LSA 7A - Photosynthesis (Week 4a)

Overall equation of photosynthesis

6 CO2 + 6 H2O + light energy -> C6H12O6 + 6 O2 (low free energy reactants -> high free energy glucose). Energy and mass are still conserved. The pre-class worksheet writes it as 6 CO2 + 12 H2O -> C6H12O6 + 6 O2 + 6 H2O, which nets out to the same thing.

Overall equation of cellular respiration

C6H12O6 + 6 O2 -> 6 CO2 + 6 H2O + free energy (stored in ATP). It is roughly the reverse of photosynthesis.

How are photosynthesis and cellular respiration related?

The products of one are the reactants of the other. Photosynthesis (chloroplast) makes glucose and O2 from CO2 and H2O using light. Respiration (mitochondria) breaks glucose down with O2 into CO2 and H2O and makes ATP.

Photosynthesis in one sentence

Energy from the sun is used to build complex food molecules (sugar) out of carbon dioxide.

Why does light energy help organisms work against entropy?

Light energy powers the building of high-order, high-free-energy molecules (sugars), which lets organisms maintain internal order.

Oxidation

Loss of electrons. Compound A loses e- and is oxidized; it is the reducing agent.

Reduction

Gain of electrons. Compound B gains e- and is reduced; it is the oxidizing agent.

Reducing agent

The molecule that donates (loses) electrons and becomes oxidized.

Oxidizing agent

The molecule that accepts (gains) electrons and becomes reduced.

What is oxidized and what is reduced in photosynthesis?

Water is oxidized (loses electrons, releases O2). Carbon dioxide is reduced (gains electrons) to form carbohydrate.

Redox potential

The tendency of a molecule to acquire electrons (be reduced). Higher (more positive) redox potential = stronger pull on electrons.

Which direction do electrons flow in a redox chain?

From molecules with lower redox potential to molecules with higher redox potential (downhill, exergonic). Delta G has the opposite sign of delta redox potential.

True or False: Pq accepting an electron from PSII means Pq is acting as a reducing agent

False. When Pq accepts an electron it is being reduced, so it is acting as an oxidizing agent. Fix: when Pq donates an electron to the cytochrome complex it acts as a reducing agent.

True or False: Electrons would flow through the photosynthetic redox chain (+820, +1200, -400, -200, -80, +370, +400, -430, -380, -320 mV) with no light input

False (clicker Q2). The chain goes uphill at two points (to -400 after P680 and to -430 after P700), so electrons only flow because photons boost P680 and P700.

What does a photon do at P680 and P700 in the Z-scheme?

Photon energy raises the reaction center chlorophyll to a very low redox potential (P680: +1200 to -630 mV; P700: +400 to -1200 mV on the slide), making it a strong electron donor so electrons can flow downhill to the next acceptor.

Where does the light-dependent stage occur?

In the thylakoid membrane of the chloroplast.

Where does the Calvin Cycle occur?

In the stroma of the chloroplast (all three phases).

Reactants of the light-dependent reactions

Light (photons), H2O, NADP+, ADP + Pi.

Products of the light-dependent reactions

O2, NADPH, ATP.

Reactants of the Calvin Cycle

CO2, ATP, NADPH.

Products of the Calvin Cycle

G3P (sugar), plus ADP + Pi and NADP+ which return to the light-dependent reactions.

Why is the Calvin Cycle sometimes called light-independent?

It does not use light directly, but it depends on the ATP and NADPH made by the light reactions, so it stalls without them.

Name the parts of the chloroplast

Outer membrane, inner membrane, stroma (fluid inside the inner membrane), thylakoids (stacked into grana), thylakoid membrane, and thylakoid lumen (interior space).

Photosystem

A protein complex in the thylakoid membrane made of antenna chlorophylls and a reaction center.

Antenna chlorophylls

Pigments that absorb photons and pass the energy (not electrons) from molecule to molecule to the reaction center.

Reaction center

The special chlorophyll pair (P680 in PSII, P700 in PSI) that receives the energy, gets excited, and gives up an electron to the electron transport chain.

Clicker Q1: Which arrow type represents transfer of electrons between molecules?

Arrow 3 (answer C), the electron leaving the reaction center to the ETC. Arrow 1 is light absorption and Arrow 2 is energy transfer among antenna chlorophylls, not electrons.

