Bioenergetics: Photosynthesis & Respiration

Bioenergetics is the quantitative study of energy relationships and energy conversions in biological systems. All metabolic reactions involve energy transformations.

Photosynthesis Definition:

Photosynthesis is the process in which energy-poor inorganic oxidized compounds of carbon (CO₂) and hydrogen (mainly H₂O) are reduced to energy-rich carbohydrates (glucose) using light energy absorbed and converted into chemical energy by chlorophyll and other photosynthetic pigments.

Overall Reaction of Photosynthesis:

6CO₂ + 12H₂O + Light Energy → C₆H₁₂O₆ + 6O₂ + 6H₂O

Relationship Between Photosynthesis and Respiration:

• Photosynthesis equation is almost exactly opposite to aerobic respiration
• Photosynthesis uses products of respiration (CO₂ + H₂O)
• Respiration uses products of photosynthesis (glucose + O₂)
• Photosynthesis occurs only during daytime; respiration occurs day and night

Compensation Point:

At dawn/dusk when light intensity is low, the rate of photosynthesis and respiration may become equal. At this moment, there is no net gas exchange between leaves and atmosphere.

• Sunlight is electromagnetic/radiant energy
• Full range of electromagnetic radiation = electromagnetic spectrum
• Photosynthetic pigments absorb visible light (380-750nm wavelengths)
• Light behaves as waves and as particles (photons/quanta)
• Only about 1% of light falling on leaf surface is absorbed; rest is reflected or transmitted

Two Types of Spectra:

1. Absorption Spectrum

• Graph showing relative absorption of different wavelengths by photosynthetic pigments
• Main photoreceptors: chlorophyll ‘a’ and ‘b’
• Maximum absorption in violet-blue (400-470nm) and orange-red (630-670nm) regions
• Carotenoids show more absorption at 430-500nm (blue-violet)

2. Action Spectrum

• Graph showing relative effectiveness of different wavelengths in driving photosynthesis
• First obtained by T.W. Engelmann in 1883 using Spirogyra
• Obtained by estimating CO₂ consumption or O₂ release during photosynthesis
• Most effective wavelengths: blue (430nm) and red (670nm)

Comparison of Absorption and Action Spectra:

Feature	Absorption Spectrum	Action Spectrum
Peaks	Narrower	Broader
Valley	Broader and deep	Narrower and not deep
Shows	Light absorption by pigments	Effectiveness for photosynthesis

Pigments are substances that absorb light energy. All wavelengths absorbed by pigments “disappear” (are not reflected).

Location of Pigments:

All photosynthetic pigments are embedded in thylakoid membranes/grana lamellae within chloroplasts.

Major Pigment Groups in Higher Plants:

1. Chlorophylls

• Most important photosynthetic pigments
• Insoluble in water but soluble in organic solvents
• Types: chlorophyll a, b, c, d in eukaryotic plants/algae
• Bacteriochlorophylls in photosynthetic bacteria
• Absorb violet-blue and orange-red wavelengths
• Reflect/transmit green, yellow, indigo wavelengths

Structure of Chlorophyll:

• Two parts: hydrophilic head and hydrophobic tail
• Head: porphyrin ring with magnesium as central metal ion
• Tail: phytol (C₂₀H₃₉) embedded in thylakoid membrane
• Similar to hemoglobin but with Mg instead of Fe

Chlorophyll ‘a’ vs ‘b’:

Feature	Chlorophyll ‘a’	Chlorophyll ‘b’
Formula	C₅₅H₇₂O₅N₄Mg	C₅₅H₇₀O₆N₄Mg
Functional Group	-CH₃ (methyl)	-CHO (aldehyde)
Occurrence	All photosynthetic organisms except bacteria	Green plants and green algae
Color	Blue-green	Yellow-green

2. Carotenoids (Accessory Pigments)

• Terpenoid lipids: yellow, orange, red, brown pigments
• Absorb strongly in blue-violet wavelength (430-500nm)
• Transfer energy to chlorophyll ‘a’
• Energy transfer order: Carotenoids → Chlorophyll ‘b’ → Chlorophyll ‘a’

Types of Carotenoids:

• Carotenes: Orange-red pigments (β-carotene most common)
• Xanthophylls: Yellow-orange, oxygen-containing derivatives (lutein, zeaxanthin)

Functions of Carotenoids:

• Broaden spectrum of light for photosynthesis
• Protect chlorophyll by absorbing/dissipating intense light
• Protect human eyes (macular pigments)

• Oxygen released during photosynthesis comes from water
• Important source of atmospheric oxygen for aerobic respiration

Van Niel’s Hypothesis (1930s):

Plants split water as source of hydrogen, releasing oxygen as by-product. Based on studies of bacteria that make carbohydrates but don’t release oxygen.

