BIOLOGY A - (3.5.1 - 3.5.4) ENERGY TRANSFERS BETWEEN ORGANISMS

3.5.1 PHOTOSYNTHESIS

3.5.1 PHOTOSYNTHESIS

Name the 2 stages in photosynthesis

1. LDR - Light dependent reaction

2. LIR - Light independent reaction

Where do both reactions occur

In chloroplasts

Where does LDR occur within chloroplast

Thylakoid membranes

Where does the LIR occur within a chloroplast

The stroma

What does the LDR create that is essential for use in the LIR

ATP and reduced NADP

What are the 4 main stages of the LDR

1. Photoionisation of chlorophyll

2. Photolysis

3. Chemiosmosis

4. Production of ATP and reduced NADP

What happens during the photoionisation of chlorophyll

Light energy absorbed by Chlorophyll

Absorbed energy results in electrons becoming excited and raising an energy shell to leave (break free) of the chlorophyll

Therefore what has happened to the chlorophyll and what are some of the released electrons used for

It has been ionised

Released electrons used to make ATP and reduced NADP in chemiosmosis

What are the stages in photolysis (light energy splitting water)

Water is split to release oxygen, hydrogen ions and electrons

The electrons are passed along a chain of electron carrier proteins

The hydrogen ions (protons) are accepted by NADP to make it reduced NADP (NADPH)

The oxygen is either used for respiration or diffuses out of the leaf via stomata

What does Photolysis split one molecule of H₂ O into

½ O₂ + 2e^- + 2H⁺

What happens during chemiosmosis Pt 1 (Up to the movement of protons into thylakoid lumen)

Electrons that gained energy + left chlorophyll move along electron carrier proteins embedded in Thylakoid membrane

The series of proteins that carry electrons embedded in membrane are called electron transfer chain

The electrons release energy at each protein

That energy is used to pump protons across thylakoid membrane (protons also received from photolysis of water)

This results in higher concentration of protons in the thylakoid membrane

What happens during chemiosmosis Pt 2

Due to protons being in higher concentration on inside of lumen, they diffuse out via facillitated diffusion through ATP synthase protein (enzyme)

The ATP synthase uses proton chain to catalyse reaction of ADP + Pi to make ATP

Some protons that travel across thylakoid membrane are recycled into process again

Others are picked up by NADP as well as 2 electrons to form NADPH

Why is chemiosmosis known as such

Because H⁺ ions move down conc gradient from higher to lower conc

What is the LIR also known as

The Calvin cycle

Where does the calvin cycle occur

In the stroma

What enzyme does the stroma contain

RuBisCo

Why is this stage temperature sensitive

Because it involves enzymes which can denature

What 3 ingredients does the Calvin cycle use

CO₂

reduced NADP (NADPH)

ATP

What does 6 turns of Calvin cycle result in

Synthesis of hexose sugar (Glucose)

What are the 3 stages in the Calvin cycle

Fixation

Reduction

Regeneration

What is TP the general term for

Any 3 carbon sugar with a phosphate attached to it

What is G-3P

A specific 3 - carbon sugar molecule with a phosphate group

Go over the CALVIN CYCLE DIAGRAM FROM COGNITO MENTALLY

Go over the CALVIN CYCLE DIAGRAM FROM COGNITO MENTALLY

Explain what happens during carbon fixation

CO₂ reacts with (5C) compound RuBP (using enzyme RuBisCo) to form unstable (6C) compound

This (6C) compiund splits into 2 x GP molecules

Explain what happens during the reduction (of GP)

GP reduced into triose phosphate (TP)

This uses energy from the hydrolysis of ATP

This also requires protons and electrons from NADPH (reduced NADP)

The resulting NADP is returned to the LDR to be reduced again

Explain what happens during regeneration (of RuBP)

Most TP is used to regnerate RuBP using ATP

The rest of the TP (1/6 Carbon atoms) can be used to make useful organic substances

This means that 6 turns of the calvin cycle are required to produce one molecule of a hexose sugar such as glucose

What are the 3 limiting factors of photosynthesis

Temperature

Light intensity

CO₂ Concentration

What does it mean when the graph for a specific limiting factor of photosynthesis plateaus

That another of the 3 limiting factors has become the limiting factor

What 3 techniques do agricultural practices use to help stimulate maximum rate of photpsynthesis

Artifical lighting

Heating

Paraffin burners (to release more CO₂ )

