Chapter 8: Endomembrane System

 What is the endomembrane system composed of

a series of membrane-bound organelles, including the endoplasmic reticulum, Golgi apparatus, lysosomes, and vesicles, that work together to modify, package, and transport lipids and proteins within the cell.

What are the basic characteristics of the organelles of the endomembrane system

They are membrane-bound, functional in protein and lipid transport, and have distinct structures and roles in cellular processes. organelles consist of the endoplasmic reticulum, Golgi apparatus, lysosomes, and vesicles.

What are the  difference between constitutive and regulated secretion

Constitutive secretion occurs continuously and is not regulated by external signals, while regulated secretion is triggered by specific signals and involves the storage of proteins in secretory vesicles.

What are the differences between differential centrifugation and density gradient centrifugation

Differential centrifugation separates organelles based on size and density by applying varying centrifugal forces, while density gradient centrifugation involves the use of a gradient medium to isolate organelles based on their buoyancy density.

What are the three primary characteristics if microscopy

Magnification, resolution, and contrast.

What is the relationship between wavelength and resolution

Shorter wavelengths provide higher resolution, allowing for clearer imaging of small structures.

What’s the effect on resolution of different wavelengths in relation to the Abbe equation

The Abbe equation indicates that resolution improves with shorter wavelengths, as it defines the minimum distance between two points that can be distinctly resolved.

What is meant by light-microscopy (bright field) and the limitations

Light microscopy, specifically bright field microscopy, refers to a technique that uses visible light to illuminate specimens. Its limitations include lower resolution compared to electron microscopy and difficulty in visualizing transparent or colorless specimens without staining.

Why you can use the same microscope for light microscopy and fluorescence microscopy and what the differences are

Both techniques utilize visible light and similar optical components, but fluorescence microscopy employs specific filters to detect fluorescently labeled specimens, providing enhanced contrast and specificity.

What is direct and indirect labeling using antibodies

Direct labeling involves conjugating a fluorescent dye directly to an antibody, allowing for immediate visualization. Indirect labeling uses a secondary antibody to bind to the primary antibody, which is linked to a fluorescent dye, amplifying the signal and enhancing detection.

What is Green fluorescent protein

Green fluorescent protein (GFP) is a protein that exhibits bright green fluorescence when exposed to ultraviolet or blue light. It is widely used as a marker for gene expression and protein localization in various biological research applications.

What is a cell-free system

A cell-free system is an experimental setup that allows biological processes to occur outside of living cells, typically using cell extracts or purified components to study biochemical reactions and protein functions.

What’s the difference between translation and translocation

Translation is the process of synthesizing proteins from mRNA, while translocation refers to the movement of ribosomes along the mRNA strand during protein synthesis.

what’s the difference between cotranslational and post-translational translocation

Cotranslational translocation occurs simultaneously with translation, where proteins are fed into the endoplasmic reticulum as they are synthesized, while post-translational translocation happens after the protein has been fully synthesized.

What are steps in secretory protein synthesis from cytosolic ribosome to release into the lumen of the ER (all of it)

The steps in secretory protein synthesis from the cytosolic ribosome to release into the lumen of the ER include: 1) synthesis begins on a free ribosome in the cytosol; 2) signal peptide is recognized by the signal recognition particle (SRP); 3) SRP directs the ribosome to the ER membrane; 4) the ribosome attaches to the translocon in the ER; 5) translation resumes and the growing polypeptide enters the ER lumen; 6) signal peptide is cleaved; 7) protein folds and may undergo modifications before being packaged into vesicles for secretion.

How is the integral membrane protein is synthesized

Integral membrane proteins are synthesized similarly to secretory proteins, beginning on cytosolic ribosomes, but they have specific sequences that allow them to integrate into the lipid bilayer of the membrane as they are translated and translocated into the endoplasmic reticulum.

What is the oligosaccharide precursor (in general)

The oligosaccharide precursor is a glycan structure that is assembled in the endoplasmic reticulum and serves as a foundation for the N-linked glycosylation of proteins, aiding in proper folding and stability.

What are UPR and ERAD

UPR (Unfolded Protein Response) is a cellular stress response related to the endoplasmic reticulum, activated by the accumulation of misfolded proteins, while ERAD (ER-associated degradation) is the process that targets these misfolded proteins for degradation, maintaining cellular protein homeostasis.

What is the role of the Golgi complex

The Golgi complex is responsible for modifying, sorting, and packaging proteins and lipids for secretion or delivery to other organelles. It serves as a key processing center in the endomembrane system.

