Photosynthesis and Anabolic Biosynthesis

Autotrophs: "self-feeders," these organisms are capable of producing their own food. Plants are the primary examples of autotrophs.
Heterotrophs: "other feeders," these organisms must consume organic matter from other sources to obtain food. This category includes animals, fungi, and most bacteria.
Energy Dependency: Heterotrophs rely on the sugars produced by autotrophs to meet their energy needs. For instance, a predator eating a deer receives energy that originally came from the photosynthetic vegetation consumed by that deer.

Oxidation: loss of electrons from a molecule. This process results in an increase in the molecule's net positive charge.
Reduction: gain of electrons by a molecule. This process results in a decrease in the molecule's net positive charge.
Redox Reactions: In many chemical processes, electrons are passed from one reactant to another simultaneously. Because oxidation and reduction occur together, the reaction is termed a redox reaction.
Photosynthesis as a Redox Reaction: In this process, water ( $H_2O$ ) is oxidized to produce oxygen ( $O_2$ ), and carbon dioxide ( $CO_2$ ) is fixed and reduced to form glucose ( $C_6H_{12}O_6$ ).

Overall Expanded Equation: $6 CO_2 + 12 H_2O \rightarrow C_6H_{12}O_6 + 6 H_2O + 6 O_2$
Components and Sources:
- $H_2O$ (Water): Absorbed from the soil by the roots.
- $CO_2$ (Carbon Dioxide): Acquired from the air via gas exchange through the stomata (small pores on the leaf underside).
- $O_2$ (Oxygen): Released as a waste product through the stomata.
- Sunlight: Provides the energy required to drive the process.
Comparison to Cellular Respiration: Cellular respiration is the chemical opposite of photosynthesis. In respiration, glucose is oxidized and oxygen is reduced to produce carbon dioxide, water, and energy ( $ATP$ ):
- $C_6H_{12}O_6 + 6 O_2 \rightarrow 6 CO_2 + 6 H_2O + \text{Energy (ATP)}$

Guard Cells: Specialized cells that flank the stoma (singular of stomata) to regulate gas exchange.
Main Chloroplast Components:
- Double Membrane: Consists of an outer and an inner membrane.
- Stroma: The thick fluid within the inner membrane (distinct from the stoma pores on leaves).
- Grana: Stacks of thylakoids located within the stroma.
- Thylakoids: Membrane-bound sacks where the light reactions occur.
- Lumen: The internal space inside a thylakoid.
Localization: Chloroplasts are found only in plant cells that perform photosynthesis, with the highest densities occurring in the mesophyll (middle leaf) cells.

Light Energy Properties: Light is electromagnetic energy composed of particles called photons that travel in waves.
Wavelength and Energy Relationship: Longer wavelengths (waves with crests farther apart) carry less energy, whereas shorter wavelengths carry higher energy.
Visible Spectrum: Plants utilize specific wavelengths within the fractional range of electromagnetic energy visible to humans.
Electron Excitation:
- Ground State: The initial, stable state of an electron.
- Excited State: When a photon hits a nucleus and an electron absorbs the energy, it moves to a photoexcited (high-energy) state.

Location: Occurs in the grana (specifically the thylakoid membranes).
Photosystem II (PSII):
- Functions alongside thylakoid membranes.
- Splits water ( $H_2O$ ) to release electrons, oxygen ( $O_2$ ), and hydrogen ions ( $H^+$ /protons).
- Sunlight energizes the electrons released from water.
- The energized electrons power the generation of a proton gradient.
Chemiosmosis: The process of using potential energy stored in concentration gradients to produce $ATP$ . The proton gradient ( $H^+$ ) functions like a battery, powering the enzyme $ATP\,synthase$ as protons move down their gradient to convert $ADP + P$ into $ATP$ .
Photosystem I (PSI):
- Receives electrons from Photosystem II.
- Non-cyclic Photophosphorylation: Electrons are picked up by the carrier $NADP^+$ along with $H^+$ to form $NADPH$ .
- Cyclic Photophosphorylation: Electrons cycle back to the electron transport chain of PSI to generate extra $ATP$ without producing $NADPH$ .

Location: Occurs in the stroma of the chloroplast (or the cytoplasm of prokaryotes).
Function: Acts as a "sugar factory" by performing carbon fixation—converting inert, inorganic carbon compounds into useful organic compounds like glucose.
Input Requirements: Requires $ATP$ and $NADPH$ produced during the light reactions.
Core Thermodynamics: The Calvin Cycle is a reduction process.
Key Enzyme: RuBisCO: Ribulose bisphosphate carboxylase oxygenase. It can act as a carboxylase (facilitating the Calvin Cycle) or as an oxygenase (leading to photorespiration, which does not produce sugar).
Phases of the Calvin Cycle:
1. Phase 1: Carbon Fixation: Three molecules of $CO_2$ enter the cycle one at a time and are fixed to three molecules of Ribulose 1,5-bisphosphate ( $RuBP$ , a 5-carbon compound) producing 3-Phosphoglycerate.
2. Phase 2: Reduction: $ATP$ and $NADPH$ are used to convert 3-Phosphoglycerate into Glyceraldehyde 3-phosphate ( $G3P$ ). For every three $CO_2$ molecules, one molecule of $G3P$ is the net output for glucose production.
3. Phase 3: Regeneration: Five molecules of $G3P$ are rearranged using $ATP$ to regenerate three molecules of $RuBP$ , allowing the cycle to continue.

Carbohydrate Biosynthesis: Intermediates like $G3P$ and Fructose 6-phosphate enter gluconeogenesis to produce starch, cellulose, glucose, glycogen, and peptidoglycan.
Lipid Biosynthesis:
- $G3P$ and Dihydroxyacetone phosphate ( $DHAP$ ) are used to synthesize glycerol.
- $Acetyl-CoA$ is used via the reverse of beta-oxidation to produce fatty acids.
Amino Acid Biosynthesis:
- Amination: The process of adding an amine group ( $NH_3$ ) to a precursor like oxaloacetic acid or $\alpha$ -ketoglutaric acid (from the Krebs cycle).
- Transamination: The transfer of an amine group from one amino acid (e.g., glutamic acid) to a keto acid (e.g., oxaloacetic acid) using a transaminase with a peroxidolphosphate cofactor to create a new amino acid (e.g., aspartic acid).
Nucleotide Biosynthesis:
- The Pentose Phosphate Pathway utilizes Glucose 6-phosphate to produce Ribose 5-phosphate for the synthesis of DNA and RNA.
- Purine and pyrimidine nucleotides are derived from sources including folic acid, aspartic acid, glutamine, and glycine.