Photosynthesis - Biology

Photosynthesis - Biology

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Before beginning this exercise, it is necessary to understand that photosynthesis uses light energy to synthesize carbohydrate from carbon dioxide. The equation is below.

[mathrm{6CO_2 + 6H_2O + Energy ightarrow C_6H_{12}O_6 + 6O_2}]

This process requires light for some of the reactions.

It is also necessary to understand that the plant is constantly undergoing cellular respiration according to the equation below.

[mathrm{C_6H_{12}O_6 + 6O_2 ightarrow 6CO_2 + 6H_2O + Energy}]

Notice that these two equations appear to be opposites.

When plants are exposed to light, photosynthesis and cellular respiration both occur. In the dark, only cellular respiration occurs.

We will study photosynthesis in an aquatic plant (Elodea) We can measure the rate of photosynthesis and cellular respiration by measuring the amount of CO2 given off or taken up by the plant.

Carbon dioxide combines with water to form carbonic acid (H2CO3) which dissociates into hydrogen ions (H+) and bicarbonate ions (HCO3-). The pH drops due to the presence of hydrogen ions.

[mathrm{CO_2 + H_2O leftrightarrow H_2CO_3 leftrightarrow H^+ + sideset{ }{_{3}^{-}}{HCO}}]

Respiring plants release CO2 into the water, causing the pH to decline. During photosynthesis, plants take up CO2 and the pH increases.

Using the pH Probe

Set up the pH probe by following the instructions given in the link below.

Procedure for Measuring Photosynthesis

Create a hypothesis for this experiment.

Be sure to use tap water for the experiments below. Distilled water should not be used.

After the probe is set up (see the step above), obtain two large test tubes for this experiment. A ring stand can be used to hold the tubes as shown in the photograph below.

Rinse both tubes and stoppers thoroughly with tap water to remove any traces of contaminants that might affect pH.

Fill each tube with tap water to approximately 2 cm from the top.

Cut a sprig of Elodea that is long enough to fill the entire length of one tube but not protrude from the water. The length of the stem can be adjusted, if necessary, by cutting a piece from the base of the stem. Put the plant in one of the tubes. The other tube will serve as a control.

Clamp the two tubes on a ring stand to hold them.

Insert one pH probe into each test tube.

When the pH stabilizes, record the pH in each tube and then turn on the lamp and begin timing the experiment. The pH probes can be kept in the tubes until the experiment is finished.

Record the pH of the water in each tube every 10 minutes for one hour. Your data table will have 7 pH readings for each tube.

You should begin the chromatography procedure (below) while waiting to take pH readings.


Create a hypothesis for this experiment.

During photosynthesis, light energy is absorbed by photosynthetic pigments. Chlorophyll A is the main photosynthetic pigment but chlorophyll B, carotenes, and xanthophylls also absorb light. Each pigment absorbs a specific range of colors but all of them together enable the plant to use a larger amount of light. These pigments absorb red and blue light best and absorb green the least. Plants look green; because the green light is not absorbed by the plant; it is reflected.

Chromatography is a technique used to separate the components of a mixture. In this investigation, you will use chromatography to separate and identify several photosynthetic pigments in a solution prepared from spinach leaves.

Paper chromatography can be used to separate the components of a mixture based on their polarity. Some of the mixture is placed on one end of a piece of paper and that end of the paper is immersed in a nonpolar liquid (see the diagram below).

Click on the photograph to view an enlargement.

As the liquid moves up the paper, the molecules of the sample mixture will also move. Polar molecules within the sample will spend most of their time bound to the polar surface of the paper and will therefore not move very much. Nonpolar molecules, however, will spend most of their time dissolved in the liquid as it moves up the paper. When the liquid reaches the top of the paper, these molecules will also have traveled most of the way to the top. The two types of molecules (polar and nonpolar) are now separated.


It is useful to determine the relative distance moved by a particular kind of molecule using chromatography. This value is known as Rf. For example, if the molecules move half as far as the solvent traveled, the Rf = 0.5. If the molecules moved 1/4 the distance, the Rf = 0.25. The maximum value for Rf is therefore 1.0.


Using a pencil, put a small dot in the center of a strip of chromatography paper 2 cm. from one end.

Put a hole in the other end of the paper so that it can be suspended on a wire clip inserted in a cork stopper as shown in the photograph above. The paper should be able to reach to within 1 cm of the bottom of the tube but not touch the bottom.

When the apparatus is adjusted properly, remove the paper so that you can add pigment extract.

Caution - The remainder of this procedure should be conducted under the hood because the vapors from the chemicals used are toxic and carcinogenic (cause cancer).

Use a micropipette to place a 5 ul of pigment extract on the dot that you marked on the paper. The extract should be placed directly on top of the dot. It will spread, producing a small circular spot. Allow the spot to dry for 1 minute and repeat this procedure 4 more times for a total of 5 applications of pigment extract. Allow the spot to dry between each application.

The paper in the top photograph has had one application of extract. After 5 applications, your paper should look like the one in the bottom photograph. Click on the photographs to view enlargements.

While waiting for the paper to dry after the fifth application, add chromatography solvent to the bottom of the chromatography tube. Add enough solvent so that the end of the chromatography paper will be immersed in the solvent but the spot with pigment extract will remain above the solvent. It is important not to immerse the pigment spot. This tube should be kept under the hood at all times.

When the spot has dried, suspend the paper vertically in a chromatography tube. If possible, keep the paper from touching the sides of the tube.

Check the movement of the solvent after 20 minutes. The paper should be removed before the solvent reaches the top of the paper.

Before the solvent dries, draw a line on the paper that shows how far the solvent moved. One end of the paper should have a dot that indicates where the pigments were applied and the other end should have a line that indicates how far the solvent traveled.

Allow the paper to dry under the hood. After the paper is dried, you may bring it out from under the hood.

Do not discard the chromatography solution down the drain, discard it in the beaker provided under the hood.

The photosynthetic pigments will be separated in the following order beginning with the highest Rf: beta-carotenes, xanthophylls, chlorophyll a, chlorophyll b. Beta-carotenes are orange or orange-yellow, xanthophylls are yellow, chlorophyll A is blue-green, and chlorophyll B is olive-green.

The proportion of the total distance moved by the spot is often calculated in chromatography procedures. To calculate this value, you must first measure the distance moved by the solvent. This can be done by measuring the distance from the spot to the top of the paper. Next, measure the distance moved by each of the pigments.

Rf = distance moved by the pigment/distance moved by the solvent

For each of the pigments (beta-carotenes, xanthophylls, chlorophyll a, chlorophyll b) record the distance moved and the Rf.

One member of your group should paste the chromatogram in their notebook. The names of the members of your group should be listed next to the chromatogram.


Click to enlarge


Create a graph of your results from the photosynthesis experiment. Put time on the X-axis and pH on the Y-axis. If you have a notebook with quad-ruled pages, you can draw the graph directly in your notebook. If not, use graph paper or use a computer graphing program such as Excel or LibreOffice.

Adjust the graph so that the minimum value of the Y-axis is a number that is slightly less than the minimum value observed in the table above. The maximum value should be equal to or slightly greater than the maximum value of the data. For example, suppose that the minimum pH that you measured was 5.9 and the maximum was 7.3. You could make the minimum on the graph 5.5 and the maximum 7.5.

Be sure that you clearly identify the two lines on the graph. For example, you could use circles for points on one line and squares for points on the other line.

  1. What will happen to the pH of water when CO2 is dissolved in the water?
  2. Write the equation that describes what happens when CO2 is dissolved in water.
  3. What will happen to the pH of water when CO2 is removed from the water?
  4. Two kinds of metabolic reactions caused the pH to change in the tube with the plant. One of these processes caused the pH to increase, the other caused it to decrease. Name these processes and tell which causes the pH to increase and which causes the pH to decline.
  5. The two processes listed above had opposite effects on the pH. Why did the pH increase in the light tube if both of these process were occurring at the same time?
  6. Explain why the values produced from the tube with the plant do not reflect the total photosynthesis (total CO2 consumption) of the plant. [Hint - Think about your answer to questions 4 and 5.]
  7. Explain why the pH of the tube with the plant might stop increasing toward the end of the 60 minute time period. The diagram above may be helpful for answering this question.

Photosynthesis Virtual Lab

This lab was created to replace the popular waterweed simulator which no longer functions because it is flash-based. In this virtual photosynthesis lab, students can manipulate the light intensity, light color, and distance from the light source.