Electron donor in the photosynthetic ETC

Water (H2O). It is split at PSII to replace electrons lost by P680, releasing 1/2 O2 + 2 H+.

Terminal electron acceptor in the photosynthetic ETC

NADP+ (reduced to NADPH). In respiration it is O2.

Name some electron carriers in the light reactions

Pheophytin, plastoquinone (Pq/PQ), the cytochrome b6f complex, plastocyanin (Pc), and ferredoxin (Fd).

Order of electron flow through the light reactions (Z-scheme)

H2O -> PSII (P680) -> pheophytin -> PQ -> cytochrome complex -> plastocyanin (PC) -> PSI (P700) -> ferredoxin -> NADP+ reductase -> NADPH.

What does water splitting at PSII produce?

Electrons (to replace those from P680), H+ that is released into the thylakoid lumen, and O2 as a byproduct.

How does the H+ gradient form in the thylakoid?

H+ is released in the lumen by water splitting, and the cytochrome complex (with Pq) uses energy from electron flow to pump H+ from the stroma into the lumen. NADP+ reduction also consumes H+ in the stroma.

Where is H+ concentration highest in the chloroplast?

In the thylakoid lumen (interior). The stroma has low H+.

How is ATP made in the light reactions?

H+ flows down its gradient from lumen to stroma through ATP synthase, which drives ADP + Pi -> ATP (chemiosmosis). This is called photophosphorylation.

Endergonic vs exergonic steps in the light reactions

Endergonic: photon excitation of P680/P700, pumping H+ against the gradient, making ATP, reducing NADP+. Exergonic: electrons moving downhill between carriers and H+ flowing through ATP synthase.

Direction of proton pumping in mitochondria vs chloroplasts

Mitochondria pump H+ from the matrix into the intermembrane space; ATP is made in the matrix. Chloroplasts pump H+ from the stroma into the thylakoid lumen; ATP is made in the stroma.

Why pump H+ into the smaller volume space?

A small volume means the same number of protons produces a much larger change in concentration, giving a steeper gradient and more energy to drive ATP synthase.

Study tip from lecture on ETC diagrams

Learn to read and interpret ETC diagrams instead of memorizing them.

What is NADPH?

A high-energy electron carrier made in the light reactions when NADP+ accepts electrons and H+. It delivers high-energy electrons to the Calvin Cycle.

What is ATP used for in the Calvin Cycle?

It provides the chemical energy to reduce 3-PGA to G3P and to regenerate RuBP.

Clicker Q4: Toxin makes the thylakoid membrane leaky to H+. What happens to ATP production?

Decreases (B). The H+ gradient dissipates, so there is less driving force for ATP synthase.

Clicker Q5: Leaky thylakoid membrane. What happens to G3P production?

Decreases (B). Less ATP is made, so the Calvin Cycle slows and less G3P is produced.

Clicker Q6: Toxin inhibits Rubisco. What happens to ATP production over a long time?

Decreases (B). The Calvin Cycle stops consuming ATP and NADPH, so ADP and NADP+ are not regenerated, and the light reactions run out of substrates and back up.

Short-term vs long-term effect of blocking the Calvin Cycle

Short term the light reactions may keep running briefly. Long term NADP+ and ADP run out, electron carriers stay reduced, and light-reaction output of ATP and NADPH falls.

Rubisco

Enzyme that fixes carbon: attaches CO2 to the 5-carbon sugar RuBP, forming an unstable 6-carbon intermediate that splits into two 3-phosphoglycerate (3-PGA). Delta G = -8.3 kcal/mol.

Rubisco facts

Has eight active sites, is a very slow enzyme (fixes about 3 CO2 per second), and is the most abundant enzyme on Earth.

Carbon fixation

Incorporating inorganic CO2 into an organic molecule. In the Calvin Cycle this is CO2 + RuBP -> 3-PGA, catalyzed by Rubisco.

RuBP

Ribulose 1,5-bisphosphate, the 5-carbon sugar bisphosphate that accepts CO2.

3-PGA

3-phosphoglycerate, the 3-carbon product of carbon fixation.

G3P

Glyceraldehyde 3-phosphate, the 3-carbon sugar made by the Calvin Cycle; two G3P can make glucose.

