Chloroplasts contain accessory pigments like chlorophyll b and carotenoids that help broaden the range of wavelengths of light absorbed during photosynthesis beyond just the wavelengths absorbed by chlorophyll a. These accessory pigments absorb different wavelengths of light and transfer the absorbed energy to chlorophyll a, the primary photosynthetic pigment, improving the efficiency of light absorption and energy production through photosynthesis.

1. T. Y. B.Sc. (BOTANY) SEMESTER - VI
BOTANY PAPER - I
TITLE: PLANT PHYSIOLOGY AND BIOCHEMISTRY
PAPER CODE: BOT3601
[CREDITS - 2]

2. • Plants form the basis of all life on earth and are known as producers.
• Plant cells contain structures known as plastids which are absent in animal cells.
• These plastids are double-membraned cell organelles which play a primary role in the manufacturing and storing of food. There are three
types of plastids –
1. Chromoplasts- They are the colour plastids, found in all flowers, fruits and are mainly responsible for their distinctive colours.
2. Chloroplasts- They are green coloured plastids, which comprise green-coloured pigments within the plant cell and are called chlorophyll.
3. Leucoplasts- They are colourless plastids and are mainly used for the storage of starch, lipids and proteins within the plant cell.
Chloroplast Definition
“Chloroplast is an organelle that contains the photosynthetic pigment chlorophyll that captures sunlight and
converts it into useful energy, thereby, releasing oxygen from water. “
PLANT PHYSIOLOGY
Unit - I Photosynthesis
Ultra structure of chloroplast

3. Diagram of Chloroplast
• The parts of a chloroplast such as the inner membrane, outer membrane,
intermembrane space, thylakoid membrane, stroma and lamella can be clearly
marked out.
What is a Chloroplast?
• Chloroplasts are found in all green plants and algae.
• They are the food producers of plants.
• These are found in mesophyll cells located in the leaves of the plants.
• They contain a high concentration of chlorophyll that traps sunlight.
• Chloroplast has its own extra-nuclear DNA and therefore are semiautonomous,
like mitochondria.
• They also produce proteins and lipids required for the production of chloroplast
membrane.

4. Structure of Chloroplast
• Chloroplasts are found in all higher plants.
• It is oval or biconvex, found within the mesophyll of the plant cell.
• They are double-membrane organelle with the presence of outer, inner and intermembrane space.
• There are two distinct regions present inside a chloroplast known as the grana and stroma.
• Grana are made up of stacks of disc-shaped structures known as thylakoids or lamellae.
• The grana of the chloroplast consists of chlorophyll pigments and are the functional units of chloroplasts.
• Stroma is the homogenous matrix which contains grana and is similar to the cytoplasm in cells in which all the
organelles are embedded.
• Stroma also contains various enzymes, DNA, ribosomes, and other substances.
• Stroma lamellae function by connecting the stacks of thylakoid sacs or grana.
• The chloroplast structure consists of the following parts:
Membrane Envelope
• It comprises inner and outer lipid bilayer membranes.
• The inner membrane separates the stroma from the intermembrane space.
Intermembrane Space
The space between inner and outer membranes.

5. Thylakoid System (Lamellae)
• The system is suspended in the stroma.
• It is a collection of membranous sacs called thylakoids or lamellae.
• The green coloured pigments called chlorophyll are found in the thylakoid membranes.
• It is the sight for the process of light-dependent reactions of the photosynthesis process.
• The thylakoids are arranged in stacks known as grana and each granum contains around 10-20 thylakoids.
Stroma
• It is a colourless, alkaline, aqueous, protein-rich fluid present within the inner membrane of the chloroplast present surrounding the grana.
Grana
• Stack of lamellae in plastids is known as grana.
• These are the sites of conversion of light energy into chemical energy.
Functions of Chloroplast
Following are the important chloroplast functions:
•The most important function of the chloroplast is to synthesize food by the process of photosynthesis.
•Absorbs light energy and converts it into chemical energy.
•Chloroplast has a structure called chlorophyll which functions by trapping the solar energy and is used for the synthesis of food in all green
plants.

6. Frequently Asked Questions
Where does the photosynthesis process occur in the plant cell?
In all green plants, photosynthesis takes place within the thylakoid membrane of the Chloroplast.
List out the different parts of Chloroplast?
Chloroplasts are cell organelles present only in a plant cell and it includes:
1.Stroma
2.Inner membrane
3.Outer membrane
4.Thylakoid membrane
5.Intermembrane Space
What is the most important function of chloroplast?
The most important function of chloroplast is the production of food by the process of photosynthesis.
Why is the chloroplast green?
Chloroplast contains a green pigment called chlorophyll which gives it a green colour.
How many types of plastids are there?
There are three types of plastids-chloroplast, chromoplast and leucoplast.
What is the stack of lamellae inside a plastid called?
The stack of lamellae or thylakoids inside a plastid is called grana.
•Produces NADPH and molecular oxygen (O2) by photolysis of water.
•Produces ATP – Adenosine triphosphate by the process of photosynthesis.
•The carbon dioxide (CO2) obtained from the air is used to generate carbon and sugar during the Calvin Cycle or dark reaction
of photosynthesis.

7. What are Pigments in Plants?
• Plants produce their own food, which makes them autotrophs, or any organism that produces its own
• To do this, plants undergo photosynthesis, which produces food in the form of glucose.
• During photosynthesis, the plant will absorb light from the sun, water in the roots, and carbon dioxide
glucose, with oxygen released into the atmosphere as a byproduct.
• Chloroplasts give plants the energy to perform photosynthesis.
• Chloroplasts are chemical factories in the plant's leaves that are the site of photosynthesis.
• Sunlight radiates from the sun and filters through the atmosphere as visible light.
• This visible light includes all the colors of the rainbow.
• When light meets any medium, it can be reflected, transmitted or absorbed.
• Pigments are chemical compounds that absorb visible light within the plant's chloroplast.
• Different pigments absorb light at different wavelengths.
• Pigments hide the colors they absorb.
• The color one sees is the color reflected.
• For instance, if an individual is wearing a blue shirt, then all of the colors of the rainbow except blue are
• The color blue is reflected back to one's eye, which is why the shirt appears blue.
• In a plant, light is absorbed by the chloroplast.
• There are several pigments that are most effective in driving photosynthesis: the primary pigment is
pigments, such as chlorophyll b.
• Neither chlorophyll a nor b has the ability to absorb green light, which is why the leaves of plants appear

8. What Role Do Pigments Play in the Process of Photosynthesis?
•
Photosynthesis is the process where plants convert light energy
chemical energy.
• Pigments are the light absorbing substances within the
• These pigments absorb light at different wavelengths.
• There are two types of chlorophyll pigments in leaves that are
photosynthesis: chlorophyll a and chlorophyll b.
• Chlorophyll a: the main pigment involved in photosynthesis;
this pigment is responsible for trapping light in the violet-blue
• As a result, in chlorophyll a green is the least effective color,
a is yellow-green.
• Chlorophyll b: an accessory pigment, is almost identical to
chlorophyll a, but with a slight structural difference; this
to give the two pigments a slightly different absorption spectra.
• Chlorophyll b absorbs mostly blue and yellow light and reflects

9. Introduction
• Accessory pigments are light-absorbing molecules that function in tandem with chlorophyll and photosynthetic
organisms.
• Other forms of this pigment, such as chlorophyll b in green algal and higher plant antennae, as well as chlorophyll
c and d in other algae, are included.
Accessory Pigments in Photosynthesis
• Because a plant needs to absorb light at different wavelengths, accessory pigments play a key role in
absorption of light.
• The accessory pigments are chlorophyll b, carotenoids, xanthophyll, anthocyanin, phycoerythrin, and
• These accessory pigments broaden the range of light that can be absorbed by the plant.
• However, accessory pigments cannot convert light into energy.
• Instead, they pass their absorbed energy off to chlorophyll a for energy production.
• This is an important mechanism in driving photosynthesis.

10. Examples of Accessory Pigments
• Greenlight is transmitted by chlorophyll b, while blue and red light is absorbed mostly.
• Chlorophyll a, a smaller but more abundant molecule in the chloroplast, receives the captured solar
energy
• Carotenoids are pigments that reflect light in the colours orange, yellow, and red.
• To efficiently pass absorbed photons, carotenoid pigments cluster around chlorophyll molecules in a leaf.
• Carotenoids are fat-soluble chemicals that are thought to help the body dispel surplus radiant energy
• Xanthophyll pigments operate as antioxidants by transferring light energy to chlorophyll a.
• Xanthophyll can collect or donate electrons due to its chemical structure.
• The yellow colour of fall leaves comes from xanthophyll pigments
• Chlorophyll is helped by anthocyanin pigments, which absorb blue-green light.
• Reddish, violet anthocyanin molecules give apples and autumn foliage their vibrant colour.
• Anthocyanin is a water-soluble pigment that is stored in the vacuole of plant cells
Antenna Pigments
• Photosynthetic pigments such as chlorophyll b and carotenoids build a tightly packed antenna-like
structure with protein to catch incoming photons.
• Antenna pigments collect radiant light in the same way that solar panels on a house absorb solar energy.
• As part of the photosynthetic process, antenna pigments pump light into reaction centres.
• Photons excite one electron in the cell, which is subsequently transferred to a nearby acceptor molecule
and used to produce ATP molecules.

11. Accessory Pigments in Photosynthesis
• A plant must absorb light at various wavelengths, accessory pigments play an important function in helping chlorophyll and in light
absorption
• Chlorophyll b, carotenoids, xanthophyll, anthocyanin, phycoerythrin, and phycocyanin are the accessory pigments.
• These extra pigments increase the amount of light that the plant can absorb
• Accessory pigments, on the other hand, are unable to convert light into energy.
• Instead, they send their absorbed energy to chlorophyll a, which converts it into energy.
• This is a crucial mechanism in the photosynthesis process
Role of Accessory Pigments in Photosynthesis
• Photosynthesis is the conversion of light energy from the sun into chemical energy by plants.
• The light-absorbing compounds within the chloroplasts of leaves are known as pigments
• Plants get their green hue from chlorophyll, a pigment contained in the chloroplast.
• Different wavelengths of light are absorbed by these pigments
• Chlorophyll a and chlorophyll b are two forms of chlorophyll pigments found in leaves that are involved in photosynthesis
• Chlorophyll is the most important pigment in photosynthesis, and it is responsible for capturing light in the violet-blue and red
spectrums.
• As a result, green is the least effective hue in chlorophyll a, which is why chlorophyll an is yellow-green
• Chlorophyll b is an auxiliary pigment that is nearly identical to chlorophyll except for a minor structural change that causes the two
pigments to have slightly distinct absorption spectra.
• Blue and yellow light are absorbed by chlorophyll b, while yellow-green pigments are reflected
The Function of Accessory Pigments
• Adjacent pigment molecules absorb light energy during photosynthesis
• Chlorophyll receives the energy absorbed by the accessory pigment. It also guards against light oxidation of chlorophyll molecules
• Accessory pigments include chl b, xanthophyll, and carotenoids. It also aids photosynthesis by allowing a wider spectrum of

12. • Frequently Asked Questions
• What are accessory pigments examples?
• Examples of accessory pigments are chlorophyll b and carotenoids. Chlorophyll b absorbs mostly blue and yellow light and
absorb light in the blue-green ranges and reflect the yellow, red and orange ranges.
• What are pigments and how do plants use them?
• Pigments are substances that absorb visible light. Different pigments absorb light at different wavelengths. The color one sees
absorbed by the chloroplast. There are three pigments that are most effective in driving photosynthesis: the primary pigment
chlorophyll b and carotenoids.
• What is the function of accessory pigments?
• Accessory pigments broaden the spectrum of colors that can drive photosynthesis. These light absorbing pigments work with
• What are the accessory pigments in plants?
• The accessory pigments are chlorophyll b and carotenoids. Chlorophyll b absorbs mostly blue and yellow light and reflects
light in the blue-green ranges and reflect the yellow, red and orange ranges.
Conclusion
• Accessory pigments are light-absorbing molecules that function in tandem with chlorophyll and photosynthetic
organisms.
• Photosynthesis is the conversion of light energy from the sun into chemical energy by plants.
• The light-absorbing compounds within the chloroplasts of leaves are known as pigments.
• Chlorophyll is the most important pigment in photosynthesis, and it is responsible for capturing light in the violet-
blue and red spectrums.

13. Light reaction
• Majority of autotrophs (organisms that are not dependent on external sources for their nutrition) are dependent on
light reactions for energy production.
• Such organisms are called photoautotrophs.
• Light reactions are chemical reactions that take place in the presence of light.
• In plants the process that involves a light reaction is called photosynthesis.
• This is the process of converting light energy into chemical energy.
• In this process the light energy obtained from the sun is converted into ATP (adenosine triphosphate) and NADPH
(nicotinamide adenine dinucleotide phosphate).
Light Dependent Reactions in Photosynthesis
Following is an overview of the light dependent part of the reactions in photosynthesis:
• Molecule of chlorophyll – loses one electron as it absorbs one photon
• This released electron is taken up by pheophytin(primary electron acceptor) which is a modified form of chlorophyll
• Pheophytin then passes the electron onto a quinone molecule
• This process starts the electron transport chain or a flow of electrons
• The electron transport chain ultimately causes the reduction of NADP to NADPH
• The above process causes a gradient of energy which helps ATP synthase to produce ATP.
• The chlorophyll molecule regains its lost electron when water splits to give an electron.

14. Following is the reaction for the light dependent reaction taking place in plants in the presence of non-cyclic electron
flow:
2 H2O + 2 NADP+ + 3 ADP + 3 Pi + light → 2 NADPH + 2 H+ + 3 ATP + O2
So, during light reaction in photosynthesis the following are formed:
NADPH
Proton cations
ATP
O2
There are two parts of the light dependent reactions in photosynthesis. They are the z scheme and water photolysis.
Z Scheme of Photosynthesis
• The z scheme is a scheme used to describe the light reactions that take place in photosynthesis.
• There are two types of light reactions:
Cyclic
Non-cyclic
• The cyclic reaction is called so because the electron is emitted from photosystem I, passes onto electron
acceptor molecules and finally returns to photosystem I.
• Cyclic reaction is the same as the non-cyclic process.
• Here too ATP is created but no NADPH.

15. The non-cyclic reactions (Z scheme) follow the undermentioned steps:
1. The antenna complexes such as photosystem II, chlorophyll, and accessory pigments absorb a photon and release an electron.
This antenna system is found in the photosystem II’s chlorophyll molecule.
2. This releasing of an electron is known as photoinduced charge separation.
3. This released electron is taken up by pheophytin which is the main electron acceptor molecule.
4. The electrons are now in a flow called the electron transport chain.
5. This causes the proton cations to be shuttled across the thylakoid space making an energy gradient across the chloroplast. This
gradient is also known as a chemiosmotic potential.
6. The ATP synthase uses this chemiosmotic potential to create ATP by photophosphorylation.
7. Now the electron is absorbed by photosystem I.
8. In the photosystem I the electron is further agitated by the absorption of more light.
9. This energised electron passes along other electron acceptors transferring its energy along the way.
10.This energy in the electron acceptors is used to transport hydrogen ions across the thylakoid membrane.
11.The electron is finally used to reduce NADP to NADPH. This is the part where the journey of the electron ends.

16. “Light reaction is the process of photosynthesis that converts energy from the sun into chemical energy in the form of
NADPH and ATP.”
What is Light Reaction?
• The light reaction is also known as photolysis reaction and takes place in the presence of light.
• It usually takes place in the grana of chloroplasts.
• The photosystems have pigment molecules.
• In the plants, chlorophyll is one of the primary pigments which actively takes part in the process of light reactions like photosynthesis.
• The accessory pigments include carotenoids.
• The energy from the sun is absorbed by the chlorophyll in the thylakoid membrane of the chloroplasts.
• The energy is then transferred to ATP and NADPH that is generated by two-electron transport chains.
• Water is used and oxygen is released during the process.
Process of Light Reaction
• Light reaction is the first stage of photosynthesis process in which solar energy is converted into chemical energy in the form of ATP and NADPH.
• The protein complexes and the pigment molecules help in the production of NADPH and ATP.
• The process of light reaction is given below-
• In light reactions, energy from the sunlight is absorbed by the pigment chlorophyll and is converted into chemical energy in the form of electron charge carrier
molecules such as NADPH and ATP.
• Light energy is utilized in both the Photosystems I and II, present inside thylakoid membranes of the chloroplasts.

17. •The carbohydrate molecules are obtained from the carbon dioxide from the use of chemical energy gathered during the reactions.
•The Light energy tends to split into the water and later extracts the electrons from the photosystem II; then the electrons move from the PSII to
b6f (cytochrome) to the photosystem I (PSI) and reduce in the form of energy.
•The electrons are re-energized in the Photosystems I and the electrons of high energy reduce NADP+ into NADPH.
•In the process of non-cyclic photophosphorylation, the cytochrome uses the electron energy from Photosystem II to pump the ions of hydrogen
from the lumen to stroma; later, this energy allows the ATP synthase to bind to the third phosphate group to the ADP molecule, which then forms
the ATP.
•In the process of cyclic photophosphorylation, the cytochrome b6f uses electron energy from both the Photosystems I and II to create a number
of ATP and stops the production of the NADPH, thus maintaining the right quantities of ATP and NADPH.
•Thus, the light reactions harness the light energy to drive the transport of electrons and the pumping of the proton, to convert the energy from
the light into the biologically useful form ATP and produces a usable source of reducing the power NADPH.
Key Points on Light Reaction
•The light reaction traps the energy from the sun and converts it into chemical energy that is stored in NADPH and ATP.
•Oxygen is released as the waste product.

