Extracellular Matrix (ECM) Questions PDF

Extracellular Matrix (ECM) Questions 1.​ What is the extracellular matrix (ECM)? ○​ The ECM is a network of extracellular materials that surrounds cells. It regulates cell shape, adhesion, migration, growth, and differentiation. It consists of proteins such a...

Extracellular Matrix (ECM) Questions 1.​ What is the extracellular matrix (ECM)? ○​ The ECM is a network of extracellular materials that surrounds cells. It regulates cell shape, adhesion, migration, growth, and differentiation. It consists of proteins such as collagen and other components like proteoglycans​. 2.​ How are cells affected by interactions between cells and the ECM? ○​ The ECM influences cellular behavior by regulating activities such as migration, growth, and differentiation through cell-surface receptors​. 3.​ What happens when mammary gland epithelial cells in culture are treated with enzymes that digest the surrounding ECM? ○​ Cells lose their differentiated state, appear flattened, and their secretory activities decrease. Reintroducing ECM materials restores differentiation​. 4.​ Where is the ECM most prominent? ○​ In connective tissues such as cartilage, bones, tendons, and the corneal stroma. These tissues derive their properties (e.g., flexibility, hardness, tensile strength, transparency) from the ECM​. 5.​ What are the functions of the basement membrane? ○​ Provides mechanical support, generates survival signals, facilitates cell migration, separates tissues, and acts as a barrier to cancer cells and macromolecules​. 6.​ What is the most abundant protein in the human body? ○​ Collagen, constituting more than 25% of total protein​. 7.​ What is the structure of collagens? ○​ Collagen molecules are trimers of three polypeptide chains that form a triple helix. Some assemble into fibrils and then into fibers​. 8.​ When individual collagen molecules in a collagen fibril are arranged in a staggered manner, what happens as a result? ○​ This staggered arrangement provides strength and creates a characteristic banding pattern through covalent cross-links between lysine and hydroxylysine​. 9.​ What happens to the elderly with continued cross-linking of collagen fibrils? ○​ Cross-linking reduces skin elasticity and increases bone brittleness​. 10.​How are collagen fibers in tendons arranged? ○​ Collagen fibers in tendons are aligned parallel to the tendon’s long axis, optimizing resistance to pulling forces during muscle contraction​. 11.​How are the layers of collagen in the corneal stroma organized? How does this affect the corneal stroma? ○​ Collagen fibrils are arranged in orthogonal layers (fibers in each layer are parallel but perpendicular to adjoining layers), providing strength and maintaining transparency by reducing light scattering​. 12.​The Type IV collagen trimer has some interspersed nonhelical segments in basement membranes. How does this affect the basement membranes?  ○​ These nonhelical segments allow flexibility and a lattice-like structure, facilitating ECM material deposition​. 13.​What are the characteristics of glycosaminoglycans (GAGs)? ○​ GAGs are acidic polysaccharides with repeating disaccharides. Their negative charges attract cations and water, forming hydrated gels that resist compression forces​. 14.​Why can proteoglycans occupy a lot of space? What are the functions of proteoglycan aggregates? ○​ Proteoglycans’ hydrated gels occupy space due to their ability to bind water. They provide resistance to compression and contribute to the mechanical strength of tissues like cartilage​. 15.​How are cells affected by laminin? ○​ Laminin supports cell migration, growth, and differentiation. It provides migration paths for specific cells, such as primordial germ cells during development​. 16.​What is the enzyme involved in the degradation of the ECM? ○​ Matrix metalloproteinases (MMPs) degrade ECM components, facilitating processes like tissue remodeling​. 17.​What are the roles of integrins? ○​ Integrins attach cells to the ECM and mediate bidirectional signaling (inside-out and outside-in), influencing adhesion, migration, and intracellular signaling cascades​. 18.​When cells from two different developing organs are mixed, they form a mixed clump. What happens next? ○​ Cells self-sort into homogeneous clusters, differentiating into the structures they would form in an intact embryo​. 19.​What is the area called where tight junctions, gap junctions, and desmosomes are arranged in a specific array? ○​ This is called the junctional complex​. 20.​Where are desmosomes particularly abundant? ○​ In tissues subject to mechanical stress, such as the skin, cardiac muscle, and epithelial layers of the gums and uterine cervix​. 