Photosynthesis & ATP synthesis

Heterotroph: Organisms which feed on organic matter (mammals)

Autotroph: Organisms which make food using inorganic matter (plants)
Respiration: Process of converting inorganic matter into energy

CO2 diffusion: Stomata ------> Air spaces ------> mesophll ------> chlorophyll

(Contains Chlorophyll)

Leaf necessities:
1. Contain chlorophyll and other pigments arranged to absorb light
2. Be able to absorb CO2 and dispose of oxygen
3. Have decent water supply
4. Be able to transport manufactured carbohydrates to the rest of the plant
Large surface area and thinness allow for maximum light absorption

The upper epidermis has thin flat transparent cells which secrete a waxy
transparent cuticle that prevents water loss.
(The lower epidermis contains more stomata since they don’t directly face the
sun; Upper has less to avoid excess water loss.)

Stomata (pores) regulate diffusion of gases. They are

surrounded by 2 guard cells that regulate the rate of
transpiration by swelling up and spreading out when
turgid and absorbing water, allowing gases to diffuse
through stomata, then, shrinking and closing up when
flaccid as it releases water.

A decrease in water potential is needed for more water to be absorbed; this is achieved by
removing hydrogen ions using energy from ATP and the addition of potassium ions using indirect
active transport.

Palisade cell light adaptation:

1. Long & cylinderal position 90* from epidermis
2. Large vacuole restricts chloroplasts to edges
3. Proteins in cytoplasm can move chloroplasts to
absorb enough light or protect against excessive sun
(Palisade cell)
[Photosynthesis only occues in spongy
Palisade cell gaseous exchange adaptation
mesophll during high light intensities since
1. Long narrow air spaces providing surface area their air spaces provide a large surface area
2. Thin cell walls containing moist cell walls ]
Chlorophyll structure and function

Also contain ribosomes and dna

Starch grains store carbohydrates

The membrane contains chlorophyll (type a & b) which is a pigment that absorbs
certain wavelengths (colours) of light (unabsorbed colours are reflected and seen)
NB: Chlorophyll A absorbs slightly longer wavelengths than B.

Carotenoids such as carotene and xanthophlls are pigments that absorb shorter
wavelengths but aren’t completely necessary.
 Light dependant stage

Location: Thylakoids in chloroplasts

-these thylakoids contain phoyosystems (chlorophyll cluster) which absorb and
transfer light to form ATP

Photophosphorylation: photo (using light) phosphorylation (phosphate addition)

Cyclic photophosphorylation

-Only Ps1 is used

- No NADPH formed

1. Light is absorbed
2. Electron gains energy and moves
across carriers
3. Energy is used to form ATP
4. Electron returns and cycle repeats
ADP: Adenosine diphosphate
ATP: Adenosine triphosphate
680nm : PSII
I700nm : PSI
 Non- cyclic photophosphorylation
(Z scheme)
-PSI & PSII
- forms NADPH

1. Cyclic photophosphorylation
2. Electron go to PSI
3. Energy is used to form NADPH
(photolysis)
Background: H2O splits: “O” is disposed, H+ reacts with NADP & E- entered PS

Light Independent stage (dark)

Location: stroma of chloroplasts

- it contains the enzyme Rubisco (Ribulose bisphosphate carboxylase) which catalyzes the
combination reaction between CO2 & RuBP (Ribulose bisphosphate)

ATP & NADPH are used in this process to produce carbohydrates (glucose etc)
1. 6RuBP (5C) + 6CO2= 6C (unstable) which
then splits into (12) 3C GP/ PGA
(6C split into 2- 3Cs) (phosphosglycerate)
(GP/ PGA)

2. 12 ATP gives a phosphate to 12 GP (3C)

forming 12/TP (3C) and NADPH2 is oxidized.

3. 5/6 of TP rearranges to regenerate RUBP

83%
by 6 ATP giving phosphates, 1/6 form glucose
(Sugar)
Ribulose-5-phosphate 1,3- biphosphoglycerate
Factors affecting rate of photosynthesis

A limiting factor is what limits the rate of reaction during Photosynthesis. If enough
isn't supplied to the plant the rate would increase .

