PHOTOSYNTHESIS

Photosynthesis is the process by which plants, some bacteria, and some protistans use the
energy from sunlight to produce sugar, which cellular respiration converts into ATP, the "fuel"
used by all living things. The conversion of unusable sunlight energy into usable chemical
energy, is associated with the actions of the green pigment chlorophyll. Most of the time, the
photosynthetic process uses water and releases the oxygen that we absolutely must have to
stay alive. Oh yes, we need the food as well!

We can write the overall reaction of this process as:

6H2O + 6CO2 ----------> C6H12O6+ 6O2
Most of us don't speak chemicalese, so the above chemical equation translates as:

six molecules of water plus six molecules of carbon dioxide produce one molecule of sugar
plus six molecules of oxygen

Leaves and Leaf Structure

Plants are the only photosynthetic organisms to have leaves (and not all plants have leaves).
A leaf may be viewed as a solar collector crammed full of photosynthetic cells.

The raw materials of photosynthesis, water and carbon dioxide, enter the cells of the leaf,
and the products of photosynthesis, sugar and oxygen, leave the leaf.
Cross section of a leaf, showing the anatomical features important to the study of photosynthesis: stoma, guard
cell, mesophyll cells, and vein

Water enters the root and is transported up to the leaves through specialized plant cells
known as xylem (pronounces zigh-lem). Land plants must guard against drying out
(desiccation) and so have evolved specialized structures known as stomata to allow gas to
enter and leave the leaf. Carbon dioxide cannot pass through the protective waxy layer
covering the leaf (cuticle), but it can enter the leaf through an opening (the stoma; plural =
stomata; Greek for hole) flanked by two guard cells. Likewise, oxygen produced during
photosynthesis can only pass out of the leaf through the opened stomata. Unfortunately for
the plant, while these gases are moving between the inside and outside of the leaf, a great
deal water is also lost. Cottonwood trees, for example, will lose 100 gallons of water per hour
during hot desert days. Carbon dioxide enters single-celled and aquatic autotrophs through
no specialized structures.

The Nature of Light

White light is separated into the different colors (=wavelengths) of light by passing it through
a prism. Wavelength is defined as the distance from peak to peak (or trough to trough). The
energy of is inversely porportional to the wavelength: longer wavelengths have less energy
than do shorter ones.

Wavelength and other aspects of the wave nature of light

The order of colors is determined by the wavelength of light. Visible light is one small part of
the electromagnetic spectrum. The longer the wavelength of visible light, the more red the
color. Likewise the shorter wavelengths are towards the violet side of the spectrum.
Wavelengths longer than red are referred to as infrared, while those shorter than violet are
ultraviolet.

The electromagnetic spectrum

Light behaves both as a wave and a particle. Wave properties of light include the bending of
the wave path when passing from one material (medium) into another (i.e. the prism,
rainbows, pencil in a glass-of-water, etc.). The particle properties are demonstrated by the
photoelectric effect. Zinc exposed to ultraviolet light becomes positively charged because
light energy forces electrons from the zinc. These electrons can create an electrical current.
Sodium, potassium and selenium have critical wavelengths in the visible light range. The
critical wavelength is the maximum wavelength of light (visible or invisible) that creates a
photoelectric effect.

Chlorophyll and Accessory Pigments

A pigment is any substance that absorbs light. The color of the pigment comes from the
wavelengths of light reflected (in other words, those not absorbed). Chlorophyll, the green
pigment common to all photosynthetic cells, absorbs all wavelengths of visible light except
green, which it reflects to be detected by our eyes. Black pigments absorb all of the
wavelengths that strike them. White pigments/lighter colors reflect all or almost all of the
energy striking them. Pigments have their own characteristic absorption spectra, the
absorption pattern of a given pigment.

Chlorophyll is a complex molecule. Several modifications of chlorophyll occur among plants

and other photosynthetic organisms. All photosynthetic organisms (plants, certain protistans,
prochlorobacteria, and cyanobacteria) have chlorophyll a. Accessory pigments absorb energy
that chlorophyll a does not absorb. Accessory pigments include chlorophyll b (also c, d, and e
in algae and protistans), xanthophylls, and carotenoids (such as beta-carotene). Chlorophyll
a absorbs its energy from the Violet-Blue and Reddish orange-Red wavelengths, and little
from the intermediate (Green-Yellow-Orange) wavelengths.
Carotenoids and chlorophyll b absorb some of the energy in the green wavelength. Why not
so much in the orange and yellow wavelengths? Both chlorophylls also absorb in the orange-
red end of the spectrum (with longer wavelengths and lower energy). The origins of
photosynthetic organisms in the sea may account for this. Shorter wavelengths (with more
energy) do not penetrate much below 5 meters deep in sea water. The ability to absorb some
energy from the longer (hence more penetrating) wavelengths might have been an advantage
to early photosynthetic algae that were not able to be in the upper (photic) zone of the sea
all the time.

