geocities.com/CapeCanaveral/Lab/2948/orgel.html
The Original Origin-of-Life Experiment
In the early 1950s
Stanley L. Miller … did the first experiment
designed to clarify the chemical reactions
that occurred on the primitive earth.
In the flask at the bottom,
he created an "ocean" of water,
which he heated, forcing water vapor to circulate …
The flask at the top contained an "atmosphere"
consisting of methane (CH4), ammonia (NH3),
hydrogen (H2) and the circulating water vapor.
Next he exposed the gases to a continuous
electrical discharge ("lightning"),
causing the gases to interact.
… products … passed through a condenser
and dissolved in the mock ocean.
The experiment yielded many amino acids …
Years after this experiment, a meteorite that struck near Murchison, Australia,
was shown to contain a number of the same amino acids that Miller identified …
Discovery
of fell
amino
acids Australia
from Didwana-Rajod
meteorite
This meteorite, that
near Murchison,
on 28 September 1969, turned
out to contain a variety of organic molecules including
bothand
purines
pyrimidines as well
the aminoof
acids
listed here. The amino acids and their relative proportions were quite similar to
itsandimplication
onasorigin
life.
the products formed in Miller's experiments. The question is: were these molecules simply terrestrial contaminants that got into the
Tewari
et al.
meteorite after
it fell2002.
to earth. J. GEOLOGICAL SOCIETY OF INDIA 60:107-110.
Abstract:
Probably not:
Aromatic
amino
Tyrosine
Tryptophan
•Some of the samples
wereacids
collectedPhenylalanine,
on the same day it fell and
subsequentlyand
handled
with great care to avoid contamination.
have
been
identified
for
the
time
Didwana-Rajod meteorite
•The samples
lacked
certain amino
acids
that first
are found
in allfrom
earthly the
proteins.
which
fell on
(most
probably
from
asteroid
beltcontain
between
Jupiter
•Only L amino
acidsEarth
occur in earthly
proteins,
but the amino
acids
in the meteorite
both D andMars
L formsand
(although
L forms in
were
slightly
more prevalent).
our
Solar
system) in 1991 near Didwana in Nagaur district of Rajasthan.
Margulis & Sagan (1995)
“Of the six kinds of atoms crucial to life on earth
- carbon, nitrogen, oxygen, sulfur and phosphorus - all have been detected in space.
Hydrogen is the most common element in DNA, RNA, proteins, fats
… is also the most common element in the universe.
Ammonia (NH3) was discovered in interstellar space in 1968.
H3C2N, cyanoacetylene, was detected in 1970.
Alcohol (CH3CH2OH) abounds in the constellation Orian.
Other compounds found both in space and in living things include
water, acetylene, formaldehyde, cyanide, methanol, and formic acid. “
{from spectraphotometry}
1999 Kuiper Prize Lecture:
Cometary origin of the biosphere.
Delsemme AH
ICARUS 146: (2) 313-325 AUG 2000
Abstract:
{Not the O2 - Gaia}
Most of the biosphere was brought on the primitive
Earth by an intense bombardment of comets.
This included the atmosphere, the seawater and
those volatile carbon compounds
needed for the emergence of life. …
http://www.mbl.edu/Astrobiology/Teske/Habitat_Diversity.html
http://www.geocities.com/CapeCanaveral/Lab/2948/orgel.html
… recent investigations indicate
the earth's atmosphere was never as reducing as Urey and Miller presumed.
… it seems prudent to consider other mechanisms for the accumulation of
the constituents of proteins and nucleic acids in the prebiotic soup.
For instance,
the amino acids and nitrogen-containing bases
needed for life on the earth might have been delivered
by interstellar dust, meteorites and comets. …
… some of the organic materials required for life …
may have arisen in deep-sea vents,
the submarine fissures in the earth's crust
through which intensely hot gases are cycled.
Initial indications of abiotic formation of hydrocarbons
in the Rainbow ultramafic hydrothermal system,
Mid-Atlantic Ridge.
Holm NG, Charlou JL. 2001.
Earth and Planetary Science Letters 191:1-8.
End of the Leslie E. Orgel essay.
Jeffrey L. Bada and Antonio Lazcano
Science Jun 14 2002:1982-1983.
Ever since the pioneering work of
Aleksandr Oparin and John Haldane
the prebiotic soup theory has dominated thinking
about how life emerged on Earth.
According to the modern version of this theory,
organic compounds accumulated in the primordial oceans
and underwent polymerization, producing increasingly complex macromolecules
that eventually evolved the ability to catalyze their own replication.
The prebiotic soup scenario thus suggests that the first living entities appeared,
and evolved through the RNA world to DNA/protein biochemistry,
when Earth was cool rather than boiling hot.