A plant is shown in a beaker and test tube which bubbles to indicate the rate of photosynthesis. Students can measure the rate over time. There is an included data table for students to type into the simulator, but I prefer to give them their own handout, where they can answer other questions and get further instructions on how to run the simulator. The document is made with google docs so that it can be shared with remote students.

There are several experiments that can be done in the lab that would complement this virtual experiment. For example, students can use elodea and measure the number of bubbles released when the plant is under a bright light. Algae beads can also be used to measure changes in pH as the plants consume carbon dioxide.

In experiment 2, students specifically look at light color to determine which wavelength of light increases the rate of photosynthesis. Students should discover that green light has a very slow rate. Their collected data is then compared to a graph of the absorption spectrum of light.


General Process of Photosynthesis

  • Sunlight is absorbed by chlorophyll (found in thylakoidmembranes of the chloroplast).
  • Chlorophyll molecules are arranged into photosystems.
  • This absorbed energy is used to split water into three different components:
    1. Hydrogen ions (also called protons) are stored in the chloroplast – an area called the proton pool.
    2. Oxygen passes out of plant cell and leaf into the atmosphere.
    3. Electrons are given to chlorophyll.
  • Chlorophyll that has energy because of sunlight transfers that energy to its electrons, creating high-energy electrons.
  • These high-energy electrons are combined with protons and carbon dioxide to make glucose.

Detailed Process of Photosynthesis

Photosynthesis occurs in the chloroplast in two stages:

  • Light stage – requires the direct input of light and occurs in the thylakoid membranes.
  • Dark stage (light-independent stage OR Calvin Cycle) – does not require the direct input of light and occurs in the stroma.

Light Stage

  • Sunlight photon strikes a cluster of chlorophyll molecules called a photosystem.
  • The chlorophyll molecules transfer the energy to a reaction center chlorophyll (RCC).
  • The energy is absorbed by an electron which becomes a ‘high-energy electron‘.
  • The energised electron is released from the RCC and can take one of two paths:

1. Cyclic pathway (pathway 1)
2. Non-cyclic pathway (pathway 2)

A photosystem

1. Cyclic pathway
  • The energised electron is picked up by an electron acceptor.
  • It is passed from electron acceptor to electron acceptor losing energy along the way.
  • This energy is used to power the production of ATP from ADP and a phosphate.
  • Once the electron has been passed through it is taken back up by the RCC (chlorophyll).
  • The ATP is passed onto the next stage of photosynthesis – the dark stage.
2. Non-cyclic pathway (pathway 2)
  • The energised electron is picked up by an electron acceptor.
  • It is passed from electron acceptor to electron acceptor losing energy along the way.
  • This energy is used to power the production of ATP from ADP and a phosphate.
  • The photosystem is deficient in electrons and splits water into electrons, protons and oxygen gas (photolysis).
  • The electrons are taken up by the photosystem, the protons are stored in a proton pool within the chloroplast and the oxygen gas is either released into the atmosphere or used in respiration.
  • The electrons that passed through the electron acceptors are now low-energy electrons and are now passed onto another photosystem.
  • Light strikes this second photosystem and the electrons are re-energised.
  • The electrons are released and captured by NADP + to become NADP – .
  • Protons are attracted towards and taken up by NADP – to become NADPH.
  • NADPH and ATP are passed onto the next stage of photosynthesis – the dark stage.

Dark Stage (Calvin cycle)

  • NADPH and ATP from the light stage are used to reduce (addition of protons and electrons) carbondioxide in the stroma of the chloroplast.
  • Glucose isformed in this reaction.
  • As a result, NADPH is converted back to NADP + and ATP is converted back to ADP and a phosphate.

Mandatory Experiment: to investigate the effect of light intensity OR carbon dioxide concentration on the rate of photosynthesis


  • Pondweed (Elodea)
  • Metre stick
  • Pond water
  • Thermometer
  • Paperclip
  • Sodium hydrogen carbonate
  • Stopwatch
  • Backed blade
  • Strong fluorescent light source
  • Beaker and test tube


  • Obtain fresh pondweed.
  • Cut a small section using the backed blade and crush the cut end slightly between your fingers.
  • Place pondweed in a test tube with pond water.
  • Ensure the cut end is facing upwards and weigh the pondweed down by attaching a paperclip.
  • Shine the strong light source on the pondweed for 5 minutes to allow the pondweed to adjust.
  • Move the light source various distances from the pondweed.
  • Allow the pondweed to adjust to each new light intensity for 5 minutes before counting the number of bubbles per minute.
  • Count the number of bubbles per minute at each distance.
  • Calculate the light intensity at each distance by using the following formula: 1 /d 2 (where d is the distance from the light source)
  • Fill in the table below:
Apparatus setup for examining the effect of light intensity on the rate of photosynthesis


Photosynthetic organisms are photoautotrophs, which means that they are able to synthesize food directly from carbon dioxide and water using energy from light. However, not all organisms use carbon dioxide as a source of carbon atoms to carry out photosynthesis photoheterotrophs use organic compounds, rather than carbon dioxide, as a source of carbon. [4] In plants, algae, and cyanobacteria, photosynthesis releases oxygen. This is called oxygenic photosynthesis and is by far the most common type of photosynthesis used by living organisms. Although there are some differences between oxygenic photosynthesis in plants, algae, and cyanobacteria, the overall process is quite similar in these organisms. There are also many varieties of anoxygenic photosynthesis, used mostly by certain types of bacteria, which consume carbon dioxide but do not release oxygen.

Carbon dioxide is converted into sugars in a process called carbon fixation photosynthesis captures energy from sunlight to convert carbon dioxide into carbohydrate. Carbon fixation is an endothermic redox reaction. In general outline, photosynthesis is the opposite of cellular respiration: while photosynthesis is a process of reduction of carbon dioxide to carbohydrate, cellular respiration is the oxidation of carbohydrate or other nutrients to carbon dioxide. Nutrients used in cellular respiration include carbohydrates, amino acids and fatty acids. These nutrients are oxidized to produce carbon dioxide and water, and to release chemical energy to drive the organism's metabolism. Photosynthesis and cellular respiration are distinct processes, as they take place through different sequences of chemical reactions and in different cellular compartments.

The general equation for photosynthesis as first proposed by Cornelis van Niel is therefore: [14]

CO2 carbon
dioxide + 2H2A electron donor + photons light energy → [CH2O] carbohydrate + 2A oxidized
donor + H2O water

Since water is used as the electron donor in oxygenic photosynthesis, the equation for this process is:

CO2 carbon
dioxide + 2H2O water + photons light energy → [CH2O] carbohydrate + O2 oxygen + H2O water

This equation emphasizes that water is both a reactant in the light-dependent reaction and a product of the light-independent reaction, but canceling n water molecules from each side gives the net equation:

CO2 carbon
dioxide + H2O water + photons light energy → [CH2O] carbohydrate + O2 oxygen

Other processes substitute other compounds (such as arsenite) for water in the electron-supply role for example some microbes use sunlight to oxidize arsenite to arsenate: [15] The equation for this reaction is:

CO2 carbon
dioxide + (AsO 3−
3 )
arsenite + photons light energy → (AsO 3−
4 )
arsenate + CO carbon
monoxide (used to build other compounds in subsequent reactions) [16]

Photosynthesis occurs in two stages. In the first stage, light-dependent reactions or light reactions capture the energy of light and use it to make the energy-storage molecules ATP and NADPH. During the second stage, the light-independent reactions use these products to capture and reduce carbon dioxide.