Light intensity
-Light provides energy for the light dependant reaction. (Doesn't affect LIDS)
-increased light = increased rate
-too much light = optimum rate (light saturation)

Carbon dioxide concentration

-Air= 0.04% CO2
-Absorbed through stomata
-The diffusion gradient keeps gases moving in as the [inside] < [
outside]

Temperature
-Mainly affects light independant stage since enzymes are present & denature
exceeding optimum temp (Doesn't affect LDS)
Photorespiration: Rubisco catalyzes a reaction bonding O2 to RuBP instead of
CO2 if the temperature is too high
-Affects kinetic energy, higher temp = more motion & collisions = increased rate

Quanitiy of chlorophll
-More chlorophyll = more absorbtion of light energy
-Lack of nutrients, disease and environmental stress cause damage to
chloroplasts, resulting in decrease in chlorophyll
Light effect on Calvin cycle
- Light isn't needed, but the products (ATP & NaDP) from photophosprylation are
-When light isn't supplied, ATP & NADPH is no longer given to the calvin cyle
-ATP & NADP are used as fuel for the conversion of GP (PGA) to TP
- GP piles up and the process continues till TP is used up
 Respiration & ATP synthesis
Active transport: moving substances against concentration gradient (requires energy)

ATP: Adenosine Triphosphate, ADP: Adenosine Diphosphate (energy currency)

Hydrolysis: When ATP loses a phosphate, 30.5kJ of energy is released.

(This is catalyzed by the enzyme ATPases)
Glycolysis (breaking glucose apart)

Location: cytoplasm

1. Phosphorylation (glucose -------> glucose-6-phosphate)

2. Isomerisation (glucose-6-phosphate -------> fructose-6-phosphate)
3. Phosphorylation (fructose-6-phosphate --------> fructose biphosphate)
4. Lysis (fructose biphosphate -------> Dihydroxyacetone phosphate & Glyceradehyde phosphate
5. Oxidation, loss of H (NAD ------> NADH)
6. Phosphorylation (Glyceradehyde phosphate -------> Glyceradehyde biphosphate)
7. Dephosphorylation (Glyceradehyde biphosphate -------> 3-phosphosglycerate
8. Isomerisation ( 3-phosphosglycerate ------> 2-phosphosglycerate)
9. Dephosphorylation (2-phosphosglycerate -------> pyruvate)
Mitochondria

Link reaction: Oxidative Decarbonization

Pyruvate enters mitochondria once O2 is available to continue aerobic respiration
1. Decarbonization & Dehydrogenation of pyruvate: "C" excreted, "H" reduces
(NAD-------> NADH)
2. Combination of Coenzyme A (CoA) forming acetyl CoA
Krebs Cycle

Location: matrix of mitrondria

-Produces ATP, CO2, FADH2 NADH2

1. Carboxylation (oxaloacetate (4C) + acetyl CoA (2C) -------> citrate (6C)

2. Isomerisation (citrate ------> Isocitrate)
3. Oxidatative Decarboxylation (Isocitrate (6C)------> alpha ketoglutarate (5C)
4. Oxidatative Decarboxylation (alpha ketoglutarate (5C) -------> succinate (4C)
5. Oxidation (succinate (4C) ------->fumerate (4C) (2FAD------>FADH2)
6. Isomerisation (fumerate (4C) -------> malate (4C) (in the presence of water)
7. Oxidation (malate (4C) -------> oxaloacetate (4C) (NAD-----> NADH2)
Oxidative decarboxylation forms (2NAD -------> 2NADH2, 2CO2)

(Inorganic phosphates (Pi)

flow freely in the cytoplasm)

X2
2
Electron transport chain: Oxidative Phosphorylation

Location: Inner membrane (cristae) of Mirochondria

-Contains complex molecule, proteins and cytochromes known as electron carries
- NADH and FADH2 from Krebs cycle are oxidized in this process
- Once oxidized, NAD and FAD return to the Krebs cycle to be reused
- ATP Synathases & Complexes 1, 3 & 4: intrinsic proteins, Complex 2: extrinsic
- Coenzyme Q & cytochrome C: transfer molecules

1. Oxidation: NADH donates electron to EC1 and H+ moves to intermembrane

2. Transportation: Electron goes to CoQ
3. Oxidation: FADH donates electron to EC2 then sends it to CoQ
4. Transportation: Electron moves from CoQ to EC3 & H+ moves to intermembrane
5. Transportation: Electron moves to Cyt C, then EC4 & H+ moves to intermembrane
6. H2O Formation: Electron moves to oxygen which splits to form 2H2O
7. Chemiosomosis: H+ moves down ATP synthase catalyzing formation of ATP
8. Cycle repeats

4H= 1 ATP
Oxygen has 6 v.e therefore if you add to that it'll gain a full
she'll and no longer be reactive
Therefore an O ion / 1/2O is used so it wouldn't lose reactivity
 Aerobic Respiration (Presence of air)

