# Biology, Answering the Big Questions of Life/Photosynthesis/Photosynthesis3

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* ADVANCED

## Atoms, Orbitals and Light

An Atom is made of protons, neutrons, and electrons. The electrons circle the nucleus staying within Atomic Orbitals, descrete regions where the electron is most likely to be. Under normal conditions the electrons stay as close to the atom as possible. At this configuration, electrons are at their the lowest energy level. This low energy level is called the Ground State.
Atoms can absorb light energy and jump to a higher energy level. When they do so, they are said to be in an Excited state To do this the light must be of exactly the right wavelength to allow it to jump to a higher orbital. These higher orbitals are further from the nucleus of the atom.
That is why water is so important. H2O is not at habitable temperature it is actually a complex molecule comprising OH- & H+. Add common salt and you get NaCl + H2O which solution is OH-/Na+ (Sodium Hyroxide [alkaline bleach]) plus Cl-/H+ (Hydrochoric Acid) a nice balance.
The electron will later fall back down to the ground state. When they do, they will reemit a lower energy wavelength of light. This is called fluorescence. Chlorophyll fluoresces in the far red.
Reading
* Wikipedia:Electron_shell
* Absorption (electromagnetic radiation)
* Wikipedia:Energy_level
* Wikipedia:Fluorescence

## Photosystems

When an atom in a chlorophyll molecule, absorbs light and jumps to a higher energy level, the electron gets far enough from the atom that it can be stolen away by nearby molecules carrying the electron down an electron transport chain. The chlorophyll that loses the electron is situated in a particular location called the photosynthetic reaction center. It is in the center of a sort of inverted umbrella of molecules in the thylakoid membrane. The tip of that umbrella is very near the first molecule in the photosynthetic electron transport chain. Once the electron is stolen, the chlorophyll gets a new electron from nearby chlorophylls and other accessory pigments. These pigments all group together in a structure called a photosystem.
The photosystem works together as a group. Electrons flow across the photosystem getting discharged into the reaction center, while elsewhere electrons are taken from water, or from other membrane proteins in the electron transport chain. The thylakoid membrane is simply coursing with electricity.

## The Z scheme

* A chlorophyll molecule has a heme containing a mg+ (magnesium) atom in the center. It also has a long tail.
* When light is absorbed by chlorophyll, an electron in the magnesium atom jumps from the ground state to an excited state. This electron is farther away from the center of the atom.
* The chlorophyll molecule is right next to another molecule which grabs electrons. When the electron gets far enough away from the center of the atom, this molecule steals the electrons and passes it from molecule to molecule.
* The energy of the electron transfer is used to pump hydrogen atoms across the thylakoid membrane. A high H$^+$ concentration is made in the inner thylakoid space. This high H$^+$ concentration is used to make ATP using the proton channel ATP synthase.
* There are two chlorophyll reactive centers that absorb chlorophyll at different wavelengths. One reactive center dumps the electrons on the other, and the second one finally dumps the electrons on the high energy molecule NADP which forms NADPH+H
* NADP is the final electron acceptor in photosynthesis.
* The magnesium ion that lost the electron in the chlorophyll atom at the beginning is now a very unhappy ion. It steals an electron from water to get back to a normal state. Water breaks apart into hydrogen ions and oxygen gas. This is why plants release oxygen.
* Water is the initial electron donor in photosynthesis
Reading
* Wikipedia:Photosystem
* Wikipedia:Photophosphorylation
* Photosynthetic reaction center
* Wikipedia:Light_harvesting_complex
* Wikipedia:Photosynthetic_pigment
* Wikipedia:Chemiosmosis

