Chapter 7: Inside the Cell

Major Components of Prokaryotic Cells

Prokaryotic cells, such as bacteria and archaea, lack a membrane-bound nucleus and organelles. Their structure is simpler than eukaryotic cells.

• Plasma Membrane: Phospholipid bilayer that controls entry and exit of substances.

• Cell Wall: Provides structural support and protection; composed of peptidoglycan in bacteria.

• Cytoplasm: Gel-like substance containing water, enzymes, nutrients, and the cell's genetic material.

• Ribosomes: Sites of protein synthesis; smaller than eukaryotic ribosomes.

• Nucleoid: Region where the single, circular DNA molecule is located.

• Flagella: Used for movement.

• Pili/Fimbriae: Structures for attachment to surfaces or other cells.

Components of Eukaryotic Cells (Including Non-Animal Cells)

Eukaryotic cells have membrane-bound organelles and a nucleus. Plant, fungal, and protist cells may have additional structures.

• Nucleus: Contains DNA; site of transcription.

• Mitochondria: Site of cellular respiration; produces ATP.

• Endoplasmic Reticulum (ER): Rough ER synthesizes proteins; Smooth ER synthesizes lipids.

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

• Lysosomes: Digestive organelles (mainly in animal cells).

• Peroxisomes: Break down fatty acids and detoxify harmful substances.

• Chloroplasts: (Plants and algae) Site of photosynthesis.

• Vacuoles: Storage and structural support (large central vacuole in plants).

• Cell Wall: (Plants, fungi, some protists) Provides support and protection.

Flow of Molecules Into and Out of the Nucleus

The nucleus is surrounded by a double membrane (nuclear envelope) with nuclear pores that regulate transport.

• Transported Molecules: mRNA, tRNA, ribosomal subunits (out); proteins, nucleotides (in).

• Mechanism: Nuclear pores allow selective transport via nuclear localization signals and transport proteins.

Endomembrane System Organelles and Functions

The endomembrane system includes organelles involved in synthesis, modification, and transport of proteins and lipids.

• Endoplasmic Reticulum (ER): Protein and lipid synthesis.

• Golgi Apparatus: Protein modification and sorting.

• Lysosomes: Digestion and recycling.

• Vesicles: Transport materials between organelles.

Signal Hypothesis: Protein Targeting to the Endomembrane System

Proteins destined for secretion or for organelles in the endomembrane system follow a specific pathway.

1. Protein synthesis begins on free ribosomes.

2. Signal sequence emerges from ribosome.

3. Signal recognition particle (SRP) binds signal sequence.

4. SRP binds to SRP receptor on ER membrane.

5. Ribosome docks on ER; translation resumes.

6. Protein is threaded into ER lumen.

7. Signal sequence is removed.

8. Protein folds and undergoes modifications.

9. Protein is packaged into vesicles.

10. Vesicles transport protein to Golgi for further processing.

Endocytosis, Phagocytosis, and Autophagy

• Receptor-Mediated Endocytosis: Uptake of specific molecules via receptor binding.

• Phagocytosis: Engulfment of large particles or cells.

• Autophagy: Digestion of cell's own damaged organelles or proteins.

Chapter 11: Cell-Cell Interactions

Extracellular Matrix (ECM) of Animal and Plant Cells

The ECM provides structural support and mediates cell signaling.

• Animal ECM: Composed of proteins (collagen, elastin) and polysaccharides.

• Plant ECM: Cell wall made of cellulose, hemicellulose, and pectin.

• Function: Support, protection, cell communication.

Types of Cell-Cell Connections

Cells connect via specialized structures to maintain tissue integrity and facilitate communication.

• Tight Junctions: Seal cells together, preventing passage of molecules.

• Desmosomes: Provide mechanical strength by linking cytoskeletons.

• Gap Junctions: (Animals) Allow direct transfer of ions and small molecules.

• Plasmodesmata: (Plants) Channels for transport between cells.

Cell-Cell Connections Facilitating Transfer

• Gap Junctions: Facilitate transfer of molecules and signals in animal cells.

• Plasmodesmata: Facilitate transfer in plant cells.

Long-Distance Cell Signaling

Cells communicate over long distances using signaling molecules (hormones, neurotransmitters).

• Reception: Signaling molecules bind to receptors (e.g., G-protein-coupled receptors).

