Comprehensive Notes on C1.3 Photosynthesis

C1.3 Photosynthesis

C1.3.1 Transformation of Light Energy to Chemical Energy

Photosynthesis converts light energy into chemical energy.
Sunlight is the main source of light energy.
Light energy is transformed into the chemical energy of organic compounds like glucose.
Energy is required to produce carbohydrates, such as glucose, from inorganic substances like carbon dioxide and water.
Glucose is used to create other compounds, including fructose, sucrose, cellulose, lipids, proteins, and nucleic acids.

C1.3.2 Conversion of Carbon Dioxide to Glucose

Glucose contains carbon, hydrogen, and oxygen.
Carbon dioxide and water are used to produce glucose during photosynthesis.
Hydrogen is obtained through photolysis, where light energy splits water into hydrogen ions (protons), electrons, and oxygen.
Hydrogen from water is used to reduce carbon dioxide in the Calvin cycle (light-independent reactions), resulting in glucose.
Glucose is converted to sucrose for transport in the phloem.
It's then polymerized to starch and stored in fruits and seeds.

C1.3.3 Oxygen as a By-Product

Photosynthesis is carried out by plants, algae, and cyanobacteria.
Light energy is absorbed as photons.
Light splits water into hydrogen ions, electrons, and oxygen.
Oxygen is released as a by-product through photolysis.
Photolysis increases oxygen concentration inside chloroplasts.
Oxygen diffuses out of chloroplasts, then out of leaf cells into air spaces inside the leaf.
Oxygen diffuses through stomata to the outside air.
In terrestrial organisms, oxygen is released into the air via diffusion.
In aquatic organisms, oxygen emerges as bubbles.

C1.3.4 Separation and Identification of Photosynthetic Pigments by Chromatography

Chromatography separates mixtures of substances based on their movement on paper via capillary action.
It uses a mobile phase (solvent) and a stationary phase (paper).
Pigments are separated using an alcohol/solvent mixture.
Two types of chromatography exist: paper and thin-layer (TLC).
TLC uses a plastic strip coated with a porous material like silica gel, aluminum oxide, or cellulose.
$R_f$ (retardation factor) is the ratio of the distance traveled by the pigment to the distance traveled by the solvent.
Pigments move at different rates based on their solubility in the solvent.
The rate depends on the pigment's attraction to the hydrophobic running solvent versus the hydrophilic chromatography strip.

Chloroplasts and Pigments

Chloroplasts are organelles that absorb light energy for photosynthesis.
They contain pigments like chlorophyll a and b, and carotenoids (xanthophyll, carotene, and phaeophytin).
These pigments absorb different wavelengths of light, resulting in different colors.

Chromatography Procedure

Cut a leaf into pieces.
Grind leaves with sand and propanone to extract pigments using a mortar and pestle.
Draw a line 10 mm from the end of chromatography paper and apply drops of pigment extract.
Suspend the strip in a test tube with solvent, ensuring the strip's base touches the solvent.
Remove the strip and mark the solvent front.
Calculate $Rf$ values using the formula: $Rf = \newline \newline \frac{Distance \, travelled \, by \, pigment}{Distance \, travelled \, by \, solvent}$
Use $R_f$ values to identify the pigments.

Absorption of Light by Chlorophyll

Blue and red light are absorbed the most.
Greatest absorption occurs in blue light.
Red light is absorbed in high amounts.
Green light is least absorbed and is reflected/transmitted.

Absorption Spectrum of Chlorophyll

X-axis: Wavelength/color
Y-axis: Absorbance/% absorption
Peak between 400 and 500 nm (blue light)
Peak between 600 and 700 nm (red light)
Blue peak is higher than the red peak.

Action Spectrum of Photosynthesis

X-axis: Light wavelength/frequency
Y-axis: Rate of photosynthesis
Curve increases, decreases, then increases again and decreases.
Peak around 450 nm (blue region)
Peak around 670 nm (red region)
First peak is higher than the second peak.