What’s the basic differences between the Vesicular transport model and the cisternal maturation model

The vesicular transport model suggests that cargo is transported between stable, separate compartments via vesicles, while the cisternal maturation model posits that cisternae of the Golgi complex change identity and function over time as they mature, processing cargo as they move from the cis to trans side.

What’s the basic structure and the role of COPI and COPII

COPI (Coat Protein Complex I) and COPII (Coat Protein Complex II) are protein complexes that coat vesicles transporting materials between the endoplasmic reticulum and the Golgi apparatus. COPII is involved in the anterograde transport from the ER to the Golgi, while COPI is responsible for retrograde transport from the Golgi back to the ER.

What is the role of KDEL sequence and KDEL receptor (in detail)

The KDEL sequence is a short peptide signal present on proteins that directs their retrieval from the Golgi apparatus back to the endoplasmic reticulum. The KDEL receptor recognizes this sequence and facilitates the transport of KDEL-containing proteins in vesicles, ensuring proper localization within the cell.

What’s the roles of V-SNARES and T-SNARES – the example of synaptobrevin receptor

V-SNAREs (vesicle-soluble N-ethylmaleimide-sensitive factor attachment protein receptors) and T-SNAREs (target membrane SNAREs) are proteins that mediate the fusion of vesicles with their target membranes. Synaptobrevin is an example of a V-SNARE found in synaptic vesicles, which interacts with T-SNAREs on the presynaptic membrane to facilitate neurotransmitter release.

What is the role of a mannose 6-phosphate tag and a mannose 6-phosphate receptor (in detail)

The mannose 6-phosphate (M6P) tag is a molecular marker that directs lysosomal enzymes to their appropriate destination in the lysosome. The M6P receptor identifies this tag in the Golgi apparatus, facilitating the sorting and transport of these enzymes in vesicles to lysosomes for degradation of substrates.

What’s the role of lysosome and how hydraulic enzymes are targeted (the mannose 6-phosphate tag and receptor)

Lysosomes are membrane-bound organelles that contain hydrolytic enzymes for breaking down waste materials and cellular debris. Hydraulic enzymes are targeted to lysosomes by the mannose 6-phosphate tag, which is recognized by mannose 6-phosphate receptors in the Golgi apparatus, ensuring their delivery to lysosomes.

What’s the difference between bulk phase endocytosis and receptor mediated endocytosis

Bulk phase endocytosis involves the nonspecific uptake of extracellular fluid and solutes, while receptor-mediated endocytosis is a selective process that uses specific receptors to internalize particular molecules or ligands.

What’s the formation and role of clathrin coated adaptor proteins

Clathrin-coated adaptor proteins are essential components in the process of vesicular transport, facilitating the budding of vesicles from membranes. They help recruit cargo and clathrin to form a coated vesicle, which is necessary for proper trafficking within the endomembrane system.

What is the 4 compartments of mitochondria

The four compartments of mitochondria are the outer membrane, intermembrane space, inner membrane, and mitochondrial matrix. Each compartment has distinct functions, including energy production and metabolic processes.

What are the basics of mitochondrial import including the role of TOM and the TIMs and location of signal sequences

Mitochondrial import involves the translocation of proteins into mitochondria, facilitated by the Translocase of the Outer Membrane (TOM) complex and the Translocase of the Inner Membrane (TIM) complexes. Signal sequences on precursor proteins direct their import and dictate their final localization within the mitochondria.

What’s the structure of the nuclear envelope

The nuclear envelope consists of two lipid bilayer membranes, the inner and outer membranes, separated by the perinuclear space. It serves as a barrier that regulates the exchange of materials between the nucleus and the cytoplasm, and contains nuclear pore complexes that facilitate the transport of molecules.

What’s the role of nuclear pores

Nuclear pores are large protein complexes that span the nuclear envelope, regulating the transport of ions, RNA, and proteins between the nucleus and cytoplasm. They allow selective entry and exit, ensuring proper cellular function and communication.

Interpret slides 8.11 and 8.12

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What’s protein transport in and out of the nucleus (extent of 8.13)

Protein transport in and out of the nucleus involves the movement of proteins through nuclear pores, where they are selectively imported or exported to maintain cellular function and compartmentalization.

What kind of protein is Ran

Ran is a small GTPase involved in the transport of proteins and RNA across the nuclear envelope, playing a critical role in the regulation of nuclear import and export.

What are Ran-GAP and Ran-GEF and what do they do

Ran-GAP (GTPase-activating protein) stimulates the hydrolysis of Ran-GTP to Ran-GDP, promoting export, while Ran-GEF (guanine nucleotide exchange factor) facilitates the exchange of GDP for GTP on Ran, promoting import. Together, they regulate the cycle of nuclear transport.