B2.2 Organelles and compartmentalization

An organelle is a discrete cell subunit adapted for a specific function. In this syllabus, nuclei, chloroplasts, mitochondria, endoplasmic reticulum, Golgi apparatus, vesicles, ribosomes and the plasma membrane count as organelles; cell wall, cytoskeleton and cytoplasm do not.

Compartmentalization concentrates enzymes, substrates and metabolites, maintains conditions such as a suitable pH, and separates biochemical processes that would interfere with one another.

Lysosomes keep acidic hydrolytic enzymes separated from cytoplasm. A phagocytic vacuole can fuse with a lysosome so engulfed material is digested inside a controlled compartment rather than throughout the cell.

Cell fractionation followed by ultracentrifugation separates organelles by physical properties, allowing their structures and functions to be investigated independently.

A useful cell structure is not automatically an organelle under the IB convention. State the compartment, the concentrated or separated process, and the functional advantage.

The nuclear envelope separates transcription from cytoplasmic translation, so RNA can be processed after transcription and before it reaches ribosomes.

DNA remains in the nucleus. Pre-mRNA can be capped, polyadenylated and spliced to remove introns; mature mRNA is then exported through nuclear pores for translation.

Route in a eukaryote: DNA transcription in nucleus → post-transcriptional mRNA modification → selective pore export → translation on cytoplasmic ribosomes.

An intron can be removed from pre-mRNA before the mature transcript meets a ribosome, preventing the intron sequence from being translated.

Prokaryotes lack a nuclear compartment, so a newly made mRNA can meet ribosomes and begin translation immediately; this spatial processing interval is not available.

A mitochondrion's double membrane creates a small intermembrane space, a highly folded inner membrane and a separate matrix, each adapted for aerobic ATP production.

Cristae provide a large area for electron-transport chains and ATP synthase. Proton pumping into the small intermembrane space rapidly builds an electrochemical gradient; proton return through ATP synthase drives ATP formation.

The matrix concentrates enzymes and substrates for the link reaction and Krebs cycle, while transport proteins regulate entry of pyruvate and movement of required metabolites across membranes.

A mitochondrion in a high-energy cell can have extensive cristae, accommodating more electron-transfer and ATP-synthase complexes when oxygen and respiratory substrates are available.

Cristae increase capacity but do not guarantee ATP production: oxygen, substrates, ADP, phosphate and functioning electron carriers are also required.

Chloroplasts separate light-dependent reactions on thylakoid membranes from Calvin-cycle carbon fixation in the stroma.

Grana provide a large thylakoid-membrane area for photosystems, electron carriers and ATP synthase. The small fluid volume inside thylakoids allows protons to accumulate rapidly and generate a steep gradient.

The stroma concentrates Calvin-cycle enzymes and substrates at a suitable pH. ATP and reduced NADP produced by thylakoid reactions are then used to reduce and assimilate carbon in the stroma.

Stacking thylakoids expands photosystem surface without requiring a much larger chloroplast, while the surrounding stroma remains a distinct enzyme-rich compartment.

Photosystems absorb light on thylakoid membranes, not in the stroma; Calvin-cycle enzymes do not replace the membrane electron-transfer machinery.

The nuclear envelope is a double membrane that separates nucleoplasm from cytoplasm while nuclear pores provide rapid, regulated exchange.

Compartmentalization protects DNA and permits RNA processing before translation. Pores selectively export RNA and import nuclear proteins, while the nuclear lamina supports envelope shape and chromosome organization.

During mitosis and meiosis in many eukaryotic cells, the envelope breaks into membrane vesicles or fragments so spindle microtubules can access chromosomes; it re-forms around daughter nuclei later.

Mature mRNA exits through a pore, whereas a transcription factor bearing a nuclear-localization signal can be selectively imported.

The envelope is neither freely permeable nor permanently intact. Pores enable controlled interphase exchange, and regulated disassembly supports nuclear division.

Free ribosomes make proteins used in the cytosol, while ribosomes bound to rough ER make proteins entering the secretory pathway or membranes.

A signal sequence directs a translating ribosome to the ER. The growing chain can then enter the ER lumen or membrane rather than remaining in the cytoplasm.

Decide by destination: cytosol suggests free ribosome; secretion, lysosome or membrane suggests rough ER.

A digestive enzyme destined for secretion is translated on rough ER, whereas a cytosolic metabolic enzyme is made on a free ribosome.

Free and bound ribosomes are not permanently different machines; targeting determines their location during translation.

The Golgi apparatus receives vesicles, modifies their contents and sorts them into new vesicles for different destinations.

Different cisternae contain enzymes that alter proteins or lipids as cargo moves through the stack. Sorting signals direct cargo to the plasma membrane, lysosome or another compartment.

Follow cargo: arrival vesicle; cisternal modification; sorting signal; destination vesicle.

A protein processed in the ER can be glycosylated further in the Golgi and packaged for secretion.

The Golgi is not simply storage: its value is sequential processing plus destination-specific sorting.

Vesicles move membrane and soluble cargo by budding from one compartment and fusing with a specific target while keeping cargo enclosed.

Clathrin proteins assemble as a coat on the cytoplasmic face of a budding membrane, helping curve it into a coated pit and select cargo through adaptor proteins. The coat is removed before targeting and fusion.

Trace vesicle traffic: cargo selection → clathrin-coated bud → membrane scission → uncoating → target recognition → fusion and cargo delivery.

In receptor-mediated endocytosis, receptors and bound cargo cluster in a clathrin-coated pit that pinches off; in secretion, a Golgi-derived vesicle later fuses with the plasma membrane.

Clathrin helps form and select coated vesicles; it does not determine every later target by itself, and vesicle traffic is not random diffusion.