2.3 Bioenergetics, Cellular Respiration & Photosynthesis

2.3 Bioenergetics, Cellular Respiration & Photosynthesis

Bioenergetics is the study of energy transformations in biological systems. Living organisms maintain highly ordered cellular structures through continuous coupling of exergonic and endergonic reactions. For the AMC exam, mastering the metabolic machinery of photosynthesis and cellular respiration is essential.

---

1. ATP & Biological Oxidation-Reduction

• Adenosine Triphosphate (ATP): The universal energy currency of cells, consisting of adenine, ribose, and three phosphate groups. Hydrolysis of the terminal phosphoanhydride bond releases $\sim 7.3\text{ kcal/mol}$ ($30.5\text{ kJ/mol}$) under standard conditions: $\text{ATP} + H_2O \xrightarrow{\text{ATPase}} \text{ADP} + P_i + 7.3\text{ kcal/mol}$
• Redox Reactions: Biological energy release occurs via transfer of electrons (hydrogen atoms). Oxidation is the loss of electrons/hydrogen atoms; reduction is the gain of electrons/hydrogen atoms. Principal electron coenzymes include $NAD^+ / NADH$, $NADP^+ / NADPH$, and $FAD / FADH_2$.

---

2. Photosynthesis: Converting Solar Energy to Chemical Energy

Photosynthesis occurs in chloroplasts and consists of two interconnected phases: the Light-Dependent Reactions (thylakoid membrane) and the Light-Independent Reactions (Calvin Cycle) (stroma).

$\text{Overall Reaction: } 6CO_2 + 12H_2O \xrightarrow[\text{Chlorophyll}]{\text{Light}} C_6H_{12}O_6 + 6O_2 + 6H_2O$

A. Photosynthetic Pigments

• Chlorophyll a: Primary photosynthetic pigment present in all oxygenic photosynthetic organisms; absorbs blue-violet and red light, reflecting green.
• Accessory Pigments: Chlorophyll b and carotenoids (carotenes and xanthophylls) absorb wavelengths not absorbed by chlorophyll a and transfer excitation energy to the reaction center, while protecting against photo-oxidation (photoprotection).
• Action Spectrum vs. Absorption Spectrum: Absorption spectrum measures light absorption by isolated pigments; action spectrum measures overall photosynthetic rate across different wavelengths (demonstrated by T.W. Engelmann using Spirogyra and aerobic bacteria).

B. Light-Dependent Reactions (Photophosphorylation)

Located in the thylakoid membranes, utilizing Photosystem II (P680) and Photosystem I (P700):

1. Non-Cyclic Photophosphorylation (Z-Scheme):
   • Photon absorption by Photosystem II (PS II) excites electrons, which are passed down an electron transport chain (pheophytin, plastoquinone $PQ$, cytochrome $b_6f$ complex, plastocyanin $PC$) to Photosystem I (PS I).
   • Photolysis of Water: An enzyme on the thylakoid lumen side of PS II splits water: $2H_2O \rightarrow O_2 + 4H^+ + 4e^-$ This releases $O_2$ as a byproduct, donates $e^-$ to replace lost P680 electrons, and accumulates $H^+$ in the lumen.
   • Electrons from PS I are passed via ferredoxin ($Fd$) to $NADP^+$ reductase, forming $NADPH$.
   • Proton Pumping & Chemiosmosis: Proton accumulation in the thylakoid lumen creates a proton gradient. Protons flow back into the stroma through $CF_0CF_1$-ATP Synthase, driving ATP formation.
2. Cyclic Photophosphorylation:
   • Involves PS I only. Excited electrons from P700 pass to ferredoxin, then return via cytochrome $b_6f$ to PS I.
   • Generates ATP only—no $NADPH$ is produced and no photolysis of water occurs ($no\ O_2\ release$). Used when cell ATP requirements exceed NADPH supply.

C. Light-Independent Reactions (Calvin Cycle / C3 Pathway)

Occurs in the chloroplast stroma, divided into three stages:

1. Carbon Fixation: Enzyme RuBisCO (Ribulose-1,5-bisphosphate carboxylase-oxygenase) catalyzes the addition of $CO_2$ to 5-carbon Ribulose 1,5-bisphosphate (RuBP), forming an unstable 6-carbon intermediate that immediately splits into two 3-carbon molecules of 3-phosphoglycerate (3-PGA).
2. Reduction Phase: 3-PGA is phosphorylated by ATP to 1,3-bisphosphoglycerate, then reduced by $NADPH$ to Glyceraldehyde 3-phosphate (G3P / TP).
3. Regeneration of RuBP: Out of every 6 G3P molecules produced, 1 G3P exits to form glucose/starch, while 5 G3P molecules undergo ATP-dependent rearrangement to regenerate 3 RuBP acceptors.