The structure of the chloroplast and photosynthetic membranes

The thylakoid is the structural unit of photosynthesis. Both photosynthetic prokaryotes and
eukaryotes have these flattened sacs/vesicles containing photosynthetic chemicals. Only
eukaryotes have chloroplasts with a surrounding membrane.

Thylakoids are stacked like pancakes in stacks known collectively as grana. The areas between
grana are referred to as stroma. While the mitochondrion has two membrane systems, the
chloroplast has three, forming three compartments.

Structure of a chloroplast

Stages of Photosynthesis

Photosynthesis is a two stage process. The first process is the Light Dependent Process (Light
Reactions), requires the direct energy of light to make energy carrier molecules that are used
in the second process. The Light Independent Process (or Dark Reactions) occurs when the
products of the Light Reaction are used to form C-C covalent bonds of carbohydrates. The
Dark Reactions can usually occur in the dark, if the energy carriers from the light process are
present. Recent evidence suggests that a major enzyme of the Dark Reaction is indirectly
stimulated by light, thus the term Dark Reaction is somewhat of a misnomer. The Light
Reactions occur in the grana and the Dark Reactions take place in the stroma of the
chloroplasts.
 Overview of the two steps in the photosynthesis process.
Light Reactions

In the Light Dependent Processes (Light Reactions) light strikes chlorophyll a in such a way as
to excite electrons to a higher energy state. In a series of reactions the energy is converted
(along an electron transport process) into ATP and NADPH. Water is split in the process,
releasing oxygen as a by-product of the reaction. The ATP and NADPH are used to make C-C
bonds in the Light Independent Process (Dark Reactions).

In the Light Independent Process, carbon dioxide from the atmosphere (or water for
aquatic/marine organisms) is captured and modified by the addition of Hydrogen to form
carbohydrates (general formula of carbohydrates is [CH2O]n). The incorporation of carbon
dioxide into organic compounds is known as carbon fixation. The energy for this comes from
the first phase of the photosynthetic process. Living systems cannot directly utilize light
energy, but can, through a complicated series of reactions, convert it into C-C bond energy
that can be released by glycolysis and other metabolic processes.

Photosystems are arrangements of chlorophyll and other pigments packed into thylakoids.
Many Prokaryotes have only one photosystem, Photosystem II (so numbered because, while
it was most likely the first to evolve, it was the second one discovered). Eukaryotes have
Photosystem II plus Photosystem I. Photosystem I uses chlorophyll a, in the form referred to
as P700. Photosystem II uses a form of chlorophyll a known as P680. Both "active" forms of
chlorophyll a function in photosynthesis due to their association with proteins in the thylakoid
membrane.

Action of a photosystem

Photophosphorylation is the process of converting energy from a light-excited electron into

the pyrophosphate bond of an ADP molecule. This occurs when the electrons from water are
excited by the light in the presence of P680. The energy transfer is similar to the chemiosmotic
electron transport occurring in the mitochondria. Light energy causes the removal of an
electron from a molecule of P680 that is part of Photosystem II. The P680 requires an electron,
which is taken from a water molecule, breaking the water into H+ ions and O-2 ions. These O-
2 ions combine to form the diatomic O2 that is released. The electron is "boosted" to a higher
energy state and attached to a primary electron acceptor, which begins a series of redox
reactions, passing the electron through a series of electron carriers, eventually attaching it to
a molecule in Photosystem I. Light acts on a molecule of P700 in Photosystem I, causing an
electron to be "boosted" to a still higher potential. The electron is attached to a different
primary electron acceptor (that is a different molecule from the one associated with
Photosystem II). The electron is passed again through a series of redox reactions, eventually
being attached to NADP+ and H+ to form NADPH, an energy carrier needed in the Light
Independent Reaction. The electron from Photosystem II replaces the excited electron in the
P700 molecule. There is thus a continuous flow of electrons from water to NADPH. This
energy is used in Carbon Fixation. Cyclic Electron Flow occurs in some eukaryotes and
primitive photosynthetic bacteria. No NADPH is produced, only ATP. This occurs when cells
may require additional ATP, or when there is no NADP+ to reduce to NADPH. In Photosystem
II, the pumping to H ions into the thylakoid and the conversion of ADP + P into ATP is driven
by electron gradients established in the thylakoid membrane.

Noncyclic photophosphorylation (top) and cyclic photophosphorylation (bottom). These processes are better
known as the light reactions.

The above diagrams present the "old" view of photophosphorylation. We now know where
the process occurs in the chloroplast, and can link that to chemiosmotic synthesis of ATP.
Chemiosmosis as it operates in photophosphorylation within a chloroplast

Halobacteria, which grow in extremely salty water, are facultative aerobes, they can grow
when oxygen is absent. Purple pigments, known as retinal (a pigment also found in the human
eye) act similar to chlorophyll. The complex of retinal and membrane proteins is known as
bacteriorhodopsin, which generates electrons which establish a proton gradient that powers
an ADP-ATP pump, generating ATP from sunlight without chlorophyll. This supports the
theory that chemiosmotic processes are universal in their ability to generate ATP.

