Study Guide for BIO 344 Exam II (2026)

Chapter 12: Protein Transport and Membrane Dynamics

  • Protein Movement Between Nucleus and Cytosol

    • Proteins are moved through the nuclear envelope via nuclear pore complexes that facilitate transport.

  • Nuclear Pore Complexes

    • Large protein complexes that span the nuclear envelope, allowing the selective exchange of molecules between the nucleus and cytosol.

  • Nuclear Import Receptor

    • A specific protein that binds to nuclear localization signals (NLS) on proteins destined for the nucleus, facilitating their transport through nuclear pore complexes.

  • Energy Molecule for Protein Transport

    • GTP (guanosine triphosphate) provides the energy necessary for the import of large proteins into the nucleus, and it is attached to the protein Ran, which regulates the transport process.

  • Subcompartments of Mitochondria

    • Mitochondria consist of the outer membrane, intermembrane space, inner membrane, and mitochondrial matrix, each with distinct functions.

  • Protein Translocators

    • Protein complexes located in mitochondrial membranes that facilitate the import of proteins into the mitochondria.

  • Mitochondrial Signal Sequence

    • The mitochondrial signal sequence is critical for protein import, forming an alpha helix that is hydrophobic and plays a significant role in the translocation process.
    • The alpha helix possesses properties such as having a hydrophobic core, allowing it to interact with the lipid bilayer during import.

  • Importing Proteins into Mitochondrial Matrix

    • Proteins are synthesized in the cytosol and then imported by unfolding and passing through translocators in the inner and outer membranes into the mitochondrial matrix.

  • Targeting Proteins to Intermembrane Space

    • Proteins are directed to the intermembrane space via specific signals in their sequences and translocators that guide them into the space between the inner and outer membranes.

  • Difference Between Smooth ER and Rough ER

    • Smooth ER is involved in lipid synthesis and lacks ribosomes, while Rough ER has ribosomes on its surface, making it the site of protein synthesis.

  • Initiation of Protein Synthesis

    • Protein synthesis begins in the cytosol with ribosomes, then proteins destined for secretion or for a membrane start their journey toward the ER.

  • Directing Proteins to the ER

    • Proteins are directed to the ER by their signal sequences that are recognized by the signal recognition particle (SRP).

  • Signal Recognition Particle and SRP Receptor Functions

    • The SRP binds to the signal sequence and pauses translation, directing the ribosome to the SRP receptor on the ER membrane to facilitate translocation into the ER.

  • Fate of Signal Sequence Post-ER Entry

    • The signal sequence is typically cleaved off by a signal peptidase once the protein has been translocated into the lumen of the ER.

  • Transmembrane Protein Insertion

    • Transmembrane proteins have start transfer and stop transfer sequences that determine their placement within the lipid bilayer of the ER membrane.

  • Start Transfer and Stop Transfer Signal Sequences

    • Start transfer sequences initiate the translocation of a polypeptide into the membrane, while stop transfer sequences halt this process, anchoring the protein in the membrane.

  • Insertion of Multipass Membrane Proteins

    • Proteins that pass through the ER membrane multiple times have several alternating start and stop transfer sequences that dictate their topology.

  • Glycosylation in the ER

    • Proteins undergo glycosylation in the ER where oligosaccharides are attached, mainly to asparagine residues (N-glycosylation).

  • Link Between Protein Glycosylation and Folding

    • Glycosylation aids in proper protein folding and stability and aids in quality control mechanisms of the ER.

  • Consequences of Incorrect Protein Folding

    • Proteins that do not fold correctly are targeted for degradation via the proteasome or retained in the ER.

  • Assembly of Membrane Lipids

    • Membrane lipids are assembled in the smooth ER and then distributed to various organelles through vesicular transport.

  • Phospholipid Transfer to Organelles

    • Phospholipid exchange proteins are required to transfer phospholipids from the ER to mitochondria but not to the Golgi, likely due to the close proximity of the ER and Golgi apparatus allowing simpler diffusion.

Chapter 13: Endocytosis and Secretory Pathways

  • Endocytic and Secretory Pathways

    • The secretory pathway involves the transport of proteins from the ER to the outside of the cell, while the endocytic pathway imports materials into the cell from the extracellular environment.

  • Vesicular Transport vs. Transmembrane Transport

    • Vesicular transport utilizes membrane-bound vesicles to move substances, while transmembrane transport involves direct passage through the membrane.

  • Intracellular Compartments in Pathways

    • Major compartments include the ER, Golgi apparatus, endosomes, and lysosomes, involved in processing and transport of cellular materials.

  • Coated Vesicles

    • Specialized transport vesicles with a protein coat that aids in cargo selection and packaging. Three types include:
    • Clathrin-coated vesicles that transport materials from the plasma membrane to endosomes.
    • COPI-coated vesicles that transport materials from the Golgi back to the ER.
    • COPII-coated vesicles that transport materials from the ER to the Golgi.