Most organisms that utilize oxygenic photosynthesis use visible light for the light-dependent reactions, although at least three use shortwave infrared or, more specifically, far-red radiation. [17]

Some organisms employ even more radical variants of photosynthesis. Some archaea use a simpler method that employs a pigment similar to those used for vision in animals. The bacteriorhodopsin changes its configuration in response to sunlight, acting as a proton pump. This produces a proton gradient more directly, which is then converted to chemical energy. The process does not involve carbon dioxide fixation and does not release oxygen, and seems to have evolved separately from the more common types of photosynthesis. [18] [19]

  1. outer membrane
  2. intermembrane space
  3. inner membrane (1+2+3: envelope)
  4. stroma (aqueous fluid)
  5. thylakoid lumen (inside of thylakoid)
  6. thylakoid membrane
  7. granum (stack of thylakoids)
  8. thylakoid (lamella)
  9. starch
  10. ribosome
  11. plastidial DNA
  12. plastoglobule (drop of lipids)

In photosynthetic bacteria, the proteins that gather light for photosynthesis are embedded in cell membranes. In its simplest form, this involves the membrane surrounding the cell itself. [20] However, the membrane may be tightly folded into cylindrical sheets called thylakoids, [21] or bunched up into round vesicles called intracytoplasmic membranes. [22] These structures can fill most of the interior of a cell, giving the membrane a very large surface area and therefore increasing the amount of light that the bacteria can absorb. [21]

In plants and algae, photosynthesis takes place in organelles called chloroplasts. A typical plant cell contains about 10 to 100 chloroplasts. The chloroplast is enclosed by a membrane. This membrane is composed of a phospholipid inner membrane, a phospholipid outer membrane, and an intermembrane space. Enclosed by the membrane is an aqueous fluid called the stroma. Embedded within the stroma are stacks of thylakoids (grana), which are the site of photosynthesis. The thylakoids appear as flattened disks. The thylakoid itself is enclosed by the thylakoid membrane, and within the enclosed volume is a lumen or thylakoid space. Embedded in the thylakoid membrane are integral and peripheral membrane protein complexes of the photosynthetic system.

Plants absorb light primarily using the pigment chlorophyll. The green part of the light spectrum is not absorbed but is reflected which is the reason that most plants have a green color. Besides chlorophyll, plants also use pigments such as carotenes and xanthophylls. [23] Algae also use chlorophyll, but various other pigments are present, such as phycocyanin, carotenes, and xanthophylls in green algae, phycoerythrin in red algae (rhodophytes) and fucoxanthin in brown algae and diatoms resulting in a wide variety of colors.

These pigments are embedded in plants and algae in complexes called antenna proteins. In such proteins, the pigments are arranged to work together. Such a combination of proteins is also called a light-harvesting complex. [24]

Although all cells in the green parts of a plant have chloroplasts, the majority of those are found in specially adapted structures called leaves. Certain species adapted to conditions of strong sunlight and aridity, such as many Euphorbia and cactus species, have their main photosynthetic organs in their stems. The cells in the interior tissues of a leaf, called the mesophyll, can contain between 450,000 and 800,000 chloroplasts for every square millimeter of leaf. The surface of the leaf is coated with a water-resistant waxy cuticle that protects the leaf from excessive evaporation of water and decreases the absorption of ultraviolet or blue light to reduce heating. The transparent epidermis layer allows light to pass through to the palisade mesophyll cells where most of the photosynthesis takes place.

In the light-dependent reactions, one molecule of the pigment chlorophyll absorbs one photon and loses one electron. This electron is passed to a modified form of chlorophyll called pheophytin, which passes the electron to a quinone molecule, starting the flow of electrons down an electron transport chain that leads to the ultimate reduction of NADP to NADPH. In addition, this creates a proton gradient (energy gradient) across the chloroplast membrane, which is used by ATP synthase in the synthesis of ATP. The chlorophyll molecule ultimately regains the electron it lost when a water molecule is split in a process called photolysis, which releases a dioxygen (O2) molecule as a waste product.

The overall equation for the light-dependent reactions under the conditions of non-cyclic electron flow in green plants is: [25]

Not all wavelengths of light can support photosynthesis. The photosynthetic action spectrum depends on the type of accessory pigments present. For example, in green plants, the action spectrum resembles the absorption spectrum for chlorophylls and carotenoids with absorption peaks in violet-blue and red light. In red algae, the action spectrum is blue-green light, which allows these algae to use the blue end of the spectrum to grow in the deeper waters that filter out the longer wavelengths (red light) used by above-ground green plants. The non-absorbed part of the light spectrum is what gives photosynthetic organisms their color (e.g., green plants, red algae, purple bacteria) and is the least effective for photosynthesis in the respective organisms.

Z scheme

In plants, light-dependent reactions occur in the thylakoid membranes of the chloroplasts where they drive the synthesis of ATP and NADPH. The light-dependent reactions are of two forms: cyclic and non-cyclic.

In the non-cyclic reaction, the photons are captured in the light-harvesting antenna complexes of photosystem II by chlorophyll and other accessory pigments (see diagram at right). The absorption of a photon by the antenna complex frees an electron by a process called photoinduced charge separation. The antenna system is at the core of the chlorophyll molecule of the photosystem II reaction center. That freed electron is transferred to the primary electron-acceptor molecule, pheophytin. As the electrons are shuttled through an electron transport chain (the so-called Z-scheme shown in the diagram), it initially functions to generate a chemiosmotic potential by pumping proton cations (H + ) across the membrane and into the thylakoid space. An ATP synthase enzyme uses that chemiosmotic potential to make ATP during photophosphorylation, whereas NADPH is a product of the terminal redox reaction in the Z-scheme. The electron enters a chlorophyll molecule in Photosystem I. There it is further excited by the light absorbed by that photosystem. The electron is then passed along a chain of electron acceptors to which it transfers some of its energy. The energy delivered to the electron acceptors is used to move hydrogen ions across the thylakoid membrane into the lumen. The electron is eventually used to reduce the co-enzyme NADP with a H + to NADPH (which has functions in the light-independent reaction) at that point, the path of that electron ends.

The cyclic reaction is similar to that of the non-cyclic but differs in that it generates only ATP, and no reduced NADP (NADPH) is created. The cyclic reaction takes place only at photosystem I. Once the electron is displaced from the photosystem, the electron is passed down the electron acceptor molecules and returns to photosystem I, from where it was emitted, hence the name cyclic reaction.

Water photolysis

Linear electron transport through a photosystem will leave the reaction center of that photosystem oxidized. Elevating another electron will first require re-reduction of the reaction center. The excited electrons lost from the reaction center (P700) of photosystem I are replaced by transfer from plastocyanin, whose electrons come from electron transport through photosystem II. Photosystem II, as the first step of the Z-scheme, requires an external source of electrons to reduce its oxidized chlorophyll a reaction center, called P680. The source of electrons for photosynthesis in green plants and cyanobacteria is water. Two water molecules are oxidized by four successive charge-separation reactions by photosystem II to yield a molecule of diatomic oxygen and four hydrogen ions. The electrons yielded are transferred to a redox-active tyrosine residue that then reduces the oxidized P680. This resets the ability of P680 to absorb another photon and release another photo-dissociated electron. The oxidation of water is catalyzed in photosystem II by a redox-active structure that contains four manganese ions and a calcium ion this oxygen-evolving complex binds two water molecules and contains the four oxidizing equivalents that are used to drive the water-oxidizing reaction (Dolai's S-state diagrams). Photosystem II is the only known biological enzyme that carries out this oxidation of water. The hydrogen ions are released in the thylakoid lumen and therefore contribute to the transmembrane chemiosmotic potential that leads to ATP synthesis. Oxygen is a waste product of light-dependent reactions, but the majority of organisms on Earth use oxygen for cellular respiration, including photosynthetic organisms. [26] [27]

Calvin cycle

In the light-independent (or "dark") reactions, the enzyme RuBisCO captures CO2 from the atmosphere and, in a process called the Calvin cycle, it uses the newly formed NADPH and releases three-carbon sugars, which are later combined to form sucrose and starch. The overall equation for the light-independent reactions in green plants is [25] : 128

Carbon fixation produces the intermediate three-carbon sugar product, which is then converted into the final carbohydrate products. The simple carbon sugars produced by photosynthesis are then used in the forming of other organic compounds, such as the building material cellulose, the precursors for lipid and amino acid biosynthesis, or as a fuel in cellular respiration. The latter occurs not only in plants but also in animals when the energy from plants is passed through a food chain.

The fixation or reduction of carbon dioxide is a process in which carbon dioxide combines with a five-carbon sugar, ribulose 1,5-bisphosphate, to yield two molecules of a three-carbon compound, glycerate 3-phosphate, also known as 3-phosphoglycerate. Glycerate 3-phosphate, in the presence of ATP and NADPH produced during the light-dependent stages, is reduced to glyceraldehyde 3-phosphate. This product is also referred to as 3-phosphoglyceraldehyde (PGAL) or, more generically, as triose phosphate. Most (5 out of 6 molecules) of the glyceraldehyde 3-phosphate produced is used to regenerate ribulose 1,5-bisphosphate so the process can continue. The triose phosphates not thus "recycled" often condense to form hexose phosphates, which ultimately yield sucrose, starch and cellulose. The sugars produced during carbon metabolism yield carbon skeletons that can be used for other metabolic reactions like the production of amino acids and lipids.

