Core Concepts in Cell Structure, Metabolism, and Photosynthesis

Cell Structure and Function

Prokaryotic vs. Eukaryotic Cells

Cells are the fundamental units of life, classified as either prokaryotic or eukaryotic based on their structural features.

• Prokaryotic cells lack a membrane-bound nucleus and organelles. Their DNA is located in a region called the nucleoid. Examples: Bacteria and Archaea.

• Eukaryotic cells have a true nucleus enclosed by a nuclear envelope and possess membrane-bound organelles. Examples: Plants, Animals, Fungi, and Protists.

• Key differences: Eukaryotes are generally larger, have complex internal structures, and can form multicellular organisms.

Example: Escherichia coli (prokaryote) vs. Homo sapiens skin cell (eukaryote).

Structure and Function of Organelles

Organelles are specialized structures within eukaryotic cells that perform distinct functions necessary for cellular life.

• Nucleus: Stores genetic material (DNA) and coordinates cell activities.

• Mitochondria: Site of cellular respiration and ATP production.

• Chloroplasts: Conduct photosynthesis in plant cells.

• Endoplasmic Reticulum (ER): Synthesizes proteins (rough ER) and lipids (smooth ER).

• Golgi Apparatus: Modifies, sorts, and packages proteins and lipids.

• Lysosomes: Contain digestive enzymes for waste breakdown.

Additional info: Prokaryotes lack these membrane-bound organelles but may have specialized internal membranes.

Organelle Function and Cellular Activity

Each organelle contributes to the overall function and survival of the cell.

• Mitochondria generate ATP, the cell's energy currency, through aerobic respiration.

• Chloroplasts convert solar energy into chemical energy via photosynthesis.

• Endoplasmic Reticulum and Golgi Apparatus are involved in protein and lipid synthesis, modification, and transport.

Endosymbiosis Theory

The endosymbiosis theory explains the origin of mitochondria and chloroplasts as formerly free-living prokaryotes engulfed by ancestral eukaryotic cells.

• Evidence: Both organelles have their own DNA, double membranes, and reproduce independently within the cell.

• Significance: This theory highlights the evolutionary relationship between prokaryotes and eukaryotes.

Energy and Metabolism

Potential vs. Kinetic Energy in Chemical Reactions

Energy exists in two main forms relevant to biology: potential and kinetic.

• Potential energy: Stored energy due to position or structure (e.g., chemical bonds).

• Kinetic energy: Energy of motion (e.g., movement of molecules).

• During chemical reactions, potential energy in bonds is converted to kinetic energy (heat, movement) and vice versa.

Endergonic vs. Exergonic Reactions and Gibbs Free Energy

Chemical reactions are classified by their energy changes, described by Gibbs free energy ($\Delta G$).

• Exergonic reactions: Release energy; $\Delta G < 0$; spontaneous.

• Endergonic reactions: Require energy input; $\Delta G > 0$; non-spontaneous.

• Gibbs free energy equation:

$\Delta G = \Delta H - T\Delta S$

• Where $\Delta H$ = change in enthalpy, $T$ = temperature (Kelvin), $\Delta S$ = change in entropy.

Enzyme Catalysis and Activation Energy

Enzymes are biological catalysts that speed up reactions by lowering the activation energy barrier.

• Activation energy ($E_a$): The minimum energy required to initiate a chemical reaction.

• Enzymes bind substrates, stabilize the transition state, and reduce $E_a$.

Additional info: Enzymes are highly specific and can be regulated by various factors.

Factors Affecting Enzyme Function

Enzyme activity is influenced by environmental conditions.

• pH: Each enzyme has an optimal pH; deviations can denature the enzyme.

• Temperature: Higher temperatures increase reaction rates up to a point, but excessive heat denatures enzymes.

Cellular Respiration

Stages of Cellular Respiration

Cellular respiration is a multi-step process that converts glucose into ATP.