{
Glucose
Glycolysis in cytoplasm

{
Pyruvate
Link reaction in matrix

Acetyl CoA

Matrix
{ Krebs Cycle

Electron transport chain NaDPH2 & FADH2 --------> ATP

Structure and function of mitochondria

Shape, size and quantity of mitochondria in a cell depends on cell activity/ purpose
Anaerobic Respiration/ Lactic fermentation
Location: cytoplasm in absence of oxygen
Amount of ATP formed: 2

Pyruvate + NADH ------> lactate + NAD

-Lactate produces in muscle cells during excersise since more O2 is needed, it

diffuses into blood to be carried around the body.
-High lactate concentration affects the brain & causes disorientation & nausea
- Too much lactate stops muscle contraction

- Hepatocytes (liver cells) absorb lactate and convert it to pyruvate.

-Removal of lactate by hepatocytes requires oxygen (why athletes breathe so hard
after excersice to provide extra oxygen to cells)
-Extra oxygen needed: oxygen debt

Lactic fermentation Fermentation in yeast

Uses of Anaerobic Respiration

-Yeast fermentation: Alcohol, rum (sucrose) , wine (grapes) , beer (starch from
barley grain broken into maltose), yogurt (lactic fermentation of milk)
Respiratory substrate
Substance used to make ATP
-Carbohydrates & proteins: 17kJg of energy
- Lipids 39kJg of energy
-Molecules with more H release more energy since it's stored in the e- of H
-Red blood and brain cells entirely depend on glucose as a substrate

Measuring rate of Aerobic Respiration

-Uses O2 to make CO2
-If a respiring organism is placed in a closed system and CO2 is removed, volume
of gas will reduce as O2 is used up.
-CO2 is removed with soda lime / KOH
-Water baths are used to maintain temperature

-gas volumes are sensitive to temp and pressure, ensure to maintain it for
accurate results
-
 Energy flow and Nutrient Cycling

Terms
- Ecology: study of interactions of organisms in an environment
- Abiotic: Non-living, Biotic: Living
- Fauna: Animals
- Flora: Plants
- Habitat: Area organisms live
- Species: Organisms capable of interbreeding with one another, have similar
characteristics and have fertile offspring
- Population: Members of same species living in a habitat
- Community: Different species living in a habitat
- Ecosystem: A natural unit of living and non living organisms through which energy
flows in a Nutrient cycle
- Niche: role of an organism in an ecosystem
-Trophic level: Feeding level
- Food chain: linear feeding relationship/ transfer of energy
- Food web: Combined food chain
- Biomass: Total mass of organisms of a species living in an area of the environment

NB: Only 10% of energy is passed up each Trophic level

Types of coral
Light absorption loss
-sunlight not hitting leaves
-sunlight being reflected from leaf surface
-sunlight passing through leaves but missing chlorophyll
-some wavelengths not being absorbed
-energy loss during reactions of photosynthesis

Energy loss
-not all parts of plant consumed
-not all plant material is digested, remaining material is excreted for decomposers
-energy lost through heat

Productivity
-Rate at which plants convert light to chemical potential energy
-Units: kJm-2year-1 (kilojoules of energy transfered per square meter per year)
-Gross primary productivity (GPP): Total energy transfered
-Net primary productivity (NPP): Energy remaining after respiration
-Primary productivity is used only for producers however GPP & NPP is for all
-All energy is recycled in an ecosystem, dead cells are broken down into inorganic
materials by decomposers
Nitrogen cycle

-Nitrogen exists as a triple bonded molecule making it unreactive and unusable.

-It must be converted to ammonia (NH3) or nitrate (NO3) (nitrogen fixation)

Nitrogen fixation (organisms)

-Only prokaryotes and archeans are capable of nitrogen fixation eg. Rhizobium
(This bacteria is found in nodules of plant roots sharing a mutualist relationship. During
germination, lectin (protein) is produced binding to polysaccharides on the surface of
Rhizobium. The bacteria invades and spreads along the root hairs causing cells to separate
forming nodules (lumps) for bacteria to live)

Nitrogenase catalyzes conversion of Nitrogen (N2) to Ammonium ions (NH4+)

-Hydrogen (from NADPH)
-ATP (from metabolism of sucrose during photosynthesis )
- Absence of oxygen (leghaemoglobin protein absorbing oxygen)
-Nitrogen fixation (atmosphere): lightning providing energy to form (NO3) which is
dissolved in rain and carried to the ground
-Nitrogen fixation (Haber process): In the production of fertilizer, ammonia is
produced and often converted to ammonium nitrate for fertilizer (cheaper)

