Photosynthesis

Describe how coenzyme Q accepts electrons

• Antioxidant because it can accept electrons from things so they don’t oxidise other things

• Ubiquinone has a rign structure, this is where everything is sp2 hybridised

• But it is not aromatic, in the ring there are only 4π electrons

• Electron source can be accepted by an oxygen, this triggers a breaking of bonds throughout the molecule

• This produces a negative charge on the oxygen that accepted the electron and forms a radical

• Radical can accept another electron, producing another negative charge

• This produces an aromatic product, the gain of aromaticity is the driving force in the reaction

• Protons can be shuttles across the membrane to neutralise the O- charges

• Can be oxidised back to the original molecule

• Has a repeating unit, this aids membrane association.

Describe the 2 stage process of photosynthesis

• Light dependent reaction

  • Building up molecules of ATP, producing oxygen - net oxidation from water, and we are reducing NADP+ --> NADPH, this gives us reducing equivalents

  • This uses energy from light

• Dark reaction - this is light independent

  • Redyce carbon dioxide, hydrogen is used to redice the charge build up

Describe how chlorophyll absorbs light

• Light absorption by the porphyrin ring around the magnesium centre

• In the ring there is a large conjugated system

• The energy gap for the homo-lumo is small, matching the energy of visible light

Describe b-carotene

• Long conjugated system for the electrons to have a small energy gap, can absorb light

Describe the absorption spectra in the solar spectrum

• Different molecules can absorb a large amount of different wavelengths, maximising their rate of photosynthesis

• Combination of molecules act as an antenary complex

Describe the z scheme

• P680 absorbs light, this excites electrons into thr LUMO (higher energy)

• Electrons are transferred through a series of carriers, this is down a electrochemical gradient to a lower energy, this releases energy for proton pumping which allows ATP synthesis

• P700 then excites the electrons again using energy from light absorption, they are passed to ferredoxin and then NADP+ reductase which produces NADPH

• The electrons from P680 are replaced by oxidising water, as the P680 has a highest oxidising agent

• P700 is the strongest reducing agent

Describe the reaction of rubisco

• Conversion of ribulose-1,5-bisphosphate to 3-phosphoglycerate

• Kcat is 3/s, very slow but a key enzyme

• For every carbon dioxide in, ypou get two molecules of 3phosphoglycerate

 

Describe the mechanism of Rubisco

• Mg2+ is coordinated, 3 with active site residues that are negatively charged, one of these is a lysine hat has been carboxylated due to such a high concentration of CO2

• If there are no substrates, 3 waters will also coordinate

• Substrate enters and replaces two waters

• Donate lysine lone pair, allos oxygn attack and deprotonation

• Form an enolate that is coordinated to the magnesium

• One histidine aids the deprotonation of the alcohol and a lysine aids alcohol formation

• Flipping the sterochem

• Forming the carbon-carbon bond

• Enolate increases nucleophicity of the alkene

• Water deprotonated to make a bettwe nucleophile

• Attacks carbonyl and can form a tetrahedral intermediate

• Tetrahedral intermediate forms

• Reforms the carbonyl and break a C-C bond

• Negative chartge is protonated by a protonated basic residue

• Formed 2 x 3 phosphoglycerates

Describe the Calvin cycle with 3CO2

• Incorporating 3CO2 means we've made 6G3P

• If one carbon dioxide comes in, 2x3GP come out

• For 3CO2, 1/6 G3P goes to central metabolic pathways and the other 5 go the rest of the pathway

How is fructose 6 phoshate regenerated?

• 

Describe the transketolase reaction

Another G3P is used with fructose 6phosphate to produce a 4C sugar and a 5C sugar

Describe the transketolase mechanism

• TPP is an illid, -ve charge acts as a nucelophile and attacks the carbonyl

• Can be protonated to form a protonated tetrahedral intermediate

• Deprotonate alchol and reform the carbonyl.

• Then kcik out LG, electrons are accepted by the N+ on the TPP

• TPP allows the breaking of the C-C bond

• Have a 4C sugar and 2 carbons attached to the TPP intermediate

• Nitrogen donates e- via resonance

• Attacks aldehyde and protonates the oxygen

• Tetrahedral intermediate forms

• Deprotonate alcohol

• Form ketone

• Kick out TPP as a LG

• Forms a 5C sugar

Describe the second aldolase reaction

• Aldolase combins a 4C and 3C to a 7C sugar - sedoheptulose 1,7 bisphosphate

Describe the reaction of sedoheptulose 1,7 bisphosphate

• Phosphatase cannot be used for SLP as not a good LG

• Form an inorganic phosphate

Describe th second transketolase reaction with sedoheptulose 7 phosphate

 

• Second transketonase allows two 5C molecules to be produced

• Overall 3X5C sugars

Describe the conversion of ribose5phosphate to ribulose5phosphate

• Conversion of ribose5phosphate (an aldose) to ribulose5phosphate (a ketone)

• Isomerisation from an aldehyde to a ketone

Describe the conversion of xyulose5phosphate to ribulose5phosphate

• Attempting to change the stereochemistry of a carbon

• Deprotonate a-to carbonyl to give us an enolate

• Then kick oxygen electrons down and reprotonates on the other side, produces the epimer

• Once we have deprotonates, the carbon is not planar - so have to add to the opposite face to get the opposite stereoisomer

Describe the conversion of ribulose5phosphate to ribulose1,5bisphosphate

• Phosphorylate using a kinase

• Produced 3 molecules of ribulose1,5bisphosphate and have one G3P left for the central metabolic pathways

Why is rubisco slow?

• Not overly selective

• Can also do photorespiration

• Enolate attacks oxygen and gives a peroxide compound