Light Independent Reaction

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• Happens in the stroma
• Does not require light
• ATP and NADPH from light dependent reaction is used to reduce carbon dioxide to triose phosphate and regenerate ribulose biphosphate (RuBP)
• Carbon dioxide reacts with RuBP to form an unstable 6-carbon intermediate which breaks down into two molecules of 3 phosphoglycerate (PGA) catalysed by ribulose biphosphate carboxylase/oxygenase (Rubisco)
• ATP and NADPH reduces PGA to form triose phosphate (G3P), forming ADP and NADP in the process
• Most of the triose phosphate is used to regenerate RuBP
• Some triose phosphate exit the cycle and is used to synthesise other products like starch and glucose
• ADP and NADP are channeled back into the light dependent reaction to produce more ATP and NADPH

Light Dependent Reaction

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• There are two photosystems at the thylakoid membranes of the chloroplast.
• Photosynthetic pigments (eg. chlorophyll and carotenoids) are organized into the two photosystems, PSII and PSI.
• Photosynthetic pigments absorb light energy which cause the excitation of their electrons (photoactivation).
• Excited electrons are ejected from PSI and PSII due to their high energy.
• The excited electrons produce adenosine triphosphate (ATP) from adenosine diphosphate (ADP) using ATP synthase.
• Nicotinamide adenine dinucleotide phosphate (NADPH) is also produced from nicotinamide adenine dinucleotide phosphate ion (NADP+).
• The electron transport chain and the ATP synthase complex at the thylakoid membrane are involved in the production of ATP and NADPH.
• As light is involved in the production of ATP, it is known as photophosphorylation.
• At PSII, the electrons used to produced ATP and NADPH are replenished by electrons from water molecules. 
• Splitting of water (photolysis) results in the release of oxygen gas.

In simpler terms, when light falls on the thylakoid membrane,

• Light causes photoactivation, which is the excitement of electrons by absorption of light energy, at the photosynthetic pigments at PSII and PSI.
• Excited electrons are ejected from the reaction centers of PSII and PSI.
• Ejected electrons are used to produce ATP and NADPH.
• Electrons lost are replenished from photolysis of water.
• Oxygen gas is released in the process.

Chloroplasts

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Chloroplasts

• found in mesophyll cells
• site for photosynthesis
• surrounded by double membrane called chloroplast envelope
• thylakoids are fluid-filled sacs
• a stack of thylakoids is called a granum
• stroma is a gel-like fluid that surrounds the grana
• stroma contains soluble enzymes of the Calvin cycle, sugars, organic acids, etc.
• excess carbohydrates from photosynthesis is stored as starch grains in the chloroplast
• the two main photosynthetic pigments, chlorophyll and carotenoids, are embedded at the surface of thylakoid membranes

Chlorophyll

• converts light energy to chemical energy
• absorb mainly red and blue-violet light 
• reflects green light which gives leaves their green colour

Carotenoids

• yellow, orange, red or brown pigments
• absorb strongly in blue-violet light

Leaf Structure

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Cuticle 

• thin waxy layer of lipids
• prevents water loss through evaporation
• allows light to pass through

Epidermis

• transparent layer of cells
• allows light to pass through
• protects the cells underneath from damages

Palisade Mesophyll Cells

• contains a large number of chloroplasts
• tightly packed together vertically to allow as many cells as possible to absorb light

Spongy Mesophyll Cells

• contains few chloroplasts
• loosely packed with intercellular air spaces for fast diffusion of carbon dioxide

Stoma

• surrounded by two guard cells
• allows exchange of gases 

Vascular Bundle (Vein of leaf)

• made up of xylem and phloem vessels
• xylem transports water and mineral salts
• phloem transports nutrients

Inhibitors

Many drugs and poisons are inhibitors of enzymes in the nervous system.

Competitive Inhibitor

• resembles shape of substrate closely
• competes with substrate for active site
• binds to active site either reversibly or irreversibly
• prevents substrate from binding to enzyme active site, reducing rate of reaction

Non-competitive Inhibitor

• has a different structure from substrate
• binds to an allosteric site, causing a change in the shape of active site
• substrates can no longer bind to the active site and no enzyme-substrate complex can be formed

Factors affecting enzyme reactions

Substrate concentration

• At low substrate concentration, increasing the substrate concentration will result in a proportional increase in the rate of reaction.
• As there are sufficient active sites, the increase in substrate concentration will increase the frequency of effective collisions between the enzyme and substrate molecules, increasing the rate of formation of enzyme-substrate complex.
• However, at high substrate concentration, increasing the substrate concentration will no longer speed up the reaction.
• All the active sites of the enzyme molecules will be occupied at any given moment.
• Any added substrates have to ‘wait’ until existing enzyme-substrate complexes are dissociated and the active sites become available for binding.
• The rate of reaction can only be increased with the addition of enzymes.

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Enzyme concentration

• At low enzyme concentration, increasing the enzyme concentration will result in a proportional and linear increase in the rate of reaction.
• The increase in enzyme concentration provides more active sites which the substrate molecules can bind to, increasing the rate of effective collision and the formation of enzyme substrate complex.
• However, at high enzyme concentration, increasing the enzyme concentration will no longer have effect on the reaction as all the substrate molecules would already have been converted into their products.
• The rate of reaction can only be increased with the addition of substrates.

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Temperature

• Enzymes work best at their optimum temperature, which is usually 40°C.
• Below the optimum temperature, the rate of reaction increases linearly with the increase in temperature.
• As the temperature increases, kinetic energy of the molecules increase. This increases the rate of effective collisions between enzyme and substrate molecules and the formation of enzyme-substrate complex.
• Beyond the optimum temperature, the rate of reaction decreases even though the frequency of collisions increases.
• Thermal agitation of the enzymes break the hydrogen bonds, ionic bonds and hydrophobic interactions that stabilize the specific 3D conformation of the enzyme.
• The enzyme becomes denatured as the shape of the enzyme's active site is altered and is no longer complementary to that of the substrate.

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pH

• Enzymes work best at their optimum pH level.
• A change in pH level will result in the alteration of the ionic charge of the R groups of the amino acid residues.
• This breaks the ionic bonds and hydrogen bonds that are responsible for maintaining the specific 3D conformation of the enzyme.
• The enzyme becomes denatured as the shape of the enzyme's active site is altered and is no longer complementary to that of the substrate.

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