A2 BIOLOGY

SEMESTER THREE 2021

Student Notes
12s8

PHOTOSYNTHESIS
Learning objectives:
I. 5.1 understand the overall reaction of photosynthesis as requiring energy
from light to split apart the strong bonds in water molecules, storing the
hydrogen in a fuel (glucose) by combining it with carbon dioxide and
releasing oxygen into the atmosphere
II. 5.2 understand how photophosphorylation of ADP requires energy and that
hydrolysis of ATP provides an immediate supply of energy for biological
processes
III. 5.3 understand the light-dependent reactions of photosynthesis, including
how light energy is trapped by exciting electrons in chlorophyll and the role
of these electrons in generating ATP, reducing NADP in cyclic and non-cyclic
photophosphorylation and producing oxygen through photolysis of water
IV. 5.4 (i) understand the light-independent reactions as reduction of carbon
dioxide using the products of the light-dependent reactions (carbon fixation
in the Calvin cycle, the role of GP, GALP, RuBP and RUBISCO)

(ii) know that the products are simple sugars that are used by plants,
animals and other organisms in respiration and the synthesis of new
biological molecules (polysaccharides, amino acids, proteins, lipids and
nucleic acids)

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 V. 5.5 understand the structure of chloroplasts in relation to their role in
photosynthesis
VI. 5.6 understand what is meant by the terms absorption spectrum and action
spectrum
VII. 5.7 understand that chloroplast pigments can be separated using
chromatography and the pigments identified using Rf values

ATP molecule

★ Made up of adenine (nitrogenous base), a

ribose sugar and three phosphate groups.
★ Second and third covalent bonds are unstable and can be broken down
easily.
★ Break down of ATP release energy - Hydrolysis (exergonic)
★ Synthesis of ATP from ADP and phosphate – Phosphorylation (endergonic)

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Structure of a chloroplast

3
Structure of a thylakoid

4
Photosystems

★ On the thylakoid membrane photosensitive pigments

are organized into complex systems.
★ Primary pigments, accessory pigments and electron
carriers are assembled together in this chlorophyll
complex.
★ These chlorophyll complexes are called photosystems.
★ There are two photosystems:- PSI and PSII

Photosystem I

★ Accessory pigments or antennae pigments (chlorophyll a, carotenoid,

chlorophyll b) are arranged around the primary pigment chlorophyll a.
★ PSI is found on the single thylakoids.
★ The absorption peak of this chlorophyll a is 700 nm and it is the reaction
centre.
★ Antennae pigments absorb light energy (different wavelengths), transfer to
the reaction centre.
★ Reaction centre molecule (Chlorophyll) gets oxidized and releases high
energy electrons.

Photosystem II

★ It is larger than PSI.

★ PSII is found on the thylakoids
which are stacked into grana.
★ The reaction centre is chlorophyll a, with an absorption peak of 680 nm.

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Chlorophyll

★ Chlorophyll is present in the thylakoid membrane.

★ Have a polar porphyrin head and a nonpolar hydrocarbon tail.
★ Tail is lipid soluble.
★ The hydrocarbon tail anchors the
pigment molecules into the lipid bilayer.
★ The head absorb light energy

Adaptations of leaf for photosynthesis

Thin lamina

★ Fast / maximum gas exchange /uptake of carbon dioxide

★ Help in the penetration of light ;
★ Carbon dioxide is used in the Calvin cycle
★ Light is used in light-dependent stage / photolysis / photophosphorylation.

Veins / vessels in the midrib

★ Xylem transport water to the leaves

★ Phloem transport sucrose / sugar /carbohydrates away from the leaves
★ Water is the source of hydrogen ions in light-dependent reactions.
★ Transporting sugar to make more room for more carbohydrate synthesis

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Adaptations of Spongy mesophyll for gas exchange

★ The gas exchange surface is the cell wall and membrane

★ The spongy mesophyll cells are loosely packed and have air spaces between
them and large surface area to volume ratio.
★ So the diffusion distance is small between air space and cytoplasm
★ Air spaces and loosely packed cells make diffusion fast
★ Carbon dioxide can continuously enter the leaf and circulate around the cells
★ This maintains a concentration gradient between air space and cell

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Chloroplast

★ A double membrane bound organelle found in green plant cells.

