Topic2 Full Handwritten Notes
Topic2 Full Handwritten Notes
A2 Biology ( 9700)
nov-2023
18/11/2023
Part 1
Introduction
Structure of chloroplast
Chloroplast pigments
Chromatography
Photosystems
1. chloroplast
A) double membrane ( envelope )
B) stroma …( loop of DNA ..genes …RUBISCO / ATP synthase
70 S ribosomes
Light independent reaction …RUBISCO ..Co2 fixation
C) granal membrane : L.S.A
ETC ….
ATP synthase
Photosystems ..light energy ..light dependent reaction
2. Light dependent :
Thylakoid
Water ….photolysis …..2e- + 2H+ + 1/2O2
3. Light independent
Stroma
CO2 ..ATP + NADPH….TP
6. Chromatography
7. Photosystem ( PSI / PSII)
Accessory pigments + primary pigment …light harvesting clusture
Photosynthesis Read
Way of nutrition
Heterotrophs Autotrophs
Feed on other living organisms to get their Organisms that make their own food
energy Autotrophic nutrition : involves the building
Heterotrophic nutrition : involves the break up organic complex compounds
down of organic matter into small soluble ones carbohydrates, lipids , proteins from
Example : animals, fungi, and some bacteria inorganic molecules ( CO2 and water ) using
energy from sun
Chemo autotrophs
Photo autotrophs
Stroma
Photosynthesis
Thylakoid
Light dependent reaction Light independent reaction
Thylakoid
Stroma
O2
H2O
Reduced NADP
2. Light independent ATP
stage
ATP and reduced Light independent stage
NADP ..reduce CO2 ..to Reduction of CO2
Triose phosphate
produce TP CO2
( TP )
6CO2 + 6H2O…………….C6H12O6 +6O2
Light dependent
• light independent In thylakoid
• Stroma H2O photolysis
• CO2 reduced Using light energy
using NADPH A) oxygen …an excretory waste producr
and ATP to B) 2e-… enter the ETC ..produce ATP
produce TP C) H+ ….to produce reduced NADP
Inter granal lamella Circular DNA
Structure of chloroplast
Granum
Thylakoid
Thylakoid
ATP synthase
Stroma Colorless fluid contain starch grains , lipid droplets , 70S ribosomes and circular DNA
Site of light independent reaction …..contain enzyme ( RUBISCO ) cataylse CO2 fixation
Stacks of Granal membrane provide large surface area for light absorption and
thylakoid photosynthetic pigments for light dependent stage .
( granum )
Granal membrane has many ATP synthase to form ATP by chemiosmosis in
light dependent stage
Has electron carriers for ETC
Circular loop of DNA Codes for proteins such as RUBISCO / ATP synthase
Chloroplast pigments
The photosynthetic pigments
Chlorophyll a………………..yellow green ………………..430, 662nm …………….absorb red and blue violet
Chlorophyll b ……………….blue green …………………..453, 642 nm ……………absorb red and blue violet
Carotenoids ……………….Orange ……………………….450 nm ……………………absorb blue violet light
Effectiveness
A) absorption
B) energy content
Absorption of different wave lengths of light Graph that shows the rate of photosynthesis at
by different photosynthetic pigments different wave lengths
How much each wave each wave is absorbed Show effectiveness of different wave lengths
which is related to their absorption and energy
The higher the absorption the higher rate of photosynthesis content , where the shorter wave length , the
greater the energy it contains
When white light is shone on a suspension of chloroplast made from leaf ….light in the regions blue
violet and red is absorbed and light in green region will be reflected , so leaves appear green …..as
they contain chlorophyll that reflects the green light
Chromatography
B) each photosystem
1. Has accessory pigments ( carotenoids + chlorophyll b)
They will absorb wave length not readily absorbed by chlorophyll a in
primary pigment ( reaction center ) ..pass the energy to reaction
center containing chlorophyll a molecules
In photosystem I and pHotosystem II ( PSI and PSII)
PSII
PSI
Accessory pigments.