18. Cyclic and non cyclic
• We all are well aware of the complete process of photosynthesis.
• Yes, it is the biological process of converting light energy into chemical energy.
• In this process, light energy is captured and used for converting carbon dioxide and water into glucose and oxygen gas.
• The complete process of photosynthesis is carried out through two processes:
Light reaction
• The light reaction takes place in the grana of the chloroplast.
• Here, light energy gets converted to chemical energy as ATP and NADPH.
• In this very light reaction, the addition of phosphate in the presence of light or the synthesizing of ATP by cells is known as
photophosphorylation
Dark reaction
• While in the dark reaction, the energy produced previously in the light reaction is utilized to fix carbon dioxide into carbohydrates.
• The location where this happens is the stroma of the chloroplasts.
Photophosphorylation
• Photophosphorylation is the process of utilizing light energy from photosynthesis to convert ADP to ATP.
• It is the process of synthesizing energy-rich ATP molecules by transferring the phosphate group into ADP molecule in the presence of light.
Photophosphorylation is of two types:
• Cyclic Photophosphorylation
• Non-cyclic Photophosphorylation

19. Cyclic Photophosphorylation
• The photophosphorylation process which results in the
movement of the electrons in a cyclic manner for synthesizing
ATP molecules is called cyclic photophosphorylation.
• In this process, plant cells just accomplish the ADP to ATP for
immediate energy for the cells.
• This process usually takes place in the thylakoid membrane and
uses Photosystem I and the chlorophyll P700.
• During cyclic photophosphorylation, the electrons are
transferred back to P700 instead of moving into the NADP from
the electron acceptor.
• This downward movement of electrons from an acceptor to
P700 results in the formation of ATP molecules.

20. Non-Cyclic Photophosphorylation
• The photophosphorylation process which results in the movement of the
electrons in a non-cyclic manner for synthesizing ATP molecules using the
energy from excited electrons provided by photosystem II is called non-
cyclic photophosphorylation.
• This process is referred to as non- cyclic photophosphorylation because the
lost electrons by P680 of Photosystem II are occupied by P700 of
Photosystem I and are not reverted to P680.
• Here the complete movement of the electrons is in a unidirectional or in a
non- cyclic manner.
• During non-cyclic photophosphorylation, the electrons released by P700 are
carried by primary acceptor and are finally passed on to NADP.
• Here, the electrons combine with the protons – H+ which is produced by
splitting up of the water molecule and reduces NADP to NADPH2.

21. Cyclic Photophosphorylation Non-Cyclic Photophosphorylation
Only Photosystem I is involved. Both Photosystem I and II are involved.
P700 is the active reaction centre. P680 is the active reaction centre.
Electrons travel in a cyclic manner. Electrons travel in a non – cyclic
manner.
Electrons revert to Photosystem I Electrons from Photosystem I are
accepted by NADP.
ATP molecules are produced. Both NADPH and ATP molecules are
produced.
Water is not required. Photolysis of water is present.
NADPH is not synthesized. NADPH is synthesized.
Oxygen is not evolved as the by-product Oxygen is evolved as a by-product.
This process is predominant only in
bacteria.
This process is predominant in all green
plants.
Difference between Cyclic and Non-Cyclic Photophosphorylation

22. Electron Transport Chain
• Electron Transport Chain is a series of compounds
where it makes use of electrons from electron carrier
to develop a chemical gradient.
• It could be used to power oxidative phosphorylation.
• The molecules present in the chain comprises
enzymes that are protein complex or proteins,
peptides and much more.
• Large amounts of ATP could be produced through a
highly efficient method termed oxidative
phosphorylation.
• ATP is a fundamental unit of metabolic process.
• The electrons are transferred from electron donor to
the electron acceptor leading to the production of
ATP.
• It is one of the vital phases in the electron transport
chain.
• Compared to any other part of cellular respiration the
large amount of ATP is produced in this phase.

23. • Electron transport is defined as a series of redox reaction that is similar to the relay race.
• It is a part of aerobic respiration.
• It is the only phase in glucose metabolism that makes use of atmospheric oxygen.
• When electrons are passed from one component to another until the end of the chain the electrons reduce molecular oxygen thus producing
water.
• The requirement of oxygen in the final phase could be witnessed in the chemical reaction that involves the requirement of both oxygen and
glucose.
Electron Transport Chain in Mitochondria
• A complex could be defined as a structure that comprises a weak protein, molecule or atom that is weakly connected to a protein.
• The plasma membrane of prokaryotes comprises multi copies of the electron transport chain.
Complex 1- NADH-Q oxidoreductase: It comprises enzymes consisting of iron-sulfur and FMN (Flavin mononucleotide).
• Here two electrons are carried out to the first complex aboard NADH.
• FMN is derived from vitamin B2.
Q and Complex 2- Succinate-Q reductase: FADH2 (flavin adenine dinucleotide) that is not passed through complex 1 is received directly from
complex 2.
• The first and the second complexes are connected to a third complex through compound ubiquinone (Q)(nutrient).
• The Q molecule is soluble in water and moves freely in the hydrophobic core of the membrane.
• In this phase, an electron is delivered directly to the electron protein chain.
• The number of ATP obtained at this stage is directly proportional to the number of protons that are pumped across the inner membrane of the
mitochondria.

24. Complex 3- Cytochrome c reductase: The third complex is comprised of Fe-S protein, Cytochrome b, and Cytochrome c proteins.
• Cytochrome proteins consist of the heme group.
• Complex 3 is responsible for pumping protons across the membrane.
• It also passes electrons to the cytochrome c where it is transported to the 4th complex of enzymes and proteins.
• Here, Q is the electron donor and Cytochrome C is the electron acceptor.
Complex 4- Cytochrome c oxidase: The 4th complex is comprised of cytochrome c, a and a3.
• There are two heme groups where each of them is present in cytochromes c and a3.
• The cytochromes are responsible for holding oxygen molecule between copper and iron until the oxygen content is reduced completely.
• In this phase, the reduced oxygen picks two hydrogen ions from the surrounding environment to make water.

25. Calvin cycle and its regulation
• Photosynthesis is the biochemical process that occurs in all green plants or autotrophs producing organic molecules from carbon dioxide (CO2).
• These organic molecules contain many carbon-hydrogen (C–H ) bonds and are highly reduced compared to CO2.
There are two stages of Photosynthesis –
Light-dependent reactions – As the name suggests, it requires light and mainly occurs during the daytime.
Light-independent reactions – It is also called the dark reaction or Calvin cycle or C3 cycle.
• This reaction occurs both in the presence and absence of sunlight.
“Calvin cycle or C3 cycle is defined as a set of chemical reactions performed by the plants to reduce carbon
dioxide and other compounds into glucose.”

28. What is Calvin Cycle?
• Calvin cycle is also known as the C3 cycle or light-independent or dark reaction of photosynthesis.
• However, it is most active during the day when NADPH and ATP are abundant.
• To build organic molecules, the plant cells use raw materials provided by the light reactions:
1. Energy: ATP provided by cyclic and noncyclic photophosphorylation, which drives the endergonic reactions.
2. Reducing power: NADPH provided by photosystem I is the source of hydrogen and the energetic electrons required to bind
them to carbon atoms.
• Much of the light energy captured during photosynthesis ends up in the energy-rich C—H bonds of sugars.
Plants store light energy in the form of carbohydrates, primarily starch and sucrose.
The carbon and oxygen required for this process are obtained from CO2, and the energy for carbon fixation is derived from the
ATP and NADPH produced during the photosynthesis process.
The conversion of CO2 to carbohydrate is called Calvin Cycle or C3 cycle and is named after Melvin Calvin who discovered it.
The plants that undergo the Calvin cycle for carbon fixation are known as C3 plants.
Calvin Cycle requires the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase commonly called RuBisCO.
It generates the triose phosphates, 3-phosphoglycerate (3-PGA), glyceraldehyde-3P (GAP), and dihydroxyacetone phosphate
(DHAP), all of which are used to synthesize the hexose phosphates fructose-1,6-bisphosphate and fructose 6-phosphate

29. C3 Cycle Diagram
• The Calvin cycle diagram below shows the different stages of Calvin Cycle or C3 cycle that include carbon fixation, reduction, and regeneration.
Stages of C3 Cycle
Calvin cycle or C3 cycle can be divided into three main stages:
Carbon fixation
• The key step in the Calvin cycle is the event that reduces CO2.
• CO2 binds to RuBP in the key process called carbon fixation,
forming two-three carbon molecules of phosphoglycerate.
• The enzyme that carries out this reaction is ribulose
bisphosphate carboxylase/oxygenase, which is very large with a
four-subunit and present in the chloroplast stroma.
• This enzyme works very sluggishly, processing only about three
molecules of RuBP per second (a typical enzyme process of
about 1000 substrate molecules per second).
• In a typical leaf, over 50% of all the protein is RuBisCO.
• It is thought to be the most abundant protein on the earth.

30. Reduction
• It is the second stage of Calvin cycle.
• The 3-PGA molecules created through carbon fixation are converted into molecules of simple sugar – glucose.
• This stage obtains energy from ATP and NADPH formed during the light-dependent reactions of photosynthesis.
• In this way, Calvin cycle becomes a pathway in which plants convert sunlight energy into long-term storage
molecules, such as sugars.
• The energy from the ATP and NADPH is transferred to the sugars.
• This step is known as reduction since electrons are transferred to 3-PGA molecules to form glyceraldehyde-3
phosphate.
Regeneration
• It is the third stage of the Calvin cycle and is a complex process that requires ATP.
• In this stage, some of the G3P molecules are used to produce glucose, while others are recycled to regenerate the
RuBP acceptor.

31. Products of C3 Cycle
• One molecule of carbon is fixed at each turn of the Calvin cycle.
• One molecule of glyceraldehyde-3 phosphate is created in three turns of the Calvin cycle.
• Two molecules of glyceraldehyde-3 phosphate combine together to form one glucose molecule.
• 3 ATP and 2 NADPH molecules are used during the reduction of 3-phosphoglyceric acid to
glyceraldehyde-3 phosphate and in the regeneration of RuBP.
• 18 ATP and 12 NADPH are consumed in the production of 1 glucose molecule.
Key Points on C3 Cycle
• C3 cycle refers to the dark reaction of photosynthesis.
• It is indirectly dependent on light and the essential energy carriers are products of light-dependent
reactions.
• In the first stage of the Calvin cycle, the light-independent reactions are initiated and carbon dioxide is
fixed.
• In the second stage of the C3 cycle, ATP and NADPH reduce 3PGA to G3P.
• ATP and NADPH are then converted into ATP and NADP+.
• In the last stage, RuBP is regenerated.
• This helps in more carbon dioxide fixation.

32. • Frequently Asked Questions
• What is Calvin Cycle?
• Calvin cycle is also known as the C3 cycle. It is the cycle of chemical reactions where the carbon from
the carbon cycle is fixed into sugars. It occurs in the chloroplast of the plant cell.
• What are the different steps involved in the Calvin cycle?
• The different steps involved in the Calvin cycle include:
• Carbon fixation
• Reduction
• Regeneration
• What are the end products of C3 cycle?
• ADP, NADP, and glucose are the end products of the C3 cycle. ADP and NADP are produced in the
first stage of C3 cycle. In the second stage, glucose is produced.
• What is carbon fixation in the Calvin cycle?
• In the carbon fixation of the Calvin cycle, the carbon dioxide is fixed to stable organic intermediates.
• Why is the third step of the Calvin cycle called the regeneration step?
• The third step is known as regeneration because Ribulose-bis phosphate that begins the cycle is
regenerated from G3P.

33. • When the carbon dioxide concentration inside a leaf drops, photorespiration takes place.
• This takes place mostly on warm arid days when plants are compelled to shut their stomata to avert surplus water loss.
• The oxygen proportions of the leaf will automatically surge if the plants keep trying to fix carbon dioxide when their stomata are shut, all the
carbon dioxide stored will be consumed and the oxygen proportions will surge when compared to carbon dioxide levels.
What is Photorespiration
Photorespiration and its significance

34. • Photorespiration is a process that occurs in Calvin Cycle during plant metabolism.
• In this process, the key enzyme RuBisCO that is responsible for The fixing of carbon dioxide reacts with oxygen rather than carbon dioxide.
• It occurs because of the conditions in which carbon dioxide concentration falls down and rubisco does not have enough carbon dioxide to fix
and it starts fixing oxygen.
• Under suitable conditions, C3 plants have sufficient water, the supply of carbon dioxide is abundant and in such conditions, photorespiration
is not a problem.
• Photorespiration is influenced by high temperature as well as light intensity and accelerating the formation of glycolate and the flow through
the photorespiratory pathway.
• Photorespiration causes a light-reliant acceptance of O2 and discharge of CO2 and is related to the creation and metabolism of a minute
particle named glycolate.
• Photosynthesis and photorespiration are two biological processes (in flourishing plants) that can function simultaneously beside each other as
photosynthesis gives off oxygen as its byproduct and photorespiration gives off carbon dioxide as its byproduct, and the said gases are the
raw material for the said processes.
• When the carbon dioxide levels inside the leaf dip to about 50 ppm, RuBisCO begins combining Oxygen with RuBP as an alternative to
Carbon dioxide.
• The final result of this is that as an alternative to manufacturing 2 molecules of 3C- PGA units, merely one unit of PGA is fashioned with a
noxious 2C molecule termed phosphoglycolate.
• To purge themselves of the phosphoglycolate the plant takes some steps.
• Primarily, it instantly purges itself from the phosphate cluster, transforming those units into glycolic acid.
• After that, this glycolic acid is transferred to the peroxisome and then transformed into glycine.
• The conversion of glycine into serine takes place in the mitochondria of the plant cell.
• The serine produced after that is used to create other organic units.
• This causes a loss of carbon dioxide from the flora as these reactions charge plant’s energy.

35. To avert this procedure, two dedicated biochemical reactions were necessary to evolve in the flora of our world:
Photosynthesis in C4 plants
• Plants that propagate in warm, arid climates similar to sugarcane and corn have developed a dissimilar system for carbon
dioxide fixation.
• The structure of the leaves of these plants is dissimilar to that of a normal leaf.
• They are known to display Kranz anatomy.
• Dense-walled parenchyma cells termed as bundle sheath cells surround the phloem and xylem of these leaves where the
maximum amount of photosynthesis happens.
CAM – Crassulacean Acid Metabolism
• This section of flora makes use of a procedure akin to the C4 section apart from the fact that they take carbon dioxide in
nocturnal hours and convert it into malic or aspartic acid.
• The vacuoles of their photosynthetic cells provide a location to store them.
• As soon as the sun shines these plants shut their stomata and disintegrate the malic acid to keep the carbon dioxide ratio
high enough to avert photorespiration.
• This permits the leaves to have their stomata shut with the intention of preventing withering.
• This section of flora doesn’t display Kranz anatomy.

36. Important Questions on Photorespiration
• Q.1.What is Photorespiration?
Sol. Photorespiration can be defined as the evolution of carbon dioxide(CO2) during photosynthesis.
• Q.2.What is Photosynthesis?
Sol. Photosynthesis is a biological process, which uses light energy (sunlight) to synthesise organic compounds.
• Q.3.Which light range is most effective in photosynthesis?
Sol. Red light.
• Q.4.What is the function of RuBisCO in photorespiration?
• Sol. In photorespiration, RuBisCO catalyses the oxygenation of RuBP to one molecule of PGA and phosphoglycolate.
• Q.5.What is the difference between photosynthesis and photorespiration?
• Sol. Photosynthesis and photorespiration are different processes. In photosynthesis, carbon dioxide fixation takes place by the RuBisCO, whereas in the
photorespiration RuBisCO reacts with oxygen and it competes with the Calvin cycle.

37. The key difference between C3, C4 and CAM pathway is the synthesis of different products during the grasping of carbon dioxide for photosynthesis from the sunlight and
then conversion of it to glucose.
When photosynthetic plants yield 3-carbon acid or 3-phosphoglyceric acid(PGA) as their first product during the carbon dioxide fixation, it is known as C3 pathway.
When photosynthetic plants, before entering the C3 pathway, produce oxaloacetic acid or a 4-carbon compound as its primary product is known as Hatch and Slack or C4
pathway.
The pathway is CAM (crassulacean acid metabolism), when plants grasp the solar energy during the day and use the energy at night time to assimilate or fix carbon dioxide.
C3 Pathway
• These temperate or cool-season plants flourish at an optimum temperature.
• Less efficient at higher temperatures
• The primary product is 3-phosphoglyceric acid or 3-carbon acid
• It takes place in three steps – carboxylation, reduction and regeneration
• C4 Pathway
• Plants in the tropical region are observed following this pathway
• Two-step process where Oxaloacetic acid is a 4-carbon compound that is produced
• It takes place in bundle sheath and mesophyll cells found in the chloroplast
• These can either be annual or perennial, and the ideal temperature for their growth
• Examples are Indiana grass, big bluestem, Bermudagrass,
• CAM Plants
• In this type of photosynthesis, entities absorb energy during the daytime from sunlight and fix carbon dioxide at night
• This adaptation is observed during the time of drought, allowing gaseous exchange during the night when the temperature of the air is cooler, along with loss of water
vapour
• Examples are plants such as euphorbias and Cactus.
• Irregular water supply has caused bromeliads and orchids to adapt to this pathway

38. C3 C4 CAM
What it means
This pathway is observed in C3 plants wherein the
primary product from sunlight post carbon-grasping is
3-phosphoglyceric acid to produce energy
Sunlight is converted into oxaloacetic acid by some
plants prior to the C3 cycle, which is further converted
into energy. The plants are known as C4 plants. It is
the C4 pathway
Plants store solar energy post which they convert into
energy at the night, such plants are CAM plants and
the pathway is referred to as CAM pathway
Cells included
Mesophyll cells Bundle sheath cells, Mesophyll cells Mesophyll cells in C3 and C4, both
Difference Between C3, C4 and CAM pathway
Observed in
All plants carry out photosynthesis Tropical plants Semi-dry climatic conditions
Plant types that use this cycle
Hydrophytic, Mesophytic, and Xerophytic plants Mesophytic plants Xerophytic plants
Photorespiration process
Observed in higher rates Not seen as much Observed in the noon time
First-stable product produced
3-phosphoglycerate Oxaloacetate Daytime – 3-phosphoglycerate
Night time – Oxaloacetate

39. Carboxylating enzyme
In C3, RuBP carboxylase PEP carboxylase – mesophyll
RuBP carboxylase – bundle sheath
RuBP carboxylase – daytime
PEP carboxylase – nighttime
Kranz Anatomy
Not present Present Not present
Initial CO2 receptor
Ribulose-1, 5-biphosphate Phosphoenolpyruvate Phosphoenolpyruvate
Number of molecules of NADPH and ATP required to produce glucose
NADPH – 12
ATP – 18
NADPH – 12
ATP – 30
NADPH – 12
ATP – 39
The ideal photosynthetic temperature
15-25 degree celsius 30-40 degree celsius Greater than 40-degree celsius
Calvin cycle functional
Not accompanied with any other cycle Accompanied along with C4 pathway C4 pathway and C3
Example
Beans, Spinach, Sunflower, Rice, Cotton Maize, Sorghum, Sugarcane Orchids, Cacti, euphorbias

40. • Photosynthesis is the biological process by which all green plants, photosynthetic bacteria and other autotrophs convert
light energy into chemical energy.
• In this process, glucose is synthesised from carbon dioxide and water in the presence of sunlight.
• Furthermore, oxygen gas is released out into the atmosphere as the by-product of photosynthesis.
• The balanced chemical equation for the photosynthesis process is as follows:
• 6CO2 + 6H2O —> C6H12O6 + 6O2
• Sunlight is the ultimate source of energy.
• Plants use this light energy to prepare chemical energy during the process of photosynthesis.
• The whole process of photosynthesis takes place in two phases- photochemical phase and biosynthetic phase.
• The photochemical phase is the initial stage where ATP and NADPH for the biosynthetic phase are prepared.
• In the biosynthetic phase, the end product – glucose is produced.

