Transcript document

Nature and origin of Life
lecture 6
History part 2
TOPICS
1)
2)
3)
4)
5)
6)
Mendel genetics (sweet peas)
Fruit flies.
The shift to phages
Discovery of roles of nucleic acids and proteins.
DNA and the genetic code
The proteins and nucleic acid chicken and egg
problem.
7) Items of concern in the origin of life
Gregor Mendel
• Monk who investigated sweet peas
• Mendelian Inheritance:
• How sexual organisms reproduce
Causes
Loss of ½ genetic material for an offspring.
Dominant and recressive genes.
Ploidy
• The ploidy number is the number of paired
chromosomes in the cell.
• Humans are diploid.
• Plants , insects amphibians and reptiles are
often tetraploid.
• A single human may have cells of different
ploidy, so egg and sperm cells are monoploid,
most other cells are diploid, but e.g. some
muscle cells are tetraploid!
Zygosity
From Wikipedia,
Zygosity is the degree of similarity of the alleles for a trait in
an organism. If both alleles are the same, the organism
is homozygous for the trait. If both alleles are different, the
organism is heterozygous for that trait. If one allele is missing,
it is hemizygous, and, if both alleles are missing, it
is nullizygos.
Most eukaryotes have two matching sets of chromosomes; that
is, they are diploid. Diploid organisms have the same genes on
each of their two sets of homologous chromosomes, except
that the sequences of these genes may differ between the two
chromosomes in a matching pair and that a few chromosomes
may be mismatched as part of a sex-determination system.
In prokaryotes
All prokaryote Cells are haploid.
Genetic variation can only be produced by
Mutation, or
Lateral Gene Transport
Mendel interpretation
• Mendel factors = genes.
• Dominant (A) and Recessive (a)
• Possible pairings are AA, Aa, aA, aa. So dominant
features will statistically appear in ¾ of offspring.
• Mendel stated that each individual has two factors
for each trait, one from each parent. Homozygous
vs heterozygous.
• Egg and sperm each possess both genes from the
“grandparents”, but in transition to the next
generation individual ½ of the genes are lost.
Mendel First Law, Law of Segregation
• The Law of Segregation states that every
individual possesses a pair of alleles (assuming
diploidy) for any particular trait and that each
parent passes a randomly selected copy (allele) of
only one of these to its offspring. The offspring
then receives its own pair of alleles for that trait.
Whichever of the two alleles in the offspring is
dominant determines how the offspring expresses
that trait (e.g. the color of a plant, the color of an
animal's fur, the color of a person eyes).
Law of Independent Assortment
(The "Second Law")
• The Law of Independent Assortment, also
known as "Inheritance Law", states that
separate genes for separate traits are passed
independently of one another from parents to
offspring. That is, the biological selection of a
particular gene in the gene pair for one trait to
be passed to the offspring has nothing to do
with the selection of the gene for any other
trait.
Mendel 2
• Mendel's conclusions were largely ignored. Although
they were not completely unknown to biologists of the
time, they were not seen as generally applicable, even
by Mendel himself, who thought they only applied to
certain categories of species or traits. A major block to
understanding their significance was the importance
attached by 19th-century biologists to the
apparent blending of inherited traits in the overall
appearance of the progeny, now known to be due to
multigene interactions, in contrast to the organ-specific
binary characters studied by Mendel
• later work by biologists and statisticians such as R.A,
Fisher showed that if multiple Mendelian factors were
involved in the expression of an individual trait, they
could produce the diverse results observed
Fruit Flies
The D. melanogaster lifespan is about 30 days at 29 °C (84 °F).
The developmental period for fruit flies varies with temperature.
The shortest development time (egg to adult), 7 days, is
achieved at 28 °C.
Thomas Hunt Morgan began using fruit flies in experimental
studies of heredity at Columbia University in 1910. His
laboratory was located on the top floor of Schermerhorn Hall,
which became known as the Fly Room. The Fly Room was
cramped with eight desks, each occupied by students and their
experiments. They started off experiments using milk bottles
to rear the fruit flies and handheld lenses for observing their
traits. The lenses were later replaced by microscopes, which
enhanced their observations. The Fly Room was the source of
some of the most important research in the history of biology.
Morgan and his students eventually elucidated many basic
principles of heredity.
T2 phage
Molecular genetics 1
• Although genes were known to exist on chromosomes,
chromosomes are composed of both protein and
DNA—scientists did not know which of these is
responsible for inheritance. In 1928, Frederick
Griffith discovered the phenomenon of transformation:
dead bacteria could transfer genetic material to
"transform" other still-living bacteria. Sixteen years
later in1944, Avery, McLeod and McCarty identified the
molecule responsible for transformation
as DNA. The Hershey-Chase experiment in 1952 also
showed that DNA (rather than protein) is the genetic
material of the viruses that infect bacteria, providing
further evidence that DNA is the molecule responsible
for inheritance.
