Chapter 5 HISTORY OF LIFE ON EARTH
Summary of Chapter 5: EVOLUTION, D. Futuyma, 2nd Ed., 2009.
When studying this chapter keep in mind the following important patterns:
- Climates and the distribution of oceans and continents have changed over time.
- New forms of organisms have appeared and others have become extinct.
- Extinction rates have been particularly high sometimes; these are called mass extinctions.
- Especially after mass extinctions, the diversification of higher taxa has sometimes been relatively rapid.
- The diversification of higher taxa has included increases both in the number species and in the variety of their form and ecological habits.
- Extinct taxa have sometimes been replaced by unrelated ecologically similar taxa.
- The ancestral members of related higher taxa are often morphologically more similar to one another, and more ecologically generalized, than their descendants.
- Of the variety of forms in a higher taxon that were present in the remote past, usually only a few have persisted in the long term.
- The geographic distributions of many taxa have changed greatly.
- Over time, the composition of the biota resembles that of the present.
BEFORE LIFE BEGAN – some paragraphs of this section are repeated from chapter 4
The origin of the universe is shrouded in mystery.
· Science does not have the answer at present time to explain or describe how the first space and matter arose.
· Laws of nature describe the behavior of matter. Where do these laws come from?
Big Bang Theory (hypothesis?).
· The universe was a very concentrated mass of matter/energy on a very distant past.
· This mass exploded ("big bang") and hydrogen was formed.
· Hydrogen formed new elements, stars and galaxies.
· Galaxies are moving away from each other, expanding.
· The Big Bang assumes that energy, space and time already existed. The Big Bang makes no reference to where they came from.
· The Big Bang may have occurred about 14 billion years ago.
Condensation or nebular theory
· Fragmentation of an interstellar cloud forming a nebula.
· Contraction and flattening of the nebula.
· Condensation of the nebular material into protoplanets and meteorites.
· Solidification of planets and formation of our solar system about 4.6 billion years ago.
· The large condensing mass at the center became the sun.
· During condensation, elements scattered according to a density gradient with the heavy masses forming the planets near the sun and the lighter masses forming the outer planets.
· HYPERLINK "http://geol.queensu.ca/museum/index.php?option=com_content&view=article&id=50&Itemid=57" http://geol.queensu.ca/museum/index.php?option=com_content&view=article&id=50&Itemid=57
Earth Chronology, an approximation:
4.6 BY (Billion Years ago) Solar system and the earth formed
4.5 BY the earth cooled and water condensed; formation of oceans
4.06 BY there were masses of dry land; formation of oldest KNOWN rocks known.
4 - 3.8 BY life originated; small protocontinents
3.5 BY oldest known fossils; first bacterium found in Australia.
2.5 BY photosynthesis, oxygen accumulated
1.5 BY first eukaryotes
700 MY soft-bodies multicellular life
540 MY hard-bodied multicellular life; beginning of the Phanerozoic eon; many modern phyla
appeared.
Interesting site: HYPERLINK "http://www.julesberman.info/chronos.htm" http://www.julesberman.info/chronos.htm
HYPERLINK "http://anthro.palomar.edu/earlyprimates/early_1.htm" http://anthro.palomar.edu/earlyprimates/early_1.htm
HYPERLINK "http://pubs.usgs.gov/gip/geotime/contents.html" http://pubs.usgs.gov/gip/geotime/contents.html
THE EMERGENCE OF LIFE
Many scientist consider life as a group of molecules that can capture energy from the environment, use that energy to replicate itself, and therefore, capable of evolving.
Living and semi-living things might have originated more than once, we can be quite sure that all organisms we know of stem from a single common ancestor because they all share certain features that are arbitrary as far as we can tell.
Some shared features of living organisms:
· All use L optical isomers of amino acids
· The genetic code
· Same method of replication
· Same method of protein synthesis
· Same basic metabolic reactions
SOLAR SYSTEM PREREQUISITES FOR THE ORIGIN OF LIFE.
NOTE: most of the information in this section is not found in your textbook.
Our planet possessed the essential prerequisites for the development of life.
- A moderate size sun that provided a steady rate of emitted radiation over a long period of time to allow the development of life.
- A variety of elements available to form organic molecules (H, O, N, C, S, P, Ca), and the ability of carbon to form four covalent bonds and different kinds of large, stable, three-dimensional molecules.
- The orbit of the earth is nearly circular thus maintaining a uniform distance from the sun and temperature extremes are eliminated.