★ Two membranes are separated by an intermembrane space.
★ Envelope is semi permeable.
★ The matrix of the chloroplast is called stroma.
★ Stroma contains enzymes (RUBISCO) that catalyzes light independent
reactions of photosynthesis.
★ Disc shaped structures in the stroma are called thylakoids ,surrounded by
the thylakoid membrane.
★ These are the sites of light dependent reactions of photosynthesis.
★ Thylakoids contain chlorophyll molecules, accessory pigments and
electron transport systems.
★ Light absorbing molecules are arranged in photosystems.
★ This is the site of ATP synthesis in chloroplast
★ Stalks of thylakoids are called grana (granum).
★ Grana are connected with each other by lamella.
★ Lamella acts as the skeleton of the chloroplast and maximizes the efficiency
of the chloroplast.
★ Chloroplast also contains a circular DNA, lipid globules, starch granules
and 70s ribosomes.

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Thylakoid:- the site of light dependent stage of photosynthesis

★ Thylakoid membrane-
○ provide a space for accumulation of H+
○ Chlorophyll / carotenoids / photosystems / electron carrier proteins /
ATP synthase / NADP reductase are present.
○ compartmentalization from stroma
○ site of light-dependent reaction
★ Photosystem- Contains pigments for trapping light energy
★ Proteins-
○ pump the hydrogen ions into the thylakoid space.
○ Electron carrier proteins- high energy electrons pass along and
undergo redox reaction and provide energy for ATP synthesis
★ ATP synthase-
○ Channels allow hydrogen ions to pass through into stroma.
○ Energy released from this movement of hydrogen ions results in the
production of ATP
★ Lumen- provide space for the accumulation of H+ which is needed for
photophosphorylation.

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Chloroplast- structure related to function

★ Compartmentalisation (from cytoplasm);

★ Thylakoid membranes are site of
light-dependent reaction
★ Chlorophyll / carotenoids / photosystems / electron carrier proteins / ATP
synthase / NADP reductase are present within/ on thylakoid membranes
★ Thylakoid membranes provide a space for accumulation of H+ ;
★ Stroma is the site of Calvin cycle
★ Stroma contains RuBP / RUBISCO

Mechanism of photosynthesis
➔ A process of energy transduction.
➔ Light energy into electrical energy.
➔ Electrical energy into chemical energy.

Three main phases of photosynthesis

★ Light harvesting- light energy is captured by the pigments.

★ Light dependent stage (photolysis)- splitting of water into Hydrogen ion and
oxygen.

+ −
2𝐻 2𝑂 → 4𝐻 + 𝑂 2
+ 4𝑒

★ Light independent stage- the reduction of carbon dioxide and form sugars.

6𝐶𝑂 2
+ 12𝐻 2𝑂 → 𝐶 6𝐻 𝑂
12 6
+ 6 𝐻 2𝑂 + 6𝑂 2

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Light Dependent Stage of photosynthesis

★ Occurs in the thylakoid of chloroplast.

★ It involves the splitting of water by light (photolysis) and producing ATP.
★ Accessory pigments absorb light energy and transfer it into the reaction
centre.
★ The electron within the molecule gets excited and possesses high energy.
★ These electrons are emitted by the chlorophyll a molecule and are received
by the electron carriers.
★ Then passed on to other molecule.
★ The light dependent stage leads to the synthesis of ATP (phosphorylation)
and the production of reduced NADP.
★ This stage includes cyclic and non-cyclic photophosphorylation

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Non-cyclic photophosphorylation

★ Light energy is trapped in PSII and boosts electrons to higher energy levels.
★ The electrons are received by electron acceptor (TM).
★ The electrons are passed along a series of electron carriers to PSI.
+
★ 𝐻 ions pump from stroma to the lumen of the thylakoid.
+
★ Concentration of 𝐻 increases in the thylakoid which diffuse back to stroma
by chemiosmosis.
★ The energy from chemiosmosis is used for the synthesis of ATP from ADP
and Pi by the enzyme ATP synthase.
★ PSI also absorbs light and emits electrons even to a higher energy level which
are received by the electron acceptor.
★ The protons from the water molecule combine with the electron from the
electron acceptor and reduces NADP (temporary store of energized
electrons) to NADPH
★ This passes to the reactions of the light independent stage.
★ The PSI gains its lost electron from the PSII, and PSII gains its lost electron
from the splitting of water (photolysis).
★ Oxygen is produced as a waste gas during the photolysis of water.

