Unifying Concepts of Biology... CELL DOCTRINE, EVOLUTION, &
BIOENERGETICS
Modern Biology is often looked upon as... Biochemistry of the Cell next
panel
Properties of Life...
Top Ten things that characterize a Cell as Living.
1. Cells obey Laws of Energetics - i.e., they transform energy
NAS-2
2. Cells are Highly Structured
NAS-3
with emergent properties
3. Cells have an Evolutionary Origin
(from a single primordial cell)NAS-1
4. Cells Metabolize
possess metabolic pathways, process nutrients,
self adjust
to environment via metabolic regulation
5. Cells Self-Replicate (divide)
µ
6. Cells Osmoregulate
7. Cells Communicate
8. Cells show Animation (cyclosis)
9. Cells Grow, Divide, & Differentiate
10. Cells Die
next
panel
Top 10 Properties of Life...
the
basic unit of life is the CELL...
µ
"inanimate mix of biomolecules
- selected for their fitness
to perform certain (cell) biochemical functions
characteristic of life".
1. Life & Cells
OBEY physical/chemical
LAWS of Universe
NAS-2
all living things are parts of larger systems of matter & energy, and
matter continually recycles through systems as energy flows thru the systems
No
unique laws defining the Living State separate/different from natural-physical laws.
Cells
transform energy via: 1. capturing light energy, 2.
redox rxs, & 3. e-flow
a) extract energy
from surroundings
--> autotrophs
(light) & heterotrophs (food)
b) transform energy
--> to do 'work': osmotic, mechanical, electrical
c) cells
constantly expend energy to maintain a non-equilibrium ordered state
2. Cells are Highly Structured
NAS-3
all living things maintain a high degree of order & complexity
Diverse, yet similar... (all have membranes, nuclei,
& organelles)
uniqueness is
structural organization brought about by
interaction of elemental
molecules selected for by living systems next
panel
table
- elements of body*mix
--KAM--> Emergent
Properties[Table
1.1] JMM
3.
All cells are derived from a single
PRIMORDIAL cell* NAS-1 all living things are descended from a common ancestor -
Tree of Lifeview@home
a Fundamental Question of Human Inquiry has been...
Where did we come from
µ What chemical conditions
may have lead to origins of life?
How did the first cells
form?
What were the first living
entities like?
Are there
living cells elsewhere in the Universe?
There are 3 major
hypotheses of ORIGIN of LIFE...
1. Special Creation... benevolent supreme being suspends
laws of physics & chemistry to create life. [not
treatable by scientific method]
2. Extraterrestrial... life was formed or evolved
elsewhere in Universe
and was
seeded on the newly formed planet Earth,
this idea
includes such concepts as..."Panspermia". next
panel
(more later)
3.
Chemical Evolution - complexity arose from an assembly of large molecules
in the beginning... origin
of the Universe =
BIG BANG
(Explained*)
Beginning of the
Universe
approximately
13.7billion yr ago + 10%
(Hubble Constant
= 70 km/sec/MPc + 10%
and using White Dwarfs)
(MPc = megaparsec... one megaparsec equals
3.26 million light years & scale)
*
Formation of Earth
Earth coalesced from space dust
a
closer look
Chemical Evolution Origin ideas
which are based upon...
chemical
evolution is... simple chemical rx's that form complex molecular systems favoring life
1) today's known
molecules of "living cells" are made from small number
of
chemical
functional groups [ OH,
NH3, C=O, COOH, etc. ]
2) these
chemical functional groups easily form into simple monomers...
molecules
such as - amino acids, fatty acids, nucleotides, sugars.
3) these
monomers
easily make polymers or
macromolecules...
which favored the energy transforming & self-replicating
features,
so called - emergent properties that help define today's living cells...
*The exact circumstances of the origin of
life and the actual nature of first organisms may be
forever lost to science, but research can at
least help us understand what is possible as
the concept of chemical evolution
of
life conforms to scientific method,
and is EXPERIMENATLLY TESTABLE...
