Download Appendix 6 Photosynthesis and Carbon

Appendix 6
Photosynthesis and Carbon Fixing
Life cannot exist without an energy input from outside itself. That could be
organic food (products of earlier life), energy from sunlight, thermal vents, etc.
Obviously organic food is not an option for the very early species, which appear
in the geologic record at almost earliest possible moment after the earth had
cooled to a "livable" temperature, at around 3.8 Ga (Billion Years Ago)—a very
hot temperature, perhaps about that of pasteurizing (150°F)1.
The organic carbon found as early as 3.8 Ga, and the fossils of what appear to
be cyanobacteria (or their ancestors) around 3.45 Ga indicate that
photosynthesis, harvesting of energy from sunlight, appeared with the first life, or
very soon thereafter.2
Photosynthesis is an incredibly elaborate process, and the basic parts of it are
essentially the same for all photosynthetic life. The cyanobacteria conduct
photosynthesis in folded membranes called thylakoids ("light reaction" in the
following figure). Plants conduct photosynthesis in Chloroplasts as show in the
Figure.3
A number of complex molecules, some actually nano-sized motors, are involved
in photosynthesis. There are two stages: the light reaction which harvests energy
from light, and the dark reaction (Calvin Cycle in the following diagram), which
uses the products of the light process to fix carbon and make sugars. The dark
reaction does not harvest light but exchanges products with the light reaction.
1
See the Chapter 6, Life Itself. Some scientists believe that the first life was extremophiles such as live near
thermal vents in the oceans. This would move the possible time of the first life even earlier, around the
boiling point of water. Personally I think that extremophiles are a later development. See, for example, Cell
Biology, " Archaea are microbes that are more closely related to Eukaryotic cells than they are to the
Bacteria". The Archaean ribosomes appear to be closer to Eukaryotes (much later) than to bacteria—see
Margulis & Chapman, Kingdoms and Domains (2009), Figure B-3, "Ribosome morphology".
2 Haselkorn, Koonin, et al, The cyanobacterial genome core and the origin of photosynthesis (PNAS, 2006).
They assert that the earliest cyanobacteria already had both the light and Calvin processes in place. These
are two very complex and subtly linked processes and involve many specialized molecules working
together. Processes and complex molecular motors accompanying photosynthesis: energy storage
(ATPase), and carbon fixing (RuBisCO) to make sugars. Nitrogen fixing (Nitrogenase) also accompanied
photosynthesis —by necessity—but it is a separate process. According to these authors, "These are such
complex biological processes, that the complexity and early appearance on earth seems to indicate planning
and design."
3 In Eukaryotes, photosynthesis takes place in the chloroplast. In bacteria, the thylakoids, like the DNA itself,
is located in the undifferentiated general cell contents.
Photosynthesis
The following (deceptively simple) chemical equation describes the action of
photosynthesis:
6H2O+6CO2+light energy -> C6H12O6+6O2
Water + Carbon dioxide + light energy -> sugar + (waste) oxygen.
The Light Reaction.
The light process centers around chlorophyll: molecules that harvest light with
the help of a central magnesium atom. There are two forms of chlorophyll which
work cooperatively but have, remarkably, opposite characteristics—one is a
strong oxidizer, and the other is a strong reducer—each the best known design
for its particular task to be found in all of nature.
Photosystem II, involving P680 Chlorophyll: absorbs yellow (680 nm)
light. This is the strongest known biological oxidizer. It oxidizes water to
produce protons (H+) and oxygen (O2) as a waste product in the Oxygenevolving complex. It is "II" because it was discovered after Photosystem I.
The protons are used in the manufacture of ATP, the universal "energy
battery" used, in particular, in the dark process. A summary of its action is:
H2O + light energy -> 2 H+ + O2
water + light energy -> protons + oxygen.
Photosystem I, involving chlorophyll P700: absorbs orange (700 nm)
light. This is the strongest known biological reducer. It uses light energy to
prepare a precursor molecule NADPH for sugar production in the dark
process.
The protons of Photosystem II supply protons (H+) to Photosystem I to make
NADPH, and also propel a marvelous and complex rotary proton nanomotor,
ATP synthase, which prepares ATP4 (see figure).
ATP synthase proton motor
4
See an ATP Synthase animation by Donald Nicholson (Leeds University) and a more detailed molecular
view by John Walker (Cambridge). See the description from Davidson College. See also the article on ATP
Synthase from lifesorigins.com, which calls it "the smallest rotary motor in the world. ... ATP synthase was
one of the first enzymes because it is absolutely necessary for many of the organisms that are thought to
have existed on the primitive earth. All of the bacteria that oxidize non-organic chemicals to obtain energy
use ATP synthase to make ATP." The molecule is constructed from six subunits. The first recognized
nanomotor, the bacterial flagellum, was offered to an incredulous scientific world in the 1980s. At first the
discovery of this motor was met with great skepticism; it was thought that the flagellum did not rotate but
simply whipped back and forth. The proof came when a scientist found a way to glue the flagellum to a glass
slide, and when this happened, the bacterium spun around the flagellum. Since then literally thousands of
nanomotors have been identified. See also the Appendix on the Eukaryotes.
The Dark Reaction.
The dark reaction fixes carbon and then uses it to form glucose, C6H12O6, used
by the cell to form starch, amino acids and other sugars. The following remark
emphasizes the importance of carbon fixing.
"Carbon is essential to life. All of our molecular machines are built around a
central scaffolding of organic carbon. Unfortunately, carbon in the earth and
atmosphere is locked in highly oxidized forms, such as carbonate minerals and
carbon dioxide gas. In order to be useful, this oxidized carbon must be "fixed"
into more organic forms, rich in carbon-carbon bonds and decorated with
hydrogen atoms."5
This is done by a complex motor molecule, RuBisCO. It is the most common
protein on earth—about half of all the protein. The RuBisCo molecule is large
(consisting of two subunits), very slow (it can fix about 3 CO 2 molecules per
second) and very inefficient, because it spends about 20% of its time "fixing"
oxygen instead of carbon: "a wasteful process" called photorespiration.6 One
author called the molecule "dim-witted."7 Nonetheless, despite many billions
spent seeking an improved RuBisCO, no practical substitute has been found.
The RuBisCO active site uses a Magnesium atom8 to perform its function. The
overall reaction can be summarized as:
CO2 + H2O + ATP → CH2O + O2
carbon dioxide + water + ATP -> sugar (fragment) + oxygen + ADP + P+++
where ATP is the energy "battery" with three phosphates, one of which is
released generating energy, ADP and a phosphate ion. This is repeated three
times in the Calvin cycle.
RuBisCO discriminates against the isotope 13C in preference for 12C. This arises
due to slight differences in kinematics and binding energy in the CO 2 molecule.
Thus organic carbon is slightly deficient in 13C compared with inorganic carbon.
5
Buick, R. "Earliest Evidence for Life on Earth" Bulletin of the American Astronomical Society, Vol. 34, p.12
(2002).
6 Wasteful, because the cell must expend time and energy to reverse this error.
7 To fix carbon, food, energy: fix Rubicon (Biofuels Digest, 2010).
8 Occasionally Vanadium is known to substitute for the Magnesium atom.