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Midterm

BIOL 1090: Midterm Study Notes.docx
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Department
Biology
Course
BIOL 1090
Professor
Marc Coppolino
Semester
Winter

Description
BIOL 1090 Midterm Notes 50 Marks - MC - SA - Paragraph/point form/label diagram Basic Properties of Cells - Complex and organized o Contain large number of parts o Organized with respect to time and space o Interaction with little tolerance for error o Control and regulation is maintained o Complexity allows cells to be diverse o Cellular organization is consistent and conserved through evolution therefore there may be similarities between many cells in specific parts and pieces - Maintain and use a genetic program - Reproduction - Acquire and utilize energy - Support enzyme-catalyzed chemical reactions - Mechanical activities - Response to stimuli - Self-regulation - Evolve Two Classes of Cells on Earth 1) Prokaryotic - Bacteria - Structurally simpler 2) Eukaryotic - Protists, fungi, plants and animals - Structurally more complex Viruses - Non-cellular macromolecular packages - Reproduce only in living cells - Virus outside of a cell is called a virion - Virion is comprised of a small amount of DNA/RNA and a protein capsule (capsid) - Very small compared to other eukaryotic and prokaryotic cells - Can bind to a cell surface via specific proteins o Narrow host versus wide host range - Two main types of viral infections o Lytic: production of virus particles ruptures and kills the cell (e.g. influenza) o Non-lytic (or integrative): viral DNA is inserted into the host genome (provirus) and the viral progeny buds at the cell surface and the cell can survive, but often with impaired function (e.g. HIV) Fluid-Mosaic Model (Singer/Nicolson, 1972) - Bilayer of amphipathic lipids o Amphipathic: both hydrophilic and hydrophobic - Integral (transmembrane), peripheral and lipid-anchored proteins - Components are mobile and can interact The Cell Membrane - Layer of lipids interacting with another layer - Biological membranes contain a hydrated lipid bilayer - All membranes share common properties o Approximately 6nm thick (with associated water) o Stable o Flexible o Capable of self assembly - Different membranes contain different types of lipids and proteins - Membranes have different functions, in different cells and within an individual cell - Inner membrane of mitochondria contains a very high concentration of protein because it is a metabolic centre (ATP synthesis) - Myelin sheath of a neuron contains very low amounts of protein and consists of layers of plasma membrane wrapped around the nerve axon for insulation - Contain specific proteins that are needed at that specific location to complete a job - Asymmetrical - Two leaflets have distinct lipid composition - In many plasma membranes, the outer leaflet contains glycolipids and glycoproteins - Lipids move easily, laterally, within leaflet (or layer) - Lipid movement from leaflet to another leaflet is slow because of physical restriction and must be done by an enzymatic process - Membrane proteins can diffuse within the bilayer o Movement of proteins is restricted and some proteins do not move o Biochemical modification can dramatically alter protein’s mobility in the membrane Membrane Proteins - Integral Membrane Proteins o Span the lipid bilayer o Can stick out on either side o Compatible with the hydrophobic environment in the membrane o Very stable - Lipid-anchored proteins o Attached to a lipid in the bilayer o Interacts with the hydrophobic nature and holds the molecule that I associated with the membrane - Peripheral membrane proteins o Associate with the surfaces of the lipid bilayer o Not permanently attached to the membrane o Allows them to associate with hydrophilic parts of membranes or will associate with another part of another protein o Charged, electrostatic interactions and usually hydrophilic o Not as stably associated as integral membranes Membrane Fluidity - Determined by the nature of lipids in the membrane, temperature o Unsaturated lipids increase fluidity while unsaturated lipids reduce fluidity o An increase of temperature increases fluidity (because of more molecular motion) into a liquid crystal while cooling decrease fluidity, turning the membrane into a crystalline gel - Balance between ordered (rigid) structure and disordered structure - Allows mechanical support and flexibility - Dynamic interactions between components of the membrane - Important for membrane assembly and modification - Lipid composition of membranes can be altered by the desaturation of lipids or the exchange of lipid chains, but usually only occurs in response to temperature changes in eukaryotes who do not have control over their internal temperature - Cholesterol regulates membrane fluidity o Cholesterol is hydrophobic and has contrasting effects depending on the situation o Alters packing and flexibility of lipids o If added to a liquid crystal membrane, fluidity will decrease o If added to a crystalline gel membrane, fluidity will increase Lipid Rafts - Small areas of the plasma membrane that are enriched in certain types of lipids (e.g. cholesterol) - Rafts are relatively rigid - Some membrane proteins accumulate in rafts - Specialized component of the membrane - Signaling and information transduction Movement of Substances Across Cell Membranes - Lipid bilayers do not allow many compounds to pass through them freely - Small, uncharged molecules cross relatively easily - Large, polar and/or charge molecules cannot easily cross a lipid bilayer - Simple diffusion (A in diagram) o Very small molecules o Uncharged o Down a concentration gradient - Diffusion through a channel (B) o Small, charged molecules (ions) o Down a concentration gradient o Sit in the membrane o Central cavity allows the ion to pass through o The ion does not bind to the channel o Dependent on the concentration gradient o Channels are selective to specific ions o Ion channels are often gated o Three types of gated channels  Voltage-gated channels (e.g. K+ channel) where the channel responds to changes in charge across the membrane  Ligand-gated channels (e.g. CFTR) where it responds to binding of a specific molecule outside the channel to open  Mechano-gated