Carotenoids , Chlorophyll b,
Has reaction
Reaction center
center light Has reaction center
Primary pigment ( pair of chlorophyll a).
absorption peak light absorption
700nm peak 680nm
Light dependent reaction
1. The accessory pigments absorb light of many wave length that are not readily
absorbed by primary center ( pair of chlorophyll a)
And the energy transferred to the pair of chlorophyll a molecules in reaction
center in PSI and PSII
PSI
PSII
5. Electrons from PSI , are used
2. Electrons become excited raised to higher energy level NADP , to produce reduced
Electrons are being emitted from primary pigments in reaction center NADP
3. The electrons are taken by electron acceptors and pass along ETC from one carrier to another .
ATP is synthesised : energy released by carrier molecules pump proton from stroma to the thylakoid space
Creating a proton gradient , where the thylakoid membrane is impermeable to the protons so , proton diffuse through
ATP synthase down their electrochemical gradient ……the enzyme will rotate and ATP is synthesised
….phosphorylation Of ADP .
4. The primary pigments in PSI receive replacement of electrons from PSII
The primary pigments in PSII receive replacement from photolysis of water using light energy .
PSI
PSI PSII
Photolysis https://youtu.be/SnnmmKApT-c
B) the protons combine with electrons from PSI and carrier molecule
NADP to give reduced NADP
Electron acceptor
Z Scheme
Electron acceptor
ΑDP + Pi 2H+
ATP
By chemiosmosis
2e-
NADPH
P700 NADP =
reduced
PSI NADP
Photolysis
P680
H2O
Pathway for the electron in non cyclic
2H+ + 2e- + 1/2O2 photophosphorylation .
Photosystem II Path way taken by electrons in cyclic
PSII photophosphorylation
Cyclic photophsophorylation Non cyclic photophsophorylation
Products
REDUCED NADP,
ATP
ATP . Oxygen
Mitochondria Chloroplast
Oxygen act as final electron acceptor NADP is the final acceptor for H+
and e-
Produce water
Makes reduced NADP
Important notice;
Accessory pigments:
Any photosynthetic pigment that absorbs light of many wavelengths not really absorbed
by primary pigment and the energy is transferred to the pair of chlorophyll a molecules
in the reaction centers of PSI and PSII.
Photophosphorylation
The process that takes place in photosynthesis to use light energy to drive the formation
of ATP.
Cyclic photophosphorylation:
r
Involves production of ATP without photolysis of water or production of reduced NADP.
ab
Electrons travel from PSI but instead of reaching NADP , they return to PSI.
Role of thylakoid:membrane .
In thylakoid (membrane )
Dr.Nihal Gabr 41
Light independent stage
1. CO2 diffuse down its down its concentration gradient into leaves through stomata , then diffuse
through air spaces pf spongy mesophyll, then dissolve in layer of water on the cell surface membrane ,
then diffuse through cell wall and cell membrane into cytosol and through chloroplast into STROMA
CO2 7
Unstable 6C intermediate CO2 react with ribulose bisphosphate
compound.
2
( RuBP) by entering active site of
Split
v RUBISCO ..resulting in the production
quesCarboxylation
3 GP (3C )
of unstable 6C compound .
Split into two 3C compound ( GP )
Substrate
RuBP Reduction
CO2 fixation
glycerate 3 phosphate
( 5C)
Reduced NADP ATP
3. Hydrogenation ( CO2 reduction )
Regeneration NADP ADP + Pi GP is reduced and
phosphorylated using ATP
TP (3C )
ADP + Pi and reduced NADP from light
dependent stage / reaction …
ATP Amino acids to produce TP ( triose
Glycerol
Acetyl Co A
4. Fate of TP
phosphate ) which 3C sugar
1. Mostly recycled / regenerate RuBP using ATP
2. Part is converted into glycerol to be added to fatty acids to make triglycerides …to form glucose
3. Converted into acetyl Co A for use respiration
4. Converted into amino acids and fatty acids
Stroma
RUBISCO
CO2 + RUBP ………………… Unstable 6C compound
Split
Unstable 6C compound ……………….2 GP
GP ……………………………..TP
Hydrogenation using NADPH
Phosphorylation using ATP
TP …………………………….RuBP
Regeneration using ATP
Importance / role of RUBISCO enzyme : How illumination of chloroplast leads to
optimum pH conditions for Rubisco
Responsible for the fixation of carbon dioxide -
I*
coupA*
Cataylse the reaction between RuBP and CO2 Stromahim RUBISCO
PA
To give two GP
Through unstable intermediate 6C compound
1. RUBISCO is found in the stroma where
Role of NADP in light independent stage the light independent stage takes place .