Ultimate Goal may be
"creation of an artificial cell, as a model of a life system"
4
experimental approaches are active in today's origins research
...mostly searching for sources of early precursor
organic molecules of Life ???
I) classical chemical
evolution approach... [life
began when chemistry begat biology]
i.e., life formed from a chemically reactive soup... in
the early
oceans of Earth
1922 -
Oparin &
Haldane:
suggest
early Earth had a
reducing atmosphere
one rich in gases as
NH3, CH4, H2, & H2O
vapor
1953*
- Miller*
&
Urey
(U
Chicago 1953) ---> make organics in
the lab (Time
Magazine)
> abiotic origin of organic molecules from simple inorganics
> H2O, NH3, CH4,
& H2 from a reducing atmosphere
> produce HCN and formaldehyde which leads to...
>
organics*
as amino acids and sugars & Jeff
Bada reanalysis of Miller exp.* next
panel
> nucelobases can assemble spontaneously fron CN, H-C=C-H,
& water.
CRITICISM of research:
it was not
really a reducing atmosphere,
so chemically unlikely
but, experiments recently redone by J.L. Bada
& S.L. Miller using a weakly reducing
atmosphere (irradiated with protons)... have obtained bioorganic compounds
in amounts comparable to those of original Miller/Urey type
experiments. March
2007 ACS Annual Meeting Bada Presentation*
II) Deep dwelling (ocean)
hydrothermal vents*
discovered in 1979 by researchers @ Oregon
State U. - hot vents on Pacific seafloor
with minerals spewing up from pressurized, hot springs; source of chemical evolution?...
these
vent
areas (660oF) are full of organically rich molecules --->
even
with
life*
(tube worms @ vents)
& bacteria living in hydrothermal vents.
speculation is that life's
molecules may have originated in
the hydrothermal vents
regions.
next
panel
A role for the
hydrothermal vents in
?...
Origin
of Metabolism
Gunter
Wachterschauser (German biochemist) has
speculated that origins of
bioorganic chemical reactivity may have
originated near hydrothermal vents
before genetics - a cycle of chemical reactions that produce energy. > earliest primordial biochemical
cycles may have functioned there... > metabolic cycles likely predate cells...
took place on mineral surfaces
that acted
as catalysts & surfaces for early reactions √ key reaction may have been a
reductive reaction like citric acid cycle...
Researchers including M.J. Russell, M.M. Hanczyc, D. Deamer, C. Huber, and G. Cody
have synthesized amino acids and assembled/disassembled polypeptides
under vent like conditions,
all crucial metabolic processes that might have arisen at hydrothermal vents
so maybe the bioorganic molecules evolved at hydrothermal vents.
next
panel
What is source of
bioorganic molecules ?
(chemical evolutionary precursors to life)
a) Miller &
Urey - abiotic synthesis in tidal pools of Earth's
early oceans
b)
hydrothermal vents (spewed up from "middle
Earth")
C)
SPACE
DEBRIS:
chemical evolution
vs.
meteorites
early bombardment with dust, meteorites, asteroids, & comets
may have
deposited organics on newly forming planet Earth.
Asteroids rocky objects, that hit Earth &
contain molecules such as kerogen...
[an organic material known as -
PAH*
-
polycyclic aromatichydrocarbons*],
nucleobases, quinones, carboxylic acids, and
amines & amides
= some 70 amino acids, including
8 of common 20 aa's. Comets
are mostly ice crystals on cores of silicates & carbon NASA-Stardust
contain about 10% CO, CO2, CH4, CH3OH, and NH3
Thus the origin of the molecules of life may have been from space. next
panel Campbell -
Concept Activities - chapter 2.1 - How space rocks are analyzed for the
signs of life*
PANSPERMIA - idea that living microbes drifted in from space & colonized Earth; Svante Arrhenius (1908) radiation emitted
by stars carried
microbes thru
space; (also supported by
Francis Crick)
"Life
Happens*"
bumper stickers now have more
meaning in terms of chemical evolution.