Dark Reaction

Carbon-Fixing Reactions are also known as the Dark Reactions (or Light Independent
Reactions). Carbon dioxide enters single-celled and aquatic autotrophs through no specialized
structures, diffusing into the cells. Land plants must guard against drying out (desiccation)
and so have evolved specialized structures known as stomata to allow gas to enter and leave
the leaf. The Calvin Cycle occurs in the stroma of chloroplasts (where would it occur in a
prokaryote?). Carbon dioxide is captured by the chemical ribulose biphosphate (RuBP). RuBP
is a 5-C chemical. Six molecules of carbon dioxide enter the Calvin Cycle, eventually producing
one molecule of glucose.

The first step in the Calvin Cycle

The first stable product of the Calvin Cycle is phosphoglycerate (PGA), a 3-C chemical. The
energy from ATP and NADPH energy carriers generated by the photosystems is used to attach
phosphates to (phosphorylate) the PGA. Eventually there are 12 molecules of glyceraldehyde
phosphate (also known as phosphoglyceraldehyde or PGAL, a 3-C), two of which are removed
from the cycle to make a glucose. The remaining PGAL molecules are converted by ATP energy
to reform 6 RuBP molecules, and thus start the cycle again. Remember the complexity of life,
each reaction in this process, as in Kreb's Cycle, is catalyzed by a different reaction-specific
enzyme.

C-4 Pathway

Some plants have developed a preliminary step to the Calvin Cycle (which is also referred to
as a C-3 pathway), this preamble step is known as C-4. While most C-fixation begins with
RuBP, C-4 begins with a new molecule, phosphoenolpyruvate (PEP), a 3-C chemical that is
converted into oxaloacetic acid (OAA, a 4-C chemical) when carbon dioxide is combined with
PEP. The OAA is converted to Malic Acid and then transported from the mesophyll cell into
the bundle-sheath cell, where OAA is broken down into PEP plus carbon dioxide. The carbon
dioxide then enters the Calvin Cycle, with PEP returning to the mesophyll cell. The resulting
sugars are now adjacent to the leaf veins and can readily be transported throughout the plant.

C-4 photosynthsis involves the separation of carbon fixation and carbohydrate systhesis in space and time

The capture of carbon dioxide by PEP is mediated by the enzyme PEP carboxylase, which has
a stronger affinity for carbon dioxide than does RuBP carboxylase When carbon dioxide levels
decline below the threshold for RuBP carboxylase, RuBP is catalyzed with oxygen instead of
carbon dioxide. The product of that reaction forms glycolic acid, a chemical that can be broken
down by photorespiration, producing neither NADH nor ATP, in effect dismantling the Calvin
Cycle. C-4 plants, which often grow close together, have had to adjust to decreased levels of
carbon dioxide by artificially raising the carbon dioxide concentration in certain cells to
prevent photorespiration. C-4 plants evolved in the tropics and are adapted to higher
temperatures than are the C-3 plants found at higher latitudes. Common C-4 plants include
crabgrass, corn, and sugar cane. Note that OAA and Malic Acid also have functions in other
processes, thus the chemicals would have been present in all plants, leading scientists to
hypothesize that C-4 mechanisms evolved several times independently in response to a
similar environmental condition, a type of evolution known as convergent evolution.
 Photorespiration

The Carbon Cycle

Plants may be viewed as carbon sinks, removing carbon dioxide from the atmosphere and
oceans by fixing it into organic chemicals. Plants also produce some carbon dioxide by their
respiration, but this is quickly used by photosynthesis. Plants also convert energy from light
into chemical energy of C-C covalent bonds. Animals are carbon dioxide producers that derive
their energy from carbohydrates and other chemicals produced by plants by the process of
photosynthesis.

The balance between the plant carbon dioxide removal and animal carbon dioxide generation
is equalized also by the formation of carbonates in the oceans. This removes excess carbon
dioxide from the air and water (both of which are in equilibrium with regard to carbon
dioxide). Fossil fuels, such as petroleum and coal, as well as more recent fuels such as peat
and wood generate carbon dioxide when burned. Fossil fuels are formed ultimately by organic
processes, and represent also a tremendous carbon sink. Human activity has greatly increased
the concentration of carbon dioxide in air. This increase has led to global warming, an increase
in temperatures around the world, the Greenhouse Effect. The increase in carbon dioxide and
other pollutants in the air has also led to acid rain, where water falls through polluted air and
chemically combines with carbon dioxide, nitrous oxides, and sulfur oxides, producing rainfall
with pH as low as 4. This results in fish kills and changes in soil pH which can alter the natural
vegetation and uses of the land. The Global Warming problem can lead to melting of the ice
caps in Greenland and Antarctica, raising sea-level as much as 120 meters. Changes in sea-
level and temperature would affect climate changes, altering belts of grain production and
rainfall patterns.