- Large amounts of water present on the surface of the earth. Water is an excellent solvent that enables acids, bases and salts to ionize and react. It remains liquid over a wide range of temperatures. Its solid phase floats on the liquid phase.
- Large amount of hydrogen compounds that allowed protons to be donated to carbon.
· There was molecular preadaptation for the biochemical processes leading to the formation of biomolecules.
· Oparin and Haldane (1920s) independently proposed that the primitive atmosphere of the Earth was reducing and that organic compounds formed in such an atmosphere might be similar to those presently used by living organisms.
- The early atmosphere contained very little oxygen and was rich in hydrogen (H2) and compounds that can donate hydrogen atoms to other substances: a reducing atmosphere.
Oparin's and Haldane's ideas inspired the famous Miller-Urey experiment, which in 1953 began the era of experimental prebiotic chemistry.
There are serious doubts at present that the original atmosphere of the Earth was reducing. Rocks from the Archaean contain ferrous and ferric oxides, and sulfates, all of which contain oxygen.
THE MILLER EXPERIMENT
Harold C. Urey of the University of Chicago and Stanley L. Miller, a graduate student in Urey's laboratory, wondered about the kinds of reactions that occurred when the earth was still enveloped in a reducing atmosphere.
In 1953, Stanley Miller demonstrated that amino acids and other organic compounds could be synthesized spontaneously from hydrogen gas, ammonia, methane and other compounds presumed to have been present in the second atmosphere of the Earth if energy is provided.
Miller found that as much as 10 percent of the carbon in the system was converted to a relatively small number of identifiable organic compounds, and up to 2 percent of the carbon went to making amino acids of the kinds that serve as constituents of proteins.
Variants of Miller’s experiment are many. The results have been similar to Miller’s, a large number of organic molecules, some found in living organisms and others not.
In reproducing Miller’s experiment or its variants, it is important to keep O2 out of the reaction. Aldehydes and cyanides are first products, and then more complex organic compounds are synthesized.
Glycine was the most abundant amino acid, resulting from the combination of formaldehyde (CH2O), ammonia and hydrogen cyanide. A surprising number of the standard 20 amino acids were also made in lesser amounts.
A variety of organic compounds are produced when a heated mixture of carbon monoxide and hydrogen is passed over a catalyst. Adding ammonia produces purine and pyrimidine nucleotide bases that the Miller reactions do not produce.
Simple organic molecules have been found in carbonaceous meteorites called chondrites.
· The Murchison meteorite that fell in Australia in 1963 contained 80 kg of carbonaceous material and 1% of this material is organic carbon.
· The interior portion of this meteorite contains fatty acids up to eight carbons long.
· Practically all the amino acids found in the meteorite, protein and non-protein, are similar to the amino acids produced by sparking mixtures in laboratory experiments.
Since then, workers have subjected many different mixtures of simple gases to various energy sources. The results of these experiments can be summarized neatly:
· Under sufficiently reducing conditions, amino acids form easily.
· Conversely, under oxidizing conditions, they do not arise at all or do so only in small amounts.
Requirements for polymerization:
· Adequate concentration of monomers.
· Dehydration
· Protection against decomposition due to external factors.
Most polymerization involves the removal of water (dehydration) from the condensing molecules.
Condensing agents are molecules that help condensation (e.g. formation of a peptide bond) by removing water from the reactants (e.g. two amino acids) and releasing energy during the hydration of the condensing agent. The result is a dipeptide and a new organic molecule derived from the hydration of the condensing agent.
· Cyanide compounds have been identified as condensing agents.
e. g. cyanamide (CN2H2), cyanogen (C2H2), cyanic acid (HCN), cyanoacetylene (C2N2H).
· Condensing agents provide the energy for the formation of dipeptides and other dimers.
e. g. formation of dipeptide bond can couple to the hydrolysis of cyanamide.
· Condensing agents accept water resulting from the condensing molecules: dehydration process.
Cyanogen and cyanamide can cause nucleotides to form by the phosphorylation of adenosine, uridine, and cytosine.
Oró had found that heating a mixture of hydrogen cyanide and ammonia in an aqueous solution could yield adenine.
Later studies established that the remaining nucleic acid bases could be obtained from reactions among hydrogen cyanide and two other compounds that would have formed in a reducing prebiotic atmosphere: cyanogen (C2N2) and cyanoacetylene (HC3N).
