B2.2 Organelles and compartmentalization

Organelles and compartmentalization explain how eukaryotic cells divide work among specialized structures, controlled internal spaces, and directed vesicle transport routes.

Syllabus
First assessment 2025
Topic
B2.2
Level
HL

Learning objectives

B2.2.1Organelles as discrete subunits• Organelles are discrete cell subunits adapted for specific functions• Nuclei, chloroplasts, mitochondria, vesicles, ribosomes, and plasma membrane are organelles• Cell wall, cytoskeleton, and cytoplasm are not usually considered organellesB2.2.2Nucleus-cytoplasm separation• The nuclear envelope protects DNA and separates transcription from translation• Introns can be removed from pre-mRNA by RNA splicing before translation• Nuclear pores regulate mRNA export and protein import using selective transportB2.2.3Advantages of compartmentalization• Compartmentalization concentrates enzymes, substrates, and suitable pH for specific reactions• It separates incompatible biochemical processes so they can be controlled• Lysosomes and phagolysosomes contain acidic hydrolytic digestion away from cytoplasmB2.2.4(HL)—Mitochondrion adaptations• The outer membrane contains transport proteins for pyruvate entry• Folded cristae increase surface area for electron transport chains and ATP synthase• The intermembrane space stores protons; the matrix contains Krebs cycle enzymesB2.2.5(HL)—Chloroplast adaptations• Thylakoid membranes in grana hold photosystems, electron transport chains, and ATP synthase• Small thylakoid spaces allow rapid proton accumulation• The stroma contains enzymes and suitable pH for the Calvin cycleB2.2.6(HL)—Nuclear membrane benefits• The nuclear envelope is a double membrane continuous with the ER• Numerous nuclear pores allow rapid regulated exchange between nucleus and cytoplasm• The nuclear lamina supports the nucleus, and the envelope breaks into vesicles during divisionB2.2.7(HL)—Free ribosomes vs. rough ER• Free ribosomes synthesize proteins retained and used in the cytoplasm• Polysomes allow many ribosomes to translate the same mRNA at once• RER-bound ribosomes synthesize proteins for secretion, membranes, or lysosomesB2.2.8(HL)—Golgi apparatus• The Golgi is a stack of flattened cisternae receiving vesicles from the RER• Different cisternae modify proteins by glycosylation, sulfation, or phosphorylation• Vesicles from the Golgi deliver proteins to lysosomes, membranes, or secretion pathwaysB2.2.9(HL)—Vesicles in cells• Vesicles move materials between organelles, plasma membrane, and extracellular space• Receptor-mediated endocytosis can form clathrin-coated pits and vesicles• Vesicle fusion is essential for secretion and neurotransmitter release

Compartments Turn One Cell into Many Workspaces

An organelle is a distinct cellular subunit adapted for a particular function. Membranes create local conditions, concentrate enzymes and substrates, and isolate incompatible reactions.

Cutaway diagram of a eukaryotic cell showing the nucleus, mitochondrion, rough endoplasmic reticulum, Golgi apparatus and lysosome as distinct compartments.

boundary → controlled composition → efficient reaction conditions; vesicles and transport proteins then connect the separate spaces into one coordinated cell

The Nucleus Separates RNA Processing from Translation

The nuclear envelope keeps DNA and transcription in the nucleus while translation occurs on cytoplasmic ribosomes. This separation permits pre-mRNA processing before mature mRNA reaches a ribosome.

The figure shows a polysome.

DNA transcription → 5′ cap, intron removal and poly-A tail → mature mRNA export through a nuclear pore → several ribosomes can translate it as a polysome

SL Summary: Explain the Advantage, Not Just the Organelle

  • organelle membrane → selected molecules and conditions → faster, regulated pathways
  • nucleus separated from cytoplasm → RNA processing before translation → controlled gene expression
  • distinct cytoplasmic spaces → incompatible reactions remain apart → simultaneous specialized work

For any compartment: name its boundary → state what differs across it → connect that difference to a function.

Mitochondrial Architecture Couples Oxidation to ATP Synthesis

HL only

The matrix contains enzymes for the link reaction and Krebs cycle. The inner membrane carries electron-transfer chains and ATP synthase; cristae enlarge its area, while the narrow intermembrane space permits rapid H⁺ accumulation.

