Molecular Biology
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Molecular biology 1. Cytoskeleton 2. Motor proteins 3. Signal sequences-navigated protein transport 4. Apoptosis 5. RNA: structure and function 6. RNAinterference 7. Control of gene expression 8. Cojugative gene transfer 9. DNA damage response 10. Cell –cell signaling 11. Bacterial chemotaxis 12. Bacterial cell motility 13. Bacterial toxins 14. Viroids Vladimír Jirků 1. Cytoskeleton The Cytoskeleton is a highly dynamic (complex, responsive) filamentous structure, acting as an intracellular scaffolding organizing the cell's contents to maximize inner-cell differentiation, transport and coordination of cell processes, as well as maintaining or altering cell shape and cell motion. In addition, interactions with the cytoskeleton influence a number of other behaviors, including signaling pathways (But one of the most important roles of the microtubule cytoskeleton is that it regulates and thus coordinates actin polymerization. Without this coordination, cells can't maintain their ability to have front ends and back ends – this front / back dichotomy is referred to as “cell polarity”). It is contained in all eukaryotic cells. While the cytoskeleton is an interconnected network, it is conventionally broken into three distinct cytoplasmic systems: microtubules, actin filaments ( microfilaments) and intermediate filaments. Microtubules: They are hollow filaments of about 25 nm, formed by 13 protofilaments which, in turn, are polymers of alpha and beta tubulin. They have a very dynamic behaviour, binding GTP for polymerization. They are organized by the microtubule organizing centre (MTOC, centrosome , - spindle pole body in yeast cell). They play key roles in: intracellular transport (associated with motor proteins) - transport cell compartments; the axoneme of cilia and flagella; the mitotic spindle; synthesis of the cell wall in plant cell, among others. Microtubules have + end / - end (MTOC) polarity. Actin filaments These filaments (around 7 nm in diameter) are composed of two actin chains oriented in an helicoidal shape. They are mostly concentrated just beneath the plasma membrane, as they keep cellular shape, form cytoplasmatic protuberances (like pseudopodia and microvili), and participate in some cell-to-cell or cell-to-matrix junctions and in the transduction of signals. They are also important for cytokinesis and, along with myosin, muscular contraction. G- actin (globular actin) with bound ATP can polymerize, to form F-actin (filamentous actin). F-actin may hydrolyze its bound ATP to ADP + Pi and release Pi. ADP release from the filament does not occur because the cleft opening is blocked. ADP/ATP exchange: G-actin can release ADP and bind ATP, which is usually present in the cytosol at higher concentration than ADP. Actin filaments have polarity. The actin monomers all orient with their cleft toward the same end of the filament (designated the minus end). Actin monomers spiral around the axis of the filament, with a structure resembling a double helix. At the ends of actin filaments are boud capping proteins. Different capping proteins may either stabilize an actin filament or promote disassembly. They may have a role in determining filament length. Cross-linking proteins organize actin filaments into bundles or networks. Actin- binding domains of several of the cross-linking proteins (e.g., filamin, -actinin, spectrin, dystrophin and fimbrin) are homologous. Most cross-linking proteins are dimeric or have 2 actin-binding domains. Some actin-binding proteins such as -actinin, villin and fimbrin bind actin filaments into parallel bundles. Depending on the length of a cross-linking protein, or the distance between actin-binding domains, actin filaments in parallel bundles may be held close together, or may be far enough apart to allow interaction with other proteins such as myosin. Filamins dimerize, through antiparallel association of their C-terminal domains, to form V-shaped cross-linking proteins that have a flexible shape due to hinge regions. Filamins organize actin filaments into loose networks that give some areas of the cytosol a gel-like consistency. Filamins may also have scaffolding roles relating to their ability to bind constituents of signal pathways such as plasma membrane receptors, calmodulin, caveolin, protein kinase C, transcription factors, etc. Nucleation. three 'barbed'-end nucleators of F actin have been described. The ARP2/3 complex, made up of two ARP proteins and five associated subunits (ARPC1–5/p41–16), serves as a template for F-actin formation and can also interact with the sides of existing actin filaments, forming branched F-actin arrays. Upstream regulation: cofilins are inhibited in their activity and dynamics by specific kinases (such as