Carbon concentrating mechanisms

On land

In hot and dry conditions, plants close their stomata to prevent water loss. Under these conditions, CO
2 will decrease and oxygen gas, produced by the light reactions of photosynthesis, will increase, causing an increase of photorespiration by the oxygenase activity of ribulose-1,5-bisphosphate carboxylase/oxygenase and decrease in carbon fixation. Some plants have evolved mechanisms to increase the CO
2 concentration in the leaves under these conditions. [28]

Plants that use the C4 carbon fixation process chemically fix carbon dioxide in the cells of the mesophyll by adding it to the three-carbon molecule phosphoenolpyruvate (PEP), a reaction catalyzed by an enzyme called PEP carboxylase, creating the four-carbon organic acid oxaloacetic acid. Oxaloacetic acid or malate synthesized by this process is then translocated to specialized bundle sheath cells where the enzyme RuBisCO and other Calvin cycle enzymes are located, and where CO
2 released by decarboxylation of the four-carbon acids is then fixed by RuBisCO activity to the three-carbon 3-phosphoglyceric acids. The physical separation of RuBisCO from the oxygen-generating light reactions reduces photorespiration and increases CO
2 fixation and, thus, the photosynthetic capacity of the leaf. [29] C4 plants can produce more sugar than C3 plants in conditions of high light and temperature. Many important crop plants are C4 plants, including maize, sorghum, sugarcane, and millet. Plants that do not use PEP-carboxylase in carbon fixation are called C3 plants because the primary carboxylation reaction, catalyzed by RuBisCO, produces the three-carbon 3-phosphoglyceric acids directly in the Calvin-Benson cycle. Over 90% of plants use C3 carbon fixation, compared to 3% that use C4 carbon fixation [30] however, the evolution of C4 in over 60 plant lineages makes it a striking example of convergent evolution. [28]

Xerophytes, such as cacti and most succulents, also use PEP carboxylase to capture carbon dioxide in a process called Crassulacean acid metabolism (CAM). In contrast to C4 metabolism, which spatially separates the CO
2 fixation to PEP from the Calvin cycle, CAM temporally separates these two processes. CAM plants have a different leaf anatomy from C3 plants, and fix the CO
2 at night, when their stomata are open. CAM plants store the CO
2 mostly in the form of malic acid via carboxylation of phosphoenolpyruvate to oxaloacetate, which is then reduced to malate. Decarboxylation of malate during the day releases CO
2 inside the leaves, thus allowing carbon fixation to 3-phosphoglycerate by RuBisCO. Sixteen thousand species of plants use CAM. [31]

Calcium oxalate accumulating plants, such as Amaranthus hybridus and Colobanthus quitensis, showed a variation of photosynthesis where calcium oxalate crystals function as dynamic carbon pools, supplying carbon dioxide (CO2) to photosynthetic cells when stomata are partially or totally closed. This process was named Alarm photosynthesis. Under stress conditions (e.g. water deficit) oxalate released from calcium oxalate crystals is converted to CO2 by an oxalate oxidase enzyme and the produced CO2 can support the Calvin cycle reactions. Reactive hydrogen peroxide (H2O2), the byproduct of oxalate oxidase reaction, can be neutralized by catalase. Alarm photosynthesis represents an unknown photosynthetic variation to be added to the already known C4 and CAM pathways. However, alarm photosynthesis, in contrast to these pathways, operates as a biochemical pump that collects carbon from the organ interior (or from the soil) and not from the atmosphere. [32] [33]

In water

Cyanobacteria possess carboxysomes, which increase the concentration of CO
2 around RuBisCO to increase the rate of photosynthesis. An enzyme, carbonic anhydrase, located within the carboxysome releases CO2 from the dissolved hydrocarbonate ions (HCO −
3 ). Before the CO2 diffuses out it is quickly sponged up by RuBisCO, which is concentrated within the carboxysomes. HCO −
3 ions are made from CO2 outside the cell by another carbonic anhydrase and are actively pumped into the cell by a membrane protein. They cannot cross the membrane as they are charged, and within the cytosol they turn back into CO2 very slowly without the help of carbonic anhydrase. This causes the HCO −
3 ions to accumulate within the cell from where they diffuse into the carboxysomes. [34] Pyrenoids in algae and hornworts also act to concentrate CO
2 around RuBisCO. [35]

The overall process of photosynthesis takes place in four stages: [13]

Stage Description Time scale
1 Energy transfer in antenna chlorophyll (thylakoid membranes) femtosecond to picosecond
2 Transfer of electrons in photochemical reactions (thylakoid membranes) picosecond to nanosecond
3 Electron transport chain and ATP synthesis (thylakoid membranes) microsecond to millisecond
4 Carbon fixation and export of stable products millisecond to second

Plants usually convert light into chemical energy with a photosynthetic efficiency of 3–6%. [36] [37] Absorbed light that is unconverted is dissipated primarily as heat, with a small fraction (1–2%) [38] re-emitted as chlorophyll fluorescence at longer (redder) wavelengths. This fact allows measurement of the light reaction of photosynthesis by using chlorophyll fluorometers. [38]

Actual plants' photosynthetic efficiency varies with the frequency of the light being converted, light intensity, temperature and proportion of carbon dioxide in the atmosphere, and can vary from 0.1% to 8%. [39] By comparison, solar panels convert light into electric energy at an efficiency of approximately 6–20% for mass-produced panels, and above 40% in laboratory devices. Scientists are studying photosynthesis in hopes of developing plants with yield increases. [37]

The efficiency of both light and dark reactions can be measured but the relationship between the two can be complex. [40] For example, the ATP and NADPH energy molecules, created by the light reaction, can be used for carbon fixation or for photorespiration in C3 plants. [40] Electrons may also flow to other electron sinks. [41] [42] [43] For this reason, it is not uncommon for authors to differentiate between work done under non-photorespiratory conditions and under photorespiratory conditions. [44] [45] [46]

Chlorophyll fluorescence of photosystem II can measure the light reaction, and Infrared gas analyzers can measure the dark reaction. [47] It is also possible to investigate both at the same time using an integrated chlorophyll fluorometer and gas exchange system, or by using two separate systems together. [48] Infrared gas analyzers and some moisture sensors are sensitive enough to measure the photosynthetic assimilation of CO2, and of ΔH2O using reliable methods [49] CO2 is commonly measured in μmols/(m 2 /s), parts per million or volume per million and H2O is commonly measured in mmol/(m 2 /s) or in mbars. [49] By measuring CO2 assimilation, ΔH2O, leaf temperature, barometric pressure, leaf area, and photosynthetically active radiation or PAR, it becomes possible to estimate, "A" or carbon assimilation, "E" or transpiration, "gs" or stomatal conductance, and Ci or intracellular CO2. [49] However, it is more common to used chlorophyll fluorescence for plant stress measurement, where appropriate, because the most commonly used measuring parameters FV/FM and Y(II) or F/FM' can be made in a few seconds, allowing the measurement of larger plant populations. [46]

Gas exchange systems that offer control of CO2 levels, above and below ambient, allow the common practice of measurement of A/Ci curves, at different CO2 levels, to characterize a plant's photosynthetic response. [49]

Integrated chlorophyll fluorometer – gas exchange systems allow a more precise measure of photosynthetic response and mechanisms. [47] [48] While standard gas exchange photosynthesis systems can measure Ci, or substomatal CO2 levels, the addition of integrated chlorophyll fluorescence measurements allows a more precise measurement of CC to replace Ci. [48] [50] The estimation of CO2 at the site of carboxylation in the chloroplast, or CC, becomes possible with the measurement of mesophyll conductance or gm using an integrated system. [47] [48] [51]

Photosynthesis measurement systems are not designed to directly measure the amount of light absorbed by the leaf. But analysis of chlorophyll-fluorescence, P700- and P515-absorbance and gas exchange measurements reveal detailed information about e.g. the photosystems, quantum efficiency and the CO2 assimilation rates. With some instruments, even wavelength-dependency of the photosynthetic efficiency can be analyzed. [52]

A phenomenon known as quantum walk increases the efficiency of the energy transport of light significantly. In the photosynthetic cell of an algae, bacterium, or plant, there are light-sensitive molecules called chromophores arranged in an antenna-shaped structure named a photocomplex. When a photon is absorbed by a chromophore, it is converted into a quasiparticle referred to as an exciton, which jumps from chromophore to chromophore towards the reaction center of the photocomplex, a collection of molecules that traps its energy in a chemical form that makes it accessible for the cell's metabolism. The exciton's wave properties enable it to cover a wider area and try out several possible paths simultaneously, allowing it to instantaneously "choose" the most efficient route, where it will have the highest probability of arriving at its destination in the minimum possible time.