42. • During the biosynthetic phase, carbon dioxide and water combine to give carbohydrates i.e. sugar molecules.
• This reaction of carbon dioxide is termed as carbon fixation. Different plants follow different pathways for carbon fixation.
• Based on the first product formed during carbon fixation there are two pathways: the C3 pathway and C4 pathway.
The Pathway of Photosynthesis
C3 Pathway (Calvin Cycle)
• The majority of plants produce 3-carbon acid called 3-phosphoglyceric acid (PGA) as a first product during carbon dioxide
fixation.
• Such a pathway is known as the C3 pathway which is also called the Calvin cycle.
Calvin Cycle occurs in three steps:
• carboxylation
• reduction
• regeneration
• In the first step, the two molecules of 3-phosphoglyceric acid (PGA) are produced with the help of the enzyme called RuBP
carboxylase.
• Later in the second and third steps, the ATP and NADPH phosphorylate the 3-PGA and ultimately produces glucose.
• Then the cycle restarts again by regeneration of RuBP.
• Beans, Rice, Wheat, and Potatoes are an example of plants that follow the C3 pathway

43. C4 Pathway (Hatch and Slack Pathway)
• Every photosynthetic plant follows Calvin cycle, but in some plants, there is a primary stage to the Calvin Cycle
known as C4 pathway.
• Plants in tropical desert regions commonly follow the C4 pathway.
• Here, a 4-carbon compound called oxaloacetic acid (OAA) is the first product by carbon fixation.
• Such plants are special and have certain adaptations as well.
• The C4 pathway initiates with a molecule called phosphoenolpyruvate (PEP) which is a 3-carbon molecule.
• This is the primary CO2 acceptor and the carboxylation takes place with the help of an enzyme called PEP
carboxylase.
• They yield a 4-C molecule called oxaloacetic acid (OAA).
• Eventually, it is converted into another 4-carbon compound known as malic acid.
• Later, they are transferred from mesophyll cells to bundle sheath cells.
• Here, OAA is broken down to yield carbon dioxide and a 3-C molecule.
• The CO2 thus formed, is utilized in the Calvin cycle, whereas 3-C molecule is transferred back to mesophyll cells
for regeneration of PEP.
• Corn, sugarcane and some shrubs are examples of plants that follow the C4 pathway.
• Calvin pathway is a common pathway in both C3 plants and C4 plants, but it takes place only in the mesophyll cells
of the C3 Plants but not in the C4 Plants.

44. Key points:
• Photorespiration is a wasteful pathway that occurs when the Calvin
cycle enzyme rubisco acts on oxygen rather than carbon dioxide.
• The majority of plants are C3 plants, which have no special features to
combat photorespiration.
• C4 plants minimize photorespiration by separating initial CO2​ fixation and
the Calvin cycle in space, performing these steps in different cell types.
• Crassulacean acid metabolism (CAM) plants minimize photorespiration
and save water by separating these steps in time, between night and day.

46. Bacterial photosynthesis
1. Photosynthesis in prokaryotes
• The photosynthetic prokaryotes are green bacteria puple bacteria and
cyanobacteria
• They differ fundamentally in the pathways of photosynthetic reactions
• Photosynthetic bacteria have comparatively primitive systems essentially to the
activities carried out by photosystem I in eukaryotic plants.
• Lacking a water splitting activity equivalent to photosystem II, photosynthetic bacteria
bacteria cannot use water as an electron donor and do not evolve oxygen in
photosynthesis.
Cyanobacteria
• Oxygenic photosynthetic bacteria perform photosynthesis in a similar manner to plants.
to plants.
• They contain light-harvesting pigments, absorb carbon dioxide, and release oxygen.
oxygen.
• Cyanobacteria typically prokaryotic in cellular organization , have two photosystems
photosystems equivalent to eukaryotic photosystems I and II and carry out
photosynthesis by same mechanisms as eukaryotic plants.
• Cyanobacteria or Cyanophyta are the only form of oxygenic photosynthetic bacteria
bacteria
• Cyanobacteria can use water as a electron donor and evolve oxygen in photosynthesis.

47. Photosynthetic bacteria-
• Purple bacteria An oxygenic photosynthetic bacteria consume carbon dioxide but do not release oxygen.
• These include Green and Purple bacteria as well as Filamentous Anoxygenic Phototrophs (FAPs), and
Phototrophic Heliobacteria.
• Purple bacteria classified into two types • Purple sulfur bacteria the Chromatiaceae which produce sulfur
particles inside their cells.
• It use sulfur containing compounds such as H2S as electron donors for non cyclic photosynthesis is called
Photolithotrophy.
• Purple non sulfur bacteria Ectothiorhodospiraceae, which produce sulphur particles outside their cells.
• It use complex sulfur free organic substances such as malate and succinate as electron donors, the process
is called photoorganotrophy.
• While these bacteria can tolerate small amounts of sulfur, they tolerate much less than purple or green
sulfur bacteria, and too much hydrogen sulfide is toxic to them.
• Purple bacteria cannot photosynthesize in places that have an abundance of oxygen, so they are typically
found in either stagnant water or hot sulfuric springs.
• Instead of using water to photosynthesize, like plants and cyanobacteria, purple sulfur bacteria use
hydrogen sulfide as their reducing agent, which is why they give off sulfur rather than oxygen.
Photosynthetic bacteria-Green bacteria
• Green sulfur bacteria generally do not move (non-motile), and can come in multiple shapes such as
spheres, rods, and spirals
• These bacteria have been found deep in the ocean
• They have also been found underwater near Indonesia.
• These bacteria can survive in extreme conditions, like the other types of photosynthetic bacteria, suggesting
an evolutionary potential for life in places otherwise thought uninhabitable.
• Green bacteria which may be use either inorganic sulfate containing compounds or nonsulfur organic

48. 7. Other bacteria
• Phototrophic Heliobacteria are also found in soils, especially water- saturated fields, like rice paddies.
• They use a particular type of bacteriochlorophyll, labelled g, which differentiates them from other types of
photosynthetic bacteria.
• They are photoheterotroph, which means that they cannot use carbon dioxide as their primary source of
carbon.
• Green and red filamentous anoxygenic phototrophs (FAPs) were previously called green non-sulfur
bacteria, until it was discovered that they could also use sulfur components to work through their
processes.
• This type of bacteria uses filaments to move around.
• The color depends on the type of bacteriochlorophyll the particular organism uses.
• What is also unique about this form of bacteria is that it can either be photoautotrophic, meaning they
create their own energy through the sun’s energy; chemoorganotropic, which requires a source of carbon;
or photoheterotrophic, which, as explained above, means they don’t use carbon dioxide for their carbon
source.
8. Types of bacterial Photosynthesis
• There are two types of photosynthetic processes: • oxygenic photosynthesis • Anoxygenic photosynthesis
• The general principles of anoxygenic and oxygenic photosynthesis are very similar, but oxygenic
photosynthesis is the most common and is seen in plants, algae and cyanobacteria.
9. oxygenic photosynthesis
• During oxygenic photosynthesis, light energy transfers electrons from water (H2O) to carbon dioxide
(CO2), to produce carbohydrates.
• In this transfer, the CO2 is "reduced," or receives electrons, and the water becomes "oxidized," or loses
electrons.
• Ultimately, oxygen is produced along with carbohydrates.

49. 10. Anoxygenic photosynthesis
• Purple and green sulfur bacteria carry out anoxygenic photosynthesis i.e. there is no evolution of oxygen.
• There is only one photosystem involved in photosynthesis
• The electron donors sulphur, reduced sulphur compounds, molecular hydrogen or simple organic
compounds.
• These are substances with lower redox potentials than water.
• Even in cyanobacteria , there may be anoxygenic photosynthesis with only one photosystem when
hydrogen sulphide is the electron donor.
• The general equation for Anoxygenic photosynthesis is: • 2H2A +CO2 ↔C(H2O) +H2O+2A
11. Photosynthetic structures
• In eukaryotic cells of higher plants, multicellular red, green and brown alge, dinoflagellates and diatoms
the photosynthetic structures are the chlorpplasts.
• Chlorplasts enclose membraneous sacs called thylakoids which contain the units of photosynthesis
12. Photosynthetic structures
• In Prokaryotes(blue green bacteria, prochlorphyta, purple and green bacteria), the photosynthetic structures
are called Chromatophores
• In the Rhodospirillaceae (purple non- sulfur bacteria) and chromatiaceae (purple sulfur bacteria) the
thylakoids are extensions of the cell membrane.
• They may be in the form of vesicles , tubular bodies or lamellae
13. In chlorobiaceae (green sulfur bacteria) the sacs like membraneous structures called chlorosomes forming
the photosynthetic apparatus are not continuous with the cell membrane i.e. it is attached to the cytoplasmic

50. Photosynthetic structures Natural and artificial chlorosomal systems.
(a) Schematic of photosynthetic apparatuses in photosynthetic green bacteria.
(b) Molecular structures of bacteriochlorophyll-c–f molecules.
(c) Synthetic chlorophyll derivatives reported as models of bacteriochlorophyll-d.
14. Photosynthetic pigments Three main classes of photosynthetic pigments:
• Chlorphylls(Chl)(including bacteriochlorophyll, BChl), • Carotenoids and • phycobilins (Phycobiliproteins,PBPs)
15. Bacateriochlorophylls
• The photosynthetic pigments of the purple and green bacteria are bacteriochlorphylls a,b,c,d or e and a variety of
carotenoids.
• Bacteriochlorophylls ,like chlorphylls of eukaryotic plants are built on a terapyrrole ring containing a central magnesium
atom and differ only in minor substitutions in side groups attached to the ring.
• purple bacteria contain bacteriochlorphylls a and b.
• Green bacteria predominately c, d and e and also contain small quantities of bacteriochlorophylls a, which occur in
reaction centers
• Bacteriochlorphyll pigments absorb light most strongly in the near UV and far red regions of the spectrum and transmit
most of the UV wavelengths.
Carotenoids
• The distinctive colors of green and purple bacteria come primarily from different carotenoids occuring as accessory
pigments in association with bacteriochlorophylls.
• The carotenoids are found in almost all photsynthetic orgnaisms.
• They are yellow and orange pigments which are soluble in organic solvents.
• There are two types of carotenoids, carotene and carotenols. Carotenes, e.g. ß-carotene.
• Most of the carotenes are present in Photosystem I.
• Carotenols (Xanoathophylls) are alcohols.
• Fucoxanthol is present in diatoms and other brown algae.

51. 17. Phycobilins
• Phycobilins are water soluble open chain tetrapyyroles which are present in red algae and blue
green bacteria (cyanobacteria).
• There are two kinds of phycobilins, phycocyanins and phycoerythrins
. • Phycocyanins are predominate in the blue green algae, while phycoerythrins predominate in
the red algae.
• Phycobilins are mainly present in PS II, but also present in PS I.
18. • The light harvesting complexes of both purple and green bacteria like the LHC-I and LHC-II
antennas of higher plants, absorb light and pass excitation energy to the reaction centers of the
photosystem
19. Electron transport carriers in Bacterial photosynthesis
• The electron transport System of photosynthetic bacteria differs from that of aerobic bacteria.
• Cytochrome a and other types of Cytochrome oxidase are absent in the photosynthetic
electron transport system, because photosynthesis takes place under anaerobic conditions.
• Hence there is no need of a cytochrome which interacts with molecular oxygen.
20. Electron transport carriers The electron transport system consists of an
• intermediate electron acceptor (I) , • a primary electron acceptor (X), • a secondary acceptor (Y),
generally believed to be ubiquinone (UQ) and • b and c type cytochrome
21. Electron transport carriers and its location
• The electron transport carriers are asymmetrically located in the membrane.
• This is necessary for setting up in the hydrogen ion gradient.
• The reaction centre spans the membrane of the chromatophore.

52. • The primary acceptor (X) is believed to be associated with the reaction center on the outer side of the
membrane.
• The secondary acceptor Y (probably UQ) takes proton from the medium.
• It is thus located on the outer side of the membrane.
• The b type cytochrome is probably located in the interior of the membrane.
• The c-type cytochrome interacts with the reaction centre and is located on the inside of the membrane.
22. Primary acceptor
• The electron from P870 is received by an intermediate acceptor (I) and transferred to a primary acceptor(X).
• The purified P870 reaction centre has been shown to contain nonhaeme iron and ubiquinone.
• This has led to possibly both acts as primary acceptors.
• X is therefore likely to be an iron-sulfur protein or iron-quinone complex.
• It may or may not be ferredoxin (Clostridium have ferredoxin).
• Bacterial ferredoxins are blackish brown in color with absorption maxima around 390nm
23. Quinone
• The secondary acceptor (Y) is generally believed to be ubiquinone (UQ).
• UQ has also been considered to be a primary acceptor in the bacterial reaction centre, probably in an iron
quinone complex. • UQ consists of a 1-4 benzoquinone nucleus with n isoprenoid side chain at the second
carbon atom
24. Cytochrome b
• Cytochrome b is present in the photosynthetic electron transport system.
• It is adjacent to cytochrome c in the cyclic system.
• Cytochrome b may be present even in organisms where it has been previously reported to be absent.
• Small amounts of cytochrome b could be masked by other substances.
• One molecule of Cytochrome b present per reaction centre
• Cytochrome b has a role in cyclic photosynthetic flow in the chromatiaceae, Chlorobiaceae aswell as in the

53. • C-type Cytochrome
• A number of different c type cytochromes have been found in the electron transport system of
photosynthetic bacteria.
• In the purple non-sulphur bacterium Rhodospirillum rubrum a soluble c-type cytochrome is associated
with P870 of the reaction centre.
• This cytochrome is referred to as cytochrome c2 and has a high mid point potenitial of about +300mv.
• Cytochrome c2 is the electron donor to P870.
• In PS I of higher plants , Plastocyanin(PC) is the electron donor to P700.
• Rodospirillum also contains cytochrome cc’ with two different haeme groups
• Purple sulphur bacteria like Chromatium contain cytochrome c552 in addition to cytochrome c2 and cc’.
• Cytochrome c552 (MW 72000) has two haeme groups and one FMN.
• The green sulphur bacterium Chlorobium has three cytochromes of C-type.
26. Photophosphorylation
• Photophosphorylation is the process of utilizing light energy from photosynthesis to convert ADP to ATP
i.e light energy is converted into chemical energy
• It is the process of synthesizing energy-rich ATP molecules by transferring the phosphate group into ADP
molecule in the presence of light
• Two photosystems are involved in eukaryotes but only one photosystem is involved in prokaryotes.
Photophosphorylation is of two types: • Cyclic Photophosphorylation • Non-cyclic Photophosphorylation
27. Reaction centre
• The photosynthetic unit consists of ‘antenna’ or ‘light harvesting’ molecules for gathering light photons
and a reception centre where energy conversation takes place.
• Light energy harvested by the antenna pigments is transferred to the reaction centre.
• The pigments and proteins, which convert light energy to chemical energy and begin the process of

54. • In the chloroplasts of green plants of the reaction centre chlorophylls are P700(PS I) and P680(PS II).
• In green and purple bacteria some 40 or more bacteriochlorophyll molecules makes up the
photosynthetic unit .
• The reaction centre complex is commonly referred to as P870, although the wavelength may vary in
different species.
• The reaction centre generally contains BChl a(2-5% of the total) or rarely ,BChl b.
• In the purple non sulfur bacterium Rhodospirillum rubrum the principal light harvesting pigment is BChl a
and the reaction centre molecule is P890
29. • In Rhodopseudomonas spheroides the light harvesting bacteriochlorophyll absorbs maximally at
850nm and the reaction centre BChl is P870. in the R-26 mutant of R.sphaeroides, which lacks carotenoids,
the reaction centre pigment P870 constitutes 5% of the total pigment.
• In green sulphur bacteria the principal light harvesting pigment is BChl c (650nm) or BChl d (660nm) in the
green species and BChl e in the brown species
30. Light reactions in purple bacteria
• The single photosystem of purple bacteria is built around three membrane spanning polypeptides known
as the light(L), medium(M), heavy(H) polypeptides.
• These polypeptides organize a reaction center containing either bacteriochlorophyll a or b and a short
series of electron which is closely resembles those of photosystem II of green plants.
31. • In Purple bacteria , the bacteriochlorophyll molecyules at the reaction center undergo a change in
absoption at a wavelength of 870 or 960nm, depending on the species , as they undergo cycles of oxidation
and reduction in connections with the excitation of electrons.
• The reaction center bacteriochlorophyll of these bacteria are identified accordingly as P870 or P960.
• The reaction center consists of a pair of specialized bacteriochlorophyll b molecules.
• After excitation in the reaction center , electrons flow to the bacteriopheophytin b, which resembles
bacteriochlorophyll b without a central magnesium atom.