Isotope Experiments (1940s):

Confirmed Van Niel’s hypothesis using heavy oxygen isotope O¹⁸:

• Group 1: H₂O with O¹⁸ + CO₂ with O¹⁶ → Produced O¹⁸
• Group 2: H₂O with O¹⁶ + CO₂ with O¹⁸ → Did not produce O¹⁸

Conclusion: Oxygen produced during photosynthesis comes from water, not CO₂.

• Acts as carbon source for synthesis of organic compounds
• Reduced during light-independent reactions using ATP and NADPH
• About 10% of total photosynthesis occurs in terrestrial plants; 90% in aquatic systems

Sources of CO₂:

• Aquatic organisms: Dissolved CO₂, bicarbonates, carbonates
• Terrestrial plants: Atmospheric CO₂ (0.03-0.04%)

Passage of CO₂ in Plants:

• Enters leaves through stomata
• Dissolves in water absorbed by mesophyll cell walls
• Stomata cover only 1-2% of leaf surface but allow proportionally more CO₂ diffusion

Stomatal Regulation:

• Stomata open during daytime when CO₂ required for photosynthesis
• Stomata close at night when photosynthesis stops
• Regulated by guard cells with peculiar structure

Photosynthesis is a ‘redox process’ with two main parts:

1. Light-Dependent Reactions:

• Occur in grana on thylakoid membrane
• Use light energy to make ATP and NADPH
• Input: Water; Output: Oxygen

2. Light-Independent Reactions (Dark Reactions):

• Occur in stroma of chloroplast
• Use ATP and NADPH to convert CO₂ to G3P (sugar)
• Also occur in daytime when light reaction products available

Photosynthetic pigments organized into clusters called photosystems on thylakoid membranes for efficient light absorption.

Photosystem Structure:

• Antenna Complex (Peripheral): Accessory pigments (chl b, carotenoids) channel energy to reaction centre
• Reaction Centre (Central): Chlorophyll ‘a’ with primary electron acceptor and electron carriers

Types of Photosystems:

• PS-I (P700): Chlorophyll ‘a’ absorbs maximum at 700nm
• PS-II (P680): Chlorophyll ‘a’ absorbs maximum at 680nm
• Named in order of discovery, not occurrence

Energy Transfer Mechanism:

1. Pigments in antenna complex absorb light of various wavelengths
2. Energy passed to chlorophyll ‘a’ in reaction centre
3. Chlorophyll ‘a’ electrons become excited and escape
4. Electrons move to electron transport chain, oxidizing chlorophyll

Predominant pathway in higher plants using both photosystems. Also called Z-scheme due to Z-shaped electron flow.

Mechanism Steps:

1. Absorption by PS-II and Electron Excitation

• Photons strike PS-II antenna complex
• Energy reaches P680 reaction centre
• Electrons excited and captured by primary electron acceptor
• Creates “electron holes” in chlorophyll

2. Photolysis of Water

• Water splitting complex (manganese cluster) on luminal side of thylakoid
• Water breaks into: 2H⁺ + 2e⁻ + ½O₂
• Electrons fill holes in PS-II
• Oxygen released as by-product

3. Electron Flow from PS-II to PS-I

• Electrons flow through electron transport chain:
• Primary acceptor → Plastoquinone (Pq) → Cytochrome complex → Plastocyanin (Pc) → PS-I
• Cytochrome complex acts as proton pump: moves H⁺ from stroma to thylakoid interior
• Creates proton gradient for ATP synthesis via ATP synthase (chemiosmosis)

4. Absorption by PS-I and Electron Excitation

• P700 absorbs photons, electrons excited to higher energy
• Electrons captured by primary acceptor of PS-I
• Holes filled by electrons from PS-II

5. Electron Flow from PS-I to NADP⁺

• Electrons flow: PS-I → Ferredoxin (Fd) → NADP reductase → NADP⁺
• NADP⁺ + 2e⁻ + H⁺ → NADPH
• One photon excites one electron

End Products of Light Reactions:

• NADPH/NADPH₂
• ATP
• Molecular oxygen (O₂)

Occurs when ATP supply needs to catch up with demand (high NADPH, low ATP). Uses only PS-I.