2. Excited electron leave chlorophyll a /
Hydrogen carrier ..donate the hydrogen atom ( H++ e-) photosystems
Reduce GP to TP 3. And pass through ETC
4. The protons present from photolysis ,
Role of ATP in light independent stage are pumped from the stroma into the
Supplies energy / phosphate thylakoid space
To convert GP to TP
TP regenerated into RuBP using ATP So protons leave the stroma causing the
ph to rise
How products of photophosphorylation are used in Calvin Cycle :
There are three environmental factors that have the most influence on the rate of photosynthesis.
Temperature
r
Influences the activity of enzymes, so an
ab
increase leads to an increase in enzyme activity
up to optimum temperature . Both light Temp …Rubisco ..Light
dependent and light independent stages independent.
lG
involves enzymes , but temperature has a much
greater effect on the light independent stage.
Optimum temperature of plants is 25°C . Rubisco
iha
Carbon dioxide concentration
Dr.Nihal Gabr 45
Light intensity ……….source of energy absorbed by chloroplast pigments in thylakoid and used in light
dependent reaction …..to produce ATP and reduced NADP
CO2 concentration………..raw material / substrate , where its used in light independent reaction for
CO2 fixation …optimum conc 0.1%
Temperature …… affects both light dependent and light independent stages as they both involves
enzymes ….but temperature has greater effect on light independent stage …RUBISCO ( 25 C)
A) at low light intensity…small or no effect ..as light intensity is a limiting factor …less ATP and
reduced NADP from light dependent stage
B) at high light intensity …increase in temperature will increase rate of photosynthesis …more kinetic
energy for RUBISCO and CO2 so more effective collisions and so more CO2 fixation .
Limiting factors
• An external environmental factor that is present in shortest Read
supply and limits the rate of reaction(photosynthesis).
Photosynthesis is affected by more than one limiting factor .
• The rate of the process at any given moment is not affected by a combination of all the factors , but
rather by just one- the one whose level is at the least favourable value.This factor is called the
limiting factor because it only limits the rate at which the process can take place .However much
the levels of the other factors change , they don’t alter the rate of the process.
Example of light intensity limiting the rate of
photosynthesis:
3
1. In complete darkness, it is the absence of light
alone that prevents photosynthesis occurring.
2. No matter how much we raise or lower the
temperature or change the concentration of
r
carbon dioxide, there will be no photosynthesis .
Light or rather the absence of it, is the factor
ab
determining the rate of photosynthesis at that
moment.
3. If we provide light ,however the rate of
photosynthesis will increase.
4. lG
As we add more light, the more the rate
increases.This doesn’t continue indefinitely,
however, because there comes a point at which
further increase in light intensity have no effect on
iha
the rate of photosynthesis. • By looking at graph 1, the rate of photosynthesis
5. At this point some other factor , such as the increases as the light intensity increases (0 to A). light
concentration of carbon dioxide, is in short supply intensity is the LIMITING FACTOR. Beyond point A,
and so limits the process. light intensity is no longer the LIMITING FACTOR
6. Carbon dioxide now is the limiting factor and only since the rate remains constant even though the light
.N
an increase in its level will increase the rate of intensity increases. So, we have to consider other
photosynthesis. factors that could cause the rate to become constant
7. Further increase in carbon dioxide concentration (A to B).
levels will fail to have any effect.
Dr
8. At this point a different factor ,e.g temperature is • Graph 2 shows that the rate does not increase so
the limiting factor and only an alteration in its level much despite the temperature being increased from
will affect the rate of photosynthesis. 20 to 30°C (with the carbon dioxide being kept
constant). This means that temperature is not the
actual LIMITING FACTOR. But if the conditions are
reversed, the temperature being constant and the
carbon dioxide being increased from 0.03% to 0.13%,
the rate increases (Look at graph 3). Both of these
indicate that carbon dioxide concentration is the
LIMITING FACTOR in A to B (Graph 1).
Dr.Nihal Gabr 46
A: on increasing carbon dioxide concentration, rate of
~
photosynthesis increases steeply , as carbon dioxide is
O a rate limiting factor , where most Rubisco active sites
are free so more chance of effective collision and more
Carbon dioxide fixation.
r
concentration is no more a limiting factor, another
Substrate conc is limiting.
ab
limiting factor has been introduced , which is Rubisco
concentration , as all enzyme active sites are occupied
with substrate (carbon dioxide so Rubisco is working at
maximum capacity (v max.)
lG
• As light intensity increased, the volume of
iha
oxygen produced and carbon dioxide
absorbed due to photosynthesis will increase
to a point at which exactly balanced by the
oxygen absorbed and carbon dioxide
·
.N
t
increase in light intensity will have no effect
on photosynthesis . At this point some other
factor such as carbon dioxide concentration
or temperature is limiting the reaction .
