Chapter 3 Part 3: Eukaryotic Cell Structures & Endomembrane System

“Endomembrane” = any structure built from a phospholipid bilayer that is continuous or can fuse with other bilayers.
Only found in eukaryotic cells; prokaryotes lack these internal membranes.
Key advantage: organelles can bud off (vesicles) and merge seamlessly, creating an efficient intracellular transport network.

Nuclear envelope
• Double membrane (inner & outer); outer layer is continuous with rough ER.
Nuclear pores
• Regulated gateways.
• Permit exit of all RNA types (mRNA, tRNA, rRNA).
• Import nucleotides & proteins; strictly exclude DNA export.
Nucleolus
• Dense region where rRNA is processed & combined with proteins → ribosomal subunits.
• Ribosomal subunits exit via nuclear pores.
Chromatin vs. chromosomes
• Chromatin = DNA in loose, thread-like state (functional form for gene expression).
• Condenses into chromosomes only during cell division for ease of segregation.

Continuous with nuclear envelope; interior cavity = lumen (aka cisternal space).

Rough ER (RER)

Studded with ribosomes → easy to spot in micrographs.
Functions
• Initial protein synthesis (polypeptide elongation) & insertion into lumen.
• Early folding/processing steps.
• Phospholipid biosynthesis to expand its own membrane.
Morphology: broad, flattened sacs with large lumens.

Smooth ER (SER)

Lacks ribosomes.
Functions
• Carbohydrate synthesis/modification (e.g., glycogen metabolism).
• Steroid & lipid synthesis.
• Detoxification of drugs/poisons (especially in liver cells).
• Additional phospholipid production.
Morphology: narrow, tubular, coral-like branching pockets.

Stack of flattened membrane sacs (“cisternae” → pancake metaphor).
Receives transport vesicles from RER; contents enter the cis-face, exit the trans-face.
Final protein assembly: tertiary/quaternary folding, glycosylation, tagging for destination.
Generates new vesicles for delivery to lysosomes, plasma membrane, or secretion.

Transport Vesicles

Bud from RER/SER or Golgi; fuse with target membranes (Golgi, lysosome, plasma membrane).
Showcase of membrane continuity.

Lysosomes

Vacuoles

Large central vacuole in plants
• Water storage → produces turgor pressure that stiffens stems/leaves.
• Loss of water = wilting; refill = leaves re-extend for optimal light capture.
Animal examples: adipocytes store lipids in large vacuole-like droplets, but vacuoles are rare in animals overall.

Composition: rRNA + ~80 proteins.
Two subunits (large & small) separate when idle, join on mRNA during translation.
Free ribosomes
• Float in cytoplasm; synthesize proteins retained inside the cell (e.g., enzymes for glycolysis).
Bound ribosomes (on RER)
• Make proteins destined for secretion, lysosomes, or membrane insertion.

Double-membrane organelle
• Outer membrane (smooth)
• Inner membrane folded into cristae → ↑ surface area.
Internal compartments
• Matrix (innermost, enzyme-rich; site of citric acid cycle).
• Intermembrane space (between inner & outer; crucial for proton gradient).
Primary role: aerobic cellular respiration → $\text{Glucose} + O<em>2 \rightarrow CO</em>2 + H_2O + ATP$ .
Produces bulk of cellular ATP via oxidative phosphorylation; simplified energy equation: $ATP \rightarrow ADP + P_i + \text{Energy}$ .
Has its own circular DNA & prokaryote-type ribosomes; reproduces independently by binary fission; maternally inherited.

Triple-membrane system
• Outer & inner envelopes.
• Internal thylakoid membrane folded into flat disks.
Key structures
• Thylakoid: individual disc where light-dependent reactions occur.
• Granum (pl. grana): stack of thylakoids; resemble stack of coins.
• Stroma: fluid outside thylakoids; contains enzymes for Calvin cycle (light-independent reactions).
Own DNA & ribosomes; replicate similarly to mitochondria.

Timeline: > 2 \text{ billion years} ago.
Steps
1. Early ancestor of eukaryotes formed internal membranes → primitive nucleus & ER.
2. Engulfed aerobic heterotrophic prokaryote → became symbiotic mitochondrion.
3. Lineage leading to plants later engulfed photosynthetic prokaryote → became chloroplast.
Evidence
• Organelle size ≈ modern bacteria.
• Double/triple membranes (outer from host’s phagocytic membrane, inner from original bacterium).
• Own circular DNA, prokaryotic ribosomes, independent division.
Implications: cooperation (symbiosis) drove cellular complexity; underpins energy & food webs today.

Identify easily:
• Nucleus (large circular), nucleolus (dark center).
• Mitochondria: kidney-bean shape with cristae; cross-sections appear circular.
• Rough ER: parallel sheets studded with dots (ribosomes).
• Smooth ER: thin, branching tubes.
• Golgi: curved, stack of flattened sacs.
• Vesicles: small, spherical, membrane-bounded.
• Cytoplasm: background matrix.
Practice: print unlabeled images and annotate to reinforce spatial understanding.

Group organelles by membrane status:
• Membranous: nucleus, ER, Golgi, vesicles, lysosomes, vacuoles, mitochondria, chloroplasts.
• Non-membranous: ribosomes, cytoskeleton (covered elsewhere).
Understand flow of protein production & export: DNA → mRNA (nucleus) → ribosome (RER) → lumen → vesicle → Golgi → vesicle → plasma membrane.
Link function to structure (e.g., cristae & thylakoid folds maximize surface area for energy reactions).
Remember exceptions: animal cells lack cell walls & chloroplasts; plant cells possess both mitochondria & chloroplasts.
Next lecture focus: detailed structure & chemistry of the plasma membrane.