Ch 20 - Calvin Cycle

What does the Calvin cycle use?

ATP and NADPH from light reactions to fix CO2.

Where does the Calvin cycle occur?

Chloroplast stroma (dark reactions).

Three stages of the Calvin cycle

Fixation, reduction, regeneration.

Stage 1 (fixation) does what?

CO2 is fixed to RuBP to form 3-phosphoglycerate.

Stage 2 (reduction) does what?

3-PG is converted to triose phosphates using ATP and NADPH.

Stage 3 (regeneration) does what?

Triose/hexose intermediates regenerate RuBP.

Rubisco stands for what?

Ribulose 1,5-bisphosphate carboxylase/oxygenase.

Rubisco substrate (5-carbon acceptor)

Ribulose 1,5-bisphosphate (RuBP).

Immediate product after CO2 fixation

An unstable 6-carbon intermediate that splits into two 3-PG.

Rubisco is considered “rate-limiting” for what?

Hexose synthesis/overall carbon fixation pace.

Rubisco problem (concept)

It binds sugar phosphates too tightly and is slow (low kcat).

Why is Rubisco so abundant?

It’s inefficient, so plants make lots to get enough flux.

Rubisco active site needs what to be active?

Carbamate formation and Mg2+ binding.

Which residues help bind Mg2+ in Rubisco?

Carbamate plus acidic residues (Asp/Glu) coordinate Mg2+.

Rubisco mechanism key intermediate

Enediol/enediolate intermediate of RuBP.

Why form an enediol intermediate?

Makes RuBP reactive so it can form a new C–C bond with CO2.

Rubisco makes what two identical molecules?

Two 3-phosphoglycerate molecules.

What is photorespiration?

Rubisco uses O2 instead of CO2, producing phosphoglycolate.

Why does photorespiration happen?

O2 and CO2 are similar and both can enter Rubisco’s channel.

Carboxylation vs oxygenation (concept)

Carboxylation is only ~4× faster than oxygenation (so oxygenation is significant).

Product of Rubisco oxygenase reaction

Phosphoglycolate (not very useful directly).

Why is photorespiration “wasteful”?

Organic carbon is oxidized to CO2 without generating high-energy electrons; ~25% waste.

Photorespiration carbon salvage (example)

Some carbon can be recovered; serine can be converted to 3-PG.

Concept: If O2 rises or CO2 falls, what happens to photorespiration?

Photorespiration increases.

Concept: If temperature rises, what happens to Rubisco oxygenase activity?

Oxygenase activity increases (more photorespiration).

Q1 concept: photons per CO2 fixed

Plants need ~8 photons absorbed per CO2 fixed (as framed in the slide question).

Net result of 3 CO2 fixed (carbon product)

One triose phosphate equivalent (DHAP).

Stoichiometry for hexose formation (C3)

6 CO2 + 18 ATP + 12 NADPH + 12 H2O → C6H12O6 + 18 ADP + 18 Pi + 12 NADP+ + 6 H+.

How many cycles to make one hexose?

Six Calvin cycles (fixing 6 CO2).

What fraction of GAP exits regeneration (concept)

About 1 out of 6 GAP is not used for regeneration.

“Catch-22” idea of Calvin cycle

Needs intermediates to regenerate RuBP while also needing output for sugar synthesis.

Stage 2 “looks familiar” because…

It overlaps with glycolysis/gluconeogenesis-type steps and intermediates.

What molecules store fixed carbon in plants?

Starch and sucrose.

Starch resembles what storage polymer?

Glycogen (but less branched).

Sucrose synthesis uses what activation?

UDP is used to activate glucose for sucrose formation.

How do light reactions “prime” the stroma?

Provide ATP, NADPH, Mg2+, and reduced ferredoxin (Fdred) to activate enzymes.

What happens to stroma pH in the light?

It increases to ~8 (becomes more basic).

How does higher stroma pH help Rubisco?

Deprotonates an active-site lysine and favors carbamate formation for Mg2+ binding.

Thioredoxin links what processes?

Light reactions to activation of Calvin cycle enzymes.

Many Calvin cycle enzymes are inactive because…

They contain regulatory disulfide bonds.

What does thioredoxin do to activate enzymes?

Reduces disulfide bonds (turns enzymes “on”).

How is thioredoxin reduced?

By electrons from ferredoxin (Fdred).

Concept: If ferredoxin is not reduced, what happens to Calvin cycle regulation?

Thioredoxin stays oxidized → Calvin cycle enzymes remain less active.

Concept: If stroma does NOT alkalinize in light, what happens?

Reduced Rubisco activation and slower Calvin cycle flux.

Concept: If Mg2+ is limited, what happens to Rubisco?

Lower activation and decreased CO2 fixation.

Q2 concept: Does higher CO2 automatically solve climate change?

Not fully; fixation is limited by ATP/NADPH, enzyme capacity, water/nutrients, and photorespiration constraints.

Engineering Rubisco faster: likely tradeoff (concept)

Faster often means less specific (more oxygenation) or other kinetic penalties.

