Cell Biology: The Cell and Its Organelles

The MCAT loves to test the cell as a system of specialized compartments, each with a structure that predicts its function. If you can map every organelle to what it makes, breaks, or moves, and connect that to the membranes that separate it from everything else, you can reason through most cell-biology items without pure memorization.

Core Idea

• Structure predicts function. Membranes create compartments so incompatible reactions (digestion, oxidation, ATP synthesis) can run side by side; the shape of each organelle reflects the job it does.
• Eukaryotic = membrane-bound organelles and a true nucleus; prokaryotic = none. This single distinction drives many exam questions about where DNA lives and where processes occur.
• The endomembrane system is a pathway, not a pile of parts: nucleus → rough ER → Golgi → vesicles → membrane/lysosome/secretion.

Prokaryotic vs. Eukaryotic Cells

Prokaryotes (bacteria, archaea) have no membrane-bound nucleus and no membrane-bound organelles; their circular DNA sits in a nucleoid, and they use 70S ribosomes. Eukaryotes have a true nucleus, an endomembrane system, mitochondria, and 80S ribosomes (cytoplasmic). Both share a plasma membrane, cytoplasm, and ribosomes. The 70S vs. 80S distinction is high-yield: mitochondrial ribosomes are 70S, evidence for the endosymbiotic origin of mitochondria.

The Plasma Membrane

The fluid mosaic model describes a phospholipid bilayer — polar phosphate heads facing outward toward water, nonpolar fatty-acid tails facing inward — studded with proteins that drift laterally. Cholesterol buffers fluidity (increasing it at low temperature, decreasing it at high temperature). The membrane is selectively permeable: small nonpolar molecules cross freely, while ions and large polar molecules need transport.

• Passive transport (no ATP): simple diffusion, facilitated diffusion through channels/carriers, and osmosis, all moving down the gradient.
• Active transport (uses ATP or a gradient): moves solutes against the gradient, e.g. the Na+/K+ ATPase (3 Na+ out, 2 K+ in).

The Nucleus and Nucleolus

The nucleus stores DNA and is the site of replication and transcription. Its double membrane (nuclear envelope) is perforated by nuclear pores that regulate mRNA and protein passage. Inside, the dense nucleolus assembles ribosomal subunits (rRNA synthesis and packaging). No mRNA is translated here — translation happens in the cytoplasm.

The Endomembrane System: ER and Golgi

• Rough ER is coated with ribosomes and synthesizes and folds secreted and membrane-bound proteins; it is continuous with the nuclear envelope.
• Smooth ER lacks ribosomes and handles lipid/steroid synthesis, detoxification (liver), and calcium storage (the sarcoplasmic reticulum in muscle).
• The Golgi apparatus modifies, sorts, tags (e.g. glycosylation), and packages proteins from the ER into vesicles. Material enters the cis face (near the ER) and exits the trans face toward its destination.

Mitochondria and Energy

Mitochondria are the site of oxidative phosphorylation and the bulk of ATP production. They have a double membrane: a smooth outer membrane and a folded inner membrane whose folds (cristae) hold the electron transport chain and ATP synthase. The matrix contains the enzymes of the citric acid (Krebs) cycle and the cell's own mitochondrial DNA and 70S ribosomes. The proton gradient across the inner membrane drives chemiosmotic ATP synthesis.

Digestion, Detox, and Ribosomes

• Lysosomes contain acidic hydrolytic enzymes for intracellular digestion, autophagy, and apoptosis; membrane failure can release these enzymes ("suicide sacs").
• Peroxisomes break down fatty acids (beta-oxidation) and neutralize hydrogen peroxide and other reactive species using catalase.
• Ribosomes (free in cytosol or bound to rough ER) are the site of translation; free ribosomes tend to make cytosolic proteins.

The Cytoskeleton and Cell Junctions

Three filament systems give shape and enable movement: microtubules (thickest; tracks for motor proteins kinesin/dynein, form the spindle, cilia, and flagella in a 9+2 arrangement), microfilaments (actin; thinnest; muscle contraction and cytokinesis), and intermediate filaments (mechanical strength, e.g. keratin). Cell junctions include tight junctions (seal cells, block leakage), desmosomes (anchor cells against stress), and gap junctions (channels for direct cell-to-cell communication).

High-Yield Exam Patterns

• 70S vs. 80S ribosomes and mitochondrial/chloroplast DNA are tested as evidence for endosymbiotic theory.
• Expect a secretory-pathway question: trace a protein nucleus → rough ER → Golgi → vesicle → membrane/secretion.
• Cristae and inner-membrane surface area are linked to ATP output — more cristae, more oxidative phosphorylation.
• Distinguish passive vs. active transport by whether ATP is used and whether movement is with or against the gradient.
• Match each junction to its role: tight = seal, desmosome = anchor, gap = communicate.
• Cholesterol's effect on fluidity ("fluidity buffer") is a favorite conceptual twist.

Common Traps to Avoid

• Assuming translation happens in the nucleus — the nucleolus makes ribosomes, but proteins are translated in the cytoplasm.
• Confusing rough ER (protein synthesis) with smooth ER (lipids, detox, calcium).
• Calling all transport "active" — facilitated diffusion uses a protein but no ATP.
• Mixing up the cytoskeletal filaments — microtubules move cargo and form the spindle, actin drives contraction, intermediate filaments provide strength.
• Forgetting that prokaryotes lack membrane-bound organelles but still have ribosomes and a plasma membrane.