Molecular Genetics 2
Watson and Crick determined the structure of DNA in
1953, using the X-ray crystallography work of Rosalind
Franklin and Maurice Wilkins that indicated DNA had
a helical structure (i.e., shaped like a corkscrew). Their
double-helix model had two strands of DNA with the
nucleotides pointing inward, each matching a
complementary nucleotide on the other strand to form
what looks like rungs on a twisted ladder. This structure
showed that genetic information exists in the sequence
of nucleotides on each strand of DNA. The structure
also suggested a simple method for duplication: if the
strands are separated, new partner strands can be
reconstructed for each based on the sequence of the old
strand.
Genetic Code discovery
The Crick, Brenner et al. experiment was the first to demonstrate
that codons consist of three DNA bases.
Marshall Nirenberg and Heinrich J. Matthai were the first to
elucidate the nature of a codon in 1961 at the National
Institutes of Health. They used a cell-free system to translate a
poly-uracil RNA sequence (i.e., UUUUU...) and discovered
that the polypeptide that they had synthesized consisted of
only the amino acid phenylalanine. They thereby deduced
that the codon UUU specified the amino acid phenylalanine.
This was followed by experiments in Severo Ochoa's
laboratory that demonstrated that the poly-adenine RNA
sequence (AAAAA...) coded for the polypeptide poly-lysine
and that the poly-cytosine RNA sequence (CCCCC...) coded
for the polypeptide poly-proline. Therefore the codon AAA
specified the amino acid lysine, and the codon CCC specified
the amino acid proline. Using different copolymers most of
the remaining codons were then determined.
Jacques Monod
• In 1971 two works appeared that created
roadblocks for new theories of the origin of life.
• Monod wrote a book “Chance and Necessity”.
• He first created a problem by stating that organisms
have purpose or “teleonomy”. He then stated that
variation had to arise on top of a stationary state.
• He also pointed to the chicken and egg situation
between genes and enzymes. He found that he had
boxed himself into an arguement in which life could
have only arisen by an impossibly rare event.
Issues
• Eigen did not accept Monod’s view of the rarity
of life, but somehow imagined that a hypercycle
would develop spontaneously!
• Such a view was followed by Stuart Kauffmann,
who imagined that the occasional rare event
permitted by thermodynamics could be quite
common. ( As with Bill Clinton’s comment, he
failed to bring arithmetic to the problem.)
Manfred Eigen 1
Eigen wrote a very long paper
“Self-organization of Matter and the origin of
biological macromolecules”
Eigen argued that “we would not attribute the
attribute of being alive to anything less than the
hypercycle in part VI which is characterized by
ten properties.
Three are metabolism, reproduction and mutability.
The other 7 are associated with the chicken and egg
aspects, and a cycle of enzymatic behavior which
he called a hypercycle.
Eigen 2
At the start of the paper, Eigen asks ‘ Which came
first, the protein or the nucleic acid?”
And the words protein and nucleic acid may be
replaced by function and information.
He then states “This is absurd, because function
cannot occur in an organized manner unless
information is present, and this information
only acquires its meaning through the function
for which it encodes.”
Christian De Duve 1
• Following this, in 1995 De Duve wrote “Vital
Dust” In which he argued that since there are a
relatively small number of molecules involved in
life, and they are made by common paths, life
should be easy to create.
• He ignored the ultra low probability of creating
an exact sequence of amino acids in a protein.
• E.g. with 20 amino acids, an exact string of 100
Would have a probability of 20-100 , or 10-300.
De Duve 2
• In a later book, Singularities , De Duve gets
into his own chicken and egg problem. First
he quotes Leslie Orgel saying that enzyme
metabolism being totally different than preenzyme metabolism, could shed no light on the
original metabolism.
• He then has a problem as to how enzyme
metabolism could arise.
Hoyle
• Hoyle also looked at the probability of making
a single simple prokaryote, and decided that it
was similar to a tornado travelling through a
junk-yard and creating a Boeing airliner
complete and working!
What went wrong?
1) A process of survival of a mutable material in
a dissipative environment MAY create a
survival line of it may not.
2) If a survival line is created, mutable materials
will change roles as well as forms.
3) The first survival state does not need to
employ efficient reactions, it merely needs to
grow faster than it is destroyed.
4) Therefore Eigen is wrong.
Variations
1 Soup is not alive.
2 Play the movie backwards as far as replanting
the potatoes and carrots in the yard - this
corresponds to creating life.
3 Play the movie forward and keep the soup on
the heat without adding water. The black stuff
produced is called “tar” or “kerogen”.
Conclusion
The recipe for life not only requires the
ingredients. It also has issues of how and when
ingredients are added, the quantities that are
added. The storage of ingredients. The rate and
form in which energy is added, and the nature of
pauses where the less fit fail to survive.
Life is not a foregone conclusion. From the
statistics of 1 planet, and it has life, the
probability of a planet having life is:
1 +/- 1 !