Because that quantum walking takes place at temperatures far higher than quantum phenomena usually occur, it is only possible over very short distances, due to obstacles in the form of destructive interference that come into play. These obstacles cause the particle to lose its wave properties for an instant before it regains them once again after it is freed from its locked position through a classic "hop". The movement of the electron towards the photo center is therefore covered in a series of conventional hops and quantum walks. [53] [54] [55]

Early photosynthetic systems, such as those in green and purple sulfur and green and purple nonsulfur bacteria, are thought to have been anoxygenic, and used various other molecules than water as electron donors. Green and purple sulfur bacteria are thought to have used hydrogen and sulfur as electron donors. Green nonsulfur bacteria used various amino and other organic acids as an electron donor. Purple nonsulfur bacteria used a variety of nonspecific organic molecules. The use of these molecules is consistent with the geological evidence that Earth's early atmosphere was highly reducing at that time. [56]

Fossils of what are thought to be filamentous photosynthetic organisms have been dated at 3.4 billion years old. [57] [58] More recent studies, reported in March 2018, also suggest that photosynthesis may have begun about 3.4 billion years ago. [59] [60]

The main source of oxygen in the Earth's atmosphere derives from oxygenic photosynthesis, and its first appearance is sometimes referred to as the oxygen catastrophe. Geological evidence suggests that oxygenic photosynthesis, such as that in cyanobacteria, became important during the Paleoproterozoic era around 2 billion years ago. Modern photosynthesis in plants and most photosynthetic prokaryotes is oxygenic. Oxygenic photosynthesis uses water as an electron donor, which is oxidized to molecular oxygen ( O
2 ) in the photosynthetic reaction center.

Symbiosis and the origin of chloroplasts

Several groups of animals have formed symbiotic relationships with photosynthetic algae. These are most common in corals, sponges and sea anemones. It is presumed that this is due to the particularly simple body plans and large surface areas of these animals compared to their volumes. [61] In addition, a few marine mollusks Elysia viridis and Elysia chlorotica also maintain a symbiotic relationship with chloroplasts they capture from the algae in their diet and then store in their bodies (see Kleptoplasty). This allows the mollusks to survive solely by photosynthesis for several months at a time. [62] [63] Some of the genes from the plant cell nucleus have even been transferred to the slugs, so that the chloroplasts can be supplied with proteins that they need to survive. [64]

An even closer form of symbiosis may explain the origin of chloroplasts. Chloroplasts have many similarities with photosynthetic bacteria, including a circular chromosome, prokaryotic-type ribosome, and similar proteins in the photosynthetic reaction center. [65] [66] The endosymbiotic theory suggests that photosynthetic bacteria were acquired (by endocytosis) by early eukaryotic cells to form the first plant cells. Therefore, chloroplasts may be photosynthetic bacteria that adapted to life inside plant cells. Like mitochondria, chloroplasts possess their own DNA, separate from the nuclear DNA of their plant host cells and the genes in this chloroplast DNA resemble those found in cyanobacteria. [67] DNA in chloroplasts codes for redox proteins such as those found in the photosynthetic reaction centers. The CoRR Hypothesis proposes that this co-location of genes with their gene products is required for redox regulation of gene expression, and accounts for the persistence of DNA in bioenergetic organelles. [68]

Photosynthetic eukaryotic lineages

Symbiotic and kleptoplastic organisms excluded:

  • The glaucophytes and the red and green algae—clade Archaeplastida (unicellular and multicellular)
  • The cryptophytes—clade Cryptista (unicellular)
  • The haptophytes—clade Haptista (unicellular)
  • The dinoflagellates and chromerids in the superphylum Myzozoa—clade Alveolata (unicellular)
  • The ochrophytes—clade Heterokonta (unicellular and multicellular)
  • The chlorarachniophytes and three species of Paulinella in the phylum Cercozoa—clade Rhizaria (unicellular)
  • The euglenids—clade Excavata (unicellular)

Except for the euglenids, which is found within the Excavata, all of them belong to the Diaphoretickes. Archaeplastida and the photosynthetic Paulinella got their plastids— which are surrounded by two membranes, through primary endosymbiosis in two separate events by engulfing a cyanobacterium. The plastids in all the other groups have either a red or green algal origin, and are referred to as the "red lineages" and the "green lineages". In dinoflaggelates and euglenids the plastids are surrounded by three membranes, and in the remaining lines by four. A nucleomorph, remnants of the original algal nucleus located between the inner and outer membranes of the plastid, is present in the cryptophytes (from a red algae) and chlorarachniophytes (from a green algae). [69] Some dinoflaggelates which have lost their photosyntethic ability have later regained it again through new endosymbiotic events with different algae. While able to perform photosynthesis, many of these eukaryotic groups are mixotrophs and practice heterotrophy to various degrees.

Cyanobacteria and the evolution of photosynthesis

The biochemical capacity to use water as the source for electrons in photosynthesis evolved once, in a common ancestor of extant cyanobacteria (formerly called blue-green algae), which are the only prokaryotes performing oxygenic photosynthesis. The geological record indicates that this transforming event took place early in Earth's history, at least 2450–2320 million years ago (Ma), and, it is speculated, much earlier. [70] [71] Because the Earth's atmosphere contained almost no oxygen during the estimated development of photosynthesis, it is believed that the first photosynthetic cyanobacteria did not generate oxygen. [72] Available evidence from geobiological studies of Archean (>2500 Ma) sedimentary rocks indicates that life existed 3500 Ma, but the question of when oxygenic photosynthesis evolved is still unanswered. A clear paleontological window on cyanobacterial evolution opened about 2000 Ma, revealing an already-diverse biota of Cyanobacteria. Cyanobacteria remained the principal primary producers of oxygen throughout the Proterozoic Eon (2500–543 Ma), in part because the redox structure of the oceans favored photoautotrophs capable of nitrogen fixation. [ citation needed ] Green algae joined cyanobacteria as the major primary producers of oxygen on continental shelves near the end of the Proterozoic, but it was only with the Mesozoic (251–66 Ma) radiations of dinoflagellates, coccolithophorids, and diatoms did the primary production of oxygen in marine shelf waters take modern form. Cyanobacteria remain critical to marine ecosystems as primary producers of oxygen in oceanic gyres, as agents of biological nitrogen fixation, and, in modified form, as the plastids of marine algae. [73]

Although some of the steps in photosynthesis are still not completely understood, the overall photosynthetic equation has been known since the 19th century.

Jan van Helmont began the research of the process in the mid-17th century when he carefully measured the mass of the soil used by a plant and the mass of the plant as it grew. After noticing that the soil mass changed very little, he hypothesized that the mass of the growing plant must come from the water, the only substance he added to the potted plant. His hypothesis was partially accurate – much of the gained mass also comes from carbon dioxide as well as water. However, this was a signaling point to the idea that the bulk of a plant's biomass comes from the inputs of photosynthesis, not the soil itself.

Joseph Priestley, a chemist and minister, discovered that, when he isolated a volume of air under an inverted jar, and burned a candle in it (which gave off CO2), the candle would burn out very quickly, much before it ran out of wax. He further discovered that a mouse could similarly "injure" air. He then showed that the air that had been "injured" by the candle and the mouse could be restored by a plant. [74]

In 1779, Jan Ingenhousz repeated Priestley's experiments. He discovered that it was the influence of sunlight on the plant that could cause it to revive a mouse in a matter of hours. [74] [75]

In 1796, Jean Senebier, a Swiss pastor, botanist, and naturalist, demonstrated that green plants consume carbon dioxide and release oxygen under the influence of light. Soon afterward, Nicolas-Théodore de Saussure showed that the increase in mass of the plant as it grows could not be due only to uptake of CO2 but also to the incorporation of water. Thus, the basic reaction by which photosynthesis is used to produce food (such as glucose) was outlined. [76]

Cornelis Van Niel made key discoveries explaining the chemistry of photosynthesis. By studying purple sulfur bacteria and green bacteria he was the first to demonstrate that photosynthesis is a light-dependent redox reaction, in which hydrogen reduces (donates its – electron to) carbon dioxide.