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Differences between PS I andPS II

PS I PS II

Found mainly on the lamellae and the Found mainly on the inner surface of
outer surface of grana. granal thylakoid.

Reaction centre is P700. Reaction centre is P680

Both cyclic and non-cyclic Participate only in non-cyclic

photophosphorylation. photophosphorylation.

Can undergo cyclic photophosphorylation No independent function.

independently.

Lost electron is regained from PSII Lost electrons are regained from
photolysis of water.

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Cyclic photophosphorylation
★ Cyclic photophosphorylation involves only photosystem I (PSI).
★ Light hits a chlorophyll molecule in PSI and energizes electrons.
★ Light-excited electrons leave the chlorophyll molecule and are collected by
the electron acceptor.
★ These high energy electrons pass down directly along an electron transport
chain and the energy released is used to pump hydrogen ions from the
stroma into the lumen of the thylakoid.
★ Hydrogen ion concentration increases within the lumen of the thylakoid.
★ So, these hydrogen ions diffuse back into the stroma through a protein
channel on the thylakoid membrane.
★ Diffusion of Hydrogen ions from lumen to stroma (chemiosmosis) activates
ATP synthase to phosphorylate ADP to form ATP.This is called
photophosphorylation.
★ The electron will be returned to the
chlorophyll molecule in PSI.

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Light Independent Stage of photosynthesis

★ Takes place whether or not light is present.

★ The details of this stage were analyzed by Melvin Calvin.
★ It is the reduction of 𝐶𝑂 2
using the reduced NADP and ATP from the light

reaction.
★ The light-independent reactions of photosynthesis take place in the stroma
of the chloroplasts, using the reduced NADP and ATP from the
light-dependent reactions.
★ NADP acts as a hydrogen carrier.
★ Carbon dioxide is reduced to carbohydrate.
★ This stage consists of a series of reactions known as the Calvin cycle and
each stage of the cycle is controlled by enzymes.

LIS

★ 𝐶𝑂 2
diffuse into the leaf through stomata.

★ 𝐶𝑂 2
combine with a 5C compound- Ribulose bisphosphate (RuBP) and

form an unstable 6C compound. (Ribulose bisphosphate carboxylase-

RuBISCO)
★ The 6C compound breaks down into two molecules of 3C compound –
Glycerate-3-phosphate (GP).
★ GP is converted (reduced) to Glyceraldehyde-3-phosphate (GALP) by using
reduced NADP and ATP.
★ From every 12 GALP formed 10 are used to regenerate RuBP and the
remaining two into Glucose.
★ The high concentration of RuBP keeps running the Calvin Cycle at a high rate.

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 IN OUT

six 𝐶𝑂 2
One glucose

18 ATP 18 ADP

12 NADPH 12 NADP

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Interdependence between light dependent and Calvin
cycle

Summary of photosynthesis

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Fate of glucose

Glucose can be converted, using enzymes, into starch, cellulose, fats, amino
acids/proteins and nucleic acids. The extra elements needed to make some of these
compounds, such as nitrogen and phosphorus, are taken up by the roots of the
plant from the soil

The calvin cycle is the starting point for making all the organic substances a plant
needs. Glyceraldehyde-3-phosphate (GALP) and glycerate-3-phosphate (GP)
molecules are used to make essential biological molecules:

★ Carbohydrates:- simple sugars (eg. glucose) are made by joining two GALP
molecules together, and polysaccharides (eg. starch and cellulose) are made
by joining hexose sugars together in different ways.

The production of glucose is very important as it's used in respiration, which

provides energy needed for biological processes.