• Transduction: Second messengers relay the signal inside the cell.

• Response: Cellular changes occur (gene expression, metabolism).

G-Protein-Coupled Receptors and Second Messengers

• G-Protein-Coupled Receptors (GPCRs): Activate G-proteins, which trigger second messenger pathways.

• Second Messengers: Small molecules (e.g., cAMP, Ca2+) that amplify the signal.

Chapter 8: Energy and Enzymes

Potential Energy, Enthalpy, Entropy, and Gibbs Free Energy

Biological systems obey the laws of thermodynamics. Gibbs free energy determines whether reactions are spontaneous.

• Potential Energy: Stored energy due to position or structure.

• Enthalpy (H): Total heat content.

• Entropy (S): Measure of disorder.

• Gibbs Free Energy (G): Energy available to do work.

Equation:

• Exergonic/Spontaneous:

• Endergonic/Non-Spontaneous:

Redox Reactions and Phosphorylation

• Redox Reactions: Transfer of electrons; oxidation (loss), reduction (gain).

• Phosphorylation: Addition of phosphate group; often activates molecules.

• Coupling: Endergonic reactions are driven by exergonic reactions (e.g., ATP hydrolysis).

Biological Reaction Hurdles and Enzyme Function

• Activation Energy: Energy barrier to starting a reaction.

• Proper Orientation: Reactants must be correctly aligned.

• Enzymes: Lower activation energy and orient substrates.

Enzyme Activity and Regulation

• Substrate Saturation: Maximum rate when all enzyme active sites are occupied.

• Covalent Regulation: Enzyme activity modified by covalent attachment (e.g., phosphorylation).

• Noncovalent Regulation: Temporary binding of regulators.

• Competitive Regulation: Inhibitor binds active site.

• Allosteric Regulation: Inhibitor or activator binds elsewhere, changing enzyme shape.

Example: Enzyme Activity in Bamboo Shark

Enzyme activity can be affected by environmental conditions such as temperature and pH.

Additional info: Enzyme studies often measure reaction rates under varying conditions to determine optimal activity.

Chapter 9: Cellular Respiration and Fermentation

Catabolic vs. Anabolic Processes

• Catabolic: Breakdown of molecules to release energy (e.g., cellular respiration).

• Anabolic: Synthesis of molecules, requiring energy (e.g., photosynthesis).

Inputs and Outputs of Cellular Respiration

• Inputs: Glucose, oxygen.

• Outputs: Carbon dioxide, water, ATP.

Four Steps of Cellular Respiration

1. Glycolysis: Cytosol.

2. Pyruvate Processing: Mitochondrial matrix.

3. Citric Acid Cycle: Mitochondrial matrix.

4. Electron Transport Chain & Oxidative Phosphorylation: Inner mitochondrial membrane.

Redox Chemistry, Phosphorylation, and Feedback Inhibition

• Redox: Electron transfer (NAD+ to NADH).

• Phosphorylation: ATP synthesis.

• Feedback Inhibition: End product inhibits earlier steps (e.g., ATP inhibits phosphofructokinase).

Importance of Oxygen

• Oxygen: Final electron acceptor in electron transport chain; essential for efficient ATP production.

Fermentation in Low Oxygen Conditions

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

• Example: Lactic acid fermentation in muscle cells.

Chapter 10: Photosynthesis

Role of Chlorophyll in Capturing Light Energy

• Chlorophyll: Pigment that absorbs light energy, initiating photosynthesis.

• Location: Thylakoid membranes of chloroplasts.

Locations of Photosynthesis Reactions

• Light-Dependent Reactions: Thylakoid membranes.

• Light-Independent Reactions (Calvin Cycle): Stroma of chloroplast.

Oxygen Production and Carbon Fixation

• Oxygen: Produced during light-dependent reactions (splitting water).

• Carbon Fixation: Occurs during Calvin cycle (light-independent reactions).

Comparison: Photosynthesis vs. Cellular Respiration

Importance of Rubisco and Photorespiration

• Rubisco: Enzyme that catalyzes carbon fixation in Calvin cycle.

• Photorespiration: Occurs when Rubisco binds O2 instead of CO2, reducing efficiency of photosynthesis.

Additional info: Photorespiration is more common under high temperatures and low CO2 concentrations.