Chemistry for Biologists: Photosynthesis
Leaves and leaf       structure | The structure of the chloroplast       and photosynthetic membranes | Stages of       photosynthesis | Non-cyclic phosphorylation       (the Z scheme) | Chemiosmosis and ATP       synthesis | Cyclic phosphorylation | The light-independent reactions | Summary of stages of photosynthesis | Factors affecting the rate of photosynthesis | Test your knowledge
Photosynthesis
Photosynthesis is the process by which plants, some       bacteria and some protistans use the energy from sunlight to produce glucose       from carbon dioxide and water. This glucose can be converted into pyruvate       which releases adenosine triphosphate (ATP) by cellular respiration. Oxygen is       also formed.
Photosynthesis may be summarised by the word equation:
carbon dioxide +         water
glucose + oxygen
The conversion of usable sunlight energy into chemical energy       is associated with the action of the green pigment chlorophyll.
Chlorophyll is a complex molecule. Several modifications of       chlorophyll occur among plants and other photosynthetic organisms. All       photosynthetic organisms 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.
Chlorophyll - click on image to open
All chlorophylls have:
a lipid-soluble hydrocarbon tail       (C20H39 -)
a flat hydrophilic head with a magnesium ion at its centre;       different chlorophylls have different side-groups on the head
The tail and head are linked by an ester bond.
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.
Water enters the root and is transported up to the leaves       through specialized plant cells known as xylem vessels. Land plants must guard       against drying out 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 the stoma (the singular of stomata),       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 of water is also lost. Cottonwood trees, for example, will lose       100 gallons (about 450 dm3) of water per hour during hot desert       days.
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
When chlorophyll a absorbs light energy, an electron gains       energy and is 'excited'. The excited electron is transferred to another       molecule (called a primary electron acceptor). The chlorophyll molecule is       oxidized (loss of electron) and has a positive charge. Photoactivation of       chlorophyll a results in the splitting of water molecules and the transfer of       energy to ATP and reduced nicotinamide adenine dinucleotide phosphate       (NADP).
The chemical reactions involved include:
condensation reactions - responsible for water molecules       splitting out, including phosphorylation (the addition of a phosphate group to       an organic compound)
oxidation/reduction (redox) reactions involving electron       transfer
Photosynthesis is a two stage process.
The Light dependent reactions, a light-dependent series       of reactions which occur in the grana, and require the direct energy of       light to make energy-carrier molecules that are used in the second process:
light energy is trapped by chlorophyll to make ATP         (photophosphorylation)
at the same time water is split into oxygen, hydrogen ions         and free electrons:
2H2O  
  4H+ +         O2 + 4e- (photolysis)
the electrons then react with a carrier molecule         nicotinamide adenine dinucleotide phosphate (NADP), changing it from its         oxidised state (NADP+) to its reduced state (NADPH):
NADP+ + 2e- +         2H+  
  NADPH + H+
The light-independent reactions, a light-independent       series of reactions which occur in the stroma of the chloroplasts, when the       products of the light reaction, ATP and NADPH, are used to make carbohydrates       from carbon dioxide (reduction); initially glyceraldehyde 3-phosphate (a       3-carbon atom molecule) is formed.
The light-dependent reactions
When light energy is absorbed by a chlorophyll molecule its       electrons gain energy and move to higher energy levels in the molecule       (photoexcitation). Sufficient energy ionises the molecule, with the electron       being 'freed' leaving a positively charged chlorophyll ion. This is called       photoionisation.
In whole chloroplasts each chlorophyll molecule is associated       with an electron acceptor and an electron donor. These three       molecules make up the core of a photosystem. Two electrons from a       photoionised chlorophyll molecule are transferred to the electron acceptor. The       positively charged chlorophyll ion then takes a pair of electrons from a       neighbouring electron donor such as water.
An electron transfer system (a series of chemical reactions)       carries the two electrons to and fro across the thylakoid membrane. The energy       to drive these processes comes from two photosystems:
Photosystem II (PSII) (P680)
Photosystem I (PSI) (P700)
It may seem confusing, but PSII occurs before PSI. It       is named because it was the second to be discovered and hence named second.
The energy changes accompanying the two sets of changes make a       Z shape when drawn out. This is why the electron transfer process is sometimes       called the Z scheme. Key to the scheme is that sufficient energy is released       during electron transfer to enable ATP to be made from ADP and phosphate.
Chemiosmosis and ATP synthesis
The components of non-cyclic phosphorylation are found in the       thylakoid membranes of the chloroplast. Electrons passing through the transport       chain provide energy to pump H+ ions from the stroma, across the       thylakoid membrane into the thylakoid compartment. H+ ions are more       concentrated in the thylakoid compartment than in the stroma. We say there is an       electrochemical gradient. H+ ions diffuse from the high to the low       regions of concentration. This drives the production of ATP.
 
Cyclic phosphorylation
The net effect of non-cyclic phosphorylation is to pass       electrons from water to NADP. Energy released enables the production of ATP.       But much more ATP is needed to drive the light-independent reactions.
This extra energy is obtained from cyclic phosphorylation.       This involves only Photosystem I which generates excited electrons. These are       transferred to the electron transport chain between PSII and PSI, rather than       to NADP+ and so no NADPH is formed. The cycle is completed by       electrons being transported back to PSI by the electron transport system.
The light-independent reactions
In the Light-Independent Process (the Dark reaction) carbon       dioxide from the atmosphere (or water for aquatic/marine organisms) is captured       and modified by the addition of hydrogen to form carbohydrates. 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.
Carbon dioxide combines with a five-carbon sugar, ribulose       1,5-biphosphate (RuBP). A six-carbon sugar forms but is unstable. Each molecule       breaks down to form two glycerate 3-phosphate (GP) molecules.
These glycerate 3-phosphate (GP) molecules are phosphorylated       by ATP into glycerate diphosphate molecules.
These are reduced by NADPH to two molecules of glyceraldehyde       3-phosphate (GALP).
Of each pair of GALP molecules produced:
one molecule is the initial end product of photosynthesis;       it is quickly converted to glucose and other carbohydrates, lipids or amino       acids
one molecule forms RuBP through a series of chemical       reactions
The first steps 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 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 six RuBP molecules, and thus start the cycle again.
Factors affecting the rate of       photosynthesis
The main factors are light intensity, carbon dioxide       concentration and temperature, known as limiting factors.
As light intensity increases, the rate of the light-dependent       reaction, and therefore photosynthesis generally, increases proportionately. As       light intensity is increased however, the rate of photosynthesis is eventually       limited by some other factor. Chlorophyll a is used in both photosystems. The       wavelength of light is also important. PSI absorbs energy most efficiently at       700 nm and PSII at 680 nm. Light with a high proportion of energy concentrated       in these wavelengths will produce a high rate of photosynthesis.
An increase in the carbon dioxide concentration increases the       rate at which carbon is incorporated into carbohydrate in the light-independent       reaction and so the rate of photosynthesis generally increases until limited by       another factor.
Photosynthesis is dependent on temperature. It is a reaction       catalysed by enzymes. As the enzymes approach their optimum temperatures the       overall rate increases. Above the optimum temperature the rate begins to       decrease until it stops.