Chapter 15: Intracellular Compartments and Protein Sorting: Study Guide for Cell Biology

Membrane-Enclosed Organelles

Cellular Strategies for Compartmentalization

Cells employ strategies to isolate and organize their chemical reactions, ensuring efficiency and regulation. Eukaryotes have more highly developed compartmentalization than prokaryotes.

• Strategy 1: Use of membrane-enclosed organelles to separate processes.

• Strategy 2: Assembly of multi-enzyme complexes in the cytosol.

• Example: Eukaryotic cells contain organelles such as the nucleus, mitochondria, and endoplasmic reticulum, while prokaryotes rely mainly on cytosolic complexes.

Major Membrane-Enclosed Organelles and Their Functions

• Nucleus: Contains genetic material; site of DNA replication and transcription.

• Mitochondria: Site of cellular respiration and ATP production.

• Chloroplasts: Site of photosynthesis (in plants and algae).

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

• Golgi Apparatus: Modification, sorting, and packaging of proteins and lipids.

• Lysosomes: Degradation of macromolecules.

• Peroxisomes: Breakdown of fatty acids and detoxification.

• Vesicles: Transport of materials within the cell.

Double-Membrane Organelles

• Nucleus

• Mitochondria

• Chloroplasts

Cell Volume and Membrane Area

• Membrane-enclosed organelles occupy a significant portion of cell volume (up to 50%).

• The endoplasmic reticulum has a much larger membrane area than the plasma membrane.

Relationship Between ER and Nuclear Membrane

• The nuclear envelope is continuous with the endoplasmic reticulum.

Rough ER vs. Smooth ER

• Rough ER: Studded with ribosomes; synthesizes proteins for secretion or membrane insertion.

• Smooth ER: Lacks ribosomes; synthesizes lipids and detoxifies chemicals.

• Example: Liver cells have abundant smooth ER for detoxification.

Endomembrane System and Communication

• Includes the ER, Golgi apparatus, lysosomes, endosomes, and plasma membrane.

• Organelles communicate via vesicular transport.

Evolution of Nucleus, Mitochondria, and Chloroplasts

• Nucleus: Thought to have evolved by invagination of the plasma membrane.

• Mitochondria and Chloroplasts: Originated from endosymbiotic events.

Protein Sorting

Mechanisms of Protein Entry into Organelles

Proteins are sorted to organelles by specific mechanisms, depending on their destination.

• Transport through nuclear pores (nucleus).

• Translocation across membranes (mitochondria, chloroplasts, ER, peroxisomes).

• Vesicular transport (between ER, Golgi, lysosomes, plasma membrane).

Direct Protein Reception from Cytosol

• Nucleus

• Mitochondria

• Chloroplasts

• Peroxisomes

Proteins Lacking Sorting Signals

• Remain in the cytosol.

Protein Synthesis for Mitochondria and Chloroplasts

• Proteins are synthesized in the cytosol and imported into these organelles.

Effects of Signal Sequence Manipulation

• Removing an ER signal sequence prevents ER targeting; attaching it to a cytosolic protein redirects it to the ER.

• Proteins with both nuclear localization and export signals shuttle between nucleus and cytosol.

• Proteins with both ER and nuclear signals are typically directed to the ER.

Nuclear Envelope Structure

• Double membrane with nuclear pores for transport.

Protein Conformation During Transport

• Proteins remain folded during nuclear transport.

• Proteins are unfolded during transport into mitochondria and chloroplasts.

Nuclear Pore Function

• Allow free passage of small, water-soluble molecules.

• Restrict larger molecules unless they have specific signals.

Nuclear Import Receptors

• Bind proteins with nuclear localization signals and escort them through nuclear pores.

Mitochondrial Protein Import and Chaperones

• Proteins are recognized by import receptors and translocated into the matrix.

• Chaperones assist in protein folding inside mitochondria.

Peroxisomal Protein Transport

• Proteins are imported via direct translocation or vesicular transport.

Entry Point for Secretory Proteins

• Endoplasmic reticulum is the entry point for proteins destined for secretion or organelles.

Destinations of Transmembrane vs. Water-Soluble Proteins

• Transmembrane proteins: Inserted into membranes.

• Water-soluble proteins: Released into organelle lumen or extracellular space.

Free vs. Membrane-Bound Ribosomes

• Free ribosomes: Synthesize cytosolic proteins.

• Membrane-bound ribosomes: Synthesize proteins for membranes or secretion.

Energy Source for ER Protein Transport

• Energy is provided by GTP hydrolysis and ATP.

Polyribosomes and Rough ER

• Polyribosome: Multiple ribosomes translating a single mRNA.

• Rough ER: Membrane with attached ribosomes.

SRP and SRP Receptor Function

• Signal Recognition Particle (SRP): Binds ER signal sequence and pauses translation.

• SRP Receptor: Located on ER membrane; guides ribosome to translocation channel.

ER Signal Sequence Fate

• Usually cleaved off after protein enters ER.

Transmembrane Protein Signal Sequences

• Single-pass: Have ER signal and stop-transfer sequence.

• Multipass: Have multiple start-transfer and stop-transfer sequences.