55. • From bacteriopheophytin electrons from through two quinones QA and QB each are associated with an iron
atom.
• At this point electrons pass from the photosystem to carriers of the electron transport system.
• Thus, the electron pathway within the R.viridis photosystem is equivalent to the P680 pheophytin QA QB
pathway of eukaryotic photosystem II (& cyanobacterial photosystem II) Electrons may flow cyclically or noncylically
around the single photosystem of purple sulfur bacteria.
33. Cyclic electron transport in purple bacteria
• In cyclic electron transport (figure 1) , electrons released from the photosystem enter a quinone pool.
• The electrons are later transferred from the quinone pool to a b/c1 complex.
• The bacterial b/c1 complex contains a b-type and c-type cytochrome linked with an iron sulfur protein and a
group of polypeptides.
• Electrons flow through the bacterial b/c1 complex pumps H+ gradient linked to electron transport as in
eukaryotic systems.
• In most purple bacteria electrons flow from the b/c1 complex to another c-type cytochrome c2 , a peripheral
membrane protein .
• From cytochrome c2 electrons return at lower energy levels to the reaction center of the single photosystem
• After another energy boost through light absorption, that may repeat the cyclic pathway
34. Quinone pool b/c1 complexP870 or P960 Cyt c2 Photosystem Figure 1 . Cyclic electron transport in purple
photosynthetic bacteria H+
35. Noncyclic electron transport in purple bacteria
• In noncyclic flow in purple bacteria(Figure 2), electrons derived from various sulfur or nonsulfur donors depending
on their energy level may be passed by a carrier, usually a cytochrome to the photosystem and then to the quinone
pool.
• In either case electrons in the quinone pool initially contain too little energy to directly reduce NAD+.
• Some electrons in the pool, however receive an additional energy boost from the membrane potential built up by
cyclic electron transport

56. 36. • Noncyclic flow results in the one way transfer of electrons from donor substances to NAD+.
• The NADH produced by the reduction provides a source of electrons for reductions in the cell as in the
dark reactions fixing Co2 into carbohydrates.
• Alternatively electrons carried by NADH can enter electron transport linked to the synthesis of ATP.
• The same F0F1 ATPase active in oxidative phosphorylation uses the H+ gradient built up by
photosynthetic electron transport as an energy source for ATP synthesis in purple bacteria.
• ATP produced by the F0F1 ATPase along with NADH formed by noncyclic photosynthesis provides energy
and reducing power for Co2 fixation in the dark reactions.
• The molecules and complexes of the light reactions including light harvesting photosystems and electron
transport carriers associated with saclike invaginations of the plasma membrane in purple bacteria.
37. b/c1 complex P870 or P960 Quinone pool Cyt c2 Sulfur or nonsulfur donors Photosystem.
• Noncyclic electron transport in purple photosynthetic bacteria.
• Electron donors for noncyclic photosynthesis may be sulfur containing compounds sucha s hydrogen
sulphide or non sulfur organic substances such as succinate.
• The Star indicates the excited from the photosystem. H+ NAD
38. Light reactions in Green Bacteria
• The photosynthetic systems of green bacteria appear to be two fairly well defined groups with respect to
photosystem and electron transport system
• One group is anaerobic and possesses a photosystem resembling photosystem II of eukaryotic plants
• Second group is aerobic , with a photosystem similar to eukaryotic photosystem

57. 40. photosynthetic electron flow in anaerobic bacteria which progresses primarily or exclusively by a cyclic pathway P870
P870* Various cytochromes Photosystem
41. Aerobic Green bacteria
• The photosystem of aerobic green bacteria contains specialized bacteriochlorophyll a molecules absorbing light at
540nm.
• These molecules identified as P840, pass electrons to a primary acceptor and a chain of Fe/S centers rather than
quinones .
• The more complex electron transport systems of these bacteria may include ferredoxin, a b/c1 complex and the
ferredoxin –NAD oxidoreductase complex.
• Electron carriers are arranged in aerobic bacteria may be either Cyclic or noncyclic electron transport
42. Aerobic green bacteria- Cyclic electron transport
• In cyclic transport , electrons flow to ferredoxin after excitation and movement through the internal carriers of the
photosystem.
• The direct reduction of ferredoxin at the first carrier reflects the fact that electrons excited to significantly higher energy
levels by the photosystem in these bacteria.
• Electrons then flow to NAD+ via the ferredoxin-NAD oxidoreductase complex which may contain FAD as an internal
carrier as in the equivalent complex of higher plants.
39. Anaerobic Green bacteria
• Within the photosystem of anaerobic group of bacteria, bacteriochlorophyll a molecules forming the a
reaction center change in absorbance at a wavelength of 870nm and are identified as P870
• Following excitation in the reaction center, electrons flow through a group of internal carriers including
bacteriopheophytin and iron associated quinones
• Electron transport around the photosystem of anaerobic green bacteria appears to be primarily by cyclic
pathway
• Only a few different cytochromes are in the electron transport system of these bacteria in connection
between this electron flow and ATP synthesis or reduction of NAD+.
• It is doubtful that electrons excited by the photolysis have enough energy to reduce NAD directly.
• However NADH may still be formed

58. • Transfer from the b/c1 complex to the photosystem may be direct or may occur via additional cytochromes;
the cytochromes on this side of the b/c1 complex, like those delivering electrons to the complex from NADH
.
• Because the b/c1 complex is present in the loop, H+ is pumped across the membrane housing system each
time electrons cycle around the photosystem.
43. Various cytochromes b/c1 complex P840 Cyt c2 Photosystem
• Cyclic electron transport in aerobic green bacteria H+ P840* NAD FD-NAD reductaseFD
44. Non-cyclic electron flow in aerobic green bacteria
• In non-cyclic electron flow in aerobic green bacteria (fig 5) uses electrons removed from inorganic sulfur
compounds.
• This flow occurs through cytochromes that vary widely in different species, electron pass from the donors
through one or more of these cytochromes to reach the b/c1 complex.
• From this point electrons enter the photosystem and, after excitations are delivered at high energy levels
to ferredoxin.
• The electrons may remain with ferredoxin with ferredoxin which serves directly as an electron donor for
dark reactions to green bacteria.
• Alternatively electrons may be delivered from ferredoxin to NAD
• The NADH produced may provide electrons for the dark reactions or may enter the respiratory electron
transport system leading to oxygen as the final electron acceptor
• Alternatively the electrons may reenter the photosynthetic pathway from NADH and travel cyclically
through one or more loops around photosystem.
• The same F0F1 ATPase active in oxidative phosphorylation uses the H+ gradient established by
photosynthetic electron transport as the energy source for ATP synthesis.
• All components of the light reactions are associated with the plasma membrane in green bacteria.

59. 47. Calvin Cycle (Dark reactions) Calvin cycle takes place in three steps: • Carbon Fixation • Reduction • Regeneration
48. Calvin cycle-Carbon Fixation
• In carbon fixation, a CO2 molecule from the atmosphere combines with a five-carbon acceptor molecule called ribulose-1,5- bisphosphate (RuBP).
• The resulting six-carbon compound is then split into two molecules of the three-carbon compound, 3-phosphoglyceric acid (3-PGA).
• This reaction is catalyzed by the enzyme RuBP carboxylase/oxygenase, also known as RuBisCO.
• Due to the key role it plays in photosynthesis, RuBisCo is probably the most abundant enzyme on Earth.
49. Calvin cycle –Reduction
• In the second stage of the Calvin cycle, the 3-PGA molecules created through carbon fixation are converted into molecules of a simple sugar – glyceraldehyde-3
phosphate (G3P)
• This stage uses energy from ATP and NADPH created in the light-dependent reactions of photosynthesis
• In this way, the Calvin cycle becomes the way in which plants convert energy from sunlight into long-term storage molecules, such as sugars
• The energy from the ATP and NADPH is transferred to the sugars
• This step is called “reduction” because NADPH donates electrons to the 3-phosphoglyceric acid molecules to create glyceraldehyde-3 phosphate
• In chemistry, the process of donating electrons is called “reduction,” while the process of taking electrons is called “oxidation.”
50. Calvin cycle –Regeneration
• Some glyceraldehyde-3 phosphate molecules go to make glucose, while others must be recycled to regenerate the five-carbon RuBP compound that is used to accept
new carbon molecules
• The regeneration process requires ATP. It is a complex process involving many steps
• Because it takes six carbon molecules to make a glucose, this cycle must be repeated six times to make a single molecule of glucose
• To accomplish this equation, five out of six glyceraldehyde-3 phosphate molecules that are created through the Calvin cycle are regenerated to form RuBP molecules
• The sixth exits the cycle to become one half of a glucose molecule.
46. Dark phase of photosynthesis : Co2 utilization In bacteria the reduction of Co2 during photosynthesis takes place through two mechanisms:
1. The reductive pentose pathway or Calvin cycle 2. pyruvate synthetase reaction or reductive carboxylic acid cycle.

60. 52. PYRUVATE SYNTHETASE REACTION(REDUCTIVE CARBOXYLIC ACID CYCLE)
• In green bacterium Chlorobium thiosulfatophilum Evans et al (1966) described the pyruvate synthetase
pathway for CO2 fixation
• CO2 is used to form pyruvate by means of the pyruvatesynthetase reaction
• The ultimate reductant is hydrogen sulphide
• The light dependent oxidation of H2S provides the reducing power for the reduction of ferredoxin (fd)
• Acetyl CoA the accepts CO2 , and is reduced by ferredoxin to yield pyruvate.
53. • Formation of pyruvate by pyruvate synthetase is dependent on reduced ferredoxin Acetyl CoA +
CO2+ferredoxin (reduced) ------ Pyruvate +CoA + ferredoxin (oxidized)
• Conversion of pyruvate into oxaloacetate Pyruvate + ATP+ CO2 ---------------- Oxaloacetate +ADP+ Pi
• Carboxylation of succinyl CoA to yield α-ketoglutarate(involving reduced ferredoxin) Succinyl CoA +
CO2+ferredoxin (reduced) ---- α-ketoglutarate +CoA + ferredoxin (oxidized)
• α-ketoglutarate is converted into citrate through oxalosuccinate.
• Citrate then splits into oxaloacetate and acetate α-ketoglutarate ----- Oxalosuccinate ------------
Citrate---- Oxaloacetic acid + Acetate
54. Pyruvate Acetyl CoACoA Citrate Oxaloacetate Malate α-Ketoglutarate Succinate Fumarate Isocitrate Co2
Co2 Green bacteria can fix Co2 , by reversing reactions of Pyruvate oxidation and the Citric acid cycle
55. The net result of each cycle is that 4 molecules of CO2 are fixed (reductive fixation) and one equivalent of
oxalosuccinate is produced.
• Three molecules of ATP are required (1) for activation of acetate, (2) for Carboxylation of pyruvate and (3)
for activation of succinate, the reductive carboxylic acid cycle appears to be particularly suite to provide
the carbon skeletons for the main products of bacterial photosynthesis, which are mainly aminoacids

61. 56. Photosynthesis in Halobacteria
• Halobacteria Posses an incomplete and primitive photosynthetic mechanism that differs from purple and
green bacteria.
• Halobacteria live in extreme environments usually at high levels of salinity and too high temperature to be
tolerated by other forms, have no light harvesting antennas, no photosystems and no light driven electron
transport system
57. Photosynthetic membranes of Halobacterium contain a light absorbing molecule known as
bacteriorhodopsin(fig.8), consisting of a polypeptide chain with the light absorbing unit.
• The light absorbing unit of bacteriorhodopsin is retinal, a molecule almost identical to the visual pigment
of animals. •Bacteriorhodopsin responds to light by pumping H+ across the membrane containing the
complex.
58. • During a pumping cycle the retinal unit alternatively picks up and releases a hydrogen.
• This pickup and release may be combined with conformational changes in the protein component that
expose the retinal unit to the cytoplasm during H+ binding and to the cell exterior during H+ release.
• The H+ gradient established the light induced pumping through the bacteriorhodopsin molecule drives
ATP synthesis by FoF1ATPase.
59. Halobacterium photosynthetic system
60. Heliobacteria: • The reaction centre P798 absorbs the light energy and photosynthetic electron flow
occurs via modified form of chlorophyll a called hydroxy- chlorophyll a -Fe-S-Q-bc1 Cyt – Cyt C553 to
reaction centre which is slightly different from green sulphur bacteria.
• In both the bacteria NADH production is light- mediated.
• The primary electron acceptor in such bacteria has reduction potential of -0.5 V.
• If it is reduced, it is able to reduce NAD+ directly, hence reverse electron flow does not require for
reducing NAD+

62. • They are used in the treatment of polluted water since they can grow and utilize toxic substances such as
H2S or H2S203
• Researchers at Harvard’s Wyss Institute have engineered photosynthetic bacteria to produce simple sugars
and lactic acid.

63. UNIT-II Respiration:
Mitochondria: Ultrastructure
• In 1953, Palade and Sjostrand independently
described the ultrastructure of mitochondria.
• Mitochondria are bounded by an envelope
consisting of two concentric membranes, the outer
and inner membranes.
• The space between the two membranes is called
inter-membrane space.
• A number of invaginations occur in the inner
membrane; they are called cristae
• The space on the interior of the inner membrane is
called matrix.

64. Outer Membrane:
• The outer mitochondrial membrane has high permeability to molecules such as sugars, salts, coenzymes and
nucleotides etc
• It has many similarities with the ER but differs from it in some respects, e.g., mono-amine-oxidase is present in the
mitochondrial outer membrane but not in ER( endoplasmic reticulum)
• On the other hand, the enzyme glucose-6-phosphatase is absent from the mitochondrial outer membrane but is
present in ER
• The mitochondrial outer membrane contains a number of enzymes and proteins
Inter-Membrane Space:
The inter-membrane space is divided into two regions:
1.Peripheral space
2.Intracristal space
• Large flattened cristae are connected to the inner membrane by small tubes called peduculi cristae which are few
nanometers in diameter
• The inter-membrane space has several enzymes of which “adenylate kinase” is the chief one
• This enzyme transfers one phosphate group from ATP to AMP to produce two molecules of ADP.

65. Inner Membrane:
• The inner mitochondrial membrane invaginates inside the matrix; the invaginations
are called cristae
• This membrane has a high ratio of protein to lipid.
• “Knobs” or “spheres” of 8-9 nm diameter are spaced 10 nm apart on the cristae
membranes.
• These knobs contain F1 proteins and ATPase responsible for phosphorylation.
• They are joined to the cristae by 3 nm long stalks called “F0“.
• The F0-F1 ATPase complex” is called ATP synthase.
• The inner membrane contains large number of proteins which are involved in
electron transfer (respiratory chain) and oxidative phosphorylation
• The respiratory chain is located within the inner membrane, and consists of pyridine
nucleotides, flavoproteins, cytochromes, iron-sulphur proteins and quinones.
• Besides its role in electron transfer, and phosphorylation, the inner membrane is also
the site for certain other enzymatic pathways, such as, steroid (hormone)
metabolism.

66. Matrix:
• The interior of mitochondrion is called matrix
• It has granular appearance in electron micrographs.
• Some large granules ranging from 30 nm to several hundred
nanometers in diameter are also present in the matrix.
• The matrix contains enzymes and factors for Krebs cycle, pyruvate
dehydrogenase and the enzymes involved in β-oxidation of fatty acids.
• However, succinate dehydrogenase is present in the inner membrane
instead of matrix; this enzyme catalyses the direct transfer of
electrons from succinate to the electron transfer chain.
• The enzyme pyruvate dehydrogenase converts pyruvate to acetyl-
Coenzyme A (acetyl-CoA) which enters the Krebs cycle
• Besides above, matrix also contains DNA, RNA, ribosomes and
proteins involved in protein and nucleic acid syntheses.

67. Function of Mitochondria:
• Mitochondria is regarded as the power house of the cell as it is the site of respiration.
• The general formula for glucose oxidation is,
C6H12O6 + 6O2 ———-> 6CO2 + 6H2O + 686 kcal …
• Glucose is degraded into two pyruvate molecules through glycolysis which occurs in the cell sap (cytosol).
• Further steps in oxidation of pyruvate take place in the mitochondria.
• Pyruvate is converted to acetyl-Coenzyme A (acetyl-CoA) which is then metabolised through the Krebs cycle, also
called the citric acid cycle or tricarboxylic acid cycle.
• In this cycle, energy is liberated and CO2 is produced. Some of the released energy is used to produce ATP, while a
major part is conserved in the form of reduced coenzymes NADH and FADH2 (FAD = flavinadenine dinucleotide).
• The energy conserved in NADH and FADH2 is released by re-oxidizing them into NAD+ and FAD, respectively; the
energy so obtained is utilized to produce ATP (oxidative phosphorylation)
• This process occurs in different steps in a strict sequence called electron transfer chain or respiratory chain located
in the cristae.
• The electrons are finally transferred to oxygen, and H2O is produced at the end of this chain

68. • The carriers of electrons are organized into three complexes, viz., I, III, and IV, and the sequence of electron
transfer is as follows.
COMPLEX I (NADH ——> FMN group of NADH dehydrogenase ——> iron-sulphur centre ——> ubiquinone) ——>
COMPLEX III (ubiquinone ——> cytochrome b ——> cytochrome c1 ——> cytochrome C) ——> COMPLEX IV
(cytochrome C——> cytochrome a ——> cytochrome a3) ——> Oxygen.
• There is another complex (Complex II) which transfers electrons from succinate (produced by Krebs cycle) to
ubiquinone.
• At last O2 is reduced to water, as the following reaction.
O2 + 4e– + 4H+ —> 2H2O…
• In complete oxidation of one glucose molecule, 6 molecules of oxygen are utilized resulting in the production of 6
carbon dioxide and 6 water molecules; in addition, energy is released.
• The maximum number of ATP molecules produced during complete oxidation of one glucose molecule is 36

69. Reproduction in Mitochondria:
• Mitochondria originate by growth and division of pre-existing mitochondria.
• Their development requires the presence of oxygen.
• In the absence of O2, yeast mitochondria are replaced by “pro-mitochondria” which are double-membrane
vesicles without cristae.
• In the presence of O2, cristae and other components of mitochondria develop so that pro-mitochondria convert
into mitochondria.