Higher respiration than photosynthesis
So over all there is a net production of CO2
Little photosynthesis is taking place
Dr.Nihal Gabr 47 Due to low light intensity
7 Growing plants in protected environments
• Farmers and growers of protected crop (e.g tomatoes , lettuce and
cucumber) in temperate countries have fully automated
glasshouses with Sensore and computerised systems that maintain
suitable conditions for high rates of photosynthesis .
• These systems: Study
Control light intensity using artificial lighting and shading .
Control temperature with heaters and ventilation.
Enrich the carbon dioxide concentration of the air by burning hydrocarbons (e.g propane) or using
tanks of liquids carbon dioxide .
Temperature and Carbon dioxide regulated digitally through monitor to give optimum conditions for
r
maximum rate of photosynthesis.
ab
Supply water directly to the roots.
Use humidifiers to maintain a humidity appropriate for the crop.
Supply mineral nutrients directly( fertilisers or manure) to roots at the concentrations appropriate to the
•
growth stage of the crop.
lG
In the tropics, growers use plastic and mesh greenhouses to control the climate. Plastic protects
against heavy rain and the mesh provides protection against high light intensities and intense heat so
that salad crops are not scorched . Drip irrigation is used to reduce watering costs as water is supplied
iha
directly to the plants.
• Growing crops in protected environments has the added advantage of making it relatively easier to
control pests and diseases compared with field crops.
8
.N
C3 and C4 plants
1/
• In the lightindependent stage of photosynthesis, carbon dioxide combines with RuBP to form a six
carbon compound, which immediately splits to form two three carbon molecules GP ....these
Dr
plants are called C3 plants( plants producing C3 compounds in the reaction to fix carbon
dioxide , these are more common in temperate climate) Rubisco favors the reaction
Oxygen competes with carbon dioxide for rubisco’s active site . with oxygen )
When this happens , rubisco catalyses a different reaction (photorespiration) that
"
produces only one molecule of GP and a 2C compound.....this reaction reduce
⑦ ooo
÷÷÷÷s
efficiency of photosynthesis by reducing efficiency of rubisco considerably.
This happens most readily in high temperatures and high light intensity.
• However, maize and sorghum plants-and most other tropical grasses- do something different . et
They have evolved a method of avoiding photorespiration. The first compound that is produced in
the light dependent reaction contains four carbon atoms.....so called C4 plants.
d
in
Dr.Nihal Gabr 48
Photosynthesis
1. Structure of chloroplast
Stroma; Site of light independent reaction …containing enzyme ( RUBISCO ) catalyse
CO2 fixation.
Thylakoids / grana : Granal membrane provides large surface area for light ENERGY
absorption and photosynthestic pigements of light dependent stage .
Granal membrane has many ATP synthase to form ATP by chemiosmosis in
dependent stage .
Has electron carriers to make ETC
Loop of DNA : Codes for proteins such as Rubisco / ATP synthase
2. Chloroplast pigments
5. Steps of chromatography
1. Mixture of pigments is concentrated in a spot at one end of paper strip .
Then dry and repeat
2. Then dipped in a solvent which moves up by capillarity .
3. Measure the distance travelled by the pigment , and the distance travelled by
the solvent
Then divide: distance travelled by the pigment spot by the distance travelled by
the solvent .
Calculate the Rf value
Compare the results with known Rf values to be able to identify pigment.
2. The energy excite the the electrons in pair of chlorophyll a …and the electrons
are taken up by electron acceptors ( carriers )
Taking two pathways through ETC .
Cyclic photophosphorylation
1. CO2 fixation
2. CO2 reduction
3. TP
1. Mostly recycled / regenerate RuBP using ATP
2. Part is converted into glycerol to be added to fatty acids to make triglycerides
3. Converted into acetyl Co A for use respiration
4. Converted into amino acids and fatty acids
4. Role of RuBISCO ….
5. Role of reduced NADP in light independent stage
6. Role of ATP in light independent stage
7. How illumination of chloroplast leads to optimum pH conditions for
RuBISCO enzyme ?
- RUBISCO is found in the stroma ….site of light independent reaction
- electrons excited from pair of chlorophyll a in PSII
- and pass along the ETC
- the protons ( photolysis of water ) are pumped into the thylakoid.
- so protons leaving the stroma raise pH