Vesicular Transport

Endocytic vs. Exocytic Pathways

• Endocytic: Brings materials into cell; involves endosomes and lysosomes.

• Exocytic: Moves materials out; involves ER, Golgi, and plasma membrane.

Protein Coat Function and Fate

• Coat proteins (e.g., clathrin) help vesicle formation and are removed after budding.

Clathrin-Coated Vesicle Cargo Selection and Budding

• Adaptor proteins select cargo; clathrin forms coat; vesicle buds off parent membrane.

Vesicle Tethering, Docking, and Fusion

• Tethering: Initial contact; involves tethering proteins.

• Docking: Vesicle attaches to target membrane; involves SNARE proteins.

• Fusion: Membranes merge; SNAREs facilitate fusion.

Secretory Pathways

Covalent Modifications in the ER

• Disulfide bond formation

• Glycosylation

• Folding and assembly

Protein Glycosylation in the ER

• Proteins with specific sequences are glycosylated; sugars are attached by oligosaccharyl transferase.

Retention and Retrieval of ER Proteins

• Proteins with ER retention signals are kept or returned to ER from Golgi.

Retention of Misfolded Proteins

• Misfolded proteins are retained in ER and degraded if not properly assembled.

Unfolded Protein Response (UPR)

• Triggered by accumulation of misfolded proteins; increases chaperone production and may lead to apoptosis.

Golgi Apparatus Structure and Location

• Stacked cisternae near the nucleus; receives proteins from ER.

Protein Movement in Golgi

• Proteins move via vesicular transport between cisternae.

Sorting in Cis and Trans Golgi Networks

• Cis: Entry; sorts for further processing.

• Trans: Exit; sorts for final destination.

Oligosaccharide Addition in Golgi

• Additional sugars are added to glycoproteins in Golgi stack.

Constitutive vs. Regulated Exocytosis

• Constitutive: Continuous secretion; proteins released immediately.

• Regulated: Secretion in response to signals; proteins stored in vesicles.

Lipid Delivery and Removal at Plasma Membrane

• Lipids are delivered by vesicles and removed by endocytosis.

Protease Treatment for Protein Transport Studies

• Protease can determine if a protein is inside an organelle by digesting exposed proteins.

Temperature-Sensitive Mutants in Yeast

• Used to dissect secretory pathway by blocking steps at non-permissive temperatures.

GFP for Protein Tracking

• Green Fluorescent Protein (GFP) tags allow visualization of protein location and movement in living cells.

Endocytic Pathways

Pinocytosis vs. Phagocytosis

• Pinocytosis: Uptake of fluids and small molecules; occurs in most cells.

• Phagocytosis: Uptake of large particles; performed by specialized cells (e.g., macrophages).

Microorganism Recognition and Digestion

• Phagocytic cells recognize, engulf, and digest microorganisms using receptors and lysosomes.

Pinocytosis and Cell Surface Area

• Pinocytosis is balanced by exocytosis, maintaining cell surface area and volume.

Pinocytosis vs. Receptor-Mediated Endocytosis

• Pinocytosis: Non-specific uptake.

• Receptor-mediated: Specific uptake via receptors (e.g., LDL cholesterol).

Cholesterol Transport by Receptor-Mediated Endocytosis

• LDL binds to receptor, is internalized, and cholesterol is released in cytosol.

Viruses and Receptor-Mediated Endocytosis

• Viruses exploit this pathway to enter cells.

Fates of Receptors and Cargo After Endocytosis

• Receptors can be recycled, degraded, or transported to other locations.

• Cargo can be delivered to lysosomes for degradation.

Endosome pH and Sorting

• Endosomes maintain acidic pH, which is crucial for sorting and release of cargo.

Lysosome pH and Function

• Lysosomes are acidic; pH is essential for enzyme activity.

Lysosomal Enzymes and Transport

• Contain hydrolases; enzymes are transported via mannose-6-phosphate tagging.

Pathways to Lysosomes

• Endocytosis, phagocytosis, and autophagy deliver materials to lysosomes.

Fate of Digestion Products

• Products are transported to cytosol for reuse or excretion.

Autophagy

• Cellular process for degrading and recycling organelles and macromolecules.

• Activated during starvation or stress.

Summary Table: Major Membrane-Enclosed Organelles

Organelle	Membrane Type	Main Function
Nucleus	Double	Genetic information storage, transcription
Mitochondria	Double	ATP production, respiration
Chloroplast	Double	Photosynthesis
ER (Rough/Smooth)	Single	Protein/lipid synthesis
Golgi Apparatus	Single	Protein modification, sorting
Lysosome	Single	Macromolecule degradation
Peroxisome	Single	Fatty acid breakdown, detoxification

Key Equations

• ATP Hydrolysis:

• $\mathrm{ATP} + \mathrm{H}_2\mathrm{O} \rightarrow \mathrm{ADP} + \mathrm{P}_i + \text{energy}$

• GTP Hydrolysis:

• $\mathrm{GTP} + \mathrm{H}_2\mathrm{O} \rightarrow \mathrm{GDP} + \mathrm{P}_i + \text{energy}$

Additional info: Academic context and explanations were expanded for completeness and clarity, based on standard cell biology textbooks.