Robert Emerson discovered two light reactions by testing plant productivity using different wavelengths of light. With the red alone, the light reactions were suppressed. When blue and red were combined, the output was much more substantial. Thus, there were two photosystems, one absorbing up to 600 nm wavelengths, the other up to 700 nm. The former is known as PSII, the latter is PSI. PSI contains only chlorophyll "a", PSII contains primarily chlorophyll "a" with most of the available chlorophyll "b", among other pigments. These include phycobilins, which are the red and blue pigments of red and blue algae respectively, and fucoxanthol for brown algae and diatoms. The process is most productive when the absorption of quanta are equal in both the PSII and PSI, assuring that input energy from the antenna complex is divided between the PSI and PSII system, which in turn powers the photochemistry. [13]

Robert Hill thought that a complex of reactions consisting of an intermediate to cytochrome b6 (now a plastoquinone), another is from cytochrome f to a step in the carbohydrate-generating mechanisms. These are linked by plastoquinone, which does require energy to reduce cytochrome f for it is a sufficient reductant. Further experiments to prove that the oxygen developed during the photosynthesis of green plants came from water, were performed by Hill in 1937 and 1939. He showed that isolated chloroplasts give off oxygen in the presence of unnatural reducing agents like iron oxalate, ferricyanide or benzoquinone after exposure to light. The Hill reaction [77] is as follows:

2 H2O + 2 A + (light, chloroplasts) → 2 AH2 + O2

where A is the electron acceptor. Therefore, in light, the electron acceptor is reduced and oxygen is evolved.

Samuel Ruben and Martin Kamen used radioactive isotopes to determine that the oxygen liberated in photosynthesis came from the water.

Melvin Calvin and Andrew Benson, along with James Bassham, elucidated the path of carbon assimilation (the photosynthetic carbon reduction cycle) in plants. The carbon reduction cycle is known as the Calvin cycle, which ignores the contribution of Bassham and Benson. Many scientists refer to the cycle as the Calvin-Benson Cycle, Benson-Calvin, and some even call it the Calvin-Benson-Bassham (or CBB) Cycle.

Nobel Prize-winning scientist Rudolph A. Marcus was able to discover the function and significance of the electron transport chain.

Otto Heinrich Warburg and Dean Burk discovered the I-quantum photosynthesis reaction that splits the CO2, activated by the respiration. [78]

In 1950, first experimental evidence for the existence of photophosphorylation in vivo was presented by Otto Kandler using intact Chlorella cells and interpreting his findings as light-dependent ATP formation. [79] In 1954, Daniel I. Arnon et al. discovered photophosphorylation in vitro in isolated chloroplasts with the help of P 32 . [80] [81]

Louis N.M. Duysens and Jan Amesz discovered that chlorophyll a will absorb one light, oxidize cytochrome f, chlorophyll a (and other pigments) will absorb another light but will reduce this same oxidized cytochrome, stating the two light reactions are in series.

Development of the concept

In 1893, Charles Reid Barnes proposed two terms, photosyntax and photosynthesis, for the biological process of synthesis of complex carbon compounds out of carbonic acid, in the presence of chlorophyll, under the influence of light. Over time, the term photosynthesis came into common usage as the term of choice. Later discovery of anoxygenic photosynthetic bacteria and photophosphorylation necessitated redefinition of the term. [82]

C3 : C4 photosynthesis research

After WWII at late 1940 at the University of California, Berkeley, the details of photosynthetic carbon metabolism were sorted out by the chemists Melvin Calvin, Andrew Benson, James Bassham and a score of students and researchers utilizing the carbon-14 isotope and paper chromatography techniques. [83] The pathway of CO2 fixation by the algae Chlorella in a fraction of a second in light resulted in a 3 carbon molecule called phosphoglyceric acid (PGA). For that original and ground-breaking work, a Nobel Prize in Chemistry was awarded to Melvin Calvin in 1961. In parallel, plant physiologists studied leaf gas exchanges using the new method of infrared gas analysis and a leaf chamber where the net photosynthetic rates ranged from 10 to 13 μmol CO2·m −2 ·s −1 , with the conclusion that all terrestrial plants having the same photosynthetic capacities that were light saturated at less than 50% of sunlight. [84] [85]

Later in 1958–1963 at Cornell University, field grown maize was reported to have much greater leaf photosynthetic rates of 40 μmol CO2·m −2 ·s −1 and was not saturated at near full sunlight. [86] [87] This higher rate in maize was almost double those observed in other species such as wheat and soybean, indicating that large differences in photosynthesis exist among higher plants. At the University of Arizona, detailed gas exchange research on more than 15 species of monocot and dicot uncovered for the first time that differences in leaf anatomy are crucial factors in differentiating photosynthetic capacities among species. [88] [89] In tropical grasses, including maize, sorghum, sugarcane, Bermuda grass and in the dicot amaranthus, leaf photosynthetic rates were around 38−40 μmol CO2·m −2 ·s −1 , and the leaves have two types of green cells, i. e. outer layer of mesophyll cells surrounding a tightly packed cholorophyllous vascular bundle sheath cells. This type of anatomy was termed Kranz anatomy in the 19th century by the botanist Gottlieb Haberlandt while studying leaf anatomy of sugarcane. [90] Plant species with the greatest photosynthetic rates and Kranz anatomy showed no apparent photorespiration, very low CO2 compensation point, high optimum temperature, high stomatal resistances and lower mesophyll resistances for gas diffusion and rates never saturated at full sun light. [91] The research at Arizona was designated Citation Classic by the ISI 1986. [89] These species was later termed C4 plants as the first stable compound of CO2 fixation in light has 4 carbon as malate and aspartate. [92] [93] [94] Other species that lack Kranz anatomy were termed C3 type such as cotton and sunflower, as the first stable carbon compound is the 3-carbon PGA. At 1000 ppm CO2 in measuring air, both the C3 and C4 plants had similar leaf photosynthetic rates around 60 μmol CO2·m −2 ·s −1 indicating the suppression of photorespiration in C3 plants. [88] [89]

There are three main factors affecting photosynthesis [ clarification needed ] and several corollary factors. The three main are: [ citation needed ]

Total photosynthesis is limited by a range of environmental factors. These include the amount of light available, the amount of leaf area a plant has to capture light (shading by other plants is a major limitation of photosynthesis), rate at which carbon dioxide can be supplied to the chloroplasts to support photosynthesis, the availability of water, and the availability of suitable temperatures for carrying out photosynthesis. [95]

Light intensity (irradiance), wavelength and temperature

The process of photosynthesis provides the main input of free energy into the biosphere, and is one of four main ways in which radiation is important for plant life. [96]

The radiation climate within plant communities is extremely variable, with both time and space.

In the early 20th century, Frederick Blackman and Gabrielle Matthaei investigated the effects of light intensity (irradiance) and temperature on the rate of carbon assimilation.

  • At constant temperature, the rate of carbon assimilation varies with irradiance, increasing as the irradiance increases, but reaching a plateau at higher irradiance.
  • At low irradiance, increasing the temperature has little influence on the rate of carbon assimilation. At constant high irradiance, the rate of carbon assimilation increases as the temperature is increased.

These two experiments illustrate several important points: First, it is known that, in general, photochemical reactions are not affected by temperature. However, these experiments clearly show that temperature affects the rate of carbon assimilation, so there must be two sets of reactions in the full process of carbon assimilation. These are the light-dependent 'photochemical' temperature-independent stage, and the light-independent, temperature-dependent stage. Second, Blackman's experiments illustrate the concept of limiting factors. Another limiting factor is the wavelength of light. Cyanobacteria, which reside several meters underwater, cannot receive the correct wavelengths required to cause photoinduced charge separation in conventional photosynthetic pigments. To combat this problem, a series of proteins with different pigments surround the reaction center. This unit is called a phycobilisome. [ clarification needed ]

Carbon dioxide levels and photorespiration

As carbon dioxide concentrations rise, the rate at which sugars are made by the light-independent reactions increases until limited by other factors. RuBisCO, the enzyme that captures carbon dioxide in the light-independent reactions, has a binding affinity for both carbon dioxide and oxygen. When the concentration of carbon dioxide is high, RuBisCO will fix carbon dioxide. However, if the carbon dioxide concentration is low, RuBisCO will bind oxygen instead of carbon dioxide. This process, called photorespiration, uses energy, but does not produce sugars.

