E2 Lec3 part1

Intracellular compartments provide distinct spaces for specific types of biochemistry.
Key organelles include the nucleus, mitochondria, endoplasmic reticulum (ER), Golgi apparatus, and various vesicles.
Vesicles serve as transport units and reserve membrane material, allowing the cell to regulate the size of the plasma membrane.
Volume statistics in a typical liver hepatocyte:
- Mitochondria: Approximately $1\,700$ per cell, accounting for $22\%$ of total cell volume.
- Endoplasmic reticulum (ER): Accounts for approximately $12\%$ of total cell volume.
- Lysosomes, endosomes, and peroxisomes: Small individual volumes but high in total number.

Archaeon: An ancient precursor cell type that evolved into eukaryotes.
Endosymbiosis: The process by which an archaeon absorbed an aerobic bacterium, which became the mitochondria. Evidence includes the mitochondrial double membrane and its own genome.
Invagination: The cell membrane folded inward to surround genetic material, forming the nucleus and the endomembrane system (ER, Golgi, and associated vesicles).
Historical Context: These theories were discussed by evolutionary biologist Ann Druyan (identified as Carl Sagan's ex-wife) and Dorian Sagan.

Protein synthesis typically begins in the cytosol before proteins are directed to specific compartments.
Transport across membranes: Selective process for moving proteins into the ER, mitochondria, and chloroplasts using specific membrane proteins.
Nuclear Transport: Proteins slip through specialized nuclear pores.
Vesicular Transport: Selective ferrying of proteins in vesicles originating from the ER to other destinations.

Signal sequences: Primary structures within proteins that act as an addressing system.
ER Import Sequence: Found at the N-terminus; proteins without a signal sequence are retained in the cytoplasm.
ER Retention Sequence: Located at the C-terminus, often called the "KDEL" sequence based on its amino acids:
- Lysine ( $K$ )
- Asparatic acid ( $D$ )
- Glutamic acid ( $E$ )
- Leucine ( $L$ )
Mitochondrial Import Sequence: Located at the N-terminus, distinct from the ER sequence.
Nuclear Localization Sequence (NLS): Directs proteins to the nucleus. It can be hidden within protein folds and exposed by events like hormone binding (e.g., steroid hormone receptors).

Membrane Structure: The nucleus is enclosed by a double lipid bilayer (inner and outer membranes).
Continuity: The outer nuclear membrane is continuous with the endoplasmic reticulum membrane; both bilayers are continuous at the points where nuclear pores are located.
Nuclear Pores: Large, selective filtering channels through the double lipid bilayer.
Nuclear Lamina: A layer of cytoskeletal proteins on the inner aspect of the nuclear membrane that maintains nuclear shape (e.g., round, dog bone, or dumbbell shapes).