★ Lipids:- these are made using glycerol, which is synthesised from GALP, and
fatty acids which are synthesised from GP.
★ Amino acids:- some amino acids are made from GP.
★ Nucleic acids:- the sugar in RNA (ribose) is made using GALP.

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Using the products of photosynthesis

★ Two molecules of GALP join to form glucose (gluconeogenesis).

★ This glucose may be converted into disaccharides such as sucrose for
transport round the plant.
★ (Alpha glucose molecule joins with fructose by 1,2-glycosidic bond through
condensation reaction and forms sucrose).
★ (starch is a polymer of alpha glucose. Glucose monomers join together by
glycosidic bond through condensation reaction. Starch has two polymers-
unbranched amylose with only 1,4-glycosidic bond and branched
amylopectin with 1,4 and 1,6-glycosidic bond).
★ (cellulose is a polymer of beta glucose. Beta glucose molecules join by
I,4-glycosidic bond through condensation reaction. This forms a long
unbranched chain of beta glucose molecule-cellulose).
★ The GALP that enters cellular respiration is used to provide energy in the
form of ATP for the functions of the cells and for the active uptake of nitrates
and phosphates from the soil.
★ The compounds from the respiration pathways are used as the building
blocks of amino acid by combining with nitrates from the soil.
★ GALP may continue round the Calvin cycle and combine with phosphates
from the soil and form nucleic acids.
★ GALP is converted to glucose which again is converted to deoxyribose.
★ Glucose is used in respiration and provides energy in the form of ATP for
DNA synthesis or active transport of substances such as nitrates.
★ GALP is also used in the synthesis of bases such as adenine, thymine,
cytosine and guanine.
★ GALP also synthesises amino acids for enzymes involved in the synthesis of
DNA.

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 ★ Some of the GALP that enters the cellular respiration pathways is converted
into a chemical called acetyl coenzyme A.
★ This compound is then used to synthesise the fatty acids.
★ GALP is converted to glycerol. One molecule of glycerol joins with three
molecules of fatty acids by ester bond through condensation reaction and
form lipids.

GP to Strach

★ Using energy from ATP and hydrogen from NADPH, GP is converted to GALP.
★ Two molecules of GALP joined to form glucose, which is alpha glucose.
★ Starch is a polymer of alpha glucose and consists of two polymers amylose
and amylopectin.
★ Glycosidic bonds are formed between glucose molecules by condensation
reaction and form two polymers.
★ amylose is straight chained with only 1.4-glycosidic bonds and amylopectin is
branched with 1,4 and 1,6-glycosidic bonds.

GALP to Cellulose

★ Two molecules of GALP joined to form glucose, which is beta glucose.

★ Cellulose is a polymer of beta glucose.
★ Beta glucose molecules joined by 1,4-glycosidic bonds through condensation
reaction and form a long unbranched chain of glucose.

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GALP to Triglycerides/lipids

★ GALP is used to produce glucose which is a source of energy for lipid/

triglyceride synthesis.
★ GALP is used to make glycerol and GP is used to make fatty acids.
★ Three fatty acids and one glycerol joined by ester bonds through
condensation reaction and form triglyceride.
★ GALP is converted to amino acids which are used to synthesise enzymes.
★ These enzymes are involved in lipid synthesis

GALP to Protein

★ Two molecules of GALP joined to form glucose.

★ Amino acids are made from glucose and nitrates.
★ Proteins are formed by joining these amino acids by peptide bond through
condensation reaction.
★ Glucose is used in respiration to produce ATP for protein synthesis

GALP to DNA

★ GALP is converted to Glucose which is converted to deoxyribose.

★ Glucose is used in respiration to produce ATP which provides energy for the
active transport of substances such as nitrates and sulphates.
★ GALP is used in the synthesis of nitrogen bases using nitrates.
★ GALP also synthesises amino acids for enzymes involved in the synthesis of
DNA.
★ DNA is polynucleotide, where mononucleotide is made up of deoxyribose,
nitrogen base and phosphate group.
★ Mononucleotides joined together by phosphodiester bond through
condensation reaction and form polynucleotide.