Life
may have originated when the mix of different molecules in the primordial
soup
passed a certain level of complexity and self-organized into living entities;
(if so, then life is not a highly improbable chance event, but almost
inevitable).
Even space
debris, as
ICE, may have been the cradle of Life... all ice contains some water... Max Berstein
(NASA - 1999)
has modeled
cryochemistry
reactions in the lab,
to look at molecular events within
comets...
he has observed...
...chemical reactions can occur even in very low temps [25K
(-400oF)],
...UV light can break
chemical bonds
- forming ketones, esters, alcohols, and quinones
(for e- transport).
...some molecules formed
spherical, capsule-like droplets when
- exposed to water, with properties akin to membranes interfaces. some experiments have shown that units
of RNA can spontaneously string themselves in ice. → so
besides abiotic or hydrothermal origins we have
a new speculation ??? maybe
extraterrestrial
aa's built 1st proteins
in space?
but
wait, recent research suggests a Role for Minerals* in
Earth's chemical evolution
next
panel
3rd experimental approach of Origins of Life research
III) study of the Origins of
Self-Replicating Chemical Systems...
i.e., Evolution of an RNA
world...
(which came 1st DNA or RNA) ►a key characteristic of life is self-replication...
Can molecules self-replicate???
in 1989 Sidney Altman and
Thomas Cech - received
Nobel Prize
for demonstrating that RNA molecules may
have
CATALYTIC ACTIVITY*(RIBOZYMES)
i.e., these RNA's catalyze hydrolysis & condensation rxs
of phosphodiester bonds.
If
RNA can
catalyze polymerization of like molecules maybe it
can be a template also,
akin
to DNA -->
figure* i.e., replicate itself, then RNA
molecules may have been the
1st SELF-REPLICATING living entity.
Researchers have been able to produce short chains of RNA, 2-40 nucleotides long
& clay minerals
enhance the process (chains of 50+ nucleotides by
bringing reactive molecules close together, concentrating
them, and thereby facilitating the formation of
bonds between them.
No self-replicating
RNA molecules exists naturally today, but lab experimentation may
establish that it was feasible, and that
RNA molecules can be selected for via
Darwinian evolutionary mechanisms (natural selection). next
panel
tba
a metabolism first - thermodynamic alternative
4th
experimental approach of Origins of Life research
IV) Knock-out Cells...ultimate
challenge: to construct an artificial organism that can reproduce & evolve.
By
modifying a simple microbe, scientists hope to create a
new form of single cell life. News
Release - new funding
>
J. Craig Venter, a principle investigator (P.I.) of
the Human Genome Project is attempting
to make a new type of bacterium using DNA manufactured in the lab;
> using the sequenced the genes of a
bacterium called
Mycoplasmagenitalium, a gram-positive
parasitic bacterium, whose primary infection site may be the human urogenital
tract.
(it probably causes
non-gonococcal urethritis
and it is also one of the simplest
known microbes with only one chromosome and
517 genes).
> researchers began
systematically
removing genes to determine how many genes
are essential for life. In 1999, they published a paper that narrowed the needs
of M. genitalium to between 265 and
350 genes using
knockout
genes concept*.
> a genomic goal will be to learn on
a molecular level the minimum genes a cell needs
to
thrive
and reproduce and how to artificially make those and other genes. > Venter plans to construct a synthetic chromosome
that is 381 genes (580,000 bp) long using lab-made chemicals,
& transplant it into bacterial cell = new synthetic life form. next
panel
Mycoplasma laboratoriumCraig Venter discusses synthetic life*view@home
current paradigm:
"simple chemical
self-assembly has lead to complex self-replicating systems"
5 Steps in Chemical Evolution of Life-
"It was a Dark and Stormy Night"
(?)Some
imProbable Steps
in Chemical Evolution of Eukaryotes... it's a long way from a research protobiont to a typical eukaryotic
cell of today the evolution of the
eukaryota was single most
important step in evolution
of multi-cellular life forms & was a key step that
lead to plant & animal life. 1. cell membrane encapsulates
genetic DNA... development of nucleus
greatest evolutionary
invention - it internalized the genome
2. loss of a rigid cell wall... cells developed ability of phagocytosis - allowed engulfing of foods
also allowed cells to clump
together --> multi-cellularity --> tissues
3. evolve a selectively permeable membrane... protects cell, allows uptake gases & nutrients & exchange with environment
4. evolve a cytoskeleton... provides framework- allowed cell to grow
larger, move, & permitted
metabolism; eukarya are 10x larger that bacteria
5. evolve aerobic respiration...