Three phases of the Calvin Cycle

1) Fixation of CO2 (RuBP + CO2 -> 3-PGA). 2) Reduction of 3-PGA to G3P (uses ATP and NADPH). 3) Regeneration of RuBP from G3P (uses ATP).

Calvin Cycle bookkeeping for 3 CO2

3 CO2 + 3 RuBP -> 6 3-PGA. Reduction uses 6 ATP and 6 NADPH to make 6 G3P. 1 G3P exits to make sugar and 5 G3P are recycled into 3 RuBP using 3 ATP.

ATP and NADPH needed per G3P made

9 ATP and 6 NADPH (6 ATP + 3 ATP, and 6 NADPH, for 3 CO2).

ATP and NADPH needed per glucose

18 ATP and 12 NADPH (two G3P, so six CO2 fixed).

Where do the ATP and NADPH for the Calvin Cycle come from?

From the light-dependent reactions. The ADP and NADP+ made by the Calvin Cycle go back to the thylakoids to be recharged.

What can a plant cell do with G3P and glucose?

Use it for respiration in mitochondria to make ATP, build sucrose for transport, store it as starch, build cellulose and other structural molecules, or make other organic molecules (amino acids, lipids).

What happens to the O2 made in photosynthesis?

It is released to the atmosphere or used by the plant's mitochondria for cellular respiration.

How do chloroplast and mitochondria ETCs compare?

Both use redox chains and a proton gradient with ATP synthase. Chloroplasts start with light and H2O and end with NADP+; mitochondria start with NADH and end with O2. Proton pumping goes opposite ways relative to the organelle compartments.

Prediction: What happens if a mutation lowers an enzyme in one step?

Trace the effect forward and backward: less product from that step, backup of its reactant, and downstream shortages of ATP, NADPH, or sugar depending on which step. Always ask what the next step needs and what recycles back.

Prediction: Light reactions stop (no light)

No ATP or NADPH, so the Calvin Cycle stalls and no G3P is made; no O2 is released.

How do herbicides affect photosynthesis? (framework)

Identify which step is blocked (PSII electron transfer, PSI electron transfer, H+ gradient/ATP synthase, or Calvin Cycle), then predict which products (O2, NADPH, ATP, G3P) fall and which reactants build up.

Herbicide that blocks electron transfer at PSII (example: DCMU/diuron)

Prevents electrons moving from PSII to plastoquinone, so no electron flow downstream: O2 evolution, H+ pumping, ATP, NADPH, and sugar all fall; PSII stays reduced and Pq stays oxidized. (From general biology, not the slides; check your lab handout.)

Herbicide that acts as an uncoupler (makes membrane leaky to H+)

Electron transport and O2 release can continue or speed up, but the H+ gradient collapses, so ATP falls (NADPH may still be made), and G3P production decreases.

Herbicide that blocks the Calvin Cycle or Rubisco

ATP and NADPH are not used up, ADP and NADP+ run out, light reactions back up, and sugar production falls. Carriers stay reduced.

How to match herbicide data to a model

Look at what is measured (O2 evolution, electron acceptor reduction, ATP, NADPH, CO2 uptake). The step where measurement drops first and upstream carriers accumulate in one redox state points to the blocked step.

Old-growth tropical forest carbon numbers (slide)

Absorbs 30.4 (photosynthesis) vs emits 24.5 (respiration) tonnes C per ha per year, so it is a net carbon sink. 10 years after deforestation, absorption falls to 12.3 and emission rises to 25.1, so it becomes a net source.

Why does deforestation turn forests from carbon sinks into sources?

Fewer photosynthesizing plants take up less CO2, while burning and decay of slash and soil erosion release stored carbon, and respiration continues.

Social inequality and deforestation (slide)

Research (Ceddia 2019, Latin America) found that inequality in income, wealth, and land ownership accelerates agricultural expansion and forest loss; more equal distribution can improve environmental protection.

Carbon forestry (slide)

Restoring trees could add about 0.9 billion hectares of canopy and store about 205 gigatonnes of carbon, making restoration one of the most effective climate mitigation strategies.

Nature of science: scientific knowledge is…

Based on observations of the natural world, subject to change, subjective, influenced by human imagination and creativity, and subject to influence by society and culture.