What must farmers consider when deciding the extent to which each technique is used

The cost effectiveness

3.5.2 RESPIRATION

3.5.2 RESPIRATION

What are the 4 main steps in Aerobic respiration and where do they occur

Glycolysis (Cytoplasm)

Link Reaction (Mitochondrial matrix)

Krebs cycle (Mitochondrial matrix)

Oxidative phosphorylation (Mitochondrial cristae)

What does respiration produce

ATP

What is the first stage in AEROBIC and ANAEROBIC respiration

Glycolysis

What are the 3 main steps of Glycolysis

1. Phosphorylating glucose to glucose phosphate (using ATP)

2. Production of triose phosphate

3. Oxidation of triose phosphate to produce pyruvate with a net gain gain of ATP and reduced NAD

How is NAD different to NADP

NADP simply contains one extra phosphate group

What type of reactions does NAD usually work in

Catabolic (breaking down) reactions

What type of reactions does NADP usually work in

Anabolic (building up) reactions such as LDR

What are NADP and NAD both

Coenzymes or “helper molecules”

What happens when phosphorylating glucose using ATP

The energy that was locked up in the ATP bond is transferred to new molecule so glucose phosphate = a high energy and highly reactive

Why do the 2 TP molecules end up with 4 phosphates (2 EACH) altogether rather than one after glucose phoshpate splits

Because a free floating inorganic phosphate from the cell’s cytoplasm attaches to each TP molecule on top of the one that is already there

Explain the oxidation process of Triose phosphate to produce pyruvate and how we end up with a net gain of ATP and reduced NAD (NADH)

Each triose phosphate molecule loses hydrogen atoms. The helper molecule NAD grabs these hydrogens and turns into reduced NAD (NADH)

Phosphate groups are handled and released from the carbon chain

The removed phosphate groups attach to ADP (adenosine diphosphate) to create ATP

Due to 4 phosphates provided from the 2 TP molecules, 4 ADPs are able to be transformed into 4 ATPs leading to a net gain of 2 ATP molecules from the start of the process

What are the 4 main stages of aerobic respiration

Glycolysis (In cytoplasm)

Link reaction (In mitochondrial matrix)

Krebs cycle (In mitochondrial matrix)

Oxidative phosphorylation (Cristae or mitochondrial inner membrane)

What happens to the products of glycolysis (Pyruvate and NADH)

They are actively transported from the cytoplasm into the mitochondrial matrix

What is NADH used for

It isn’t used in any of steps before oxidative phosphorylation

There, it will release its electrons

Most NADH is used in oxidative phosphorylation

Give difference between pyruvic acid and pyruvate

Pyruvate is simply pyruvic acid that has lose the hydrogen atom from its carboxyl group

Why is the Link reaction called as it is

Because it links glycolysis to the krebs cycle

What are the steps in the link reaction that result in formation of Acetyl CoA

An enzyme cuts off one carbon (from the 3 in pyruvate)

This removed carbon is released from cell as a waste product in form of CO₂

At the same time as carbon being cut out, NAD swoops in to collect the released electrons from the enzyme cutting the carbon, reducing the NAD to NADH

This leaves 2 carbon acetate which is immediately attached to a coenzyme A (CoA) to stabilise it

What are the products of the link reaction (one cycle)

Acetyl CoA

CO₂

NADH

Why does the link reaction occur twice for every glucose molecule

Because the glucose molecule splits into two pyruvate molecules

What are the products per CYCLE of the krebs cycle

3x NADH

1x FADH

1x ATP

2x CO₂

_{(Also regeneration of 4C compound oxaloacetate AND regeneration of CoA)}

What are the products per molecule of glucose in the krebs cycle

6x NADH

2x FADH

2x ATP

4x CO₂

What does each stage of aerobic respiration apart from oxidative phosphorylation produce

NADH

What are the steps in the krebs cycle (Overview of steps and not what happens in them)

Formation of 6C compound

First decarboxylation and dehydrogenation

Second decarboxylation and dehydrogenation

Substrate level phosphorylation

Regeneration of oxaloacetate

What happens during formation of 6C compound

1. The 2-carbon (2C) Acetyl coenzyme A from the link reaction combines with a 4-carbon (4C) oxaloacetate molecule to form a 6-carbon (6C) citrate molecule. Coenzyme A (CoA) is released and recycled back to the link reaction.