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Factors Affecting The Rate Of photosynthesis
Mainly three factors which affect the rate of photosynthesis:

01.Light intensity
02. 𝐶𝑂 2
concentration

03.Temperature

Limiting factor: Among the factors that control the rate of photosynthesis, the
factor which is closest to its minimum.The rate is limited by that factor and only a
change in that factor changes the rate of photosynthesis.

Light intensity and rate of photosynthesis

★ At very low light intensity, the rate of photosynthesis is very low.
★ Further increase in light intensity increases the rate of photosynthesis until
light saturation is reached.
★ This is the maximum rate of photosynthesis.
★ Beyond this no change in rate of photosynthesis as high light intensity
destroys chloroplast.
★ Light is trapped by chlorophyll and excites high energy electrons.
★ Light splits water molecules to produce protons
★ Electrons and protons are involved in photophosphorylation

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The effect of reduced light levels on
the relative concentrations of GP,TP
and RuBP in the Calvin cycle

1. GP cannot be reduced to TP.

2. TP levels fall and GP accumulates.
3. If TP levels fall, RuBP cannot be
regenerated.

Temperature and rate of photosynthesis

★ Calvin cycle is temperature dependent as enzyme Rubisco is involved in it.

★ The minimum temperature for photosynthesis is 0°C.
★ The optimum temperature is 25°C.
★ The rate doubles for each rise of 10°C up to an optimum temperature.
★ KE of molecules increases so does effective collision between enzyme and
substrate
★ Above 25°C bonds in
enzymes are broken
down
★ Changes the shape of
the active site.

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Concentration of 𝐶𝑂 2
and rate of photosynthesis

★ Major limiting factor to photosynthesis.

★ Increasing concentration increases the rate of photosynthesis till a certain
level.
★ Further increase in 𝐶𝑂 2
will add no effect.

1. As the amount of carbon dioxide goes

up, so does the rate. The limiting
factor is carbon dioxide.
2. Here, increasing the amount of carbon
dioxide has no effect on the rate. Light
or warmth is now the limiting factor

The effect of changing the carbon dioxide concentration on the

Calvin cycle

If the concentration carbon dioxide

falls below 0.01%:

1. RuBP cannot accept it, and

accumulates.
2. GP cannot be made.
3. Therefore, TP cannot be made.

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Absorption and action spectra

Absorption spectrum:Graph showing the degree of absorbance of different

wavelengths of light by a pigment.

Action spectrum:Graph showing the effectiveness of different wavelengths of light

stimulating photosynthesis.

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Chromatography: Separating the pigments

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 ★ The pigments can be separated by chromatography using paper or silica gel.
★ Draw a pencil line about 25 ㎜ from the bottom edge.
★ Extract the pigments from a plant by grinding up the leaves with 10㎤
propanone and then filter it.
★ The extract should be as concentrated as possible.
★ Place one small drop of this extract in the centre of the pencil line and allow
to dry before adding another drop on top.
★ Build up a pigment spot that is as small as possible but dense enough that it
contains sufficient pigment.
★ Carefully pour the chromatography solvent into a boiling tube to a depth of
no more than 1 ㎝.
★ Suspend the chromatography paper inside the boiling tube by pinning it to
the underside of the bung.
★ The bottom of the paper should be dipped into the solvent but the pigment
spot must not be immersed in the solvent at any time.
★ The pigments travel up the solid medium at different speeds and are
separated.
★ The distance travelled by the solvent needs to be marked as soon as you
remove the paper or plate from the solvent bath (Several of the pigments
fade quickly in light so you may need to draw around the spot in pencil and
label it).
★ Once the pigments are separated, determine their Rf values and compare
them to the Rf values of known pigments in the same solvent (pigments can
have very different Rf values with different solvents).
★ The Rf value is the ratio of the distance travelled by the pigment to the
distance travelled by the solvent alone.
★ The Rf value is always between 0 and 1.

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 QUESTIONS
*With reference to the structures in a chloroplast, explain how the energy
from light is made available in ATP molecules for the synthesis of organic
materials. (6)

★ Stack of thylakoids present in grana.