1. Glycolysis: Occurs in the cytoplasm; breaks glucose into pyruvate.

2. Pyruvate oxidation: Converts pyruvate to acetyl-CoA in the mitochondria.

3. Citric Acid Cycle (Krebs Cycle): Completes glucose oxidation, producing NADH and FADH2.

4. Electron Transport Chain (ETC) and Oxidative Phosphorylation: Uses electrons from NADH/FADH2 to generate ATP.

Inputs and Outputs of Cellular Respiration

Stage	Inputs	Outputs
Glycolysis	Glucose, 2 NAD+, 2 ATP	2 Pyruvate, 2 NADH, 4 ATP (net 2 ATP)
Pyruvate Oxidation	2 Pyruvate, 2 NAD+	2 Acetyl-CoA, 2 NADH, 2 CO2
Citric Acid Cycle	2 Acetyl-CoA, 6 NAD+, 2 FAD, 2 ADP	4 CO2, 6 NADH, 2 FADH2, 2 ATP
ETC & Oxidative Phosphorylation	10 NADH, 2 FADH2, O2	~34 ATP, H2O

Glycolysis: Phases and Regulation

• Energy investment phase: Consumes ATP to phosphorylate glucose.

• Energy payoff phase: Produces ATP and NADH.

• Regulation: Key enzymes (e.g., phosphofructokinase) are regulated by feedback inhibition.

Citric Acid Cycle

The citric acid cycle completes the oxidation of glucose derivatives, generating high-energy electron carriers.

• Key role: Produces NADH and FADH2 for the ETC.

Electron Transport Chain (ETC) and Oxidative Phosphorylation

The ETC uses electrons from NADH and FADH2 to pump protons, creating a gradient used by ATP synthase to produce ATP.

• Oxidative phosphorylation: ATP generation using the energy from the proton gradient.

Aerobic vs. Anaerobic Respiration and Fermentation

• Aerobic respiration: Uses oxygen as the final electron acceptor; produces more ATP.

• Anaerobic respiration: Uses other molecules as electron acceptors; less efficient.

• Fermentation: Allows ATP production without oxygen; regenerates NAD+ but yields less ATP.

Photosynthesis

Inputs and Outputs of Photosynthesis

Photosynthesis converts light energy into chemical energy in plants, algae, and some bacteria.

Stage	Location	Inputs	Outputs
Light Reactions	Thylakoid membrane	Light, H2O, NADP+, ADP	O2, ATP, NADPH
Calvin Cycle	Stroma	CO2, ATP, NADPH	Glucose (G3P), NADP+, ADP

Pigments and Light Absorption

• Chlorophyll absorbs light most efficiently in the blue and red wavelengths, reflecting green.

• Accessory pigments (carotenoids) broaden the spectrum of light absorption.

Z-Scheme and ATP/NADPH Generation

The Z-scheme describes the flow of electrons through photosystems II and I, leading to the production of ATP (via a proton gradient) and NADPH (via electron transport).

Connecting Light Reactions and Calvin Cycle

• ATP and NADPH produced in the light reactions are used as energy and reducing power in the Calvin cycle to fix carbon dioxide.

Calvin Cycle: Phases and RuBisCO

The Calvin cycle is the set of light-independent reactions in photosynthesis, consisting of three phases:

1. Fixation: CO2 is attached to ribulose bisphosphate (RuBP) by the enzyme RuBisCO.

2. Reduction: ATP and NADPH are used to convert 3-phosphoglycerate into glyceraldehyde-3-phosphate (G3P).

3. Regeneration: Some G3P is used to regenerate RuBP, enabling the cycle to continue.

C4 and CAM Plant Adaptations

C4 and CAM plants have evolved mechanisms to minimize photorespiration by separating carbon fixation from the Calvin cycle in space (C4) or time (CAM).

• C4 plants: Fix CO2 in mesophyll cells, then transfer it to bundle-sheath cells where the Calvin cycle occurs.

• CAM plants: Fix CO2 at night and store it as malate, releasing it during the day for the Calvin cycle.

Additional info: These adaptations are especially important in hot, dry environments.