21.​When a ligand binds to an integrin and induces transmembrane signaling, what kinds of responses can a cell produce? How are cells affected? ○​ Ligand binding induces changes in cytoplasmic pH, Ca²⁺ concentration, protein phosphorylation, and gene expression, altering cell behavior such as growth and differentiation​. 22.​What happens to mammary gland cells cultured in the presence of extracellular glycoproteins, like laminin? ○​ Cells regain differentiation, organize into milk-producing structures, and restore their ability to produce milk proteins​. 23.​What is the main function of gap junctions? ○​ Gap junctions mediate direct communication between cells, allowing the passage of ions and small molecules for coordinated cellular activity​. 24.​How do connexons interact to form gap junctions?  ○​ Connexons from adjacent cells align and link to form intercellular channels that connect the cytoplasms of neighboring cells​. 25.​Why can’t plants make the specialized junctions seen in animal cells? ○​ Plants lack cell adhesion molecules and are separated by rigid cell walls, unlike animal cells, which are in direct contact​. 26.​What is the structure of plasmodesmata? ○​ Plasmodesmata are cylindrical channels lined by the plasma membrane and containing a central desmotubule derived from the smooth ER​. 27.​Why can some viruses pass from cell to cell in plants through plasmodesmata even though they are bigger than the substances that normally pass through it? ○​ Viruses encode movement proteins that dilate plasmodesmata, allowing larger particles to pass through​. 28.​What cell wall component is economically important? In what way? ○​ Pectin is used commercially to provide gel-like consistency in products like jams and jellies​. 29.​How is the structure of the mature plant cell wall similar to that of the corneal stroma? ○​ Both have fibrous elements (cellulose in plants, collagen in corneal stroma) organized into perpendicular layers, providing strength​. Endomembrane Systems Questions Endomembrane Systems Questions 1.​ What kinds of membranous structures can be seen on electron micrographs of the cell interior? ○​ Membrane-bound vesicles, long channels, interconnected networks, and stacks of flattened, membrane-bound sacs called cisternae​. 2.​ What pathways of vesicle trafficking through the cytoplasm have been discovered? ○​ The biosynthetic (secretory) pathway, which transports materials synthesized in the ER to the Golgi and then to various destinations, and the endocytic pathway, which moves materials from the cell surface into cytoplasmic compartments like lysosomes​. 3.​ What substances of the biosynthetic pathway are made in the Golgi apparatus? ○​ Lipids, carbohydrates, and certain glycoproteins​. 4.​ What is the synthesis and secretion of a substance from the cell called when it happens in a continual, unregulated manner? ○​ Constitutive secretion​. 5.​ What is the pathway that allows materials or the membrane surface to move into the cell from the outside to cytoplasmic compartments? ○​ The endocytic pathway​. 6.​ How are proteins targeted to specific destinations within the cells? What types of signals are used by the cell to direct proteins to the right cellular location?  ○​ Proteins have sorting signals encoded in their amino acid sequence or attached oligosaccharides, which are recognized by receptors that direct them to their target locations​. 7.​ How is sorting of proteins in the cell facilitated? ○​ By sorting signals on the proteins, recognized by receptors on the surfaces of budding vesicles​. 8.​ Where does radiolabel first appear in the cell when a tissue is briefly incubated with radioactive amino acids? ○​ In the rough endoplasmic reticulum (RER), where proteins are synthesized​. 9.​ In studying protein transport pathways in cells, what is the step called when a brief incubation of a tissue with labeled amino acids is done? ○​ The pulse step of a pulse-chase experiment​. 10.​After a tissue has been briefly labeled with radiolabeled amino acids, it is transferred to a medium containing unlabeled amino acids. What is this step called? ○​ The chase step of a pulse-chase experiment​. 11.​Which procedure would allow for the visualization of the dynamic movements of specific proteins as they move through a single living cell? ○​ Using green fluorescent protein (GFP) fused to the gene encoding the protein to be tracked​. 12.​When cells are homogenized, the cytomembrane system is broken into fragments that can fuse into what? ○​ Microsomes​. 13.​What is the separation of different organelles or vesicles derived from different organelles called? ○​ Fractionation, often achieved using techniques like density-gradient centrifugation​. 