Core Concepts in General Biology: Cells, Energy, Respiration, 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:

• Size: Eukaryotic cells are generally larger (10–100 μm) than prokaryotic cells (0.1–5 μm).

• Complexity: Eukaryotes have compartmentalized functions via organelles; prokaryotes do not.

Structure and Function of Organelles

Organelles are specialized structures within eukaryotic cells that perform distinct functions.

• 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.

Organelle Function and Cellular Activity

Each organelle contributes to the overall function and survival of the cell. For example, mitochondria generate ATP, which powers cellular processes, while the ER and Golgi apparatus are involved in protein synthesis and transport.

Endosymbiosis Theory

The endosymbiosis theory proposes that mitochondria and chloroplasts originated from free-living prokaryotes engulfed by ancestral eukaryotic cells. Evidence includes:

• Double membranes around mitochondria and chloroplasts

• Own circular DNA similar to bacterial DNA

• Reproduction by binary fission

Energy and Enzymes in Biological Systems

Potential vs. Kinetic Energy in Chemical Reactions

Energy exists in two main forms:

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

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

In chemical reactions, potential energy in bonds is converted to kinetic energy as molecules move and react.

Endergonic vs. Exergonic Reactions and Gibbs Free Energy

Reactions are classified by their energy changes:

• Endergonic reactions: Require energy input; products have more free energy than reactants ($\Delta G > 0$).

• Exergonic reactions: Release energy; products have less free energy than reactants ($\Delta G < 0$).

Gibbs Free Energy Equation:

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

Where $\Delta G$ is the change in free energy, $\Delta H$ is the change in enthalpy, $T$ is temperature (in Kelvin), and $\Delta S$ is the change in entropy.

Enzyme Function and Catalysis

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

• They bind substrates at the active site, facilitating the conversion to products.

• Enzyme activity can be affected by pH, temperature, and substrate concentration.

Activation Energy Diagram: Enzymes lower the peak of the energy barrier, making reactions proceed faster.

Cellular Respiration

Overview and Stages

Cellular respiration is the process by which cells extract energy from glucose to produce ATP. It consists of four interconnected stages:

1. Glycolysis (cytoplasm): Glucose is split into two pyruvate molecules.

2. Pyruvate Oxidation (mitochondrial matrix): Pyruvate is converted to acetyl-CoA.

3. Citric Acid Cycle (Krebs Cycle) (mitochondrial matrix): Acetyl-CoA is oxidized, producing NADH, FADH2, and CO2.

4. Electron Transport Chain (ETC) and Oxidative Phosphorylation (inner mitochondrial membrane): Electrons are transferred to oxygen, generating ATP.

Inputs and Outputs of Each Stage

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	6 NADH, 2 FADH2, 2 ATP, 4 CO2
ETC & Oxidative Phosphorylation	NADH, FADH2, O2	~26-28 ATP, H2O

Glycolysis: Two Phases

• Energy investment phase: 2 ATP are used to phosphorylate glucose.

• Energy payoff phase: 4 ATP and 2 NADH are produced.

Regulation of Glycolysis

Key enzymes (e.g., phosphofructokinase) regulate glycolysis through feedback inhibition by ATP and other metabolites.

Citric Acid Cycle (Krebs Cycle)

This cycle completes the oxidation of glucose derivatives, generating high-energy electron carriers (NADH, FADH2).

Electron Transport Chain and Oxidative Phosphorylation

Electrons from NADH and FADH2 pass through protein complexes, creating a proton gradient used by ATP synthase to generate ATP.

Aerobic vs. Anaerobic Respiration

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

• Anaerobic respiration: Uses other molecules (not O2) as electron acceptors; less efficient.

Fermentation

Occurs when oxygen is absent; regenerates NAD+ by converting pyruvate to lactate (animals) or ethanol (yeast).

Photosynthesis

Inputs, Outputs, and Stages

Photosynthesis converts light energy into chemical energy in plants, algae, and some bacteria. It occurs in two stages:

• Light-dependent reactions: Occur in the thylakoid membranes; produce ATP and NADPH.

• Calvin cycle (light-independent reactions): Occur in the stroma; use ATP and NADPH to fix CO2 into sugars.

Pigments and Light Absorption

Chlorophyll and accessory pigments absorb specific wavelengths of light, driving photosynthesis. The absorption spectrum determines which wavelengths are most effective.

Z-Scheme and ATP/NADPH Generation

The Z-scheme describes the flow of electrons from water through photosystem II and I, generating a proton gradient (for ATP synthesis) and reducing NADP+ to NADPH.

Connecting Light Reactions to the Calvin Cycle

ATP and NADPH produced in the light reactions provide the energy and reducing power for the Calvin cycle.

Calvin Cycle: Phases and Key Enzyme

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

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

• Regeneration: RuBP is regenerated from G3P, allowing 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 for the Calvin cycle.

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

Example: Corn is a C4 plant; cacti are CAM plants.