more efficient energy transformation
6. develop various organelles
(maybe by
endosymbiosis [engulfment])... a sub-cell part that catalyzes a specific
metabolic function
7. development of sexual cell cycles
(transposons - moveable genes)... a
method to shuffle genes along chromosomes favored cellular evolution end
4
a possibleScript for Life*read?
Top 10 Characteristics of life... cont'
4. All cells METABOLIZE all life depends on
chemical reactions that take place within cells
metabolism
is chemical processes &
reactivity in living cells, where molecules are broken
down to yield energy for
vital processes & other molecules are made.
When classifying organisms, biology often looks at the mode of Nutrition,
i.e., how cells obtain
energy &
carbon from their environment [metabolism]
µ AUTOTROPHS - capable of synthesizing all
their organic molecules
using CO2 as sole
C source
1) photosynthetic autotrophs... use solar light energy
...capture light by
chlorophyll,
transfer e- from hydrogen donor
to CO
2 to reduce it to CH
2O (first
reductant H2S, now...H2O)
2) chemotrophic = use simple inorganic
molecules as their energy source
µ HETEROTROPHS - obtain energy from chemical fuels (as sugars)
by oxidation
unable to synthesize all needed molecules -
i.e., obtain nutrients by dietary means
next
panel
Cells possess Metabolic
Pathways (linked sequences of individual chemical
reactions)...
ANABOLIC - synthetic reactions... making larger from smaller molecules
CO
2 + H
20 <----> C
6H
12O
6
CATABOLIC - degradatory reactions.. breakdown of larger into smaller
Metabolic Pathways
exhibit:
A
------> B ------> C ------> D
------> E
e1 e2 e3 e4
economy & efficiency...
dynamic steady state... equal
in/out
rates of intermediates
rate of synthesis = rate of degradation
living things regulate use of energy and respond to their environment
control
is... by ENZYMES...
i.e., they are Self-Regulating...
an ex:
negative feedback (feedback inhibition*) -->
can lead to
human diseases*
Concept Activities -
Chapter 1.2 -
Positive-Negative Feedback* integration... work in a coordinated fashion...
everything at the right time
next
panel
another definition of Life
may be:
carefully orchestrated chemical reactions.
5.
Self-replication (reproduction is
single most definitive property of life) all living things share same
genetic code, which is passed from parent to offspring
genetic info is
in DNA
-
asexual* cell division = MITOSIS &
-
sexual* cell divsion = MEIOSIS
some
inanimate counterparts (or model systems)
useful
for
experimental study...
growth of crystals in chemistry
computer simulation models of evolutionary selection...
Tierra -
[digital life] is a computer simulation of evolution
by Thomas Ray @ U. Delaware - TIERRA
small computer programs of assembly code with directions on how to copy self... like a computer virus, competes for cpu time & memory space,
but
is designed to be able to mutate & evolve
next
panel
a simple computer program with
instructions allowing code changes
(mutation & evolution)
Primordial program had some 80 instructions and....