70. Types of respiration
• Respiration is a chain of chemical reactions that enables all living entities to synthesize energy required to sustain.
• It is a biochemical process wherein air moves between the external environment and the tissues and cells of the species
• In respiration, inhalation of oxygen and exhalation of carbon dioxide gas takes place
• As an entity acquires energy through oxidising nutrients and hence liberating wastes, it is referred to as a metabolic process
Do Plants Breathe?
• Yes, like animals and humans, plants also breathe.
• Plants do require oxygen to respire, the process in return gives out carbon dioxide.
• Unlike humans and animals, plants do not possess any specialized structures for exchange of gases, however, they do possess stomata
(found in leaves) and lenticels (found in stems) actively involved in the gaseous exchange
• Leaves, stems and plant roots respire at a low pace compared to humans and animals.
• Breathing is different from respiration
• Both animals and humans breathe, which is a step involved in respiration
• Plants take part in respiration all through their life as the plant cell needs the energy to survive, however, plants breathe differently, through a
process known as Cellular respiration.
• In this process of cellular respiration, plants generate glucose molecules through photosynthesis by capturing energy from sunlight and
converting it into glucose
• Several live experiments demonstrate the breathing of plants

71. The Process of Respiration in Plants
• During respiration, in different plant parts, significantly less exchange of gas takes place
• Hence, each part nourishes and fulfils its own energy requirements
• Consequently, leaves, stems and roots of plants separately exchange gases
• Leaves possess stomata – tiny pores, for gaseous exchange
• The oxygen consumed via stomata is used up by cells in the leaves to disintegrate glucose into water and carbon dioxide.

72. Respiration In Roots
• Roots, the underground part of the plants, absorbs air from the air
gaps/spaces found between the soil particles
• Hence, absorbed oxygen through roots is utilized to liberate the
energy that in the future, is used to transport salts and minerals from
the soil.
• We know that plants possess a specific ability to synthesize their own
food through photosynthesis.
• Photosynthesis takes place in only those parts of the plants which
have chlorophyll, the green plant parts.
• Photosynthesis is so evident that at times it seems to mask the
respiratory process in plants.
• Respiration must not be mistaken for photosynthesis.
• Respiration occurs all through the day, but
the photosynthesis process occurs in the daytime, in the presence of
sunlight only.
• Consequently, respiration becomes evident at night time in plants.
• This is the reason we often hear people warn against sleeping under
a tree during nighttime, as it may lead to suffocation due to excess
amounts of carbon dioxide liberated by trees following respiration.

73. Respiration In Stems
• The air in case of stem diffuses into the stomata and moves through different
parts of the cell to respire
• During this stage, the carbon dioxide liberated is also diffused through the
stomata
• Lenticels are known to perform gaseous exchange in woody or higher plants.
Respiration In Leaves
• Leaves consist of tiny pores known as stomata
• Gaseous exchange occurs through diffusion via stomata
• Guard cells regulate each of the stomata
• Exchange of gases occurs with the closing and opening of the stoma between
the inferior of leaves and the atmosphere

74. Photosynthesis Respiration
This process is common to all green
plants containing chlorophyll
pigments.
This process is common to all living
things, including plants, animals,
birds, etc.
Food is synthesized. Food is oxidised.
Energy is stored. Energy is released.
Is an anabolic process. Is a catabolic process.
Cytochrome is required. Cytochrome is required here too
It is an Endothermal process. It is an Exothermal process.
It comprises products such as water,
oxygen and sugar
It comprises products such as
carbon dioxide and hydrogen
Radiant energy is converted into
potential energy.
Potential energy is converted into
kinetic energy.
Occurs during daytime in the
presence of sunlight only.
Is a continuous process, taking place
all through the lifetime
Differences between Respiration and Photosynthesis

75. “Respiration is defined as a metabolic process wherein, the living cells of an organism obtains energy (in the
form of ATP) by taking in oxygen and liberating carbon dioxide from the oxidation of complex organic
substances.”
What is Respiration?
• Respiration is a metabolic process that occurs in all organisms
• It is a biochemical process that occurs within the cells of organisms
• In this process, the energy (ATP-Adenosine triphosphate) is produced by the breakdown of glucose which is further used by cells to perform
various functions
• Every living species, from a single-celled organism to dominant multicellular organisms, performs respiration.
Types of Respiration
There are two types of respiration:
Aerobic respiration
• It is a type of cellular respiration that takes place in the presence of oxygen to produce energy
• It is a continuous process that takes place within the cells of animals and plants
• This process can be explained with the help of the chemical equation:
Glucose(C6H12O6) + Oxygen(6O2) → Carbon dioxide(6CO2) + Water(6H2O)+ Energy (ATP)
Anaerobic respiration
• It is a type of cellular respiration that takes place in the absence of oxygen to produce energy
• The chemical equation for anaerobic respiration is
Glucose(C6H12O6) → Alcohol 2(C2H5O H) + Carbon dioxide 2(CO2) + Energy (ATP )

76. Aerobic Respiration
• This type of respiration takes place in the mitochondria of all eukaryotic entities.
• Food molecules are completely oxidised into the carbon dioxide, water, and energy is
released in the presence of oxygen
• This type of respiration is observed in all the higher organisms and necessitates
atmospheric oxygen.
Anaerobic Respiration
• This type of respiration occurs within the cytoplasm of prokaryotic entities such as yeast
and bacteria
• Here, lesser energy is liberated as a result of incomplete oxidation of food in the
absence of oxygen
• Ethyl alcohol and carbon dioxide are produced during anaerobic respiration.
Types of Respiration
There are two main types of respiration.

77. Phases of Respiration in Organisms
• Respiration occurs in the cytosol and around the plasma membrane in prokaryotic cells.
• In eukaryotic cells, respiration takes place in the mitochondria, which is also considered as the powerhouse of the cells.
• This process is very much similar to internal combustion of the car engine, wherein organic compounds and oxygen go in, while water and
carbon dioxide comes out.
• The energy that is liberated powers the automotive (or cell).
• The three phases of Respiration are:
Glycolysis
• The molecules of glucose get converted into pyruvic acid which is oxidized to
carbon dioxide and water, leaving two carbon molecules, known as acetyl-CoA.
• During the process of glycolysis, two molecules of ATP and NADH are produced
• Pyruvate enters the inner matrix of mitochondria and undergoes oxidation in the
Kreb’s cycle.

78. “Glycolysis is the metabolic process that
converts glucose into pyruvic acid.”
What is Glycolysis?
• Glycolysis is the process in which glucose is broken down
to produce energy
• It produces two molecules of pyruvate, ATP, NADH and
water
• The process takes place in the cytoplasm of a cell and
does not require oxygen
• It occurs in both aerobic and anaerobic organisms.

79. • Glycolysis is the primary step of cellular respiration, which occurs in all organisms
• Glycolysis is followed by the Krebs cycle during aerobic respiration
• In the absence of oxygen, the cells make small amounts of ATP as glycolysis is followed by fermentation
• This metabolic pathway was discovered by three German biochemists- Gustav Embden, Otto Meyerhof, and Jakub Karol Parnas in the early
19th century and is known as the EMP pathway (Embden–Meyerhof–Parnas).
Glycolysis Pathway

80. Stage 1
•A phosphate group is added to glucose in the cell cytoplasm, by the action of enzyme hexokinase.
•In this, a phosphate group is transferred from ATP to glucose forming glucose,6-phosphate.
Stage 2
Glucose-6-phosphate is isomerised into fructose,6-phosphate by the enzyme phosphoglucomutase.
Stage 3
The other ATP molecule transfers a phosphate group to fructose 6-phosphate and converts it into fructose 1,6-bisphosphate by the action of
the enzyme phosphofructokinase.
Stage 4
The enzyme aldolase converts fructose 1,6-bisphosphate into glyceraldehyde 3-phosphate and dihydroxyacetone phosphate, which are
isomers of each other.
Step 5
Triose-phosphate isomerase converts dihydroxyacetone phosphate into glyceraldehyde 3-phosphate which is the substrate in the successive
step of glycolysis.
Step 6
This step undergoes two reactions:
•The enzyme glyceraldehyde 3-phosphate dehydrogenase transfers 1 hydrogen molecule from glyceraldehyde phosphate to nicotinamide
adenine dinucleotide to form NADH + H+.
• Glyceraldehyde 3-phosphate dehydrogenase adds a phosphate to the oxidised glyceraldehyde phosphate to form 1,3-bisphosphoglycerate.
Step 7
Phosphate is transferred from 1,3-bisphosphoglycerate to ADP to form ATP with the help of phosphoglycerokinase. Thus two molecules of
phosphoglycerate and ATP are obtained at the end of this reaction.

81. Step 8
The phosphate of both the phosphoglycerate molecules is relocated from the third to the second carbon to yield two molecules of 2-
phosphoglycerate by the enzyme phosphoglyceromutase.
Step 9
The enzyme enolase removes a water molecule from 2-phosphoglycerate to form phosphoenolpyruvate.
Step 10
• A phosphate from phosphoenolpyruvate is transferred to ADP to form pyruvate and ATP by the action of pyruvate kinase
• Two molecules of pyruvate and ATP are obtained as the end products.
Key Points of Glycolysis
•It is the process in which a glucose molecule is broken down into two molecules of pyruvate.
•The process takes place in the cytoplasm of plant and animal cells.
•Six enzymes are involved in the process.
•The end products of the reaction include 2 pyruvate, 2 ATP and 2 NADH molecules.

82. Pentose Phosphate Pathway
•The pentose phosphate pathway is a metabolic pathway parallel to glycolysis which
generates NADPH and pentoses (5-carbon sugars) as well as ribose 5-phosphate.
•The pentose phosphate pathway is also called as the phosphogluconate pathway or hexose monophosphate shunt.
•While it involves oxidation of glucose, its primary role is anabolic rather than catabolic.
•It is an important pathway that generates precursors for nucleotide synthesis and is especially important in red blood
cells (erythrocytes)
Location
• In plants, most steps take place in plastids.

83. The Pathway
Substrate: Glucose-6-phosphate.
There are two distinct phases in the pathway. The first is the oxidative phase, in which NADPH is generated, and the
second is the non-oxidative synthesis of 5-carbon sugars.
The Oxidative Reactions
•Glucose-6-phosphate is converted to 6-phosphogluconolactone, and NADP+ is reduced to NADPH + H+.
• Enzyme: glucose-6-phosphate dehydrogenase
• 6-Phosphogluconolactone is hydrolyzed to 6-phosphogluconate.
• Enzyme: Gluconolactonase
• 6-Phosphogluconate undergoes an oxidation, followed by a decarboxylation. CO2 is released, and a second
NADPH + H+ is generated from NADP+. The remaining carbons form ribulose-5-phosphate.
• Enzyme: 6-phosphogluconate dehydrogenase
The Non-oxidative Reactions
•Ribulose-5-phosphate is isomerized to ribose-5-phosphate or epimerized to xylulose-5-phosphate.
•Ribose-5-phosphate and xylulose-5-phosphate undergo reactions, catalyzed by transketolase and transaldolase,
that transfer carbon units, ultimately forming fructose 6-phosphate and glyceraldehyde-3-phosphate.
• Transketolase, which requires thiamine pyrophosphate, transfers two-carbon units.
• Transaldolase transfers three-carbon units.
Overall reaction of the pentose phosphate pathway
3 Glucose-6-P + 6 NADP+→ 3 ribulose-5-P + 3 CO2 + 6 NADPH
3 Ribulose-5-P → 2 xylulose-5-P + Ribose-5-P
2 Xylulose-5-P + Ribose-5-P → 2 fructose-6-P + Glyceraldehyde-3-P

84. Result of Pentose Phosphate Pathway
Oxidative portion: Irreversible.
Generates two NADPH, which can then be used in fatty acid synthesis and cholesterol synthesis and for
maintaining reduced glutathione inside RBCs.
Nonoxidative portion: Reversible.
Generates intermediate molecules (ribose-5-phosphate; glyceraldehyde-3-phosphate; fructose-6-
phosphate) for nucleotide synthesis and glycolysis.
Regulation of Pentose Phosphate Pathway
•Key enzyme in the pentose-phosphate pathway is glucose-6-phosphate dehydrogenase.
•Levels of glucose-6-phosphate dehydrogenase are increased in the liver and adipose tissue when large
amounts of carbohydrates are consumed.
•Glucose-6-phosphate dehydrogenase is stimulated by NADP+ and inhibited by NADPH and by palmitoyl-
CoA (part of the fatty acid synthesis pathway).
Purpose of Pentose Phosphate Pathway
•Pentose phosphate pathway functions as an alternative route for glucose oxidation that does not directly
consume or produce ATP.
•The pentose phosphate pathway produces NADPH for fatty acid synthesis.
•Under these conditions, the fructose-6-phosphate and glyceraldehyde-3-phosphate generated in the
pathway reenter glycolysis.
•NADPH is also used to reduce glutathione (γ-glutamylcysteinylglycine).
•Glutathione helps to prevent oxidative damage to cells by reducing hydrogen peroxide (H2O2).

85. •Glutathione is also used to transport amino acids across the membranes of certain cells by the γ-glutamyl cycle.
•Generation of ribose-5-phosphate
•When NADPH levels are low, the oxidative reactions of the pathway can be used to generate ribose-5-phosphate for
nucleotide biosynthesis.
•When NADPH levels are high, the reversible nonoxidative portion of the pathway can be used to generate ribose-5-
phosphate for nucleotide biosynthesis from fructose-6-phosphate and glyceraldehyde-3-phosphate.

86. “TCA cycle is the series of chemical reactions used by all aerobic organisms to release stored energy
through the oxidation of acetyl CoA derived from carbohydrates, fats, and proteins into ATP.”
• TCA cycle or Tricarboxylic Cycle is also known as Kreb’s Cycle or Citric Acid Cycle
• It is the second stage of cellular respiration that occurs in the matrix of mitochondria
• All the enzymes involved in the citric acid cycle are soluble
• It is an aerobic pathway because NADH and FADH2 produced transfer their electrons to the next pathway which will use oxygen
• If the transfer of electrons does not occur, no oxidation takes place
• Very little ATP is produced during the process directly
• The TCA cycle is a closed loop
• The last step of the pathway regenerates the first molecule of the pathway.
Steps of TCA Cycle
Following are the important steps of the TCA cycle:
Step 1
Acetyl Co-A combines with a four-carbon compound, oxaloacetate, and releases the CoA group resulting in a six-carbon molecule called
citrate.
Step 2
In the second step, citrate gets converted to isocitrate, an isomer of citrate. This is a two-step process. Citrate first loses a water molecule and
then gains one to form isocitrate.
Step 3
• The third step involves oxidation of isocitrate
• A molecule of carbon dioxide is released leaving behind a five-carbon molecule, ɑ-ketoglutarate
• NAD+ gets reduced to NADH. The entire process is catalyzed by the enzyme isocitrate dehydrogenase.

87. Step 6
• Succinate is oxidized to fumarate
• Two hydrogen atoms are transferred to FAD to produce FADH2
• FADH2 transfers its electrons directly to the electron transport chain since the enzyme carrying out the reaction is
embedded in the inner membrane of mitochondria.
Step 7
A water molecule is added to fumarate which is then converted to malate.
Step 8
• The oxidation of malate regenerates oxaloacetate, a four-carbon compound, and another molecule of NAD+ is reduced to
NADH in this step.
End Products of TCA Cycle
Following are the end products of TCA cycle:
1.6 NADH
2.2 ATPs
3.2 FADH2

89. Introduction
• The Krebs cycle or TCA cycle (tricarboxylic acid cycle) or Citric acid cycle is a series of enzyme catalysed reactions occurring in the
mitochondrial matrix, where acetyl-CoA is oxidised to form carbon dioxide and coenzymes are reduced, which generate ATP in the electron
transport chain.
• Krebs cycle was named after Hans Krebs, who postulated the detailed cycle
• He was awarded the Nobel prize in 1953 for his contribution
• It is a series of eight-step processes, where the acetyl group of acetyl-CoA is oxidised to form two molecules of CO2 and in the process, one
ATP is produced
• Reduced high energy compounds, NADH and FADH2 are also produced
• Two molecules of acetyl-CoA are produced from each glucose molecule so two turns of the Krebs cycle are required which yields four CO2,
six NADH, two FADH2 and two ATPs.
Krebs Cycle is a part of Cellular Respiration
• Cellular respiration is a catabolic reaction taking place in the cells
• It is a biochemical process by which nutrients are broken down to release energy, which gets stored in the form of ATP and waste products
are released
• In aerobic respiration, oxygen is required
• Cellular respiration is a four-stage process
• In the process, glucose is oxidised to carbon dioxide and oxygen is reduced to water
• The energy released in the process is stored in the form of ATPs
• 36 to 38 ATPs are formed from each glucose molecule.