-Use of Nitrogen by plants: Amino acids & proteins

-Digestion of nitrogen by animals: Proteins are broken down to amino acids,
absorbed into the blood and distrubuted to the body then built into proteins again.
Excess amino acids are deaminated in the liver and nitrogen is excreted in urea

Return of nitrate to soil from living organisms

-Decomposers break down proteins from dead animals/plants into amino acids
using protease. Some are used for growth of Decomposers while others are broken
down to release nitrogen as ammonia (Ammonification)
-This ammonia is rapidly converted to nitrite and nitrate ions (NO2- & NO3-) by
nitrifying bacteria (nitrosomonas & nitrobacter) which get energy from nitrification

Denitrification
Denitrifying bacteria get energy by reversing nitrogen fixation by converting nitrate
to nitrogen gas which is returned to the air. Common in sewage treatment plants,
compost heaps and wet soils.
 Ecological systems, biodiversity & Conservation

Biotic factors: Living

-Feeding (herbivore eats plants)
-Predation (predator kills prey)
-Parasatism (parasyte harming host) (isopods on fish skin)
-Mutalism ( associated organisms benefiting from each other)
-Commensualism (associated organisms neither harming nor benefiting)
-Competition (organisms fighting over organism in short supply)

Abiotic factors: Non-living

-Temperature (too high cause coral bleaching and oxygen solubility)
-Light intensity
-O2 concentration
-CO2 concentration (too high lowers pH, acidification)
-Water supply
-pH of water & soil
-Availability of inorganic ions (nitrate/potassium)
-Humidity
-Wind speed
-Wave action (coral reefs can be damaged due to harsh winds)
Biodiversity

-Species diversity: Number of different species in an ecosystem, quadrat/ habitat

(Habitats further from the tropics contain less species diversity since the tropics
have higher temperatures allowing for faster metabolism, all regions of the world
contain "Hotspots" where diversity is more prominent)

Plant species diversity is affected by:

⁃ Solar radiation
⁃ Rate of water loss
⁃ Humidity
⁃ Temperature

Limitations of species diversity

⁃ presence / absence of a species does not determine ecological health (does
not describe genetic diversity )
⁃ Low abundance of a species can cause extinction in that area

-Genetic diversity: Inherited species variation

(species with low genetic diversity are less likely to survive in a changing
environment)
-Genetic diversity is proportional with population size
-large population size= more genetic diversity and vice versa.

-Ecosystem diversity: Number of ecosystems

(more ecosystems give rise to more species diversity)
Ecosystem stability
Ecosystems with complex food webs with high biodiversity are more stable.

Endemic species: Found in only 1 county [Link] devil in Australia

Importance of diversity maintenance:

-maintain stability of ecosystem (can prevent climate change
-Species that can be used for medicinal purposes can be lost (over 7000 drugs
are derived from plants)
-Ecotourism: tourists observe biodiversity of a country

Conservation:
Protection of species, habitats and ecosystems to maintain biodiversity
-Situ conservation: in habitat (protection from erosion, deforestation, desertification,
sea acidification, pollution, farming etc.)
-Ex Situ conservation: out habitat ( parks, wildlife/ nature reserves, zoos, botanic
gardens, seed/embryo banks etc.)

Loss of rainforests
Deforestation is used to create plantations of rubber or oil palm, charcoal production
and subsistence farming. This leads to soil erosion leading to the land becoming
permanently degraded. When habitats are lost it may be hard for organisms to find
a new one exactly the same since they all differ in some way. In poorer areas, slash
and burn is used where an area is cleared and burned to release nutrients, if done
excessively can cause permemant damage.
Rainforests retains water in soil and when it's cleared the water runs off into rivers and streams which makes rainforests
viable for drinking water. The pressure for short-term financial gain is what pushes deforestation to continue, meaning the
government should place policies to permit this in order to conserve.
 Transport in plants

Requirements: CO2, Oxygen, Organic nutrients, Inorganic ions and water

Uptake of ions:
Inorganic ions are absorbed from between soil particles through root hairs then
transported to the xylem to be carried to parts of the plant.

