Cellular Biology I - Past Paper PDF

Subject Cellular Biology I Professor Lattanzi Wanda Author Alexander Nesterov Checker...

Subject Cellular Biology I Professor Lattanzi Wanda Author Alexander Nesterov Checker Mario Dalfino Date 02/10/2023 (11.30 am) In the cell there are many structural and functional compartments, each of those has its own task and a different level of complexity. Nearly all the organelles of an eukaryotic cell are separated by membranes that have the same gross structure of the plasma membrane (endoplasmic reticulum, Golgi complex, transport vesicles, lysosomes and peroxisomes) and compose the so- called endomembrane system. This system can be considered as a biosynthetic industry that produces everything the cell needs, but also performs some enzymatic detoxification activities, serves as a storage and produce vesicles to transport molecules in and out of the cell. Even the mitochondria have a double membrane, and they serve as power producers (cellular respiration). Finally, the nucleus is also bounded by a double membrane as well, equipped with pores that allow communication between the nucleus and the rest of the cell (cytoplasm). Plasma Membrane structure and composition Knowing the structure of the plasma membrane, it will be possible to understand most of the structural features of the other organelles. In the plasma membrane we find all the biomolecules except the nucleic acids. The membrane (and almost all the cell’s membranes) has fluid mosaic model: the fluidity of the plasma membrane is enabled because of phospholipids and a little bit of cholesterol. 1  The bilayer of the membrane is formed by phospholipids. On the outside there are hydrophilic heads which interact with extra and intracellular environment which is water-based. On the other hand, the inner part of the bilayer is composed by their hydrophobic tails, composed by fatty acids. The bilayer is very soft, so it is stabilized by proteins inside the bilayer. Proteins in the membrane structure can differ from cell to cell. Molecules in the membrane can move longitudinally, like in the ocean. Sometimes they can move from a layer to another requiring energy, that is fundamental to preserve membrane’s asymmetry. Components of the plasma membrane 1. Lipids - Types: phosphoglycerids (the most abundant); sphingolipids (less abundant); cholesterol (its quantity can vary). - Functions: structural support, because the bilayer is the key architecture of the membrane; hydrophobic barrier (gives plasma membrane selective permeability), precursors of signaling molecules (some lipids of the bilayer can serve as a substrate for enzymes which will break them into small lipidic parts and function as signaling molecules in order to communicate with other cells). 2. Proteins - Types: integral proteins (tightly fixed in the bilayer, either partially, or it goes through entire bilayer), peripheral proteins (loosely associated to the bilayer mostly on the inner layer), lipid- anchored proteins (tightly bound to the bilayer by covalent bonds). They are all differently structured. - Functions: receptors, signaling molecules, channels, ion pumps, transporters, junctional complexes (attach to a substrate). 3. Carbohydrates - Types: oligosaccharides mostly bound to proteins and lipids. 2 - Functions: signals (such as antigens), protein sorting tags (used in the transport vesicles as a tag to where the vesicle is going), structural component to interact with the environment (glycocalyx). The proportions of proteins, lipids, and carbohydrates in the plasma membrane vary with cell type: the higher the protein content, the higher the permeability (because there can be more channels and carriers); the higher the lipid content, the higher the insulation. The cell can also decide in different stages of his own life how many and what protein to express. Membrane Lipids About 50% of the mass of animal cell is composed by lipids, mainly because most of the cell’s structures are made up of membranes. Lipids represent the fluid portion of the membrane. The membrane is a lipid bilayer as it contains amphipathic lipids (phosphoglycerids, sphingolipids) with: - hydrophilic head groups pointing outwards; - hydrophilic tails point inwards. The types and amount of membrane lipids varies significantly across different cell types, as they determine the physical state of the membrane. 3  Why a double layer? Spontaneous adaptation to the environment. In aqueous solution, phospholipids tend to arrange themselves with their polar heads facing outward and their hydrophobic tails facing inward. This property allows to form the phospholipid bilayer of the cell membrane by creating a sort of sphere also called lyposome. Membrane lipids: phosphoglycerides vs sphingolipids Phosphoglycerides The most abundant in the membrane. They are built on a glycerol backbone, which has 3 hydroxyl groups: - 1 esterified to a phosphate group (forming the phosphatic acid), and can be linked to and additional polar head group (choline, serine, ethanolamine, inositol, each of which is differently present on the inner and outer layer); - 2 esterified to two fatty acid chains. Can be identical or different, can vary in length and saturated links. 4  Sphingolipids In general, they are not very abundant except in neurons and glial cells (nervous tissue). More than 80% of the plasma membrane sphingolipids are located in the outer monolayer, in order to maintain the asymmetric feature of the membrane. They are built from the ceramide (skeleton of the molecule) which is composed by a sphingosine molecule linked to a fatty acid. Ceramide can be esterified to: - Phosphorylcholine or phosphoethanolamine (sphingomyelin) - Monosaccharide (cerebroside) - Oligosaccharide (ganglioside) Cholesterol May represent up to 50% of membrane lipids in certain cells. Has a small hydroxyl group towards aqueous solution, that is the only hydrophilic part of the molecule. It is a highly hydrophobic molecule because of the presence of 4 carbon rings. It is interspersed between hydrophobic tails, which means that it will interact with them. Cholesterol can buffer and modulate their movement affecting the fluidity as well. It also influences the permeability because it makes the membrane more hydrophobic. The more hydrophobic is the membrane (due to the presence of lipids), the less will be the permeability. 