Mechanism:

1. PS-I absorbs energy, electrons excited
2. Electrons flow: PS-I → Ferredoxin → Cytochrome b₆-f complex → Plastocyanin → back to PS-I
3. ATP generated by chemiosmosis at cytochrome complex
4. Electrons return to P700 reaction centre

Key Differences from Non-Cyclic:

• No photolysis of water
• No NADPH production
• No oxygen release
• Only ATP produced
• Electrons recycled (not passed to NADP⁺)

Feature	Non-Cyclic	Cyclic
Photosystems Used	Both PS-I and PS-II	Only PS-I
Electron Source	Water (photolysis)	PS-I (recycled)
Final Electron Acceptor	NADP⁺	P700 (recycled)
Products	ATP, NADPH, O₂	ATP only
When it Occurs	Normal conditions	When ATP low, NADPH high

Also called dark reactions (but occur in daytime). Require NADPH, ATP, and CO₂. Occur in stroma of chloroplast.

1. Carbon Fixation

• CO₂ combines with RuBP (ribulose 1,5-bisphosphate, C₅)
• Catalyzed by RuBisCO (most abundant protein on Earth)
• Forms unstable 6-carbon intermediate
• Immediately splits into two 3-PGA molecules (3-phosphoglycerate)
• CO₂ + RuBP (C₅) → 6C intermediate → 2 PGA (C₃)

2. Reduction

• 3-PGA phosphorylated by ATP to form 1,3-bisphosphoglycerate
• Reduced by NADPH to form G3P (glyceraldehyde 3-phosphate)
• 6(3-PGA) + 6ATP + 6NADPH₂ → 6(3-PGAL) + 6NADP⁺ + 6ADP + 6Pᵢ
• 6 G3P produced but only 1 leaves cycle; 5 regenerate RuBP

3. Regeneration of RuBP

• 5 G3P molecules rearranged to form 3 RuBP molecules
• Requires 3 ATP molecules
• 5(3-PGAL) + 3ATP → 3(RuBP) + 3ADP + 2Pᵢ

Overall Calvin Cycle Equation:

3CO₂ + 6NADPH + 9ATP → (CH₂O)₃ + 6NADP⁺ + 9ADP + 9Pᵢ + 3H₂O

To produce one glucose molecule (C₆H₁₂O₆), need two cycles (6 CO₂ fixed).

Cellular respiration: Process by which organisms breakdown complex compounds to harvest usable energy.

External respiration: Exchange of respiratory gases between organism and environment.

Two Types of Cellular Respiration:

1. Aerobic Respiration

• Occurs in presence of O₂
• Complete breakdown of glucose to CO₂ and H₂O
• Location in eukaryotes: Mitochondria
• Net ATP: 36 or 38 ATP

2. Anaerobic Respiration (Fermentation)

• Occurs in absence of O₂
• Incomplete breakdown of glucose
• Location: Cytoplasm
• Net ATP: 2 ATP

Feature	Aerobic Respiration	Anaerobic Respiration
Oxygen Requirement	Requires O₂	No O₂ required
Glucose Breakdown	Complete to CO₂ + H₂O	Incomplete
End Products	CO₂, H₂O, energy	Lactic acid or ethanol + CO₂
ATP Yield (Net)	36 or 38 ATP	2 ATP
Location in Eukaryotes	Mitochondria	Cytoplasm

1. Alcoholic Fermentation (Yeast)

1. Glycolysis: Glucose → 2 Pyruvate + 2 ATP + 2 NADH
2. Pyruvate decarboxylation: Pyruvate → Acetaldehyde + CO₂
3. Reduction: Acetaldehyde + NADH → Ethanol + NAD⁺

2. Lactic Acid Fermentation

1. Glycolysis: Glucose → 2 Pyruvate + 2 ATP + 2 NADH
2. Reduction: Pyruvate + NADH → Lactic acid + NAD⁺

Occurs in: Anaerobic bacteria and muscle cells during strenuous exercise when oxygen supply exhausted.

Glycolysis = breakdown of glucose into two pyruvate molecules through enzymatic reactions.

Key Features:

• Location: Cytoplasm
• Occurs with or without O₂ (aerobic or anaerobic)
• Requires: Enzymes, ATP, NAD⁺

Two Phases of Glycolysis:

1. Preparatory Phase (Investment Phase)

• Consumes 2 ATP molecules
• Glucose phosphorylated and split
• End products: G3P (glyceraldehyde 3-phosphate) and DHAP (dihydroxyacetone phosphate)
• DHAP isomerizes to G3P

2. Oxidative Phase (Pay-off Phase)

• Produces ATP through substrate-level phosphorylation
• Produces NADH
• G3P oxidized to pyruvate
• Net production: 2 ATP, 2 NADH per glucose

Energy Accounting:

• ATP consumed: 2 ATP
• ATP produced: 4 ATP
• Net ATP: 2 ATP
• NADH produced: 2 NADH

Key Enzymes in Glycolysis:

• Hexokinase/Glucokinase: Phosphorylates glucose
• Phosphofructokinase (PFK): Rate-limiting enzyme
• Pyruvate kinase: Produces pyruvate and ATP

Pyruvate Oxidation (Link Reaction):

• Pyruvate enters mitochondria via pyruvate translocase
• Oxidative decarboxylation: Pyruvate → Acetyl CoA + CO₂
• Enzyme: Pyruvate dehydrogenase complex
• Produces: 1 NADH per pyruvate (2 per glucose)

Krebs Cycle Steps (per acetyl CoA):

1. Synthesis: Acetyl CoA + Oxaloacetate → Citrate (CoA released)
2. Dehydration: Citrate → cis-Aconitate
3. Hydration: cis-Aconitate → Isocitrate
4. Oxidative Decarboxylation: Isocitrate → α-Ketoglutarate + CO₂ + NADH
5. Oxidative Decarboxylation: α-Ketoglutarate → Succinyl CoA + CO₂ + NADH
6. ATP Formation: Succinyl CoA → Succinate + ATP (or GTP)
7. Dehydrogenation: Succinate → Fumarate + FADH₂
8. Hydration: Fumarate → Malate
9. Dehydrogenation: Malate → Oxaloacetate + NADH

Products per Glucose (2 turns of cycle):

• ATP: 2 (1 per acetyl CoA)
• NADH: 6 (3 per acetyl CoA)
• FADH₂: 2 (1 per acetyl CoA)
• CO₂: 4 (2 per acetyl CoA)

After Krebs cycle, most glucose energy is in NADH and FADH₂. ETC oxidizes these to produce ATP.

ETC Components (in order):

1. NADH dehydrogenase complex (I): Accepts electrons from NADH
2. FADH₂ dehydrogenase complex (II): Accepts electrons from FADH₂
3. Coenzyme Q (Ubiquinone): Mobile electron carrier
4. Cytochrome reductase complex (III): Transfers electrons to cytochrome c
5. Cytochrome c: Mobile electron carrier
6. Cytochrome oxidase complex (IV): Transfers electrons to O₂
7. ATP synthase complex (V): Produces ATP using proton gradient

Electron Flow:

• NADH → Complex I → CoQ → Complex III → Cyt c → Complex IV → O₂
• FADH₂ → Complex II → CoQ → Complex III → Cyt c → Complex IV → O₂
• O₂ is final electron acceptor: O₂ + 4e⁻ + 4H⁺ → 2H₂O

Proton Pumping and Chemiosmosis:

• Energy from electron flow used to pump H⁺ from matrix to intermembrane space
• Creates proton gradient (higher H⁺ in intermembrane space)
• H⁺ flow back through ATP synthase drives ATP production
• This mechanism = chemiosmosis

ATP Yield from Coenzymes:

• NADH: 3 ATP (when electrons enter at Complex I)
• FADH₂: 2 ATP (when electrons enter at Complex II)

ATP Production Summary (per glucose):

Pathway	Coenzyme Yield	ATP Yield	Notes
Glycolysis	2 NADH	2 ATP (net) + 4-6 ATP from NADH	NADH from cytoplasm may yield 2 or 3 ATP depending on shuttle
Pyruvate Oxidation	2 NADH	6 ATP	NADH from mitochondrial matrix
Krebs Cycle (2 turns)	6 NADH + 2 FADH₂	2 ATP + 18 ATP + 4 ATP = 24 ATP	2 ATP substrate-level + 18 from NADH + 4 from FADH₂
Total		30-32 ATP in eukaryotes 38 ATP in prokaryotes	Prokaryotes have no mitochondria so no transport costs

Prokaryotes vs Eukaryotes:

• Prokaryotes: 38 ATP (no mitochondria, all in cytoplasm)
• Eukaryotes: 36 ATP (mitochondrial membrane transport costs 2 ATP)
• NADH from glycolysis in cytoplasm must be “shuttled” into mitochondria
• Different shuttle systems yield different ATP (malate-aspartate = 3 ATP; glycerol-3-phosphate = 2 ATP)

Comparison of Chemiosmosis Sites:

Site	Proton Pumping	H⁺ Diffusion
Chloroplast	Stroma to Lumen	Lumen to Stroma
Mitochondria	Matrix to Intermembrane space	Intermembrane space to Matrix
Bacteria	Cytoplasm to Periplasmic space	Periplasmic space to Cytoplasm