Facilitated diffusion: Higher concentration of ions in the soil than in the root hair cell
Active transport: Lower concentration of ions in the soil than in the root hair cell
(energy required)

Osomosis
Movement of water through a selectively permeable membrane from high to low
concentration/potential (less negative to more negative)

Water Transport in Xylem

1. The thin layer of water covering each soil particle is absorbed by root hairs.
2. Water passively travels from the epidermis, to the cortex then to the stele
Routes:
Aploplast: Cell wall to Cell wall
Symplast: Cytoplasm through plasmodesmata
Vacuolar: Vacuole using cytoplasm and plasmodesmata
(A band of waterproof suberin that forces water through
the selectively permeable membrane to the cytoplasm)

(Vacuolar)

3. Water is actively transported through the endodermis, pericycle then xylem

Xylem vessels are made up of stacked xylem
"element". Patterns are formed by lignin
(waterproof ) which eventually kills the element as it
ages. Water is moved through the spaces/ pits of
the lignin. (Lignin keeps water within and supports
the cell)

Mechanisms of mass flow:

Capillarity: Cohesion & Adhesion
-Cohesion: Hydrogen bonds connect H2O
-Adhesion: H2O sticking to xylem vessels for
Transpiration
Water leaves xylem through a "pit" then moves to cell wall and is evaporated forming
water vapour which diffuses into the air spaces in spongy mesophyll. When the water
potential is lower in the atmosphere, a gradient forms causing vapour to the diffuse
out the leaf through the stomata.
As water evaporates from the cell walls, it's replaced by osomosis forming a
transpiration pull using Cohesion and Adhesion. (Continuous water movement is
known as the transpiration stream).

(Root pressure is osmotic/hydrostatic pressure that builds up in roots due to water

potential gradient to send water up the xylem)

Factors affecting transpiration:

-Humidity: Low atmospheric humidity = High transpiration rate
-Temperature: Increase in temp = Increase in evaporation & transpiration
-Light intensity: Stomata close at night (small aperture) reducing transpiration
-Air movements: Winds push humid air, increasing transpiration
-Plant structure & leaf anatomy: larger leaf= larger surface area
Translocation: Food Transport in Phloem
Assimilates: Substances being transported which are made by the plant (sucrose)
Symport: different substances moving in the same direction
Antiport: different substances moving in different directions

1. H+ diffuses into the mesophyll from the companion cell then back to the
companion cell with sucrose ([H+] < in companion cell while [sucrose] is = in both
which is why H+ is needed in order to pass sucrose since there is no gradient )

2. Sucrose and H+ diffuse into the sieve element through the plasmodesmata by
from the companion cell

3. Sucrose then diffuses out the phloem into the "sink" (eg. Roots)

4. Sucrose is converted to glucose/ fructose by "invertase" and used for

respiration or stored as starch.

5. Water returns to the xylem once the food reaches the sink since it's just a
carrier and the water potential gets less negative as the food is diffused to the sink
 The Circulatory System

Blood:
The body & blood contains:
-approximately 5dm3 of blood weighing 5kg
-Plasma & plasma proteins
-Erythrocytes: red blood cells (2.5 x 1013)
-Leucosytes: white blood cells (5 x 1011)
-Platelets (6 x 1012)

Erythrocytes (Red blood cells)

- Pigment: Haemoglobin (Hb): Globular protein
- Function: transporting O2 & CO2 between lungs and respiratory tissue
-Very small (7um): close to membrane allowing easy exchange
- Diconcave disc allowing larger surface area to volume ratio & fast diffusion
- No nucleus, mitochondria or reticulum, leaving more space for haemoglobin

Role of Haemoglobin
- Each Haemoglobin can bind to 8 oxygen atoms forming oxyhaemoglobin.
- When O2 is in [high], Haemoglobin combines then releases it in places with [low]

Oxygen-Haemoglobin dissolution curve

- Partial pressure: availability/ concentration of O2
- Saturation: amount of oxygen bound to blood
- Greater partial pressure = greater saturation
 Allosteric Effect: An empty Haemoglobin is tense, hence
why it is harder for the first oxygen to bind. However, Hb
begins to relax as more O2 is added, increasing affinity.
In the lungs where partial pressure is high, most Hb
molecules are fully saturated, however in respiring tissue
where partial pressure is low, Hb loses O2. (The last O2 is
only given in high demand )

Arteries: Away from heart (oxygenenated)

- Blood doesn't move slowly, but in surges (pulse) which correspond to heart beat
-As the heart's ventricles relax and blood pressure decreases, arteries recoil
inwards to give blood a little "push"
- When the ventricles contract, Arteries widen to lower blood pressure

Veins: To heart (deoxygenated)

- For blood to move to the heart, valves prevent backflow

Capillaries:
- Form networks (beds) around every tissue (except cornea & cartilage)
-Their size and thin walls allow rapid transfer of substances and allows blood to
get as close as possible to cells
The Heart

Vena cava Aorta

Pulmonary artery

Pulmonary vein

(Left)
(Right)
Pulmonary vein

Vena Cava
Aorta

Oxygenated blood: Pulmonary vein -------> Aorta

Deoxygenated blood: Vena Cava -------> Pulmonary artery