Annotated mitochondrion showing outer membrane, inner membrane folded into cristae, intermembrane space, and matrix with location-linked functions.

reduced carriers donate electrons → inner-membrane complexes pump H⁺ → electrochemical gradient forms → H⁺ returns through ATP synthase → ATP is produced

Chloroplast Compartments Link Light Capture to Carbon Fixation

HL only

Thylakoid membranes contain chlorophyll, electron carriers and ATP synthase. Their lumen accumulates H⁺; the surrounding stroma contains enzymes for the Calvin cycle. Grana increase thylakoid membrane area.

Annotated chloroplast showing grana, thylakoid membranes, thylakoid space, and stroma with matching photosynthesis functions.

light excites electrons → H⁺ accumulates in thylakoid lumen → ATP and reduced NADP form at the membrane → both enter the stroma and support carbon fixation

The Double Nuclear Envelope Protects DNA Yet Permits Exchange

HL only

The nucleus has inner and outer membranes separated by a perinuclear space. The outer membrane is continuous with rough ER; nuclear pore complexes selectively control traffic between nucleoplasm and cytoplasm.

A cutaway diagram shows the nuclear envelope surrounding chromatin and a nucleolus, with pores and continuity to ribosome-studded endoplasmic reticulum; an inset distinguishes the inner and outer surfaces.

out: processed mRNA, tRNA and assembled ribosomal subunits
in: histones, polymerases, transcription factors and other nuclear proteins
lamina: supports nuclear shape and organizes chromatin

A Targeting Signal Selects Free Ribosome or Rough ER

HL only

All cytosolic ribosomes begin translation free. A signal peptide on the growing polypeptide can redirect the ribosome to rough ER, where translation continues into the ER lumen or membrane.

Split route: free ribosome to cytoplasmic protein, rough ER ribosome to ER-Golgi-vesicle route.
  • cytosolic protein → completed on a free ribosome
  • secreted or lysosomal protein → rough ER → vesicle → Golgi
  • membrane protein → inserted into ER membrane, then trafficked

The Golgi Processes Cargo in a Directed Sequence

HL only

The Golgi is a polarized stack of flattened cisternae. The cis face receives ER vesicles; different cisternae modify proteins and lipids; the trans face sorts cargo into vesicles for distinct destinations.

RER vesicle arrives at cis Golgi, proteins modified through cisternae, sorted at trans face, vesicle leaves to target.

rough ER → transport vesicle → cis Golgi → sequential modification through cisternae → trans Golgi sorting → lysosome, plasma membrane or secretion

Vesicles Move Cargo Without Mixing Compartments

HL only

A vesicle buds with selected membrane and soluble cargo, travels to a target, and fuses so that cargo enters the correct compartment without exposure to cytosol.

Diagram shows clathrin-coated vesicles budding, docking, and fusing at the cell membrane, with a receptor and transported substance labeled.

cargo selection → membrane curvature and budding → scission → uncoating → target recognition → fusion; clathrin helps form selected coated buds during receptor-mediated endocytosis

HL Summary: Two Compartment Systems, One Design Principle

HL only
  • mitochondrion: inner-membrane H⁺ gradient → aerobic ATP
  • chloroplast: thylakoid H⁺ gradient → ATP and reduced NADP
  • endomembrane system: preserved cargo and orientation → sorting and secretion

Secreted protein: targeting signal → rough ER → vesicle → cis-to-trans Golgi → secretory vesicle → plasma membrane.

Organelles as discrete subunits

7 marks

Describe the organelles and other structures in animal cells that are visible in electron micrographs.

Advantages of compartmentalization

4 marks

Discuss the use of membranes for compartmentalization in eukaryotic cells.

Mitochondrion adaptations

HL only

3 marks

Explain the relationship between the structure of the mitochondrion and its function.

Chloroplast adaptations

HL only

4 marks

Describe how the structure of the chloroplast is adapted to its function in photosynthesis.

Nuclear membrane benefits

HL only

1 mark

What is a benefit of double membranes surrounding the nuclei of eukaryotic cells?

Free ribosomes vs. rough ER

HL only

1 mark

Which statement distinguishes between the roles of free and bound ribosomes?

Golgi apparatus

HL only

1 mark

The diagram summarizes the production and secretion of digestive enzymes in an exocrine gland cell of the pancreas.

Which cell organelle is involved at Y ?

Vesicles in cells

HL only

1 mark

What is the role of clathrin molecules in the formation of vesicles?