C1.3.5 Absorption of Specific Wavelengths of Light by Photosynthetic Pigments

Photosynthesis occurs in chloroplasts.
Chloroplasts are organelles in plant and algal cells where photons are captured.
Chlorophyll a and b reflect green light and absorb most other wavelengths in the visible light spectrum.
Accessory pigments include xanthophyll and carotenoids, reflecting yellow and orange light, respectively.

Pigment Wavelengths

Photosynthetic pigments absorb and reflect different wavelengths of light.
Reflected wavelengths give pigments their color.
Radiation energy drives photosynthesis.
Photons excite electrons in chlorophyll, powering the light-dependent stage.
Electrons are replaced by those from photolysis of water.
An absorption spectrum represents the wavelengths absorbed by each pigment.

Absorption Spectrum

An absorption spectrum is a graph of wavelength/color of light in nm (X-axis) versus percentage absorption (Y-axis).
Each pigment has a different absorption spectrum.
The graph shows overall light absorption by all pigments combined.
Light is absorbed on the blue and red ends of the spectrum.
More blue light is absorbed than red light.
Green light is not absorbed but reflected.

C1.3.6 Similarities and Differences of Absorption and Action Spectra

Both spectra have two peaks: one at the blue end and one at the red end.
In both, the peak is higher for blue light than red light.
Both have a dip for green light.
These similarities exist because wavelengths of light absorbed by chlorophyll are used in photosynthesis.

Energy and Electrons

When a pigment absorbs light energy, it raises an electron to a higher energy level (excitation).
The energy of a photon is related to its wavelength.
Longer wavelengths have less energy.
Different pigments absorb different wavelengths of light to excite electrons.
Excited electrons create chemical bonds in compounds like glucose, transforming light energy into chemical energy.

C1.3.7 Techniques for Varying Conditions to Investigate Limiting Factors

Experiment: Varying light intensity by changing the distance of a lamp from the plant.
Independent variable: Light intensity.
Dependent variable: Volume of oxygen gas.
Controlled variables: Species of plant, size of plant, number of leaves, concentration of sodium bicarbonate, temperature of water bath, volume of water in the test tube.
Using a data logger with an oxygen sensor allows for more precise measurements.
Independent variable - light intensity changed by changing distance of lamp from the plant/ power of lamp.
Dependent variable – oxygen concentration in % or ppm.
Controlled variables – species of plant/ size of plant/ number of leaves on the plant/ surface area of leaf, concentration of carbon dioxide (sensor is used for monitoring), temperature (of the surrounding).
Independent variable – light intensity changed by changing distance of lamp from the syringe.
Dependent variable – distance travelled by discs.
Controlled variables – species of plant/ size or surface area of disc/ number of discs of the plant, concentration of sodium bicarbonate, temperature of water, volume of water in syringe.

Factors Affecting Rate of Photosynthesis:

Graph illustrating the effect of light intensity on the rate of photosynthesis.
Graph illustrating the effect of carbon dioxide concentration on the rate of photosynthesis.
Graph illustrating the effect of temperature on the rate of photosynthesis.

Limiting Factor - Temperature

Increasing temperature increases molecular collisions due to increased kinetic energy, leading to an increased rate of photosynthesis.
Maximum rate of photosynthesis is reached at the 'optimal' temperature.
Breaking of bonds in enzymes' structure leads to a change in the shape of the active site (denaturation), decreasing the rate of photosynthesis.

Limiting Factor - Light Intensity

Increase in light intensity increases the rate of photosynthesis.
If the carbon dioxide concentration is increased, rate of photosynthesis will increase again until another factor becomes limiting.

Limiting Factor - Carbon Dioxide

Increase in carbon dioxide concentration increases the rate of photosynthesis.
If the light intensity is increased, rate of photosynthesis will increase again until another factor becomes limiting.

Light Compensation and Light Saturation Point

Within a certain range of light intensity, photosynthesis increases with the increase of light intensity, but after a certain light intensity, photosynthesis maintains a certain level and no longer increases. This critical point of light intensity is called the light saturation point.
Below the light saturation point, when the light intensity decreases, photosynthesis also decreases. The light intensity when the organic matter produced by the plants through photosynthesis is equal to the matter consumed by cell respiration is called the light compensation point.

