Organelles

Cytosol

The aqueous, protein

Why the cytosol is not just “empty space”

The cytosol contains cytoskeletal elements, enzymes, and metabolites that actively regulate biochemical reactions rather than simply holding organelles.

Nucleus

A double

Why separating transcription and translation is important in eukaryotes

This separation allows extensive mRNA processing and regulatory control before proteins are synthesized.

Nucleolus

A specialized nuclear region where rRNA is transcribed and ribosomal subunits are assembled, linking gene expression to protein synthesis capacity.

Chromatin

DNA

How chromatin structure affects gene expression

Tightly packed chromatin (heterochromatin) limits transcription, while loosely packed chromatin (euchromatin) allows gene expression.

Nuclear envelope

A double membrane continuous with the endoplasmic reticulum that physically separates the genome from the cytoplasm while permitting regulated transport.

Why nuclear pores are selective

Transport proteins recognize molecular signals to control which RNAs and proteins cross, preventing loss or damage to genetic information.

Ribosomes

rRNA protein complexes that catalyze peptide bond formation, converting genetic information into functional proteins.

Why rRNA is essential for ribosome function

rRNA acts as a ribozyme, meaning RNA, not protein, catalyzes peptide bond formation.

Free vs bound ribosomes

Both are structurally identical, but bound ribosomes synthesize proteins for secretion or membranes, while free ribosomes produce cytosolic proteins.

Endoplasmic Reticulum (ER)

An interconnected membrane system that increases surface area for synthesis, folding, and transport of macromolecules.

Why the ER is continuous with the nuclear envelope

This continuity allows efficient transfer of newly synthesized RNA and proteins into the endomembrane system.

Rough Endoplasmic Reticulum

Specialized ER where ribosome bound translation inserts proteins directly into the lumen or membrane for modification.

Why protein folding begins in the rough ER

Proper folding and disulfide bond formation are monitored to prevent malfunctioning proteins from reaching the Golgi.

Smooth Endoplasmic Reticulum

ER specialized for lipid synthesis, phospholipid production, detoxification, and calcium storage.

How smooth ER detoxifies substances

Enzymes modify toxins to increase solubility, allowing easier removal from the body.

Golgi Apparatus

A polarized organelle that modifies, sorts, and directs proteins based on molecular tags added during processing.

Why the Golgi has cis and trans faces

Directional flow ensures proteins are progressively modified and accurately sorted for their final destinations.

Lysosomes

Acidic, enzyme

Why lysosomal enzymes require low pH

Acidic conditions maximize enzyme activity and prevent damage if enzymes leak into the cytosol.

Autophagy

The lysosome

Peroxisomes

Organelles that carry out oxidation reactions, breaking down fatty acids and neutralizing reactive oxygen species.

Why peroxisomes are critical for detoxification

They prevent accumulation of harmful byproducts that could damage DNA and membranes.

Vacuoles

Storage organelles that regulate water balance, ion concentration, and waste sequestration.

How central vacuoles contribute to plant rigidity

Osmotic pressure against the cell wall (turgor pressure) maintains structural support without energy expenditure.

Mitochondria

Organelles that generate ATP through oxidative phosphorylation, linking metabolism to cellular energy demands.

Why mitochondria have their own DNA

They originated from free

Cristae

Folded inner mitochondrial membranes that increase surface area for electron transport chains.

How cristae structure affects ATP yield

Greater membrane surface allows more ATP synthase complexes, increasing energy production efficiency.

Chloroplasts

Photosynthetic organelles that convert light energy into chemical energy via redox reactions.

Thylakoids

Internal membrane sacs containing photosystems where light

Why photosynthesis occurs in two stages

Separating light capture from carbon fixation allows efficient energy use and regulation.

Centrioles

Microtubule organizing centers that coordinate spindle fiber formation during cell division.

Why spindle fibers are essential in mitosis

They ensure accurate chromosome segregation, preventing genetic abnormalities.

Cytoskeleton

Dynamic network of protein filaments that integrates structure, transport, and motility.

How microtubules differ from microfilaments

Microtubules provide rigidity and transport tracks, while microfilaments enable shape changes and contraction.

Motor proteins

ATP

Cilia

Short, coordinated structures that move fluid across cell surfaces through rhythmic beating.

Flagella

Long structures that generate propulsion by wave

Why cilia and flagella use a 9+2 microtubule arrangement

This arrangement allows coordinated bending powered by motor proteins (dynein).