★ Thylakoid membrane contains photosystems.
★ Chlorophyll molecule and accessory pigments in the photosystem absorb
light energy and electrons are excited from chlorophyll
★ These high energy electrons passed down through electron carrier and
undergo a series of redox reactions
★ While passing through the carriers energy level of electrons falls
+
★ The released energy is used by the proton pump to pump 𝐻 ions into the
thylakoid lumen from stroma.
+
★ Diffusion of 𝐻 ions from lumen to stroma activate ATP synthase to
phosphorylate ADP to form ATP
★ This is called photophosphorylation ;
★ Electrons from photolysis is used to replace those lost from PSII ;

Describe the structures in a chloroplast that are involved in the

light-dependent reactions of photosynthesis.

★ Chloroplast contain disc shaped structures called thylakoids ;

★ Thylakoids are made of membranes ;
★ These are arranged as stacks called grana
★ It contain pigment / chlorophyll
★ These pigments are arranged as photosystems

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Explain the role of light in the photosynthesis

★ Light results in excitation of electrons from chlorophyll / photosystems

★ This results in energy to generate in the form of ATP ;
★ Light is needed for breakdown of water (photolysis)
★ Electrons from photolysis replace electrons lost by chlorophyll /
photosystems
+
★ Photolysis produce 𝐻 ions / protons
+
★ Both ATP and reduced NADP / 𝐻 ions are needed in the light-independent
reaction / Calvin cycle to convert GP to GALP
★ ATP / reduced NADP / hydrogen ions used in production of GALP from GP .
★ Study well

Structures in a chloroplast that are involved in photophosphorylation

★ Grana present in the chloroplast

★ A granum is a stack of thylakoids and grana are connected by lamellae ;
★ Thylakoids contain electron carriers /chlorophyll / photosystems ;
★ Thylakoid membranes contain ATPase

Explain how oxygen is produced during the light-dependent reactions of

photosynthesis

★ By the photolysis of water using energy from light

Describe and explain how the products of the light dependent reaction are
involved in the production of glyceraldehyde-3-phosphate (GALP). (4)

★ In the light independent stage of photosynthesis, GP is reduced to GALP

using hydrogen from reduced NADP and energy from ATP. These ATP and
reduced NADP are the products of light dependent stage.

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One of the reactions of photosynthesis can be summarised as shown below.

Water → hydrogen ions + oxygen gas + electrons

(A) name the reaction shown.

★ Photolysis (of water) ;

(b) give one other factor, not shown above, that would be required for this
reaction to occur in a chloroplast.

★ Light / enzyme / chlorophyll /

Describe the role of the electrons in the light dependent reaction of

photosynthesis. (4)

★ Electrons passed to photosystems to replace electrons lost by chlorophyll.

★ Light energy promotes electrons to higher energy level and the electrons
emitted ;
★ High energy electrons carried through the electron transport chain.
★ Occurs as a series of redox reactions.
★ Energy released is used in ATP production ;
★ Electron is used in reduction of NADP / production of NADPH

Describe the role of the proteins in the thylakoid membrane in the formation
of ATP.

★ Electron carriers pump the hydrogen ions into the thylakoid space
★ ATPase channels allow hydrogen ions to pass through into stroma
★ Energy released from this movement of hydrogen ions results in
phosphorylation of ADP.

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GALP does not accumulate in a chloroplast during photosynthesis. Explain
how GALP is used following its production. (2)

10
★ is used for the regeneration of RuBP
12

★ Rest is used to form glucose and which is for starch / other organic chemical

The graph below shows the results of the investigationDescribe and suggest
an explanation for
the changes in the
concentrations of
RuBP and GP
shown in the
graph.

★ Both RuBP and GP levels constant until carbon dioxide lowered

★ RuBP and GP are produced in Calvin cycle ;
★ RuBP: At lower carbon dioxide levels the RuBP increases and drops and then
stays constant ;
★ Rises because being regenerated
★ Falls as being used to fix carbon dioxide ;
★ RuBP level remains constant once new equilibrium reached ;
★ GP: At lower carbon dioxide levels the GP drops and then stays constant
★ Drops because less carbon dioxide is available to convert into GP) / less
carbon fixation
★ Levels out at a lower level as carbon dioxide still available but at lower level;

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