Factors Affecting Photosynthesis

Light: Photosynthetic rate increases as light intensity increases until it reaches a plateau.
$CO2$ : Photosynthetic rate rises as $CO2$ concentration increase up to a maximum where the rate levels off.
Temperature: Photosynthetic rate increases with an increase in temperature up to an optimal level; high temperatures reduce the rate of photosynthesis.

Limiting Factors in Photosynthesis

A factor nearest its minimum/furthest from its optimum is limiting.
Increasing a limiting factor with other factors constant increases the rate.
Increasing a non-limiting factor with other factors constant has no effect on rate.

C1.3.8 Carbon Dioxide Enrichment Experiments

Carbon dioxide enrichment experiments can be achieved through: Enclosed greenhouse experiments FACE experiments

Enclosed Greenhouse Experiments

In enclosed greenhouses, the concentration of $CO_2$ can be carefully monitored and controlled.
Elevated levels of $CO_2$ can be created by burning fuels or other sources.
The effect of $CO_2$ enrichment can be measured in a variety of ways, such as total biomass produced or the yield of the fruits or vegetables grown.
Limitations: done in controlled conditions; there are natural factors and variables that are not able to be taken into account.

FACE (Free-Air CO2 Enrichment) Experiments

They must be conducted ‘in the free air’ so they are called free-air $CO_2$ experiments.
Circles of towers are built, and $CO_2$ is then released.
The concentration is monitored and whenever they drop below 550 ppm more $CO2$ is released on the upwind side to ensure the wind blows $CO2$ into the circle.
Each experiment also has control plots where air instead of $CO_2$ is released.

C1.3.9 Photosystems

Photosystems are molecular arrays of chlorophyll and accessory pigments within protein complexes, located on the thylakoid membranes within chloroplasts.
Each photosystem consists of about 100 chlorophyll molecules and 30 accessory pigments arranged in a precise molecular array.
The photosystem has a core complex with the reaction centre connected to light-harvesting antenna complexes.
Accessory pigments within the antenna complex absorb light energy and is funnelled into the core complex.
The accessory pigments absorb light of different wavelengths and pass it to the reaction centre.
Once the photon of light reaches the reaction centre (chlorophyll a), it generates and emits an excited electron.
This excited electron is accepted by the electron acceptors in the electron transport chain.
There are two types of photosystems: Photosystem II (P680) and Photosystem I (P700).

C1.3.10 Advantages of the Structured Array of Different Types of Pigment Molecules in a Photosystem

Photons of light are scattered. As the photosystem consists of a large number of pigment molecules more photons of light can be intercepted and therefore more energy supplied to the reaction centre at a faster rate.
Each pigment can only absorb a narrow range of wavelength of light. Since the photosystem consists a range of different pigment molecules, a greater proportion of light can be absorbed and a larger portion of the energy of the sun is made available for photosynthesis.
Since the pigments molecules are close and precisely oriented, it allows transfer of energy from one pigment molecule to the other till it reaches the reaction centre. This is called excitation energy transfer. Without the array most energy could be lost due to fluorescence.

C1.3.11 Generation of Oxygen by the Photolysis of Water in Photosystem II

Photolysis is the splitting of water molecule in presence of light energy and takes place in the Photosystem II/P680 (PII) next to the thylakoid space.
The PII has an oxygen-evolving complex (OEC) in the core which is where photolysis takes place.
The OEC binds two molecules of water and splits them to release 4 electrons, 4 protons and the two oxygen atoms combine to form an oxygen molecule that is released as a by-product.
Photolysis happens in the OEC on the inner surface of the thylakoid membranes. The protons produced are released into the thylakoid space to contribute to the proton gradient across the thylakoid membrane.
$2H2O \rightarrow 4H^+ + 4e^- + O2$
Oxygen molecules diffuse out from the thylakoids to the stroma and then through the cytoplasm of the cell till it eventually leaves the plants through the stomata.

