Light Independent Reaction

Image taken from: http://hyperphysics.phy-astr.gsu.edu/hbase/biology/imgbio/calvine.gif

• 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

Image taken from: http://www.shmoop.com/images/biology/biobook_photosyn_2.png

• 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

Image taken from: https://benchprep.com/blog/wp-content/uploads/2012/08/chloroplast2.jpg

Image taken from: http://blog.canacad.ac.jp/bio/BiologyIBHL1/files/1477622.jpg

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

Image taken from: https://encrypted-tbn1.gstatic.com/images?q=tbn:ANd9GcRMdbgJi7OECdEIZltQeEN-4XlpJUQnYaSeXWwa6ikEDcItbmgP

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.

Image taken from: http://alevelnotes.com/content_images/i73_Image3.gif

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.

Image taken from: http://alevelnotes.com/content_images/i74_Image4.gif

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.

Image taken from: http://alevelnotes.com/content_images/i71_gcsechem_18part2.gif

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.

Image taken from: http://alevelnotes.com/content_images/i72_enzyme_ph_graph.gif

Enzymes

What are enzymes?

• large biological molecules which catalyse chemical reactions in living organisms
• responsible for the metabolic processes which sustain life
• enzymes can be proteins or ribonucleic acid (RNA)

Properties of enzymes:

• lower the minimum amount of energy needed to start a reaction (activation energy)
• has active site of specific shape, which is complementary to its substrate 
• does not alter properties of end products of reaction
• highly efficient in small amounts
• denatured easily due to high heat

How do enzymes work?

1. After an effective collision between a substrate and an enzyme (where the substrate binds to the active site of the enzyme), an enzyme-substrate complex is formed. 
2. The substrate molecule is held in the active site by interactions such as hydrogen and ionic bonds between the R groups of the amino acids and the substrate molecule. 
3. Enzyme catalyses conversion of substrate to the end product. 
4. The alteration of chemical conformation results in the product being released from the active site since it is no longer complementary to the structure of the active site. 
5. The active site is then available for other substrates to bind to it.

"Lock and Key" Hypothesis

• there is an exact fit between the substrate and the active site of the enzyme
• the enzyme (lock) has a unique shape complementary to the substrate (key)
• enzymes are very specific; only substrates that are exactly complementary to its active site are able to bind with it

image taken from: http://katysstudynotes.files.wordpress.com/2010/11/enzymes.png

Induced Fit model

• active site of enzyme is flexible 
• active site is able to mould itself around the substrate to make the fit better
• active site returns to original shape after the products are released 

Illustration of the induced fit model

image taken from: http://zebrafish.umdnj.edu/Pre-Enrollment/Resources/Biochemistry/Enzymes%20and%20Metabolism/Images/enzyme_fit_diagram.png