14.​How do vesicles from different parts of the Golgi complex differ? ○​ They differ in their lipid and protein composition, reflecting their function and destination​. 15.​If free ribosomes are placed in a test tube with mRNAs and everything else needed to synthesize proteins, where are the proteins found after their production? ○​ Proteins remain in the cytosol or are targeted to specific locations based on signal sequences​. 16.​If a yeast cell has a mutation in the gene responsible for vesicle formation at the ER membrane, what will we see? ○​ Expanded ER cisternae due to an inability to form vesicles​. 17.​If a yeast cell has a mutation in the gene responsible for vesicle fusion, what will we see? ○​ An excess number of unfused vesicles​. 18.​How can we find out if RER and SER membranes are interconnected? ○​ By tracking the diffusion of fluorescently labeled lipids or proteins between the two compartments​. 19.​Why do different types of ER have different functions? What are these functions?  ○​ The rough ER synthesizes proteins, while the smooth ER synthesizes lipids, detoxifies substances, and regulates calcium. Their functional differences arise from their distinct enzymes and structures​. 20.​What is the arrangement of organelles in a secretory cell from the basal end to the apical end that reflects the flow of secretory products from synthesis to discharge? ○​ RER at the basal end (protein synthesis), the Golgi complex in the center (processing and sorting), and secretory vesicles at the apical end (discharge)​. 21.​Where does protein synthesis occur in the cells? ○​ On ribosomes attached to the RER and free ribosomes in the cytoplasm​. 22.​What is needed to add carbohydrates to a protein as it enters the RER lumen? ○​ The enzyme oligosaccharyltransferase transfers carbohydrate chains to nascent polypeptides​. 23.​What do molecular chaperones such as BiP and calnexin do? ○​ They assist in protein folding and prevent misfolded proteins from aggregating​. 24.​Are membranes made de novo? If not, how? ○​ No, membranes arise from pre-existing membranes by inserting newly synthesized lipids and proteins​. 25.​The phospholipid bilayers are asymmetrical. How does this happen? ○​ Asymmetry is established during synthesis in the ER and maintained during vesicle trafficking through the cell​. 26.​What causes changes in the lipid composition of membranes as they move from compartment to compartment within the cell? ○​ Enzymatic modifications, selective inclusion during vesicle budding, and phospholipid-transfer proteins​. 27.​What are the functions of carbohydrate groups on glycoproteins? ○​ They aid in proper protein folding, provide binding sites for macromolecules, and protect proteins from degradation​. 28.​Is the sequence of sugars in the oligosaccharides of a secretory glycoprotein predictable? What determines the sequence of sugar addition to glycoproteins traveling through the Golgi complex? ○​ Yes, the sequence is determined by the location and specificity of glycosyltransferases in the Golgi complex​. 29.​How does GT recognize incompletely folded or misfolded proteins? And what does GT do when it binds to a misfolded glycoprotein? ○​ GT binds to exposed hydrophobic residues of misfolded proteins, adding a glucose residue to facilitate further folding​. 30.​The accumulation of misfolded proteins in the ER causes what? ○​ It triggers the unfolded protein response (UPR), which increases chaperone production and reduces protein synthesis​. 31.​What is a model of how the sensors in the ER monitor the concentration of unfolded or misfolded proteins in the lumen? ○​ Sensors detect misfolded proteins through direct binding or by monitoring stress in the ER membrane​. 32.​How can we visualize the journey of secretory proteins from the ER to the Golgi complex? ○​ Using GFP-tagged proteins​. 33.​What model suggests that the Golgi cisternae are transient structures that travel from the cis face to the trans face, while changing during the journey? ○​ The cisternal maturation model​. 34.​What model suggests that the Golgi stack remains in place as stable compartments held together by a protein scaffold, and cargo is shuttled through the Golgi via vesicles? ○​ The vesicular transport model​. 35.​When vesicles move through the Golgi complex from trans to cis end, what is this direction called? ○​ Retrograde transport​. 36.​What is the function of the protein coat on budding vesicles? What type of vesicles are there and where do they operate? ○​ The coat assists in vesicle formation and cargo selection. Types include clathrin-coated (endocytosis), COPI-coated (retrograde transport), and COPII-coated (ER to Golgi transport) vesicles​.