C1.3.12 ATP Production by Chemiosmosis in Thylakoids

The coupling of ATP synthesis to electron transport via a concentration gradient of protons is called chemiosmosis.
When photons of light hit the reaction centre in photosystem II and I, it excites electrons which are ejected.
The excited electron from photosystem II passes down electron carriers (cytochromes) and release energy.
This energy is used to actively pump $H^+$ (protons) from stroma into the thylakoid space
$H^+$ concentration in thylakoid space becomes greater than in the stroma, a build up of potential energy.
The thylakoid membrane is impermeable to $H^+$ ions and they can diffuse back from thylakoid space into the stroma only through special membrane protein called ATP synthase
$H^+$ ions diffuse down concentration gradient from the thylakoid space back to the stroma by facilitated diffusion.
This diffusion produces energy that is used for phosphorylation of ADP to produce ATP molecules.
Since the phosphorylation is driven by light energy, it is called photophosphorylation.
The electrons from photolysis of water returns the photosystem II to its original stable state. The electron from photosystem II returns the photosystem I to its original stable state. The electrons from photosystem I are accepted by NADP which gets reduced to NADPH.

C1.3.13 Reduction of NADP by Photosystem I

Nicotinamide adenine dinucleotide phosphate (NADP) is an important electron carrier.
It functions in very much the same way as NAD does in cellular respiration.
It is able to take on electrons and become reduced, while oxidising something else.
NADP accepts two electrons from photosystem I as well as two protons/ $H^+$ from the stroma to become reduced NADP.
When photons of light hit P700/PI, the reaction centre generates and emits an excited electron.
The electron lost from PI is used to reduce NADP to reduced NADP/NADPH.
This reaction is calalysed by the enzyme NADP reductase on the thylakoid membrane.
The NADP attaches to the active site of NADP reductase and receives the electrons from PI via the electron carrier.
The emitted electrons from PSI are replaced by the electrons emitted from PSII.
This process is an essential step in photosynthesis because without it, the light- independent stage of photosynthesis could not occur.
Both ATP and reduced NADP are required to produce carbon compounds in the light-independent stage.

C1.3.14 Thylakoids as Systems for Performing the Light-Dependent Reactions of Photosynthesis

Chloroplasts are discrete organelles within plant cells that carry out photosynthesis.
It is the specialized structure of the thylakoids that allows the light-dependent stage of photosynthesis to occur effectively.
Within a chloroplast are stacks of thylakoids called grana, filling much of the space within the chloroplast.
These stacks provide a large surface area to allow for as many photosystems, electron transport chains and ATP synthases as possible.
This increases the absorption of light energy for maximum photophosphorylation.
Thylakoids are flattened membrane-bound sacs. They are considered systems because they consist of interacting and interdependent components.
Their membranes are made of phospholipids so they can hold the photosystems, electron transport chain and ATP synthase embedded in them to carry out their essential processes: photolysis, ATP production via chemiosmosis and the reduction of NADP.
The thylakoid membrane is impermeable to protons, so it allows a build-up of a proton gradient.
In addition, the small thylakoid paces within the thylakoids are ideal for allowing the establishment of electrochemical gradients as $H^+$ ions are pumped into them.
Without these spaces, the gradient could not be established as the production of ATP via chemiosmosis would not occur and there would not be sufficient energy for the production of carbon compounds.
It is also within the thylakoid space that water is split by photolysis, releasing oxygen.

C1.3.15 Carbon Fixation by Rubisco

The end-products of the light dependent reactions ATP and NADPH are used in the light-independent reactions since these reactions do not require light energy.
Carbon dioxide diffuses into the stroma of the chloroplast where it is fixed.
Atmospheric carbon dioxide is ‘fixed’ by adding it to ribulose bisphosphate (RuBP), a 5-carbon compound.
The product of the reaction is an unstable six- carbon compound that immediately splits forming two molecules of glycerate 3-phosphate (GP), a 3-carbon compound.
The reaction is catalyzed by a large enzyme, ribulose-1,5-bisphosphate carboxylase, commonly referred to as Rubisco.
This is the first step in the Calvin cycle, named after Melvin Calvin, a biochemist who worked out most of the details of this cyclic pathway.
The Calvin cycle takes place in the stroma of the chloroplasts, where there is a high concentration of Rubisco.
There are two reasons for this: Rubisco is a ‘slow’ enzyme, and the Calvin cycle is rather inefficient due to its high energy requirement, and additionally Rubisco can be competitively inhibited by oxygen, binding to it in preference to carbon dioxide, making it very inefficient at low concentrations of carbon dioxide.
To speed up the process, many molecules of Rubisco enzyme are needed.

