Unit 5 Compartments/Protein Sorting

Compartmentalization of cells

Dividing a eukaryotic cell into specialized spaces called organelles, each with specific functions.

Membrane-enclosed organelles

Organelles surrounded by one or two lipid bilayer membranes.

Cytosol/cytoplasm

Cytoplasm is the material filling the cell, containing dissolved ions, proteins, lipids, carbohydrates, and small molecules.

Mitochondria

Double-membrane organelles that produce most of the cell's ATP (usable energy).

Chloroplast

Organelle that captures sunlight and contains the molecules needed for photosynthesis.

Nucleus

Double-membrane organelle containing the cell's genomic DNA; surrounded by the nuclear envelope.

Topology of cellular organelles

How organelles are arranged and connected, determining whether molecules can move between compartments without crossing a lipid bilayer.

Topologically equivalent compartments

Compartments where molecules can move between them without crossing a lipid bilayer, through pores or vesicles. Examples: nucleus/cytoplasm and ER/Golgi.

Intracellular vesicles

Small membrane-bound sacs that transport proteins and other cargo between topologically equivalent compartments.

Endosymbiotic model

Explains how an aerobic bacterium lived inside an anaerobic archaeon, providing energy in exchange for protection and nutrients; this eventually contributed to mitochondria.

Evidence for endosymbiosis

Mitochondria have their own DNA, ribosomes, and translation factors resembling those of bacteria. Chloroplasts also likely originated from photosynthetic bacteria.

Endoplasmic reticulum (ER)

Organelle involved in protein and lipid synthesis, protein processing and transport, and Ca²⁺ storage for cell signaling.

Rough ER

ER covered with ribosomes; involved in protein synthesis, modification, and transport.

Smooth ER

ER without ribosomes; mainly involved in lipid synthesis, detoxification, and Ca²⁺ storage.

Protein translocation/transmembrane transport

Movement of a protein across a membrane, such as from the cytoplasm into the ER or mitochondria.

Signal sequences

Short amino acid sequences in proteins that act like addresses, directing proteins to the correct cellular location.

Signal recognition particle (SRP)

RNA-protein complex that recognizes the ER signal sequence, binds the ribosome making the protein, and delivers the complex to the ER.

SRP receptor

Protein in the ER membrane that binds SRP and helps deliver the ribosome and growing protein to the ER.

Translocator

Membrane protein that forms a tunnel for polypeptides to cross a membrane; hydrophobic sequences can exit sideways into the membrane.

Co-translational translocation

Transporting a protein across a membrane while it is still being translated.

Signal peptidase

Enzyme that cuts the ER signal sequence off proteins that need to be released into the ER lumen.

Post-translational translocation

Transporting a protein across a membrane after translation is complete; energy is needed to unfold the protein before transport.

N-linked glycosylation

Attaching sugars to nitrogen atoms on amino acid side chains of proteins, often in the ER.

Oligosaccharyl transferase

Enzyme that transfers an oligosaccharide (sugar chain) onto a protein during N-linked glycosylation.

Mitochondrial matrix space

The innermost compartment of a mitochondrion, enclosed by the inner mitochondrial membrane.

Mitochondrial intermembrane space

The space between the inner and outer mitochondrial membranes.

Gated transport

Selective movement of molecules between the cytoplasm and nucleus through nuclear pores without crossing a lipid bilayer.

Nuclear envelope

Double membrane surrounding the nucleus, containing nuclear pores that regulate transport between the nucleus and cytoplasm.

Nuclear pore complex (NPC)

Large protein complex in the nuclear envelope that controls movement between the nucleus and cytoplasm; small molecules pass freely, while large cargo needs help.

Nuclear localization signal (NLS)

Amino acid sequence that is necessary and sufficient to direct a protein into the nucleus with nuclear import receptors.

FG-repeats

Repeated phenylalanine-glycine sequences in the NPC that form a gel-like mesh, acting as a sieve to restrict large molecules.

Nuclear import receptors

Proteins that bind NLS-containing proteins and NPC FG-repeats, helping the cargo pass through the nuclear pore.

Exocytosis

Movement of materials out of the cell when a transport vesicle fuses with the plasma membrane; releases cargo outside or adds vesicle membrane to the plasma membrane.

Endocytosis

Movement of materials into the cell when the plasma membrane folds inward and forms a vesicle containing external cargo or membrane components.

Secretory vs. endocytic pathways

Secretory pathway moves cargo outward from the ER toward the cell surface; endocytic pathway brings cargo inward from the plasma membrane.

Transport vesicles

Small membrane-bound sacs that bud from one compartment, carry cargo, and fuse with a target compartment to deliver it.

Phosphoinositides (PIPs)

Modified phosphoinositol lipids with extra phosphate groups on the inositol ring; help identify where vesicle cargo should be delivered.

Vesicle coat proteins

Proteins that form a cage around a budding vesicle, shape the membrane, and help select cargo through adaptors; examples include clathrin, COPI, and COPII.

Clathrin

Coat protein made of heavy and light chains that assemble into a cage around vesicles and help form them.

Adaptor proteins

Proteins that connect cargo receptors in a membrane to coat proteins during vesicle formation.

Dynamin

GTP-powered protein that pinches off a budding vesicle from its original membrane.

SNARE (v- and t-SNAREs)

Complementary proteins on vesicles (v-SNAREs) and target membranes (t-SNAREs) that bind together to drive membrane fusion and help ensure correct delivery.

COPII

Vesicle coat protein that carries cargo from the ER to the Golgi; involved in forward (anterograde) transport.

COPI

Vesicle coat protein that carries cargo from the Golgi back to the ER; involved in reverse (retrograde) transport.

KDEL signal

A four-amino-acid sequence (Lys-Asp-Glu-Leu) at the C-terminus of soluble ER proteins that signals they should be returned to the ER if they reach the Golgi.

Golgi apparatus

Stack of flattened membrane compartments that modifies, processes, and sorts proteins and lipids; enzymes can add or remove sugars.