---

3. Cellular Respiration: Catabolic Energy Harvest

Aerobic respiration completely oxidizes glucose into $CO_2$ and $H_2O$, yielding ATP through four sequential metabolic stages:

Glucose (6C) ──> [1. Glycolysis (Cytosol)] ──> 2 Pyruvate (3C) + 2 ATP + 2 NADH
                                                      │
                                          [2. Pyruvate Oxidation]
                                                      │
                                           2 Acetyl-CoA (2C) + 2 CO2 + 2 NADH
                                                      │
                                            [3. Krebs Cycle (Matrix)]
                                                      │
                                           4 CO2 + 2 ATP + 6 NADH + 2 FADH2
                                                      │
                                  [4. Oxidative Phosphorylation (Inner Membrane)]
                                                      │
                                           ~28-34 ATP + 6 H2O (Final e- acceptor: O2)

A. Stage 1: Glycolysis (EMP Pathway)

• Location: Cytoplasm (anaerobic process, requires no $O_2$).
• Preparatory Phase: Glucose is phosphorylated twice (consuming 2 ATP) via hexokinase and phosphofructokinase ($PFK$, key rate-limiting enzyme) to form Fructose 1,6-bisphosphate, which splits into G3P and DHAP.
• Payoff Phase: Oxidative conversion of G3P to pyruvate yields 4 ATP (substrate-level phosphorylation) and 2 NADH.
• Net Yield: $\mathbf{2\text{ Pyruvate} + 2\text{ ATP} + 2\text{ NADH}}$ per glucose molecule.

B. Stage 2: Pyruvate Oxidation (Link Reaction)

• Location: Mitochondrial Matrix.
• Pyruvate translocates into mitochondria and undergoes oxidative decarboxylation by the pyruvate dehydrogenase complex: $\text{Pyruvate} + CoA + NAD^+ \rightarrow \text{Acetyl-CoA} + CO_2 + NADH + H^+$

C. Stage 3: Krebs Cycle (Citric Acid / TCA Cycle)

• Location: Mitochondrial Matrix.
• Acetyl-CoA (2C) combines with Oxaloacetate (4C) to form Citrate (6C). Through a cycle of oxidations and decarboxylations, oxaloacetate is regenerated.
• Yield per glucose molecule (2 turns of cycle): $\mathbf{4\text{ } CO_2 + 2\text{ ATP (GTP)} + 6\text{ NADH} + 2\text{ FADH}_2}$.

D. Stage 4: Oxidative Phosphorylation & The Electron Transport Chain (ETC)

• Location: Inner Mitochondrial Membrane (Cristae).
• Electrons from NADH and $FADH_2$ pass through four respiratory membrane complexes (Complex I: NADH dehydrogenase, Complex II: Succinate dehydrogenase, Complex III: Cytochrome $bc_1$, Complex IV: Cytochrome c oxidase).
• Terminal Electron Acceptor: Molecular oxygen ($O_2$) accepts electrons and protons to form water: $\frac{1}{2}O_2 + 2H^+ + 2e^- \rightarrow H_2O$
• Chemiosmosis (Peter Mitchell): Electron transfer pumps $H^+$ from matrix to intermembrane space. The resulting proton gradient drives $H^+$ back through $F_0F_1$-ATP Synthase, generating ATP.
• Theoretical yield: $\sim 2.5\text{ ATP per NADH}$ and $\sim 1.5\text{ ATP per } FADH_2$, producing a net total of 30–32 ATP per fully oxidized glucose molecule.

E. Anaerobic Respiration & Fermentation

When $O_2$ is deficient, cells undergo fermentation to recycle $NAD^+$ so glycolysis can continue:

• Lactic Acid Fermentation (in skeletal muscle during strenuous exercise): Pyruvate is reduced to Lactate by lactate dehydrogenase, regenerating $NAD^+$.
• Alcoholic Fermentation (in yeast): Pyruvate is decarboxylated to Acetaldehyde ($releasing\ CO_2$), which is reduced by NADH to Ethanol.