C1.3.16 Synthesis of Triose Phosphate Using Reduced NADP and ATP

The next step in the Calvin cycle is the reduction of GP. During this reaction glycerate 3-phosphate (GP) is converted to triose phosphate, another 3-carbon compound that can then be used to synthesize carbon compounds such as glucose.
This is done using ATP and reduced NADP.
Each GP molecule requires one ATP and one reduced NADP.
The ATP provides the energy and reduced NADP reduces the GP to triose phosphate (TP) through the addition of hydrogen.
This step uses up all of the products of the light-dependent reactions.
$6CO2 + 6H2O \rightarrow C6H{12}O6 + 6O2$
The oxidized NADP is reused in the light dependent reactions. Of the total number of TP molecules produced, one-sixth of these are used to synthesize glucose. The remaining five-sixth of the TP molecules are used to regenerate RuBP.

C1.3.17 Regeneration of RuBP in the Calvin Cycle Using ATP

Since the light independent reactions are a cyclic pathway, the initial compound (RuBP) must be regenerated in order for the cycle to continue.
As it is a 5-carbon compound and triose phosphate is a 3-carbon compound, we are able to make 6 RuBP from 10 triose phosphates.
From the initial six molecules of carbon dioxide 12 triose phosphates are produced, that means only two of those can be used to synthesize carbon compounds as the other 10 will be required for the regeneration of RuBP.
For every six molecules of triose phosphates produced, only one molecule is used towards the synthesis of glucose. The remaining five molecules are used for the regeneration of RuBP.
The regeneration of each RuBP also requires the energy of one ATP molecule.
The ATP produced in the light dependent reactions has two roles: reduction of GP to TP and regeneration of RuBP.

C1.3.18 Synthesis of Carbohydrates, Amino Acids and Other Carbon Compounds

All carbon compounds synthesized in plants originate from triose phosphate.
Carbohydrates like glucose or starch, amino acids or fatty acids are all produced using the intermediate products of the Calvin cycle.
Glucose is produced by linking two triose phosphates.
Glucose is converted to fructose and sucrose for transport from leaves to other parts of the plant in phloem.
Many glucose molecules are condensed into starch for storage or into cellulose to make cell walls.
Chloroplasts can also convert triose phosphate into fatty acids using enzymes from the glycolysis pathway and the link reaction to produce acetyl Co A.
Glycerol can also be made from triose phosphate and linked to fatty acids to produce triglycerides.
Nitrogen required to make amino acids from triose phosphates or glycerate-3-phosphate is obtained by absorbing sulphates, nitrates or ammonium ions.
These compounds serve various functions in plant metabolism and growth.
One important group of carbon compounds synthesized using the products of the Calvin cycle is nucleotides.
Nucleotides are the building blocks of DNA and RNA, which are vital for genetic information storage and protein synthesis.
The formation of nucleotides involves the incorporation of ribose sugar, derived from triose phosphate, along with nitrogenous bases and phosphate groups.

C1.3.19 Interdependence of the Light-Dependent and Light-Independent Reactions

The light-dependent and light-independent reactions both require the other for them to continue.
The light-independent reactions require the ATP and reduced NADP from the light-dependent reactions.
If the light-dependent reactions stop, the light- independent reactions will also stop once they use up their supplies of ATP and reduced NADP.
The reverse is also true, as the light-dependent reactions require NADP and ADP to be available to continue generating reduced NADP and ATP.
If there was a lack of carbon dioxide and the light-independent reactions stopped, the cell would run out of NADP and ADP or the supply would be so low that the reaction would slow down significantly.
Photosystem II would be most affected by this as it requires the availability of NADP at the end. Electrons would no longer be able to flow and PSII could no longer function.