5  Membrane fluidity Role of phospholipids: - Length of hydrocarbons’ chains The shorter the tails, the higher fluidity is. If tails are longer they will interact more easily with each other and make the bilayer more rigid. - Saturation of hydrocarbons’ chains The less saturated, the higher fluidity. Reduced hydrophobic interactions leads to increased fluidity because phospholipids tend to move more freely but can be varied by presence of cholesterol and temperature. Effect of temperature: - At physiological temperature the lipid bilayer behaves as bidimensional liquid crystal, like a jellified structure (fluid mosaic); - As the temperature cools down the bilayer turns into a frozen crystalline gel. - When temperature increases the extent of movement of fatty acid chains increases, thus fluidity will increase. If the fluidity is very high, the integrity of the cell will be lost; while if the fluidity is low, tissue homeostasis could collapse by reducing his rigidity. Role of cholesterol - Alters the membrane phase transition as a fluidity buffer (between fluid and solid); - Above Tm (melting temperature, between liquid state and the jelly like state), cholesterol will restrict the movement of phospholipids and decrease membrane’s fluidity; - Below Tm it disturbs the regular and tight packaging of hydrocarbon tails, and consequently cholesterol will increase fluidity. It will enable the membrane to maintain the homeostasis, but in some desperate cases in which the external environment is non-optimal, it won’t be able to avoid cell’s death. 6  To sum up, membranes rich in unsaturated fatty acids are more fluid than those rich in saturated fatty acids. Membrane Proteins They determine most of the membrane’s specific functions and contribute to membrane asymmetry. We can name them by identifying their position in the bi-layer and function: - Integral proteins: embedded in the lipid bilayer (intrinsic proteins); - Lipid-anchored proteins: outside the bilayer, but bound to it (proteolipids) interact with the membrane bilayer via covalent bonds; - Peripheral proteins: outside the bilayer, loosely bound, on the surface (extrinsic) interact with membrane bilayer via non-covalent bonds. Integral membrane proteins - Contain one or more hydrophobic domains in their secondary structure with affinity for the hydrophobic interior of the lipid bilayer. It is hydrophobic because there are regions with amino acids which have hydrophobic R-groups; - Intimately associated with the membrane and cannot be easily removed - One or more hydrophilic regions that extend outward from the membrane into aqueous phase on one or both sides of the membrane There are 2 main groups of integral membrane proteins: 1. Integral monotopic proteins – embedded in the membrane on only one side of the bilayer, quite entirely submersed, that means that it doesn’t run from one side to another of the bi-layer; 2. Transmembrane proteins - they span the membrane and have hydrophilic regions going from one side to the other of the membrane; - Single-pass proteins cross the membrane once, hydrophilic, and there is a single domain of the protein totally submerse in the bi-layer; - Multi-pass proteins cross the membrane several times (some polypeptides consist of a single polypeptide, others consist of two or more), with hydrophobic loops that connect the hydrophilic domains. 7  Lipid-anchored proteins - Anchored with covalent bond to phospholipids, either directly or through oligosaccharide to phosphatidylinositol to remain strictly attached to the membrane. Basically we can describe three main types of anchored proteins: 1. Prenylated proteins: covalently attached to the isoprene polymer, which is the hydrophobic portion; 2. Fatty acylated proteins: covalently bond to fatty acids, directly, instead of the hydrophilic head in the bi-layer. In this case, we will have a post-translational modification of a given protein. It means that after the creation of a protein, there will be a bio-synthetic step to include the fatty acid chains to the protein, so that it can be inserted in the bi-layer; 3. Glycosylphosphatidylinositol-linked proteins (GPI): phosphoglycerides to which the protein in anchored. Most of these protein have a relevant role in signaling, on both sides of the membrane. Integral protein and lipid-anchored protein are strongly stick to the membrane, which makes it difficult for us to detach and analyze them individually. Peripheral proteins - They are bound through noncovalent bonds to the membrane, as the consequence they can move rather freely. Their interaction with one of the layer (usually the inner layer) is loose. - Serve as relays in the transduction signals, once they receive an activation from the receptor, they can move to reach another effector (enzymes) that will activate the cascade of the molecular events; 8 - They can either interact with the hydrophilic portion of a protein or the hydrophilic heads of phospholipids, and in both cases we are talking about noncovalent bonds. Main functions of membrane proteins -Channels (integral) because it goes through the entire bi-layer. It can be also a transporter that recognizes a specific solute, binds it and using ATP transports it across the membrane. -Enzymatic activity: they can contain a domain that has an enzymatic activity, just like hydro pumps, that hydrolyze ATP to mediate the transport. -Cell-cell recognition (integral) -Intercellular joining (integral): integral protein is needed which has extracellular domain that has a specific region that can in turn specifically recognize a signal. Once the signal is bound, proteins undergo an allosteric activation (change in its conformation), which leads to activation of intracellular domain and leads to the cascade of chemical reaction. -Attachment to the cytoskeleton and extracellular matrix (ECM): in some tissues, cells attach to each other. In this case there will be proteins expressed on those cells which will recognize the other cell to mediate addition of the cell in that environment. In other cases we will have cells that need to attach to the extracellular matrix. -Relay molecules in signal transduction: they can be receptors. 9 Lipid Rafts There are regions of the membrane in which sphingolipids and cholesterol reduce the fluidity of the membrane, being carried as if they were in an ocean. There can be also multi molecular domains that are more rigid and can travel through the fluid mosaic without detaching from each other: this is obviously functionally useful, because there are some proteins that can’t work if not together, such as receptors and their effector proteins. 10