90. The four stages are:
1. Glycolysis:
• Partial oxidation of a glucose molecule to form 2 molecules of pyruvate
• This process takes place in the cytosol.
2. Formation of Acetyl CoA:
• Pyruvate formed in glycolysis enters the mitochondrial matrix
• It undergoes oxidative decarboxylation to form two molecules of Acetyl CoA
• The reaction is catalysed by the pyruvate dehydrogenase enzyme.
3. Krebs cycle (TCA cycle or Citric Acid Cycle):
• It is the common pathway for complete oxidation of carbohydrates, proteins and lipids as they are metabolised to acetyl coenzyme A or other intermediates of
the cycle.
• The Acetyl CoA produced enters the Tricarboxylic acid cycle or Citric acid cycle
• Glucose is fully oxidized in this process
• The acetyl CoA combines with 4-carbon compound oxaloacetate to form 6C citrate. In this process, 2 molecules of CO2 are released and oxaloacetate is
recycled
• Energy is stored in ATP and other high energy compounds like NADH and FADH2.
4. Electron Transport System and Oxidative Phosphorylation:
• ATP is generated when electrons are transferred from the energy-rich molecules like NADH and FADH2, produced in glycolysis, citric acid cycle and fatty acid
oxidation to molecular O2 by a series of electron carriers
• O2 is reduced to H2O. It takes place in the inner membrane of mitochondria.

91. Krebs Cycle Steps
It is an eight-step process. Krebs cycle or TCA cycle takes place in the matrix of mitochondria under aerobic condition.
Step 1: The first step is the condensation of acetyl CoA with 4-carbon compound oxaloacetate to form 6C citrate, coenzyme A is
released. The reaction is catalysed by citrate synthase.
Step 2: Citrate is converted to its isomer, isocitrate. The enzyme aconitase catalyses this reaction.
Step 3: Isocitrate undergoes dehydrogenation and decarboxylation to form 5C 𝝰-ketoglutarate. A molecular form of CO2 is
released. Isocitrate dehydrogenase catalyses the reaction. It is an NAD+ dependent enzyme. NAD+ is converted to NADH.
Step 4: 𝝰-ketoglutarate undergoes oxidative decarboxylation to form succinyl CoA, a 4C compound. The reaction is catalyzed by
the 𝝰-ketoglutarate dehydrogenase enzyme complex. One molecule of CO2 is released and NAD+ is converted to NADH.
Step 5: Succinyl CoA forms succinate. The enzyme succinyl CoA synthetase catalyses the reaction. This is coupled with
substrate-level phosphorylation of GDP to get GTP. GTP transfers its phosphate to ADP forming ATP.
Step 6: Succinate is oxidised by the enzyme succinate dehydrogenase to fumarate. In the process, FAD is converted to FADH2.
Step 7: Fumarate gets converted to malate by the addition of one H2O. The enzyme catalysing this reaction is fumarase.
Step 8: Malate is dehydrogenated to form oxaloacetate, which combines with another molecule of acetyl CoA and starts the new
cycle. Hydrogens removed, get transferred to NAD+ forming NADH. Malate dehydrogenase catalyses the reaction.

92. Krebs Cycle Summary
Location: Krebs cycle occurs in the mitochondrial matrix
Krebs cycle reactants: Acetyl CoA, which is produced from the end product of glycolysis, i.e. pyruvate and it condenses with 4 carbon oxaloacetate, which
is generated back in the Krebs cycle
Krebs cycle products
Each citric acid cycle forms the following products:
•2 molecules of CO2 are released. Removal of CO2 or decarboxylation of citric acid takes place at two places:
1.In the conversion of isocitrate (6C) to 𝝰-ketoglutarate (5C)
2.In the conversion of 𝝰-ketoglutarate (5C) to succinyl CoA (4C)
•1 ATP is produced in the conversion of succinyl CoA to succinate
•3 NAD+ are reduced to NADH and 1 FAD+ is converted to FADH2 in the following reactions:
1.Isocitrate to 𝝰-ketoglutarate → NADH
2.𝝰-ketoglutarate to succinyl CoA → NADH
3.Succinate to fumarate → FADH2
4.Malate to Oxaloacetate → NADH
Note that 2 molecules of Acetyl CoA are produced from oxidative decarboxylation of 2 pyruvates so two cycles are required per glucose molecule.
To summarize, for complete oxidation of a glucose molecule, Krebs cycle yields 4 CO2, 6NADH, 2 FADH2 and 2 ATPs.
Each molecule of NADH can form 2-3 ATPs and each FADH2 gives 2 ATPs on oxidation in the electron transport chain.
Krebs cycle equation
To Sum up

93. Significance of Krebs Cycle
•Krebs cycle or Citric acid cycle is the final pathway of oxidation of glucose, fats and amino acids
•Many animals are dependent on nutrients other than glucose as an energy source
•Amino acids (metabolic product of proteins) are deaminated and get converted to pyruvate and other intermediates of the Krebs cycle
•They enter the cycle and get metabolised e.g. alanine is converted to pyruvate, glutamate to 𝝰-ketoglutarate, aspartate to oxaloacetate on
deamination
•Fatty acids undergo 𝞫-oxidation to form acetyl CoA, which enters the Krebs cycle
•It is the major source of ATP production in the cells. A large amount of energy is produced after complete oxidation of nutrients
•It plays an important role in gluconeogenesis and lipogenesis and interconversion of amino acids
•Many intermediate compounds are used in the synthesis of amino acids, nucleotides, cytochromes and chlorophylls, etc.
•Vitamins play an important role in the citric acid cycle. Riboflavin, niacin, thiamin and pantothenic acid as a part of various enzymes cofactors
(FAD, NAD) and coenzyme A
•Regulation of Krebs cycle depends on the supply of NAD+ and utilization of ATP in physical and chemical work
•The genetic defects of the Krebs cycle enzymes are associated with neural damage
•As most of the biological processes occur in the liver to a significant extent, damage to liver cells has a lot of repercussions
•Hyperammonemia occurs in liver diseases and leads to convulsions and coma
•This is due to reduced ATP generation as a result of the withdrawal of 𝝰-ketoglutarate and formation of glutamate, which forms glutamine

94. Frequently Asked Questions on Krebs Cycle
What is the Krebs Cycle?
Also known as the citric acid cycle, the Krebs cycle or TCA cycle is a chain of reactions occurring in the mitochondria, through which almost all living cells produce energy in aerobic
respiration. It uses oxygen and gives out water and carbon dioxide as products. Here, ADP is converted into ATP. This cycle renders electrons and hydrogen required for electron chain
transport.
How Many ATPs are Produced In the Krebs Cycle?
2 ATPs are produced in one Krebs Cycle.
For complete oxidation of a glucose molecule, the Krebs cycle yields 4 CO2, 6NADH, 2 FADH2 and 2 ATPs.
Where Does Krebs Cycle or TCA cycle Occur?
Mitochondrial matrix.
In all eukaryotes, mitochondria are the site where the Krebs cycle takes place. The cycle takes place in a mitochondrial matrix producing chemical energy in the form of NADH, ATP,
FADH2. These are produced as a result of oxidation of the end product of glycolysis – pyruvate.
How The Krebs Cycle Works?
It is an eight-step process
1) Condensation of acetyl CoA with oxaloacetate (4C) forming citrate (6C), coenzyme A is released. 2) Conversion of Citrate to its isomer, isocitrate. 3) Isocitrate is
subjected to dehydrogenation and decarboxylation forming 𝝰-ketoglutarate (5C). 4) 𝝰-ketoglutarate (5C) experiences oxidative decarboxylation forming succinyl CoA
(4C). 5) Conversion of Succinyl CoA to succinate by succinyl CoA synthetase enzyme along with substrate-level phosphorylation of GDP forming GTP. 6) Oxidation of
Succinate to fumarate by the enzyme succinate dehydrogenase. 7) Fumarate gets converted to malate by the addition of one H2O. 8) Malate is dehydrogenated to
form oxaloacetate, which combines with another molecule of acetyl CoA and starts the new cycle.
Why Is Krebs Cycle Called As Amphibolic Pathway?
It is called amphibolic as in the Krebs cycle both catabolism and anabolism take place. The amphibolic pathway indicates the one involving both catabolic and anabolic
procedures.
How Many NADH are Produced In The Krebs Cycle?
3 NADH molecules
In one turn of the Krebs cycle, 3 molecules of NADH are produced.
For complete oxidation of a glucose molecule, Krebs cycle yields 4 CO2, 6NADH, 2 FADH2 and 2 ATPs.
What Is The Krebs Cycle Also Known As?
Krebs cycle is also known as Citric acid cycle (CAC) or TCA cycle (tricarboxylic acid cycle)
Why Krebs Cycle Is Called the Citric Acid Cycle?
Krebs cycle is also referred to as the Citric Acid Cycle. Citric acid is the first product formed in the cycle.

95. The electron transport system (ETS) in the inner mitochondrial
membrane
(A) Electron micrograph of a human cell section showing three mitochondria
(B) Scheme of the protein complexes that form the ETS, showing the mitochondrial membranes in blue and red; NADH
dehydrogenase in light green; succinate dehydrogenase in dark green; the complex formed by acyl-CoA
dehydrogenase, electron transfer flavoprotein (ETFP), and ETFP-ubiquinone oxidoreductase in yellow and orange;
ubiquinone in green labeled with a Q; cytochrome c reductase in light blue; cytochrome c in dark blue labeled with
cytC; cytochrome c oxidase in pink; and the ATP synthase complex in lilac
• The flux of electrons is represented by red arrows and e-, and the flux of protons is represented by red arrows and
H+.

96. •Electron transport chain or system is the series of electron carriers, enzyme and cytochrome that pass electron from one to another
via the redox reaction (oxidation state of substrate change)
•It is the terminal oxidation (loss of electrons)
•It consists nicotinamide adenine dinucleotide (NAD), flavin nucleotides (FAD), coenzyme Q, and cytochromes localized in F1
particles of mitochondria.
•It occurs in inner mitochondrial membrane along with cristae.
•In this process five complexes are involved namely, I- NADH-UQ reductase, II- Succinate-UQ reductase, III- UQH2-cytochrome C
reductase, IV- Cytochrome C oxidase and V is connected with F0​−F1 particles.
• In this process, NAD and FAD are reduced
Steps:
Redox at complex I: 4 protons pumped from matrix to intermembrane space.
•Redox at complex II: Coenzyme Q picks up the electrons from complex I and II, and goes to complex III.
•Redox of complex III: 4 protons again pumped from matrix to intermembrane space and cytochrome C transports electron to the
complex IV.
•Redox of complex IV: 2 protons pumped from matrix to intermembrane space and water formation occurs in the matrix.
•ATP synthase action: It pumps proton from intermembrane space to matrix and produces ATP.
•It is associated with oxidative phosphorylation.

97. THE CHEMI-OSMOTIC THEORY
• The chemi-osmatic theory is about an electrochemical link between respiration and phosphorylation
• It was proposed by Peter Mitchell in 1961
• He was awarded a Nobel prize in 1978 for his work
• Chemi – osmosis refers to the movement of chemical ions across a semi – permeable membrane down their
electrochemical gradient (from an area of higher to lower concentration) similar to movement of water
molecules by osmosis
• An example of this is the generation of ATP by the movement of hydrogen ions across a membrane during cellular
respiration or photosynthesis
• The chemi-osmotic theory deals with the generation of ATP by ATP synthase
• Chemi-osmosis involves the pumping of protons through special channels in the membranes of mitochondria
from the inner to the outer compartment
• The chemiosmotic theory explains the functioning of electron transport chains
• According to this theory, the transfer of electrons down an electron transport system through a series of
oxidation-reduction reactions releases energy
• This energy allows certain carriers in the chain to transport hydrogen ions (H+ or protons) across a membrane
• Depending on the type of cell, the electron transport chain may be found in the cytoplasmic membrane or the
inner membrane of mitochondria.

98. •In prokaryotic cells, the protons are transported from the cytoplasm of the bacterium across the cytoplasmic
membrane to the periplasmic space located between the cytoplasmic membrane and the cell wall
•In eukaryotic cells, protons are transported from the matrix of the mitochondria across the inner mitochondrial
membrane to the intermembrane space located between the inner and outer mitochondrial membranes

99. ATP Synthase Generating ATP
• The chemiosmotic theory explains the functioning of electron transport chains
• According to this theory, the tranfer of electrons down an electron transport
system through a series of oxidation-reduction reactions releases energy
• This energy allows certain carriers in the chain to transport hydrogen ions
(H+ or protons) across a membrane
• As the hydrogen ions accumulate on one side of a membrane, the
concentration of hydrogen ions creates an electrochemical gradient or potential
difference (voltage) across the membrane
• (The fluid on the side of the membrane where the protons accumulate acquires
a positive charge; the fluid on the opposite side of the membrane is left with a
negative charge.)
• The energized state of the membrane as a result of this charge separation is
called proton motive force or PMF
• This proton motive force provides the energy necessary for enzymes called ATP
synthases, also located in the membranes mentioned above, to catalyze the

100. • This generation of ATP occurs as the protons cross the membrane through the ATP synthase complexes and re-enter either
the bacterial cytoplasm or the matrix of the mitochondria
• As the protons move down the concentration gradient through the ATP synthase, the energy released causes the rotor and
rod of the ATP synthase to rotate
• The mechanical energy from this rotation is converted into chemical energy as phosphate is added to ADP to form ATP.
Figure: Development of Proton Motive Force from Chemiosmosis and Generation of ATP
• In an electron transport system, energy from electron transfer during oxidation-reduction reactions enables certain carriers to transport protons
(H+) across a membrane
• As the H+ concentration increases on one side of the membrane, an electrochemical gradient called proton motive force develops
• Re-entry of the protons through an enzyme complex called ATP synthase provides the energy for the synthesis of ATP from ADP and phosphate.

101. • Proton motive force is also used to transport substances across membranes during active transport and to rotate
bacterial flagella
• At the end of the electron transport chain involved in aerobic respiration, the last electron carrier in the membrane
transfers 2 electrons to half an oxygen molecule (an oxygen atom) that simultaneously combines with 2 protons
from the surrounding medium to produce water as an end product
• NADH and FADH2 carry protons (H+) and electrons (e-) to the
electron transport chain located in the membrane
• The energy from the transfer of electrons along the chain transports
protons across the membrane and creates an electrochemical
gradient
• As the accumulating protons follow the electrochemical gradient
back across the membrane through an ATP synthase complex, the
movement of the protons provides energy for synthesizing ATP from
ADP and phosphate
• At the end of the electron transport system, two protons, two
electrons, and half of an oxygen molecule combine to form water
• Since oxygen is the final electron acceptor, the process is called

102. Summary
1. Aerobic respiration involves four stages: glycolysis, a transition reaction that forms acetyl coenzyme A, the citric acid (Krebs) cycle,
and an electron transport chain and chemiosmosis.
2. During various steps in glycolysis and the citric acid cycle, the oxidation of certain intermediate precursor molecules causes the
reduction of NAD+ to NADH + H+ and FAD to FADH2. NADH and FADH2 then transfer protons and electrons to the electron
transport chain to produce additional ATPs by oxidative phosphorylation.
3. The electron transport chain consists of a series of electron carriers that eventually transfer electrons from NADH and FADH2 to
oxygen.
4. The chemiosmotic theory states that the transfer of electrons down an electron transport system through a series of oxidation-
reduction reactions releases energy. This energy allows certain carriers in the chain to transport hydrogen ions (H+ or protons)
across a membrane.
5. As the hydrogen ions accumulate on one side of a membrane, the concentration of hydrogen ions creates an electrochemical
gradient or potential difference (voltage) across the membrane called proton motive force.
6. This proton motive force provides the energy necessary for enzymes called ATP synthases, also located in the membranes
mentioned above, to catalyze the synthesis of ATP from ADP and phosphate.
7. During aerobic respiration, the last electron carrier in the membrane transfers 2 electrons to half an oxygen molecule (an oxygen
atom) that simultaneously combines with 2 protons from the surrounding medium to produce water as an end product.

103. Respiratory Balance Sheet:
• The balance sheet is the written statement of money earned and paid
• The balance sheet of any business gives the idea of the flow of money and
profit or loss at the end of the day, month or year
• Similarly, every living cell gains and loses energy constantly
• We can form a balance sheet for loss and gain of energy for a cell using
energy currency or ATP
• A cell generates ATP by the oxidation of substrate molecules obtained
through food consumption
• The process of oxidation of glucose molecules to produce ATP is called
respiration
• It is a complex biochemical process that occurs at the cellular scale
Fig: conversion of ADP to ATP

104. Respiration
• The entire process of respiration can be divided into 3 steps: glycolysis, Krebs cycle and electron transport system.
• These steps generate adenosine triphosphate (ATP) by the process known as phosphorylation
• Phosphorylation can be defined as the attachment of a phosphoryl group (Pi) to adenosine diphosphate (ADP)
• The process of phosphorylation can be substrate level, also known as direct phosphorylation or oxidative.
• During substrate-level phosphorylation, direct phosphorylation of ADP with a phosphate group using the energy
obtained from a coupled reaction
• Oxidative phosphorylation occurs in mitochondria resulting in the synthesis of ATP
• Oxidative phosphorylation is linked to electron transport across the mitochondrial membrane, using ATP synthase
to produce ATP molecules.

105. • Practically it has not been possible to make the calculations in a living system as it is a complex simultaneous
process, and the steps do not occur one after the another.
• Theoretically, it is possible to make calculations of the net gain of ATP during every step of oxidation of glucose
molecules.
Assumptions of ATP Balance Sheet
Theoretical calculation of ATP generation is based upon certain assumptions, which are listed below:
1.The process of respiration is sequential and orderly. The pathway involves steps glycolysis–> TCA cycle –>ETS
pathway.
2.Every NADH molecule produced during glycolysis is transferred into the mitochondria for oxidative phosphorylation
and ATP generation.
3.Respiration is an isolated pathway, and intermediates formed along the pathway are not utilised to synthesise any
other compound.
4.Glucose is the only respiratory substrate being used for ATP generation. Other substrates like protein and fat do not
enter the pathway at any stages.