[some anthropomorphic analogies]
it was stored in cpu (lived),
it consumed cpu cycles (metabolized),
copied itself (reproduced),
it moved
up in que (animation), &
it was removed (died)
New programs
(code changed) emerged (mutated & evolved)...
first variant had 79 instructions,
one
variant had 22 instructions, but replicated 6x faster,
some
variants had only 45 lines,
but lost the ability to replicate
however, it borrowed instructions from others = acted like a parasite
some programs became defensive,
ie, immunized
itself against parasites
SKIP this Material
"Life is too improbable to be due to
chance" - Creationists & Intelligent Design Theorists just as watch needs a
watchmaker, an eye, a biochemical pathways is too improbable
to be due to chance... it must be due to
intelligent design.
Richard Dawkins - "the
Blind Watchmaker"
Natural selection, is the unconscious, automatic, blind, yet essentially non-random process that
Darwin discovered, and has no purpose in mind. If it can be said to play the role of
watchmaker in nature, it is the blind watchmaker. The only watchmaker
in nature is the blind forces of physics, albeit deployed in a very special way.
A true watchmaker has foresight: he designs his cogs and springs, and plans
their interconnections, with a future purpose in his mind's eye. Natural
selection is a blind, automatic process, which scientists now know is the best explanation for the existence and
apparently purposeful form of all life, has no purpose in mind. It has no mind
and no mind's eye. It does not plan for the future. It has no vision, no
foresight, no sight at all.
By gradual, step- by-step
transformations from simple
beginnings, and with each successive change in the gradual evolutionary process,
relative to its predecessor, leads a whole sequence of cumulative steps
leads to complexity of a final end-product relative to the original starting
point. The cumulative process is directed by nonrandom survival.
Cumulative
selection is a fundamentally nonrandom process and evolution has no
long-term goal. There is no long-distance target, no final perfection to serve
as a criterion for selection.
Is it Experimentally Testable ?
Weasel Applet -
a computer "breeding"
program = possible solutions to match a supplied phrase; exhaustive search --
systematically trying all possible guesses -- that would virtually never
complete, but artificial selection via random chance can lead to a solution and
seeming great complexity. Biomorph Applet
- plausibly lifelike forms -
a variety of tree-like shapes... coded by 8 genes,
with change allowed. Result: wide variety of forms from a limited
genome - total of 1,071,794,405 different biomorphs! The accumulation of changes
turns one form into quite different forms. next
panel
6. Osmoregulate...
all life requires liquid water
(water's properties will be
covered later)
regulate exchange material across cell membrane
with the environment - solvents & solutes in/out
of cell
helps maintain differences between in/out
7. Communicate...
intra (within) & inter (between) individual cells
ex: hormones/neurons
8. show Animation... cells
reveal significant
motion,
especially @ molecular level:
vesicles moving along
MT's,
flagella, and molecules across membranes;
also cyclosis or
cytoplasmic streaming
9. cells...
all living organisms change form & function at different statges of their life
cycles
Grow...
(increase in mass), Divide...
(increase in cell number),
Develop..., &
Differentiate...
become structurally, functionally &
biochemically different
from a fertilized egg ---> to adult cells
10. Die... absence of properties of
life
Conclusions about
Life, Cells, & Living Systems
Life is manifest in the structure we call the
CELL
all cells are presumed to derive from a single primordial cell
NAS-1
born some 4 billion years ago,
√ it out reproduced its contemporary competitors,
√ and had a family resemblance to today's cells...
...all use
DNA
...all have
same
genetic code
...all possess
same basic molecules ...all have
similar properties &
metabolic functions
...all use same metabolic pathways that define properties of life
...all are very
dynamic
entities
has a number
of unique intra-cellular parts common among all cells,
√ universal
properties of all cells* next
panel
thus... a living
CELL
is a ..... *
self contained,
self assembling,
self adjusting,
self perpetuating,
isothermal mix of biomolecules,
held in a specific 3-D conformation by weak non-covalent forces,
which can extract raw materials (precursors)
& free energy from its surroundings,
and can catalyze reactions with specific
biocatalysts (enzymes), that it makes,
which shows great efficiency & economy of
metabolic regulation,
and maintains a dynamic steady state far from
equilibrium, and
that can self-replicate, using the linear information molecule DNA.
*