Because of the reduced luminosity of the young Sun,
Earth may indeed have been completely covered with ice during its early history.
The first self-replicating molecular entities may have developed
under these conditions from the prebiotic organic ingredients.
http://science.nasa.gov/newhome/headlines/ast28may99_1.htm
Apollo 12 Commander Pete Conrad inspects
Surveyor 3's camera assembly on April 20, 1967
The Surveyor 3 spacecraft's microorganisms were recovered
from inside its camera that was brought back to Earth under sterile conditions …
50-100 organisms (common bacteria - Streptococcus mitis),
survived launch, space vacuum, 3 years of radiation exposure,
deep-freeze at an average temperature of only 20 degrees above absolute zero,
and no nutrient, water or energy source.
No other life forms were found in soil samples retrieved by the Apollo missions
or by two Soviet unmanned sampling missions,
although amino acids - not necessarily of biological origin were found in soil retrieved by the Apollo astronauts.
http://science.nasa.gov/newhome/headlines/ast28may99_1.htm
Culture plate from Surveyor 3 camera foam.
The US Communicable Disease Center confirmed it as
Streptococcus mitis a common harmless bacteria
from the nose, mouth and throat in humans.
The Streptococcus genus consists of Gram-positive bacteria which
appear as chains under microscopic observation.
Members of Streptococcus can be aerobic, anaerobic, or microaerophilic.
… the largest group of bacteria isolated from the oral cavity …
almost 50% of the organisms isolated from plaque & gingival sulcus.
…streptococci are part of the normal flora and symbiotically limit
the growth of competing harmful bacteria in the mouth.
… the normal human houses about
a trillion bacteria on the skin,
10 billion in the mouth, and
100 trillion in the gastrointestinal tract.
… far in excess of the number of eukaryotic cells
in … the human host.
… there is more of "them" than "you'' in you.
The normal flora occupy available colonization sites
which makes it more difficult for other microorganisms
(nonindigenous species) to become established.
{note risk of yeast infections after antibacterial antibiotics}
Fig 26-15. Whittaker’s five-kingdom system.
Fig 27-2. The three domains of life.
The five-kingdom system recognized the
two fundamentally different types of cells,
prokaryotic and eukaryotic …
This phylogenetic tree
represents the hypothesis that
the two major prokaryotic groups
diverged very early and that
Archaea is more closely related to
Eukarya than to Bacteria.
http://www.life.uiuc.edu/Micro/woese.html
Carl R. Woese
Professor of Microbiology
B.A. (Math & Physics), Amherst College, 1950
Ph.D. (Biophysics), Yale University, 1953
Postdoc. (Biophysics), Yale University, 1953-1960
Biophysicist, General Electric Research Laboratory, 1960-1963
My evolutionary concerns center on the bacteria and the archea,
whose evolutions cover most of the planet's 4.5-billion-year history.
Using ribosomal RNA sequence as an evolutionary measure,
my laboratory has reconstructed the phylogeny of both groups,
and thereby provided a phylogenetically valid system of classification for prokaryotes.
The discovery of the archaea was in fact a product of these studies.
http://www.bact.wisc.edu/microtextbook/ClassAndPhylo/molPhylogeny.html
http://www.life.uiuc.edu/Micro/woese.html
Carl R. Woese
The archaea are unique organisms.
While prokaryotes in the cytological sense,
they are actually more closely related to eukaryotes than to the bacteria. …
{maybe; it’s not obvious from the table on the preceding slide, & …}
The group contains both the methanogens and numerous organisms that grow at
extremely high temperatures (in some cases above 100° C). As such,
they provide potential insights into mechanisms of thermophilia and methanogenesis.
B. … hot springs in Yellowstone National Park.
http://www.bact.wisc.edu/microtextbook/ClassAndPhylo/molPhylogeny.html
Large areas are covered by a biofilm
of yellow and brown coloured prokaryotes,
including Sulfolobus species.
http://helios.bto.ed.ac.uk/bto/microbes/thermo.htm#crest
Copyright 2001
The Guardian (London)
June 7, 2001
Australian scientists are to vaccinate sheep and cattle against … - flatulence.
More than 635,000 sheep and 410,000 cattle are to be treated
to reduce methanogenic archaea -primitive organisms that colonise their rumens
and help digest one of the most indigestible of substances, grass.
The organisms have only one drawback: methane, or natural gas.
A sheep can belch and fart 19 litres a day …
A cow can burp up to 280 litres a day.
Methane is a strong greenhouse gas - 21 times more potent than carbon dioxide.