106. Phase
Molecular
change
Cost per
glucose
molecule
Gain per
glucose
molecule
1. Glycolysis
Conversion of
glucose(6C) to
2 pyruvates
(3C)
2ATP
4 ATP
2 NADH
2.
Oxidation of
pyruvates
Conversion of
pyruvates(3C)
to acetyl group
(2C)
None 2 NADH
3. Krebs cycle
Conversion of
citric acid(6C)
formed by the
combination of
an acetyl
group and
oxaloacetate to
oxaloacetate(4
C)
None
2 ATP
6 NADH
2 FADH2
4.
Electron
transport
oxidation of
NADH and
FADH2 to build
ATP and water
molecules
2ATP 34 ATP
Balance Sheet
Aerobic Respiration
C6H12O6 + 6O2 → 6CO2 + 6H2O + 673Kcal
Aerobic respiration involves the complete combustion of glucose. Typically, during the electron transport system in aerobic respiration,
oxidation of each NADH molecule produces three ATP and oxidation of each FADH2 molecule produces two ATP molecules. The
numbers of ATP produced vary in prokaryotes and eukaryotes.
1NADH→3ATP
1FADH2→2ATP
Pathway
NADH (3
ATP)
FADH2 (2
ATP)
ATP Total
EMP
pathway/
glycolysis
2 x 3 = 6 —
Produced- 4
Utilised- 2
Net gain- 2
8
2 x
Pyruvate
oxidation to
acetyl CoA
2 x 3 = 6 – – 6
Krebs cycle 6 x 3 = 18 2 x 2 = 4 2 24
Total 10 x 3 = 30 2 x 2 = 4 4 38
The net gain of ATP is 36 in most eukaryotes, while it is 38 in prokaryotes.

107. Aerobic respiration Fermentation
The complete breakdown of
glucose to CO2 and H2O
Partial breakdown of glucose
The net gain is 36-38 ATP The net gain is only 2 ATP
The rate of NADH oxidation
to form NAD+
is rapid.
The rate of NADH oxidation
to form NAD+
is very slow.
Anaerobic Respiration/ Fermentation
• Anaerobic respiration or fermentation does not cause the complete combustion of glucose
• Incomplete combustion ends in the formation of ethanol in bacteria and lactic acid in muscle cells
• The difference between fermentation and aerobic respiration is given below.

108. Efficiency of Respiration
• Each glucose molecule has 2870 kJ energy stored
• Hydrolysis of ATP generates 30.5 kilojoule, which means during aerobic respiration, the total energy produced is
1159 kJ from 38 ATP molecules.
It is evident that only 40-45% of energy can be stored and utilised; what happens to the rest? It is believed that the
remaining part of the energy is lost in the form of heat.
Significance of Respiratory Balance Sheet
Theoretical calculation suggests a net gain of 38 ATP during the complete oxidation of a glucose molecule. Although the practical
calculation is not possible, we do the calculation for the following reasons:
1.To estimate the net gain of ATP
2.To understand the efficiency of the living system in extraction and storing energy
Respiratory Quotient (RQ)
• It is the ratio of the volume of carbon dioxide evolved to the volume of oxygen utilised.
• It is a quantity with no unit.
• The respiratory quotient is measured to calculate the basal metabolic rate of an individual.

109. • The respiratory quotient is different for each substrate
• For carbohydrates, the value of the respiratory quotient is 1, i.e., the volume of carbon dioxide evolved and
volume of oxygen utilized are equal
• For proteins, the value of the Respiratory quotient ranges from 0.5 to 0.9, depending upon amino acid
constituent, which implies the volume of carbon dioxide evolved is lesser than the volume of oxygen utilized
• The value of the respiratory quotient for fat is 0.7, which again implies that the volume of carbon dioxide evolved
is lesser than the volume of oxygen utilised.
• In the case of anaerobic respiration, the value of the respiratory quotient is infinity as no oxygen is utilised.
• Respirometer is used to measure the value of the respiratory quotient.
Summary
• The respiratory balance sheet deals with the gain and loss of energy in the form of an energy currency called
ATP.
• The balance sheet can be drawn only theoretically.
• There are certain assumptions considered to draw a balance sheet
• It is assumed that the process of respiration is a sequential and orderly process
• Every NADH molecule produced during glycolysis is transferred into the mitochondria for oxidative
phosphorylation and ATP generation.
• Respiration is an isolated pathway, and intermediates formed along the pathway are not utilised to synthesise any
other compound
• And glucose is the only substrate used for ATP generation
• During aerobic respiration net gain of ATP is 36 in most eukaryotes while it is 38 in prokaryotes
• During anaerobic respiration net gain of ATP is only 8.
• A respiratory balance sheet is drawn to estimate net energy gain by a cell and understand the efficiency of the

110. Frequently Asked Questions (FAQs) on Respiratory Balance Sheet
Q.1. What are the three steps of respiration?
Ans: The three steps of respiration are Glycolysis, Krebs cycle and ETS.
Q.2. How many ATPs are generated during the process of glycolysis?
Ans: During glycolysis, 2 ATP are generated by substrate-level phosphorylation and 6 by oxidative phosphorylation of
NADH.
Q.3. Why is the number of ATP generated during anaerobic respiration lower?
Ans: During anaerobic respiration, glucose is not completely oxidised; hence the number of ATP produced is
significantly lower.
Q.4. Which is the most common substrate of respiration?
Ans: Glucose is the most common substrate of respiration.
Q.5. What is the efficiency of energy during aerobic respiration?
Ans: Efficiency of energy during aerobic respiration is 40-45%.

111. • These complexes are known as NADH: ubiquinone oxidoreductase (complex I), succinate dehydrogenase (complex II),
ubiquinol–cytochrome c oxidoreductase (complex III, or cytochrome bc1 complex), cytochrome c oxidase (complex IV), and ATP
synthase (complex V)
• Complex I is the first enzyme of the respiratory chain.
Complexes of respiratory chain
• Mitochondria are the power stations of the eukaryotic cell, using the energy released by the oxidation of glucose and other sugars
to produce ATP.
• Electrons are transferred from NADH, produced in the citric acid cycle in the mitochondrial matrix, to oxygen by a series of large
protein complexes in the inner mitochondrial membrane, which create a transmembrane electrochemical gradient by pumping
protons across the membrane.
• The flow of protons back into the matrix via a proton channel in the ATP synthase leads to conformational changes in the
nucleotide binding pockets and the formation of ATP.
• The three proton pumping complexes of the electron transfer chain are NADH-ubiquinone oxidoreductase or complex I,
ubiquinone-cytochrome c oxidoreductase or complex III, and cytochrome c oxidase or complex IV.
• Succinate dehydrogenase or complex II does not pump protons, but contributes reduced ubiquinone.
• The structures of complex II, III and IV were determined by x-ray crystallography several decades ago, but complex I and ATP
synthase have only recently started to reveal their secrets by advances in x-ray crystallography and cryo-electron microscopy.
• The complexes I, III and IV occur to a certain extent as super complexes in the membrane, the so-called respirasomes.
• Several hypotheses exist about their function. Recent cryo-electron microscopy structures show the architecture of the
respirasome with near-atomic detail.
• ATP synthase occurs as dimers in the inner mitochondrial membrane, which by their curvature are responsible for the folding of the
membrane into cristae and thus for the huge increase in available surface that makes mitochondria the efficient energy plants of
the eukaryotic cell.

113. Gluconeogenesis
Definition
• Gluconeogenesis is the formation of new glucose molecules as opposed to glucose that is broken down from the long storage
molecule glycogen.
• It takes place mostly in the liver, though it can also happen in smaller amounts in the kidney and small intestine.
• Gluconeogenesis is the opposite process of glycolysis, which is the breakdown of glucose molecules into their components.

114. Function of Gluconeogenesis
• Our bodies produce glucose to maintain healthy blood sugar levels
• Glucose levels in the blood must be maintained because it is used by cells to make the energy molecule adenosine
triphosphate (ATP)
• Gluconeogenesis occurs during times when a person has not eaten in a while, such as during a period of famine or
starvation
• Without food intake, blood sugar levels become low
• During this time, the body does not have an excess of carbohydrates from food that it can break down into glucose,
so it uses other molecules for the process of gluconeogenesis such as amino acids, lactate, pyruvate, and glycerol
instead
• Once glucose is produced through gluconeogenesis in the liver, it is then released into the bloodstream, where it
can travel to cells of other parts of the body so that it may be used for energy
• The process of gluconeogenesis is sometimes referred to endogenous glucose production (EGP) because it requires
the input of energy
• Since gluconeogenesis is the opposite of glycolysis, and glycolysis releases a lot of energy, it would be expected
that gluconeogenesis would require the input of a lot of energy
• However, gluconeogenesis occurs when the body is already low on energy, so it requires workarounds in order to
use less energy
• Therefore, some steps of gluconeogenesis cannot be performed in a way that is simply the reverse of glycolysis;
instead, the cell has developed slightly different ways to perform the process, as can be seen in the
gluconeogenesis pathway when it is compared to the glycolysis pathway
• Although it may seem counterintuitive that the gluconeogenesis uses energy when the body needs more energy,
the process ultimately pays off when glucose enters cells and is used to create ATP.

115. • Glycogenolysis is another process that is used when glucose levels in the blood are low
• During glycogenolysis, the storage molecule glycogen—which is made up of long chains of glucose—is broken down
into glucose which then enters the blood
• The main difference between glycogenolysis and gluconeogenesis is that glycogenolysis involves the formation of
glucose molecules from a glucose source (glycogen), while gluconeogenesis forms glucose from non-glucose
sources, molecules that are not made up of glucose
• Also, glycogenolysis is an exergonic process; it releases energy
• Gluconeogenesis is called endogenous glucose production (EGP) in order to differentiate it from glycogenolysis
• Gluconeogenesis and glycogenolysis have a similar function, but they are used somewhat differently
• Glycogenolysis is more often used during shorter periods of fasting, such as when a person’s blood sugar drops in
between meals or after a good night’s sleep, while gluconeogenesis is used during long periods of fasting
• However, both processes are always occurring at some level in the body because glucose is important for producing
energy
• Organs such as testes, red blood cells, kidneys, and parts of the eye such as the retina use glucose as their sole
energy source, and other parts of the body also have a high demand for glucose, such as the brain and muscles.

116. Gluconeogenesis Pathway
1.Gluconeogenesis begins in either the mitochondria or cytoplasm of the liver or kidney. First, two pyruvate molecules
are carboxylated to form oxaloacetate. One ATP (energy) molecule is needed for this.
2.Oxaloacetate is reduced to malate by NADH so that it can be transported out of the mitochondria.
3.Malate is oxidized back to oxaloacetate once it is out of the mitochondria.
4.Oxaloacetate forms phosphoenolpyruvate using the enzyme PEPCK.
5.Phosphoenolpyruvate is changed to fructose-1,6-biphosphate, and then to fructose-6-phosphate. ATP is also used
during this process, which is essentially glycolysis in reverse.
6.Fructose-6-phosphate becomes glucose-6-phosphate with the enzyme phosphoglucoisomerase.
7.Glucose is formed from glucose-6-phosphate in the cell’s endoplasmic reticulum via the enzyme glucose-6-
phosphatase. To form glucose, a phosphate group is removed, and glucose-6-phosphate and ATP becomes glucose and
ADP.

117. UNIT-III: Translocation in Phloem
Phloem Sap Composition:
The major phloem sap components are carbohydrates
Analyses of the phloem exudates from various plants have shown that sucrose is the major transportable form of
carbohydrate.
In some species of Cucurbitaceous, in addition to sucrose, certain oligosaccharides like raffinose, stachyose, and
verbascose have also been found in the phloem sap composition.
Again in some cases sugar alcohols mannitol and sorbitol or dulcitol have been found in the phloem exudates.
Generally, the seaweeds produce large amounts of mannitol.
Phloem exudate rarely contains hexoses even though glucose and fructose are commonly present in phloem tissue.
They are the products of sucrose hydrolysis and are distributed in non-conducting cells to enter directly into the
metabolism.
The non-reducing sugar, sucrose, on the other hand, is a more stable compound and suitable for long-distance
transport.
For that reason, it has been found that the ratios of labelled hexoses to labelled sucrose decreased as the distance
from the leaf assimilating 14CO2 increased

118. • Exudate analyses for nitrogenous compounds of willow stems have detected the presence of glutamic acid, aspartic
acid, threonine, serine, leucine, alanine, valine, phenylalanine, asparagine, glutamine, etc.
• Phloem exudate also contains high levels of proteins, particularly P- protein and several enzymes of carbohydrate
and nitrogen metabolism
• The enzymes of glycolysis, TCA cycle, pentose phosphate pathway, transamination, peroxidase, polyphenol oxidase,
etc., have been found to be present in the sieve elements
• The protein profile also includes some proteins associated with basic cellular functions like protein kinases (protein
phosphorylation), thioredoxin (disulfide reduction), ubiquitin (protein turnover), and chaperones (protein folding)
• All these proteins are called sieve tube exudate proteins (STEPs).
These are grouped as:
(1) Enzymes related to carbohydrate metabolism,
(2) Structural proteins (“P-proteins”)
(3) “Maintenance” proteins.

119. • The structural proteins appear as either crystalline or amorphous accumulations (“P-protein bodies”) during
sieve element differentiation
• Though common, these structures are absent in some species, including many monocots
• The amorphous, fibrillar forms of this protein appear to be in equilibrium with soluble monomeric proteins, which
may be fairly abundant in phloem exudates
• Because of their abundance in cucurbit exudates, these forms have been characterized fairly extensively
• Several forms are present in phloem exudates from a given species, and exudates collected from different organs
on a plant demonstrate similar protein patterns
• However, both gel patterns and antibody cross-reactivity data suggest the existence of significant differences
among species.
• A particularly interesting aspect is the hem-agglutinating (lectin) activity of some P-proteins, which has provided
another useful diagnostic tool for probing taxonomic relationships.
• Its biological or physiological significance, however, is unclear
• Recent efforts at characterizing STEPs have focused on their possible maintenance role in SE/ CC (sieve
element/companion cell) interactions.
• Identified functions in this category include glutaredoxin, cystatin, ubiquitin, and chaperones, thioredoxin and
protein kinase activity.

120. • The phloem sap also contains high levels of K+ and Mg2 +.
• Among the anions Cl– and PO4
3-are very common.
• Traces of zinc, manganese, copper, iron and molybdenum are also present.
• Probably, due to its high K+ content the phloem exudate is slightly alkaline.
• Growth substances like indole acetic acid, gibberellic acid and abscisic acid have been detected in phloem sap.
• In addition, organic acids, particularly malic acid, nucleic acids, ATP, vitamins, etc., have also been detected in
phloem sap.
• So, phloem is an important path for the translocation of various materials.
• As a general rule the sieve-tube sap is the most concentrated solution to be found in any space of the plant body
and has the most negative osmotic potential (Ψs).( OS means the free energy of water in a system due to presence
of solute particles. This value is always negative becoz the presence of solute will always make a solution have less
water than the same volume of pure water.).

121. Girdling experiment
• Experiments now called girdling experiments were performed, in which a ring of bark is removed from a woody
plant.
• Girdling, or ringing, does not immediately interfere with upward movement of water in the xylem, but it does
interrupt phloem movement.
• In some plants surgical removal of phloem is difficult; in this case phloem may be killed by using steam (steam
girdling).
• Xylem conduction is normally not affected by such treatment, and movement in the two transport tissues can thus
easily be distinguished.
• Girdling experiments, however, are not entirely foolproof.
• The question as to whether or not mineral nutrients can ascend in the phloem illustrates the kinds of difficulties
that may be encountered.
• Much smaller amounts of mineral nutrients reach the leaves in girdled plants than in ungirdled ones.
• From this observation it might be concluded that some nutrients ascend in the phloem of ungirdled trees; girdling,
however, interrupts the flow of sugars into roots.
• Roots are thereby starved and take up fewer mineral nutrients; the reduced flow of mineral nutrients to the leaves
of girdled plants can thus be explained as a secondary effect.

122. Ringing or girdling experiment
• The experiment involves the removal of all the tissue outside
to vascular cambium (bark, cortex, and phloem) in woody
stems except xylem.
• Xylem is the only remaining tissue in the girdled area which
connects upper and lower part of the plant.
• This setup is placed in a beaker of water.
• After some time, it is observed that a swelling on the upper
part of the ring appears as a result of the accumulation of food
material
• If the experiment continues within days, the roots die first
• It is because, the supply of food material to the root is cut
down by the removal of phloem
• The roots cannot synthesize their food and so they die first
• As the roots gradually die the upper part (stem), which
depends on root for the ascent of sap, will ultimately die.

123. Pressure flow model - a passive mechanism for phloem transport
Introduction
• The Mass Flow Hypothesis was first proposed by German plant physiologist Ernst Munch in the year 1930
• He theorised the movement of sap through the phloem tissue in plants
• This theory is also known as the Pressure Flow Hypothesis
• A highly concentrated organic sugar especially sugar in the cells of the phloem from a source like a leaf forms a diffusion gradient which
draws water into the cells of phloem tissue from the adjacent xylem
• This develops turgor pressure in the phloem, which is also called hydrostatic pressure.
• Phloem movement occurs by mass flow from sources of sugar to sugar sinks
• The phloem movement is bidirectional but unidirectional in xylem cells
• Due to this multidirectional flow, it is not uncommon for sap in the sieve tubes besides to move in opposite directions based on the fact that
sap cannot travel easily between adjacent sieve tubes.
Mechanism
• When the movement of minerals and water via the xylem is driven mostly by negative pressure and movement via phloem is driven by
hydrostatic pressure.
• This process is called translocation and is accompanied by a process known as phloem loading and unloading.

125. • Cells in sugar sources load a sieve tube by osmosis developing pressure that pushes the sap low
• The cells deliver solutes out of the elements of sieve tube and produce opposite effects
• The sugar gradient from the source creates pressure-flow via the sieve tube towards the sink.
•Glucose is formed by photosynthesis in the cells of mesophyll and some glucose is utilized in the cells during respiration.
•The leftover glucose is transformed into non-reducing sugar.
•Sucrose is delivered to the neighbour cells of minute veins of the leaves.
•Sucrose diffuses from neighbour cells to the elements of the sieve tube via plasmodesmata.
• Hence, the amount of sucrose rises in the elements of the sieve tube.
•Water travels from the close xylem to the leaf vein by osmosis and raises the hydrostatic pressure of the elements of the sieve tube.
•The Hydrostatic pressure shifts the sucrose along with other substances via the cell of the sieve tube towards the sink.
•In storage sinks, sucrose is eliminated into the apoplast before entering the sink’s symplast.