  • Formation of Clathrin-Coated Vesicles

    • Involves recruitment of clathrin proteins, causing membrane invagination, followed by dynamin causing the vesicle to pinch off.

  • Role of Dynamin

    • Dynamin is a GTPase that constricts around the neck of budding vesicles, facilitating their scission from the membrane.

  • Dynamin Mutation in Fruit Flies

    • A mutation in dynamin causes vesicles to fail to bud properly, leading to paralyzed fruit flies due to impaired neuronal signaling.

  • SNARE Proteins

    • SNARE proteins facilitate the docking and fusion of vesicles with their target membranes by forming a complex that brings the membranes close enough to fuse.

  • Similarity of HIV Fusion Protein to SNAREs

    • The HIV fusion protein exhibits SNARE-like behavior by facilitating the fusion of the viral envelope with the host cell membrane, allowing viral entry into the host cell.

  • Transport from ER to Golgi

    • Cargo proteins are packaged into COPII-coated vesicles, which bud off from the ER and travel to the Golgi apparatus.

  • Cargo Protein Recruitment into Vesicles

    • Specific sequences on the cargo proteins and receptors ensure the selection of appropriate cargo for transport in the vesicles.

  • Proteins Recycled from Golgi to ER

    • Retrieval proteins, typically involved in maintaining ER functions, are recycled back to the ER for reuse, including chaperones and enzymes.

  • Cis and Trans Face of Golgi

    • The cis face is closest to the ER and is where proteins enter; the trans face is where proteins exit, often toward their final destinations.

  • Functions of the Golgi Apparatus

    • Modification of proteins, processing of polysaccharides, sorting and packaging of proteins for secretion or delivery to lysosomes.

  • Polysaccharides Added to Proteins

    • Initial polysaccharides are added in the ER as O-linked glycans, which may undergo further modifications in the Golgi.

  • Types of Polysaccharides from Golgi Modification

    • 1) N-linked glycan: attached to asparagine during synthesis in the ER.
    • 2) O-linked glycan: attached to serine or threonine in the Golgi, involving glycosylation processes that differ in their linkage and structure.

  • Enzyme Differences Across Golgi Faces

    • Enzymes in the cis face are not identical to those in the trans face, with distinct functions in glycosylation and processing.

  • Functions of Lysosomes

    • Lysosomes are organelles responsible for degradation and recycling of cellular waste, utilizing hydrolytic enzymes to break down macromolecules.

  • Difference Between Lysosomal Interior and Cytosol

    • The interior of the lysosome is acidic (pH ~5) compared to the neutral cytosol, which is critical for enzyme activity.

  • Enzymes Present in Lysosomes

    • The lysosome contains hydrolytic enzymes such as proteases, lipases, and glycosidases that facilitate degradation of cellular materials.

  • Lysosomal Protein Targeting Labels

    • Mannose-6-phosphate (M6P) residues serve as labels that direct proteins from the Golgi to the lysosome.

  • Pathways Leading to Lysosomal Degradation

    • 1) Endocytosis: uptake of extracellular materials.
    • 2) Phagocytosis: engulfing larger particles or pathogens.
    • 3) Autophagy: degradation of damaged organelles and proteins within the cell.

  • Exocytosis Definition

    • Exocytosis is the process of vesicle-mediated secretion of materials from the cell to the extracellular space.

  • Protein Coat on Endocytic Vesicles

    • The protein coat on endocytic vesicles includes clathrin, which aids in membrane invagination and vesicle formation.

  • Destination of Endocytosed Materials

    • Endocytosed materials first go to early endosomes, where they can be sorted for recycling or degradation.

  • Low-Density Lipoprotein (LDL) Particles

    • LDL particles are complexes of lipids and proteins that transport cholesterol in the bloodstream.

  • Cholesterol Uptake by Cells

    • Cells take up cholesterol through receptor-mediated endocytosis of LDL particles bound to their LDL receptors.

  • Mutations in LDL Receptor and Heart Disease

    • Mutations can lead to reduced uptake of cholesterol, increasing plasma LDL levels and contributing to the development of atherosclerosis and heart disease.

  • Types of Proteins Suspected for Recycling

    • Proteins involved in membrane trafficking, receptors for signaling molecules, and chaperones are likely candidates for recycling.

  • Transcytosis Definition

    • Transcytosis is the process where substances are transported across a cell via vesicles, moving from one side of the cell to the other.

  • Invagination for Receptor Degradation in Lysosome

    • Invagination of the membrane is crucial for creating vesicles that encapsulate receptors, allowing them to be trafficked to lysosomes for degradation.