Artificial biology carbon fixation (example)

CCR and PCC can fix carbon without competing oxygenase activity.

CETH cycle is what?

A synthetic carbon-fixation network built from naturally occurring enzymes.

Droplet microfluidics purpose (artificial chloroplasts)

Create tiny compartments (pL) to build/optimize synthetic pathways.

Reverse micelles made from what?

Oil and lipids.

C4 pathway advantage (big idea)

Reduces photorespiration by concentrating CO2 around Rubisco.

C4 pathway separates what spatially?

Initial CO2 capture vs Calvin cycle (mesophyll vs bundle-sheath).

First step in C4 CO2 capture

CO2 is converted to HCO3− in mesophyll cells.

C4 enzyme uses HCO3− + PEP to make what?

Oxaloacetate.

Oxaloacetate is converted to what in C4?

Malate.

Where is malate decarboxylated in C4?

Bundle-sheath chloroplasts (releasing CO2 for Calvin cycle).

C4 returns what back to mesophyll?

Pyruvate (then regenerated to PEP).

C4 costs extra energy how?

Uses 2 extra ATP per CO2 “transport”/concentration step.

ATP cost comparison C3 vs C4

C3: ~18 ATP per hexose; C4: ~30 ATP per hexose (per slide).

CAM pathway does what?

Fixes CO2 at night as malate and stores it in vacuoles.

CAM separates what temporally?

CO2 capture (night) from Calvin cycle (day).

Why CAM helps desert plants

Reduces water loss by opening stomata at night.

PPP overall purpose

Oxidize glucose to generate NADPH and provide pentose phosphates.

PPP is common to who?

All organisms (not just photosynthetic).

PPP diverts glucose from what pathway?

Glycolysis.

PPP key outputs

NADPH + ribose-5-P (and ribulose-5-P in some contexts).

PPP provides NADPH for what?

Reductive biosynthesis and antioxidant defense.

PPP oxidative phase makes what (per G6P)?

Ribulose-5-P + 2 NADPH + CO2.

PPP oxidative phase uses how many main enzymes?

Three (G6PD, lactonase, 6-phosphogluconate dehydrogenase).

First enzyme of oxidative PPP

Glucose-6-phosphate dehydrogenase (G6PD).

G6PD oxidizes which carbon of glucose-6-P?

C1 (forming a lactone).

What controls PPP flux strongly?

Level of NADP+ (substrate availability).

Why NADP+ matters for G6PD

G6PD is specific for NADP+ / produces NADPH.

What does lactonase do?

Opens the lactone ring.

6-phosphogluconate dehydrogenase oxidizes which carbon?

C3 of 6-phosphogluconate (per slide).

Why does CO2 release matter energetically?

CO2 release helps drive the oxidative PPP forward.

PPP non-oxidative phase does what?

Interconverts sugars (C3–C7) to balance needs for ribose vs glycolytic intermediates.

Non-oxidative PPP: isomerase makes what?

Ribose-5-P (aldose isomerization).

Non-oxidative PPP: epimerase makes what?

Xylulose-5-P (epimerization).

Transketolase transfers how many carbons?

2-carbon unit transfer.

Transaldolase transfers how many carbons?

3-carbon unit transfer.

Non-oxidative net conversion (classic)

3 pentoses (C5) → 2 fructose-6-P (C6) + 1 GAP (C3).

Does non-oxidative PPP use DHAP?

No

Transaldolase links PPP to what?

Glycolysis/gluconeogenesis via F6P and GAP production.

Transketolase cofactor

TPP (thiamine pyrophosphate).

Transketolase mechanism first step (concept)

TPP carbanion attacks ketose carbonyl carbon.

Transaldolase mechanism key feature

Uses Lys to form a Schiff base intermediate.

What breaks the C3–C4 bond in transaldolase?

Protonation of the Schiff base facilitates cleavage and aldose release.

Both transketolase and transaldolase stabilize what?

A carbanion intermediate by resonance.

PPP in plants: transaldolase can divert what?

GAP and sedoheptulose-7-P from Calvin cycle (Calvin ↔ PPP).

PPP Mode 1 goal

Make ribose-5-P only (little/no NADPH needed).

PPP Mode 2 goal

Make both ribose-5-P and NADPH.

PPP Mode 3 goal

Make NADPH only (ribose not needed).

PPP Mode 4 goal

Make both ATP and NADPH (by feeding intermediates into glycolysis).

Concept: If NADPH demand rises sharply, which mode increases?

Mode 3 (maximize NADPH production).

Concept: If ribose demand rises (DNA/RNA synthesis), which mode increases?

Mode 1 or Mode 2 (depending on NADPH need).

Warburg effect (cancer)

Increased fermentation of glucose to lactate even with oxygen.

PKM2 in cancer does what?

Low activity pyruvate kinase isoform causes glycolysis “backup.”

Why PKM2 backup increases PPP flux

More glycolytic intermediates get diverted into PPP.