RuBisCO oxygenase activity is disadvantageous to plants for several reasons:

  1. One product of oxygenase activity is phosphoglycolate (2 carbon) instead of 3-phosphoglycerate (3 carbon). Phosphoglycolate cannot be metabolized by the Calvin-Benson cycle and represents carbon lost from the cycle. A high oxygenase activity, therefore, drains the sugars that are required to recycle ribulose 5-bisphosphate and for the continuation of the Calvin-Benson cycle.
  2. Phosphoglycolate is quickly metabolized to glycolate that is toxic to a plant at a high concentration it inhibits photosynthesis.
  3. Salvaging glycolate is an energetically expensive process that uses the glycolate pathway, and only 75% of the carbon is returned to the Calvin-Benson cycle as 3-phosphoglycerate. The reactions also produce ammonia (NH3), which is able to diffuse out of the plant, leading to a loss of nitrogen.

The salvaging pathway for the products of RuBisCO oxygenase activity is more commonly known as photorespiration, since it is characterized by light-dependent oxygen consumption and the release of carbon dioxide.

Photosynthesis Light Reactions

Not all wavelengths of light are absorbed during photosynthesis. Green, the color of most plants, is actually the color that is reflected. The light that is absorbed splits water into hydrogen and oxygen:

H2O + light energy → ½ O2 + 2H+ + 2 electrons

  1. Excited electrons from Photosystem I can use an electron transport chain to reduce oxidized P700. This sets up a proton gradient, which can generate ATP. The end result of this looping electron flow, called cyclic phosphorylation, is the generation of ATP and P700.
  2. Excited electrons from Photosystem I could flow down a different electron transport chain to produce NADPH, which is used to synthesize carbohydratyes. This is a noncyclic pathway in which P700 is reduced by an exicted electron from Photosystem II.
  3. An excited electron from Photosystem II flows down an electron transport chain from excited P680 to the oxidized form of P700, creating a proton gradient between the stroma and thylakoids that generates ATP. The net result of this reaction is called noncyclic photophosphorylation.
  4. Water contributes the electron that is needed to regenerate the reduced P680. The reduction of each molecule of NADP+ to NADPH uses two electrons and requires four photons. Two molecules of ATP are formed.

The Calvin Cycle: Building Life from Thin Air

How does something like air become the wood of a tree? The answer lies in what makes up the air.

How can the air surrounding a tree be turned into tree material? Through a complex set of reactions that use the carbon from the air to make other materials. Image by André Karwath.

The air holds different elements like oxygen, carbon, and nitrogen. These elements make up molecules like carbon dioxide (CO2). Carbon dioxide is made out of one carbon atom and two oxygen atoms. Plants take the carbon atom from carbon dioxide and use it to build sugars.

This is done using the Calvin cycle. The Calvin cycle occurs inside chloroplasts, but outside the thylakoids (where ATP was created). The ATP and NADPH from the light-dependent reactions are used in the Calvin cycle.

Parts of the Calvin cycle are sometimes called light-independent reactions. But don't let the name fool you. those reactions do require sunlight to work.

The protein RuBisCO also helps in the process to change carbon from the air into sugars. RuBisCO works slowly, so plants need a lot of it. In fact, RuBisCO is the most abundant protein in the world!

The products of the Calvin cycle are used to make the simple sugar glucose. Glucose is used to build more complex sugars like starch and cellulose. Starch stores energy for the plant and cellulose is the stuff of which plants are made.


Quantum biology is an emerging field most of the current research is theoretical and subject to questions that require further experimentation. Though the field has only recently received an influx of attention, it has been conceptualized by physicists throughout the 20th century. It has been suggested that quantum biology might play a critical role in the future of the medical world. [5] Early pioneers of quantum physics saw applications of quantum mechanics in biological problems. Erwin Schrödinger's 1944 book What is Life? discussed applications of quantum mechanics in biology. [6] Schrödinger introduced the idea of an "aperiodic crystal" that contained genetic information in its configuration of covalent chemical bonds. He further suggested that mutations are introduced by "quantum leaps". Other pioneers Niels Bohr, Pascual Jordan, and Max Delbruck argued that the quantum idea of complementarity was fundamental to the life sciences. [7] In 1963, Per-Olov Löwdin published proton tunneling as another mechanism for DNA mutation. In his paper, he stated that there is a new field of study called "quantum biology". [8]

Photosynthesis Edit

Organisms that undergo photosynthesis absorb light energy through the process of electron excitation in antennae. These antennae vary among organisms. For example, bacteria use ring-like antennae, while plants use chlorophyll pigments to absorb photons. Photosynthesis creates Frenkel excitons, which provide a separation of charge that cells convert into usable chemical energy. The energy collected in reaction sites must be transferred quickly before it is lost to fluorescence or thermal vibrational motion.

Various structures, such as the FMO complex in green sulfur bacteria, are responsible for transferring energy from antennae to a reaction site. FT electron spectroscopy studies of electron absorption and transfer show an efficiency of above 99%, [9] which cannot be explained by classical mechanical models like the diffusion model. Instead, as early as 1938, scientists theorized that quantum coherence was the mechanism for excitation energy transfer.

Scientists have recently looked for experimental evidence of this proposed energy transfer mechanism. A study published in 2007 claimed the identification of electronic quantum coherence [10] at −196 °C (77 K). Another theoretical study from 2010 provided evidence that quantum coherence lives as long as 300 femtoseconds at biologically relevant temperatures (4 °C or 277 K) . In that same year, experiments conducted on photosynthetic cryptophyte algae using two-dimensional photon echo spectroscopy yielded further confirmation for long-term quantum coherence. [11] These studies suggest that, through evolution, nature has developed a way of protecting quantum coherence to enhance the efficiency of photosynthesis. However, critical follow-up studies question the interpretation of these results. Single molecule spectroscopy now shows the quantum characteristics of photosynthesis without the interference of static disorder, and some studies use this method to assign reported signatures of electronic quantum coherence to nuclear dynamics occurring in chromophores. [12] [13] [14] [15] [16] [17] [18] A number of proposals emerged trying to explain unexpectedly long coherence. According to one proposal, if each site within the complex feels its own environmental noise, the electron will not remain in any local minimum due to both quantum coherence and thermal environment, but proceed to the reaction site via quantum walks. [19] [20] [21] Another proposal is that the rate of quantum coherence and electron tunneling create an energy sink that moves the electron to the reaction site quickly. [22] Other work suggested that geometric symmetries in the complex may favor efficient energy transfer to the reaction center, mirroring perfect state transfer in quantum networks. [23] Furthermore, experiments with artificial dye molecules cast doubts on the interpretation that quantum effects last any longer than one hundred femtoseconds. [24]

In 2017, the first control experiment with the original FMO protein under ambient conditions confirmed that electronic quantum effects are washed out within 60 femtoseconds, while the overall exciton transfer takes a time on the order of a few picoseconds. [25] In 2020 a review based on a wide collection of control experiments and theory concluded that the proposed quantum effects as long lived electronic coherences in the FMO system does not hold. [26] Instead, research investigating transport dynamics suggests that interactions between electronic and vibrational modes of excitation in FMO complexes require a semi-classical, semi-quantum explanation for the transfer of exciton energy. In other words, while quantum coherence dominates in the short-term, a classical description is most accurate to describe long-term behavior of the excitons. [27]

Another process in photosynthesis that has almost 100% efficiency is charge transfer, again suggesting that quantum mechanical phenomena are at play. [18] In 1966, a study on the photosynthetic bacteria Chromatium found that at temperatures below 100 K, cytochrome oxidation is temperature-independent, slow (on the order of milliseconds), and very low in activation energy. The authors, Don DeVault and Britton Chase, postulated that these characteristics of electron transfer are indicative of quantum tunneling, whereby electrons penetrate a potential barrier despite possessing less energy than is classically necessary. [28]

Seth Lloyd is also notable for his contributions to this area of research.

DNA mutation Edit

Deoxyribonucleic acid, DNA, acts as the instructions for making proteins throughout the body. It consists of 4 nucleotides guanine, thymine, cytosine, and adenine. [29] The order of these nucleotides gives the “recipe” for the different proteins.