· The heating of aqueous solutions of ammonium cyanide produces adenine.
· Cyanoacetylene reacts with cyanates (e.g. urea) to produce the pyrimidine cytosine.
· Several researchers have proposed mechanisms for the formation of thymine and uracil from simpler cyanic molecules.
The phosphorylation of adenosine, uridine and cytosine can be accomplished in the presence of cyanogen and cyanamides. The product is adenosine monophosphate or AMP.
Thermal energy was probably the energy originally used by the early protocells.
Heat is unreliable and varied from place to place.
Chemical energy providers allowed a constant and regulated source of energy to be used in controlled and localized reactions.
Organic catalysts had to evolve to restrict reactions to the right time and place.
The cell developed a system that would provide energy in a controlled fashion when it is needed.
Proteins add speed to the process of catalysis.
THE RNA WORLD
"RNA came first. DNA and proteins came after."
In the late 1967 Carl R. Woese of the University of Illinois, Francis Crick, then at the Medical Research Council in England, and Leslie Orgel then working at the Salk Institute for Biological Studies in San Diego independently suggested a way out of this difficulty.
They 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.
In 1983 Thomas R. Cech of the University of Colorado at Boulder and, independently, Sidney Altman of Yale University discovered the first known ribozymes, enzymes made of RNA.
Ribozymes are RNA fragments that posses catalytic properties.
Ribozymes can cut, splice and elongate other oligonucleotides.
"One can contemplate an RNA world, containing only RNA molecules that serve to catalyze the synthesis of themselves" (W. Gilbert, Nature, 319:618, 1986).
Recent experiments have shown that clay particles with RNA adsorbed onto their surface can catalyze the formation of lipid envelope, which in turn can catalyze the polymerization of amino acids into polypeptides.
Some macromolecules may have evolved that catalyzed the replication of each other.
Some scientists think that within the RNA world evolution existed because replication and natural selection of molecules can occur.
Long RNA sequences would not replicate effectively because the mutation rate would be too high for them to maintain any identity.
Replication was not exact.
Some oligonucleotides could replicate themselves.
The first “genes” need not have had any particular base pair sequence.
·
Before proteins arose there were only genotypes without any particular base sequence.
Now a big jump...assuming the existence of some kind of template and polymerizing enzyme…
An RNA ribozyme binds to a cofactor made of an amino acid and short oligonucleotides, which have been joined by another ribozyme that joins specific oligonucleotides to amino acids according to a primitive code.
Amino acid and short nucleotide formed a cofactor, with the help of a ribozyme.
· Amino acid + cofactor + oligonucleotide help by a ribozyme in self replication
· The template could have a cofactor-ribozyme complex (Fig 5.2).
Many contemporary coenzymes have nucleotide components.
Selection could have led to the development of…
· The oligonucleotide component of the cofactor evolved into the transfer RNA
· The ribozyme evolved into the ribosome.
· The string of AA became a catalytic protein, en enzyme.
PRECAMBRIAN LIFE
PROKARYOTES
The Archaean, before 2.5 billion years ago, and the Proterozoic, 2.5 BYA to 542 MYA, are together referred as the Precambrian time.
Bacteria-like microfossils and stromatolites date back to 3.5 BYA
These organisms are thought to have been anaerobic.
The early atmosphere is thought to have little oxygen.
When photosynthesis evolved in bacteria and cyanobacteria, oxygen was introduced in large amounts in the atmosphere.
As oxygen increased in the atmosphere, organisms developed the aerobic respiration and mechanisms to protect the cells against oxidation.
Three domains are accepted today: one of eukaryotes, Eukarya, and two of prokaryotes, Archaea and Bacteria.
DNA provides conflicting evidence about the relationship among and within the domains, implying that there was extensive lateral gene transfer among lineages during the early history of life.
See Fig. 5.4, page 105.
The prokaryotes that descended from the last common ancestor (LCA) diversified greatly in their metabolic capacities: photosynthetic, chemoautotrophic, sulfate-reducing, methanogenic, etc.
EUKARYOTES
What makes a eukaryote a eukaryote?
The eukaryotes are distinguished from prokaryotes by being more complex and having membrane systems and compartments in which the life functions are separated from one another.
These compartments are called organelles and are bound by membranes:
· Nucleus with a nuclear envelope that is continuous with endomembrane system, endoplasmic reticulum and dictyosomes.
· Cytoskeleton containing actin and tubulin, and many other interacting proteins.