What happens during first decarboxylation and dehydrogenation

The 6C molecule is converted into a 5-carbon (5C) compound.

What happens during the second decarboxylation and deyhydrogenation

The 5C molecule is converted back into a 4-carbon (4C) compound

What happens during substrate level phosphorylation

During the conversion of the 4C intermediates, enough energy is released to transfer a phosphate group directly from an intermediate compound to ADP, synthesizing one molecule of ATP. This is called substrate-level phosphorylation.

What happens to regenerate the oxaloacetate

1. This pathway involves two final dehydrogenation steps:

   • One molecule of FAD is reduced to reduced FAD (FADH)

   • A final molecule of NAD is reduced to reduced NAD (NADH).

What do the 3 coenzymes in aerobic respiration (CoA, NAD and FAD) all have in common

They oxidise other substances and become reduced themselves by accepting electrons

NADH and FADH then donate electrons to the electron transport chain

What is the difference between NAD and FAD

NAD accepts electrons in glycolysis, link reaction and krebs cycle

FAD only accepts electrons in krebs cycle

Where does oxidative phosphorylation occur

In the mitochondrial inner membrane

Is krebs cycle catabolic or anabolic

Catabolic because it strips 6 carbon compound down via decarboxylation and dehydrogenation

What is the direction of proton pumping in chloroplasts vs in mitochondria

In chloroplasts, protons are pumped from the stroma into the thylakoid lumen

In mitochondria, protons are pumped from the matrix into intermembrane space

CORE SIMILARITIES BETWEEN PHOTOPHOSPHORYLATION AND OXIDATIVE PHOSPHRYLATION

CORE DIFFERENCES BETWEEN PHOTOPHOSPHORYLATION AND OXIDATIVE PHOSPHRYLATION

Outline the steps to oxidative phosphorylation (BROAD NAMES)

Oxidation of coenzymes

Electron transport chain

Proton pumping

Chemisosmosis

Terminal acceptor

What happens during oxidation of coenzymes

1. Reduced NAD and reduced FAD are oxidised at the inner mitochondrial membrane, splitting their hydrogen atoms into protons and electrons

What happens during the electron transport chain step

Electrons are passed along a series of electron carrier proteins in a sequence of redox reactions, losing energy as they move down the chain

What happens during the proton pumping stage

The energy released by the electrons is used to actively pump protons from the matrix into the intermembrane space, establishing an electrochemical proton gradient.

What happens during chemiosmosis

Protons diffuse down their concentration gradient back into the matrix through ATP synthase, driving the condensation of ADP and inorganic phosphate to synthesise ATP.

What happens during terminal acceptor phase

Oxygen acts as the final electron acceptor, combining with the electrons and protons at the end of the chain to form water

Why is it important that oxygen acts as a terminal electron acceptor

Because it allows electrons to keep moving down the ETC (maintaining the conc gradient and preventing build up of low energy electrons) which ensures protons keep getting pumped across

Where does anaerobic respiration occur

ONLY IN CYTOPLASM

What is pyruvate reduced to in PLANTS and MICROBES during anaerobic respiration

Ethanol and CO₂

What is pyruvate reduced to in ANIMALS

Lactate

How is the pyruvate reduced in all these organisms

By gaining the hydrogen atom from the NADH produced in glycolysis

What does this allow for when the NADH is oxidised during anaerobic respiration

For it to become NAD again which can then be re-used in glycolysis to ensure more ATP continues to be produced

Why can anaerobic respiration not be used indefintely

Because it does not produce much ATP

Lactate is an acid and this will cause enzymes to start denaturing

How many ATP molecules can be made in theory in aerobic and anaerobic respiration

Aerobic - 32

Anaerobic - 2

Why does anaerobic respiration produce such low ATP molecules

Because it only consists of glycolysis and cannot run the other 3 steps due to a lack of oxygen acting as an electron acceptor.

Why does aerobic respiration produce such high amount of ATP molecules

Because it fully extracts the energy from glucose by running glucose through all 4 stages of respiration

How efficient (as a percentage) is aerobic respiration vs anaerobic

Aerobic = 32%

Anaerobic = 2%

What are the 3 reasons why Aerobic respiration is not 100% efficient

Some protons leak across mitochondrial membrane during oxidative phosphorylation (so bypass ATP synthase)

ATP is used to actively transport pyruvate and NADH into the matrix from cytoplasm (after glycolysis)

Some energy is lost as heat