LIM (Lin-11/Isl-1/Mec-3) or TES kinases) that phosphorylate the proteins on the conserved serine residue. Dephosphorylation by phosphatases activates cofilins. ARP, actin-related protein; CAP, cyclase-associated protein; FH1, formin homology 1; FH2, formin homology Filopodia (also called microspikes) are long, thin and transient processes that extend out from the cell surface. Bundles of parallel actin filaments, with their plus ends oriented toward the filopodial tip, are cross-linked within filopodia by a small actin-binding protein such as fascin. The closely spaced actin filaments provide stiffness. Microvilli are shorter / more numerous protrusions of the cell surface found in some cells. Tightly bundled actin filaments within these structures also have their plus ends oriented toward the tip. Small cross-linking proteins such as fimbrin and villin bind actin filaments together within microvilli. Lamellipodia are thin but broad projections at the edge of a mobile cell. Lamellipodia are dynamic structures, constantly changing shape. Lamellipodia, at least in some motile cells, have been shown to contain extensively branched arrays of actin filaments, oriented with their plus (barbed) ends toward the plasma membrane. Forward extension of a lamellipodium occurs by growth of actin filaments adjacent to the plasma membrane. Cells move through the rapid rearrangement of the actin cytoskeleton. In the dendritic nucleation model, several signaling pathways converge to activate WASp/Scar proteins, which in turn activate the Arp2/3 complex. Active Arp2/3 complex binds to the side of an existing filament and nucleates new filament growth towards the cell membrane. The combined force from many growing filaments pushes the cell membrane forward, moving the cell.. ARP, actin-related protein; CAP, cyclase-associated protein; FH1, formin homology 1; FH2, formin homology Intermediate filaments These filaments, 8 to 11 nanometers in diameter, are strongly bound and very heterogeneous constituents of the cytoskeleton. They organize the internal tridimensional structure of the cell (they are structural support of the nuclear membrane for example). They also participate in some cell-cell and cell-matrix junctions. Respectively, they are made from many different types of proteins (desmin, vimentin, keratin, lamin…….). Intermediate filaments are essential for normal tissue structure and function; they provide physical resilience for cells to withstand the mechanical stresses of the tissue in which they are expressed. They are found in the nucleus (lamins) and the cytoplasm (cytoplasmic intermediate filaments). Assembly: Intermediate filaments are assembled from tetramers: two monomers form a parallel dimer by the winding of their α-helical rods into a coiled coil, oriented in register and in the same direction, and then two dimers join side-by-side in a staggered anti-parallel orientation to form a bidirectional tetramer. Each dimer is 48 nm long; because the dimers are staggered the tetramer is somewhat longer. The anti-parallel orientation of tetramers means that, unlike microtubules and microfilaments (which have a preferred assembly end), intermediate filaments do not show polarized unidirectional properties. Assembly and disassembly is regulated by cycles of phosphorylation and dephosphorylation; polymerization of intermediate filaments occurs rapidly and does not require cofactors or associated proteins. In most cells, intermediate filaments assemble into complex networks that course through the cytoplasm between the nucleus and the cell surface. Towards the cell center, they are attached to the nuclear envelope, and in the region of the plasma membrane, they are associated with various adhesion structures such as the desmosomes and hemidesmosomes of epithelial cells and the focal adhesions of fibroblasts. Cytoskeletal intermediate filaments play important roles in a wide range of cellular functions. These include the formation and maintenance of cell shape, cellular mechanical integrity, signal transduction, and the overall stability and integration of other cytoskeletal systems, i.e. microtubules and actin filaments. Types of intermediate filaments: The proteins comprising these filasments are encoded by approximately 70 different genes. This large family of proteins is subdivided into five types, four of which are located in the cytoplasm (cytoskeletal IF) and one in the nucleus (nucleoskeletal IF). In the cytoplasm, one, two or even more types of IF protein chains can polymerize into cytoskeletal IF of 10 nm diameter. Textbooks describe IF as very stable and rigid structures, only recognized for their maintenance of the mechanical stability of cells. However, the results of live cell imaging studies demonstrate the opposite. These studies have shown that