## C$_3$ and C$_4$ Plants

The steps of the Calvin cycle were discovered by Melvin_Calvin using a radioactive isotope of Carbon. An isotope is an atom that has a different number of neutrons in the nucleus. Carbon normally has 6 protons and 6 neutrons and is called carbon 12, but when it has 8 neutrons it is called carbon 14 and it will emit radiation that can expose a piece of film.
Calvin and his associates added radioactive carbon dioxide to a green algae, Chlorella pyrenoidosa and then dropped them into boiling ethanol to immediately kill the cells. They did 2D paper chromatography on the chloroplasts, and placed a piece of film over it. As the Calvin cycle incorporated the radioactive carbon dioxide, new molecules containing C$_{14}$ appeared. These molecules exposed the film directly over their location on the piece of paper. The exposed film is called an autoradiograph. Calvin and his associates later used various techniques to identify the chemicals.
They showed that carbon dioxide first appeared in a 3-carbon compound called 3-PGA. And by watching which chemicals appeared they were able to determine the order of the steps in the Calvin cycle.
The first step in the Calvin cycle is the one catalyzed by Rubisco. Where the 5-carbon compound Ribulose Bis-Phosphate is added to CO$_2$ to make a six carbon intermediate. The six carbon intermediate is very unstable and breaks apart into two 3-PGA molecules which is why it wasn't seen on the audoradiograph.
The Calvin cycle was thus considered solved, until in 1965 when some researchers in Hawaii (Kortshak, Hartt, and Burr) redid the experiment in sugarcane and got a different result. Their first intermediates were the four-carbon molecules malic and aspartic acid. They found that many tropical plants gave this same result including: Maize (corn), oats, and bamboo.
They called these plants C$_4$ plants whereas other plants were called C$_3$ plants.
Most plants including algaes, trees, and shrubs are C$_3$ plants. Only about 0.4% of species studied have C$_4$ metabolism, but they include some of the most important food crops. That is why this mechanism is considered significant.

### What is the metabolism of C4 plants?

C$_4$ plants contain a molecule called PEP carboxylase that can capture CO$_2$ from the air and place it on a molecule of Phosphoenolpyruvate(PEP - 3C) to make Oxaloacetate (4C). This is a reversible reaction and the CO$_2$ can be released if the concentration of CO$_2$ in the leaf drops.
This is used to solve a major problem with the enzyme Rubisco which forms the first step of the Calvin cycle. Rubisco was thought to have evolved when atmospheric levels of O$_2$ were low. Because of this, Rubisco cannot tell the difference between a molecule of CO$_2$ and a molecule of O$_2$. If it adds O$_2$ to RUBP, it does not make a six carbon molecule. This is a wasteful process called photorespiration.
This means if O$_2$ levels are high in the cell, then the cell will waste energy NOT making sugar. Cells are constantly making oxygen in the light reactions of photosynthesis and this O$_2$ diffuses out of the cells through pores in the bottom of the leaf called stomata.
However, when the weather is dry, leaves close their stomata to conserve water. This causes a buildup of O$_2$ in the leaves that can cause photorespiration.
C$_4$ plants capture CO$_2$ (mostly at night when the stomata are open) and store it in the stable four-carbon sugar oxaloacetate until needed. When the stomata are closed, and O$_2$ levels begin to build up, they release the CO$_2$ into the leaf so that photosynthesis can continue.
For this reason, if a C$_4$ plant and a C$_3$ plant (such as wheat and corn) are placed side by side in a dry environment, the C$_4$ plant (corn) can stay healthy and green even when the C$_3$ plant begins to wilt and brown. It is able to take harsher conditions. C$_4$ plants are known to have enlarged bundle sheathe cells, and this is where C$_4$ metabolism occurs.

### CAM metabolism (crassulacean acid metabolism)

Cactus and succulents such as lillies and orchids can also capture and store CO$_2$ with PEPcarboxylase. They store them in the leaves as malic acid (4C) and release it when needed. Unlike C4 plant, however, all of the leaf cells can do this metabolism, not just the bundle sheathe cells.
CAM and C4 are thought to be later adaptations which developed to repair defects in the original carbon fixation process.
Reading
* Wikipedia:RuBisCO
* Wikipedia:Calvin-Benson_cycle
* Wikipedia:Carbon_fixation
* Wikipedia:C4_carbon_fixation
* Wikipedia:Melvin_Calvin
* Wikipedia:Carbon-14
* Wikipedia:Paper_chromatography

## References

Salisbury, Frank B. and Cleon W. Ross.1985. Plant Physiology. Wadsworth publishing. ISBN 0-534-04482-4
Stern, Kingsley R., Shelley Jansky, and James E Bidlack.2003. Introductory Plant Biology. McGraw-Hill publishing. ISBN 0-07-290941-2

## Detail level

Easy
* Why are plants green?
* Why do leaves change color in the fall?
Intermediate
* Light and Dark reactions,
* Accessory pigments
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