An estimated 400m tonnes of methane a year wafts upwards from sheep and cattle
the world over, adding to the inexorable warming of the air.
So the Australians decided to do something. …
… we expect the vaccine will reduce methane emissions by 20% …
http://www.ucmp.berkeley.edu/alllife/threedomains.html
3 Domains
(see Fig 27.2)
Woese's Proposed Classification of Lifeforms
(see C&R Fig 26.1 & 26.16)
http://whyfiles.org/022critters/archaea.html
1998.
The pretty picture we've shown you
turns out to be a simplification of reality.
Now that the complete genomes
of more than a dozen microbes are known,
it seems that Eukarya - the higher organisms may not have sprouted off the Archaea,
as Woese supposed.
Genetic information from organisms
on the three branches of life
seem contradictory at this point.
As Woese said…
"Each picture is different,
so there's tremendous confusion."
The problem could be rooted in the ability
of organisms like bacteria to transfer groups of
genes among themselves, or even to engulf
other organisms and incorporate their genes.
That kind of transfer would make
a tree metaphor, with everything
tracing back to a common ancestor,
less appropriate than
a network metaphor, with myriad connections
between what we've been calling branches
on the tree of life.
Abstract:
The three-domain proposal of Woese ef al. …
divides all living organisms into three primary groups or domains named
Archaea (or archaebacteria), Bacteria (or eubacteria), and Eucarya (or eukaryotes),
with Eucarya being relatives (or descendants) of Archaea.
Although this proposal is currently widely accepted,
sequence features and phylogenies derived from many highly conserved proteins
are inconsistent with it and point to a close and specific relationship
between archaebacteria and gram-positive bacteria,
whereas gram-negative bacteria are indicated to be phylogenetically distinct.
…I propose that the primary division within prokaryotes is between
Monoderm prokaryotes (surrounded by a single membrane) and
Diderm prokaryotes (i.e., all true gram-negative bacteria containing both
an inner cytoplasmic membrane and an outer membrane). …
Protein phylogenies and signature sequences also show that
all eukaryotic cells have received significant gene contributions
from both an archaebacterium and a gram negative eubacterium. …
http://www.science.mcmaster.ca/biochem/faculty/gupta/mol_seq.html
Life's third domain (Archaea): An established fact or an endangered paradigm?
A new proposal for classification of organisms
based on protein sequences and cell structure.
Gupta RS. 1998. Theoretical Population Biology 54:91-104.
(see C&R Table 27.2).
Properties of
Bacteria,
Archaea
&
Eukarya
Nuclear envelope
No
No
Yes
Organelles in membrane
No
No
Yes
Mitochondria/chloroplasts
No
No
Yes
Chromosomes
1 circular
1 circular
>1 linear
Peptidoglycan in cell wall
Yes - some
No
No
Response to penicillins
Inhibited
Not inhibited
Not inhibited
Membrane lipids
Unbranched
Some branched
Unbranched
Initiator amino acid
Formyl-methionine
Methionine
Methionine
Response to linezolid (Zyvox)
Inhibited
Not inhibited
Not inhibited
non-coding Introns
No
Some
Yes
Protein synthesis inhibited
by diphtheria toxin
No
No
Yes
Meiosis and mitosis
No
No
Yes
Ribosome size
70s
70s
80s
Response to streptomycin
Inhibited
Inhibited
Not inhibited
We have been emphasizing the Unity of Life,
but the Diversity of Life is essential to antibiotic strategies.
Biological warfare
http://helios.bto.ed.ac.uk/bto/microbes/penicill.htm#crest
… natural penicillins obtained from culture filtrates of Penicillium spp.
are active only against Gram-positive bacteria
(which have a thick layer of peptidoglycan in the wall)
For a detailed description of the modes of action see:
http://www.ultranet.com/~jkimball/BiologyPages/A/Antibiotics.html#aminoglycosides
Purple bacteria:
photoautotrophic,
use light to
split H2S & CO2
release S2 & carbs
Cyanobacteria:
photoautotrophic
‘bluegreen algae’,
use light to
fix CO2 & N2
Rhizobium:
anaerobic chemoheterotroph,
use plant carbs to
split N2 & release usable nitrogen
see pg 721
Chemoheterotrophs:
ex: gut ‘flora’ - E. coli
eat your lunch & excrete
Gram +
chemoheterotrophs
endospores
ex: anthrax
Gram +
mycoplasmas,
smallest cells; lack cell wall
(not really gram +)
Chlamydias:
obligate intracellular
parasites - STD
can’t make ATP
Gram +
actinomycetes,
branching colonies in soil
ex: Streptomycetes
Spirochetes:
chemoheterotrophs,
syphilis & Lyme disease