Whenever a cell reproduces, it must copy these strands of DNA. However, sometimes throughout the process of copying the strand of DNA a mutation, or an error in the DNA code, can occur. A theory for the reasoning behind DNA mutation is explained in the Lowdin DNA mutation model. [30] In this model, a nucleotide may change its form through a process of quantum tunneling. [31] Because of this, the changed nucleotide will lose its ability to pair with its original base pair and consequently changing the structure and order of the DNA strand.

Exposure to ultraviolet lights and other types of radiation can cause DNA mutation and damage. The radiations also can modify the bonds along the DNA strand in the pyrimidines and cause them to bond with themselves creating a dimer. [32]

In many prokaryotes and plants, these bonds are repaired to their original form by a DNA repair enzyme photolyase. As its prefix implies, photolyase is reliant on light in order to repair the strand. Photolyase works with its cofactor FADH, flavin adenine dinucleotide, while repairing the DNA. Photolyase is excited by visible light and transfers an electron to the cofactor FADH-. FADH- now in the possession of an extra electron gives the electron to the dimer to break the bond and repair the DNA. This transfer of the electron is done through the tunneling of the electron from the FADH to the dimer. Although the range of the tunneling is much larger than feasible in a vacuum, the tunneling in this scenario is said to be “superexchange-mediated tunneling,” and is possible due to the protein's ability to boost the tunneling rates of the electron. [30]

Vibration theory of olfaction Edit

Olfaction, the sense of smell, can be broken down into two parts the reception and detection of a chemical, and how that detection is sent to and processed by the brain. This process of detecting an odorant is still under question. One theory named the “shape theory of olfaction” suggests that certain olfactory receptors are triggered by certain shapes of chemicals and those receptors send a specific message to the brain. [33] Another theory (based on quantum phenomena) suggests that the olfactory receptors detect the vibration of the molecules that reach them and the “smell” is due to different vibrational frequencies, this theory is aptly called the “vibration theory of olfaction.”

The vibration theory of olfaction, created in 1938 by Malcolm Dyson [34] but reinvigorated by Luca Turin in 1996, [35] proposes that the mechanism for the sense of smell is due to G-protein receptors that detect molecular vibrations due to inelastic electron tunneling, tunneling where the electron loses energy, across molecules. [35] In this process a molecule would fill a binding site with a G-protein receptor. After the binding of the chemical to the receptor, the chemical would then act as a bridge allowing for the electron to be transferred through the protein. As the electron transfers through and that usually would be a barrier for the electrons and would lose its energy due to the vibration of the molecule recently bound to the receptor, resulting in the ability to smell the molecule. [35] [36]

While the vibration theory has some experimental proof of concept, [37] [38] there have been multiple controversial results in experiments. In some experiments, animals are able to distinguish smells between molecules of different frequencies and same structure, [39] while other experiments show that people are unaware of distinguishing smells due to distinct molecular frequencies. [40] However, it has not been disproven, and has even been shown to be an effect in olfaction of animals other than humans such as flies, bees, and fish. [ citation needed ]

Vision Edit

Vision relies on quantized energy in order to convert light signals to an action potential in a process called phototransduction. In phototransduction, a photon interacts with a chromophore in a light receptor. The chromophore absorbs the photon and undergoes photoisomerization. This change in structure induces a change in the structure of the photo receptor and resulting signal transduction pathways lead to a visual signal. However, the photoisomerization reaction occurs at a rapid rate, in under 200 femtoseconds, [41] with high yield. Models suggest the use of quantum effects in shaping the ground state and excited state potentials in order to achieve this efficiency. [42]

Quantum vision implications Edit

Experiments have shown that the sensors in the retina of human eye is sensitive enough to detect a single photon. [43] Single photon detection could lead to multiple different technologies. One area of development is in quantum communication and cryptography. The idea is to use a biometric system to measure the eye using only a small number of points across the retina with random flashes of photons that “read” the retina and identify the individual. [44] This biometric system would only allow a certain individual with a specific retinal map to decode the message. This message can not be decoded by anyone else unless the eavesdropper were to guess the proper map or could read the retina of the intended recipient of the message. [45]

Enzymatic activity (quantum biochemistry) Edit

Enzymes may use quantum tunneling to transfer electrons long distances. It is possible that protein quaternary architecture may have evolved to enable sustained quantum entanglement and coherence. [46] More specifically, they can increase the percentage of the reaction that occurs through hydrogen tunneling. [47] Tunneling refers to the ability of a small mass particle to travel through energy barriers. This ability is due to the principle of complementarity, which hold that certain objects have pairs of properties that cannot be measured separately without changing the outcome of measurement. Electrons have both wave and particle properties, so they can pass through physical barriers as a wave without violating the laws of physics. Studies show that long distance electron transfers between redox centers through quantum tunneling plays important roles in enzymatic activity of photosynthesis and cellular respiration. [48] [49] For example, studies show that long range electron tunneling on the order of 15–30 Å plays a role in redox reactions in enzymes of cellular respiration. [50] Without quantum tunneling, organisms would not be able to convert energy quickly enough to sustain growth. Even though there are such large separations between redox sites within enzymes, electrons successfully transfer in a generally temperature independent (aside from extreme conditions) and distance dependent manner. [47] This suggests the ability of electrons to tunnel in physiological conditions. Further research is needed to determine whether this specific tunneling is also coherent.

Magnetoreception Edit

Magnetoreception refers to the ability of animals to navigate using the inclination of the magnetic field of the earth. [51] A possible explanation for magnetoreception is the entangled radical pair mechanism. [52] [53] The radical-pair mechanism is well-established in spin chemistry, [54] [55] [56] and was speculated to apply to magnetoreception in 1978 by Schulten et al.. The ratio between singlet and triplet pairs is changed by the interaction of entangled electron pairs with the magnetic field of the earth. [57] In 2000, cryptochrome was proposed as the "magnetic molecule" that could harbor magnetically sensitive radical-pairs. Cryptochrome, a flavoprotein found in the eyes of European robins and other animal species, is the only protein known to form photoinduced radical-pairs in animals. [51] When it interacts with light particles, cryptochrome goes through a redox reaction, which yields radical pairs both during the photo-reduction and the oxidation. The function of cryptochrome is diverse across species, however, the photoinduction of radical-pairs occurs by exposure to blue light, which excites an electron in a chromophore. [57] Magnetoreception is also possible in the dark, so the mechanism must rely more on the radical pairs generated during light-independent oxidation.

Experiments in the lab support the basic theory that radical-pair electrons can be significantly influenced by very weak magnetic fields, i.e. merely the direction of weak magnetic fields can affect radical-pair's reactivity and therefore can "catalyze" the formation of chemical products. Whether this mechanism applies to magnetoreception and/or quantum biology, that is, whether earth's magnetic field "catalyzes" the formation of biochemical products by the aid of radical-pairs, is undetermined for two reasons. The first is that radical-pairs may need not be entangled, the key quantum feature of the radical-pair mechanism, to play a part in these processes. There are entangled and non-entangled radical-pairs. However, researchers found evidence for the radical-pair mechanism of magnetoreception when European robins, cockroaches, and garden warblers, could no longer navigate when exposed to a radio frequency that obstructs magnetic fields [51] and radical-pair chemistry. To empirically suggest the involvement of entanglement, an experiment would need to be devised that could disturb entangled radical-pairs without disturbing other radical-pairs, or vice versa, which would first need to be demonstrated in a laboratory setting before being applied to in vivo radical-pairs.

Other biological applications Edit

Other examples of quantum phenomena in biological systems include the conversion of chemical energy into motion [58] and brownian motors in many cellular processes. [59]

Photosynthesis Label

This activity was designed for remote learning during the 2020 pandemic, though it is based off a similar worksheet that students would complete in class.

Remote learning makes it more challenging for students to do labeling exercises since it can be difficult to annotate text without other apps installed. I made this labeling on Google slides with the image as a background and blocks of texts that can be moved to the correct location (drag-and-drop). Students label the reactants, carbon dioxide and water, then the products, glucose and oxygen. Another slide goes into the details of the light dependent reaction and the Calvin cycle.

This activity is intended to be given after going over photosynthesis and doing the chapter reading. I encourage my students to use outside sources if they are really stuck on the labeling, like their textbook or websites. When grading, I use the paint bucket tool to fill incorrect labels with red, which can allow for students to resubmit and fix the errors.