126. •The water travels out of the cells via osmosis and lowers the hydrostatic pressure in
them.
•Hence, a gradient of pressure is developed as a result of the entry of sugar at the
source and elimination of sucrose at the sink.
•The phloem sugar is eradicated by the cortex of the root and stem and utilized by
cellular respiration.
•The starch is insoluble and does not exert any osmotic effect.
•Ultimately, pure water is left and drawn into xylem vessels by transpiration pull.

127. Overview of Translocation: Transport from Source to Sink
• Sugars move (translocate) from source to sink, but how? The most commonly accepted hypothesis to explain the
movement of sugars in phloem is the pressure flow model for phloem transport.
• This hypothesis accounts for several observations:
1.Phloem is under pressure
2.Translocation stops if the phloem tissue is killed
3.Translocation proceeds in both directions simultaneously (but not within the same tube)
4.Translocation is inhibited by compounds that stop production of ATP in the sugar source
In very general terms, the pressure flow model works like this:
• a high concentration of sugar at the source creates a low solute potential (Ψs), which draws water into the phloem
from the adjacent xylem.
• This creates a high pressure potential (Ψp), or high turgor pressure, in the phloem.
• The high turgor pressure drives movement of phloem sap by “bulk flow” from source to sink, where the sugars are
rapidly removed from the phloem at the sink.
• Removal of the sugar increases the Ψs, which causes water to leave the phloem and return to the xylem,
decreasing Ψp.

128. Phloem loading - symplast and apoplast pathways
Translocation of organic solutes such as sucrose (i.e., photosynthetic) takes place through sieve tube
elements of phloem from supply end (or source) to consumption end (or sink)
But, before this translocation of sugars could proceed, the soluble sugars must be transferred from
mesophyll cells to sieve tube elements of the respective leaves
This transfer of sugars (photosynthetic) from mesophyll cells to sieve tube elements in the leaf is called as
phloem loading
On the other hand, the transfer of sugars (photosynthetic) from sieve tube elements to the receiver cells of
consumption end (i.e., sink organs) is called as phloem unloading
Both are energy requiring processes.
Phloem Loading:
• As a result of photosynthesis, the sugars such as sucrose produced in mesophyll cells move to the sieve tubes of
smallest veins of the leaf either directly or through only 2-3 cells depending upon the leaf anatomy.
• Consequently, the concentration of sugars increases in sieve tubes in comparison to the surrounding mesophyll
cells

129. • The mechanism of phloem loading in such case has been called as sucrose-H+ symport or cotransport mechanism
• According to this mechanism protons (H+) are pumped out through the plasma membrane using the energy from
ATP and an ATPase carrier enzyme, so that concentration of H+ becomes higher outside (in the apoplast) than
inside the cell
• Spontaneous tendency toward equilibrium causes protons to diffuse
back into the cytoplasm through plasma membrane coupled with
transport of sucrose from apoplast to cytoplasm through sucrose -H+
symporter located in the plasma membrane.
• The mechanism of the transfer of sugars (sucrose) from mesophyll
cells to apoplast is however, not known.
• The movement of sugars from mesophyll cells to sieve tubes of phloem may occur either through symplast (i.e., cell
to cell through plasmodesmata, remaining in the cytoplasm) or the sugars may enter the apoplast (i.e., cell walls
outside the protoplasts) at some point en route to phloem sieve tubes
• In the latter case, the sugars are actively loaded from apoplast to sieve tubes by an energy driven transport located
in the plasma membrane of these cells

130. • Phloem loading is specific and selective for transport sugars.
• Both symplastic and apoplastic pathways of phloem loading are used in plants but in different species
• In some species however, phloem loading may occur through both the pathways in the same sieve tube element or
in different sieve tube elements of the same vein or in sieve tubes in veins of different sizes
• Experimental findings have revealed certain patterns in apoplastic and symplastic loading of sugars in phloem
which appears to be related with the type of sugar transported to phloem, type of companion cells (ordinary,
transfer or intermediary) and number of plasmodesmata (few or abundant ) connecting the sieve tubes (including
the companion cells) to surrounding cells in smaller veins.
• To some extent, phloem loading is also correlated with the family of plant, its habit (trees, shrubs, vines or herbs)
and climate such as temperate, tropical or arid climate.

131. Phloem Unloading:
It occurs in the consumption end or sinks organs (such as developing roots, tubers, reproductive structures etc.)
Sugars move from sieve tubes to receiver cells in the sink involving following steps:
(i) Sieve element unloading:
In this process, sugars (imported from the source) leave sieve elements of sink tissues.
ii)Short distance transport:
The sugars are now transported to cells in sink by a short distance pathway which has also been called as post-sieve
element transport.
(iii) Storage and metabolism:
Finally, sugars are stored or metabolized in the cells of the sink.
• As with the phloem loading process, sucrose unloading also occurs through symplast via plasmodesmata or
through apoplast at some point en route to sink cells
• Phloem unloading is typically symplastic in growing and respiring sinks such as meristems roots, and young leaves
etc. in which sucrose can be rapidly metabolized. (Young leaves act as sink until their photosynthetic machinery is
fully developed, at which point they become sources).
• Usually, in storage organs such as fruits (grape, orange etc.), roots (sugar beet) and stems (sugarcane), sucrose
unloading is known to occur through apoplast
• However, according to Oparka (1986), phloem unloading in potato tubers from sieve elements to cortical cells is a
symplastic passive process
• Because, there are wide varieties of sinks in plants which differ in structure and function, no one scheme of phloem unloading is available.

132. Phloem Unloading
• Phloem unloading occurs similar to phloem loading, either by symplast or apoplast.
• When sugar arrives at the receiving end, it is unloaded from the filter tube into the cells or sink.
• There are three types of phloem unloading mechanisms.
 Sieve Element Unloading: In this procedure, imported sugars leave sink tissue sieve components.
 Short Distance Transport: A short-distance pathway, also known as post-sieve element transfer, is now being used to transport the sugars
to the cells in the sink.
 Storage and Metabolism: Carbohydrates are finally stored or metabolized in the cells of the sink.
• Generally, when sucrose consumption rates are very high and sink cells are metabolically very active, as in the meristematic tissue of
developing roots, fruits, leaves, etc., symplast is used for phloem unloading
• When storage organs like fruits (grapes, oranges, etc.) and roots have sink cells, sucrose unloading happens through the apoplast.
Function of Phloem
• Water-based sap contains a lot of carbohydrates produced during photosynthesis
• These sugars are sent to storage organs like tubers or bulbs or non-photosynthetic plant sections like the roots by phloem
• The phloem, which transports sap, comprises still-living cells compared to the mostly-dead xylem
• Phloem is a class of complex permanent tissue that develops into a conductive or vascular system in the plant’s body
• It transports the prepared nutrients from the leaves to the growing areas and storage organs
• It is also considered that vascular plants’ phloem sap contributes to the transmission of informative signals.

134. Unit - IV Stress Physiology
Concept of Biotic stress
• Biotic stress includes attack by various pathogens such as fungi, bacteria, oomycetes, nematodes and herbivores.
• Diseases caused by these pathogens accounts for major yield loss worldwide
• Being sessile plants have no choice to escape from these environmental cues
• Expertise in tolerating these stresses is crucial for completing the lifecycle successfully.
• Therefore, to combat these threats plants have developed various mechanisms for getting adapted to such
conditions for survival
• They sense the external stress environment, get stimulated and then generate appropriate cellular responses
• These cellular responses work by relaying the stimuli from sensors, located on the cell surface or cytoplasm to the
transcriptional machinery which is situated in the nucleus, with the help of various signal transduction pathways
• This leads to differential transcriptional changes making the plant tolerant against the stress
• The signaling pathways play an indispensable role and acts as a connecting link between sensing the stress
environment and generating an appropriate physiological and biochemical response

135. • Plants are constantly exposed to a variety of potential microbial pathogens such as fungi, bacteria, oomycetes,
nematodes and herbivores
• In order to defend themselves plants have developed a variety of defense responses many of which are induced
by pathogen attack
• Penetration of the cell wall exposes the microbes to the plant plasma membrane, where they encounter
extracellular surface receptors that recognize pathogen-associated molecular patterns (PAMPs)
• Recognition a microbe at the cell surface initiates PAMP- triggered immunity (PTI), which usually halts infection
before the pathogen gains a hold in the plant
• However, pathogenic microbes have evolved the means to suppress PTI by secreting specialized proteins, called
as effectors, into the plant cell cytosol that alter resistance signaling or manifestation of resistance responses
• Bacteria Metabolomic and transcriptomic analysis of rice in response to bacterial blight pathogen Xanthomonas
oryzae pv. oryzae revealed global metabolic and transcriptomic changes in leaf tissues
• Ethylene response element binding protein (EREBP) transcription factor gets significantly expressed together with
ROS scavenging system and lower expression of alcohol dehydrogenase gene
• These factors lead to hypersensitive cell death in the resistant cultivar upon bacterial infection
• Stimulation of glutathione-mediated detoxification and flavonoid biosynthetic pathways in combination with up-
regulation of defense genes during infection inhibits pathogen from further spreading in the host tissues
• Transcripts encoding disease resistance proteins via JA/ET signaling as well as osmotic regulation via proline
synthesis genes were found differentially expressed when microarray analysis was performed in cotton associated
with Bacillus subtilis induced tolerance
• The major protein of bacterial flagella is flagellin which is a well characterized PAMP.

136. • Fungi On the basis of their lifestyles, plant pathogenic fungi have been divided into two classes: the biotrophs and the
necrotrophs
• Biotrophs feed on living host tissue, whereas necrotrophs first kill the host tissue and then feed on the dead tissues
• However, there are many plant pathogenic fungi which behave both as biotrophs and necrotrophs, depending on the
conditions in which they find themselves or the stages of their life cycles
• Such pathogens are called hemi-biotrophs
• Earlier, many fungi were commonly considered as necrotrophs whereas they had a biotrophic stage early in the infection
process and hence were basically hemi-biotrophs
• Biotrophic Fungi For resistance against biotrophs, gene-for-gene mechanism is important
• According to gene-for-gene hypothesis, given by Flor, for every gene in the plant that confers resistance, there is a
corresponding gene in the pathogen that confers avirulence
• It leads to activation of SA-dependent signaling and SAR
• In Arabidopsis, overexpression of ADR1 (NBS-LRR resistance gene) provides resistance against Erysiphe cichoracearum
• Another example is of barley and Blumeria graminis (Schulze-Lefert and Vogel 2000) where gene-for-gene resis- tance
response is evident

137. • Transcriptome data from microarray experiments suggest that during defense responses the photosynthesis-related genes are
highly down-regulated which is required to support the induction of a defence response
• The nitrogen invested in photosynthetic proteins, primarily Rubisco, is lowered or even withdrawn to provide nitrogen for the
induction of defensive compounds
• Necrotrophic Fungi Transcript profiling of various plant-pathogen systems suggest differential regulation of a large number of
transcripts in response to pathogen attack
• These transcripts included those which are associated with JA biosynthesis and signaling, ROS metab- olism, and cell wall
structure and function
• Isolation of early responsive genes of chickpea infected with blight fungus Ascochyta rabiei was carried out using PCR based
suppression subtractive hybridization (SSH) strategy and ~250 unique genes were identified
• These genes belonged to eleven different categories viz. stress, signaling, gene regulation, cellular metabolism and genes of
unknown functions
• Chitin, which is a major component of fungal cell wall, serves AU2 as a PAMP
• Therefore, chitosan (the deacetylated form of chitin) plays important role in inducing defense responses against pathogens in
many plant species
• GeneChip microarrays and quantitative RT-PCR of Botrytis cinerea infected Arabidopsis leaves revealed that chitosan has
inductive role on several genes involved in defense responses and camalexin biosynthesis

138. The basic concepts of plant stress Stress:
• stress in physical term is defined as mechanical force pe unit area applied to an object.
• In response to the applied stress ,an object_a change in the dimension, which is also known as strain.
• A biological condition which may be stress for one plant may be optimum for another plant.
• As plants are sessile, it is though to measure the exact force exerted by stress and therefore in biological term it
is difficult to define stress
• Environmental modulation of homeostasis defined as biological stress: Any change in the surrounding
environment may disrupt homeostasis
• Environmental modulation of homeostasis may be defined as biological stress
• Thus, it follows that plant stress implies some adverse effect on the physiology of a plant induced upon a sudden
transition from some optimal environmental condition where homeostasis is maintained to some suboptimal
condition which disrupts this initial homeostatic state
• Thus, plant stress is a relative term since the experimental design to assess the impact of a stress always involves
the measurement of a physiological phenomenon in a plant species under a suboptimal, stress condition
compared to the measurement of the same physiological phenomenon in the same plant specie under optimal

139. • Plant respond to stress in several different ways : Plant stress can be divided into two primary categories.
• Abiotic stress is a physical (e.g., light, temperature) or chemical insult that the environment may impose on a plant
• Biotic stress: is stress that occurs as a result of damage done to plant by other living organism Such as bacteria, virus, fungi,
beneficial and harmful insects and cultivated plant
• Abiotic stress: is defined as the negative impact of non-living factor on the living organism in a specific environment.
• Abiotic stresses such as drought (water stress), excessive watering (water logging), extreme temperatures (cold,
frost and heat), salinity and mineral toxicity negatively impact growth, development, yield and seed quality of crop
and other plants
• In future it is predicted that fresh water scarcity will increase and ultimately intensity of abiotic stresses will increase
• Hence there is an urgency to develop crop varieties that are resilient to abiotic stresses to ensure food security and
safety in coming years
• A plants first line of defense against abiotic stress is in its roots
• The chances of surviving stressful conditions will be high if the soil holding the plant is healthy and biologically
diverse
• One of the primary responses to abiotic stress such as high salinity is the disruption of the Na+/K+ ratio in the
cytoplasm of the plant cell.
• The phytohormone abscisic acid (ABA) plays an important role during plant adaptation to environmental stress such

140. Cold
• Cold stress as abiotic stress has proved to be the main abiotic stresses that decrease productivity of agricultural
crops by affecting the quality of crops and their post-harvest life
• Plants being immobile in nature are always busy to modify their mechanisms in order to prevent themselves from
such stresses
• In temperate conditions plants are encountered by chilling and freezing conditions that are very harmful to plants as
stress
• In order to adopt themselves, plants acquire chilling and freezing tolerance against such lethal cold stresses by a
process called as acclimation
• However many important crops are still incompetent to the process of cold acclimation
• The abiotic stress caused by cold affect the cellular functions of plants in every aspect
• Several signal transduction pathways are there by which these cold stresses are transduced like components of
ROS, protein kinase, protein phosphate, ABA and Ca2+, etc. and among these ABA proves to be best
Salt
• Soil salinity poses a global threat to world agriculture by reducing the yield of crops and ultimately the crop
productivity in the salt affected areas
• Salt stress reduces growth of crops and yield in many ways

141. • The osmotic pressure under salinity stress in the soil solution exceeds the osmotic pressure in plant cells due to the presence of
more salt, and thus, limits the ability of plants to take up water and minerals like K+ and Ca2+
• These primary effects of salinity stress causes some secondary effects like assimilate production, reduced cell expansion and
membrane function as well as decreased cytosolic metabolism
Drought
• Nowadays climate has changed all around the globe by continuously increase in temperature and atmospheric CO2 levels
• The distribution of rainfall is uneven due to the change in climate which acts as an important stress as drought
• The soil water available to plants is steadily increased due severe drought conditions and cause death of plants prematurely
• After drought is imposed on crop plants growth arrest is the first response subjected on the plants
• Plants reduce their growth of shoots under drought conditions and reduce their metabolic demands
• After that protective compounds are synthesized by plants under drought by mobilizing metabolites required for their osmotic
adjustment.
Heat
• Increase in temperature throughout the globe has become a great concern, which not only affect the growth of plants but their
productivity as well especially in agricultural crops plants
• When plants encounter heat stress the percentage of seed germination, photosynthetic efficiency and yield declines
• Under heat stress, during the reproductive growth period, the function of tapetal cells is lost, and the anther is dysplastic.
Toxin

142. • Anthropogenic changes and chemical pollution confront plant communities with various xenobiotic compounds or
combinations of xenobiotics, involving chemical structures that are at least partially novel for plant species
• Plant responses to chemical challenges and stimuli are usually characterized by the approaches of toxicology, ecotoxicology,
and stress physiology
• Development of transcriptomics and proteomics analysis has demonstrated the importance of modifications to gene
expression in plant responses to xenobiotics
• It has emerged that xenobiotic effects could involve not only biochemical and physiological disruption, but also the disruption
of signaling pathways
• Moreover, mutations affecting sensing and signalling pathways result in modifications of responses to xenobiotics, thus
confirming interference or crosstalk between xenobiotic effects and signalling pathways
• Some of these changes at gene expression, regulation and signalling levels suggest various mechanisms of xenobiotic sensing
in higher plants, in accordance with xenobiotic-sensing mechanisms that have been characterized in other phyla (yeast,
invertebrates, vertebrates)
• In higher plants, such sensing systems are difficult to identify, even though different lines of evidence, involving mutant
studies, transcription factor analysis, or comparative studies, point to their existence

143. • It remains difficult to distinguish between the hypothesis of direct xenobiotic sensing and indirect sensing of xenobiotic-
related modifications
• However, future characterization of xenobiotic sensing and signalling in higher plants is likely to be a key element for
determining the tolerance and remediation capacities of plant species
• This characterization will also be of interest for understanding evolutionary dynamics of stress adaptation and mechanisms of
adaptation to novel stressors.