channels (e.g. cation channels in the inner ear) - Facilitated diffusion (C) o Compound binds specifically to integral membrane protein called facilitative transporter o Change in conformation of transporter allows compound to be released on other side of membrane o Compound moves down concentration gradient - Active transport (D) o Compound binds specifically to integral membrane protein called active transporter o Change in conformation of transporter allows compound to be released on the other side of the membrane o Compound moves up the concentration gradient, therefore requiring the input of energy The Extracellular Space - Most cells have a glycocalyx o Glycocalyx: assembly of carbohydrate groups attached to proteins and lipids on the outside of the plasma membrane - Mediates cell-cell and cell-ECM interactions - Provides mechanical protection - Serves as a barrier to some particles - Binds regulatory factors - Extracellular matrix (ECM) o Many cells contact an ECM o Organized network of material produced and secreted by cells o Sites for cell attachment o Physical support for cells o Substrate through which cells can move o Contains regulatory factors (signals) o Separate/define tissues o When a cell is not attached to another cell, it must be attached to something else which is usually the ECM o Components of the ECM are produced by cells and assembled into a network  Proteins, glycoproteins (collagen, fibronectin, laminin) and proteoglycans (proteins with long chains of polysaccharides)  Long, fibrous, thread-like proteins  The cell that usually is still associated with the ECM protein it made o Dynamic environment o Binding via integrins and influences cell survival and cellular activities o Cell-ECM interactions define tissue and organ function - (Plant) cell walls o Composed of cellulose, hemicellulose, pectin and proteins o Provide structural support to cell and to the organism as a whole o Protect cell from mechanical damage and pathogens o Contain biochemical information for the cell Intracellular Compartments Compartment Function Cytosol Protein synthesis Metabolic pathways Nucleus Contains genome DNA, RNA synthesis Ribosome assembly Endoplasmic reticulum Synthesis of lipids Synthesis of proteins Golgi apparatus Protein modification Packaging of proteins and lipids Lysosomes Degradation of cellular material Endosomes Sorting Recycling Mitochondria ATP synthesis Apoptosis Chloroplasts (in plants) Photosynthesis ATP synthesis Peroxisomes Oxidation of toxic molecules - Mitochondria o Have different shapes (polymorphic), but regardless of the shape they have, they have the same basic structure and perform the same basic functions o Undergo fusion and fission (where fission can produce a new mitochondria) o Have two membranes  Outer mitochondrial membrane (OMM) contain many enzymes with diverse metabolic functions  Inner mitochondrial membrane (IMM)  High protein to lipid ratio (3:1)  Forms double-layered folds/sheets called cristae  Cristae increase membrane surface area and contain machinery for aerobic respiration and ATP formation  Rich in a phospholipid called cardiolipin (characteristic of bacterial membranes) o Aqueous compartments of the mitochondria  Intermembrane space  Matrix  High protein concentration therefore has a gel-like consistency  Mitochondrial ribosomes  Mitochondrial DNA (mtDNA) encodes polypeptides that are integrated into the IMM, ribosomes and tRNA o ATP synthesis in the mitochondria 1. Electron transport and proton pumping generate an electrochemical gradient  High-energy electrons pass from coenzymes (NADH and FADH2) in the matrix to electron carriers in IMM  Series of electron carriers (respiratory enzyme complexes I, II, III, IV) known all together as the electron-transport chain  Energy transfer at each complex used to pump H+ from matrix into intermembrane space by being carried through the inner mitochondrial membrane  Eventually low energy electron is transferred to terminal electron acceptor (O2) to produced water 2. Proton movement down electrochemical gradient powers ATP synthesis  Controlled movement of protons back across IMM via ATP synthase  Potential energy in electrochemical gradient across IMM is converted into ATP in the matrix o Apoptosis is a normal occurrence in which a coordinated sequence of evens lead to the death of a cell  Shrinkage of cell  Blebbing of the plasma membrane (creates balloon-like intrusions)  Fragmentation of DNA and nucleus  Loss of attachment to other cells  Engulfment by phagocytosis  Initiated by intracellular stimuli  Cell recognizes itself as having something wrong, such as damage in the DNA, etc.  Proapoptotic proteins stimulate mitochondria to leak proteins, such as cytochrome C (which is one of the electron carriers in the ETC)  Release of apoptotic mitochondrial proteins activates caspases and commits the cell to apoptosis Cell Biology Using GFP - Green fluorescent protein (from the jellyfish Aequorea victoria) can be genetically fused with a cellular protein - Fusion protein can be expressed in cells - Fluorescence from the fusion protein can be visualized microscopically - Monitoring the fusion protein provides information about the endogenous protein Cytoplasmic Membrane Systems - Organization allows material to be made, processed, packaged, delivered, etc. - Vesicular transport o ER to Golgi o Organelle to plasma membrane (exocytosis) o Secretion of neurotransmitter, secretion of collagen o Plasma membrane to organelle (endocytosis) o Organelle to organelle - Endoplasmic reticulum (ER) o Interconnected network of membrane- enclosed tubules and flattened sacs (it is reticular) o Interior, called the lumen, is separate from the cytosol o ER membrane is continuous with outer membrane of the nucleus o Smooth ER  Production of steroid homrones  Detoxification (in liver cells)  Sequestration (storage) of calcium ions  In muscle cells, the smooth ER is called the sarcoplasmic reticulum o Rough ER  Ribosomes cover the rough ER  Protein synthesis, modification and transport for proteins targeted to the ER  Synthesis of membrane phospholipids  Glycosylation of proteins and the addition of carbohydrate chains  Protein folding (quality control) o Protein translation in the cytoplasm beings on free ribosomes and is then completed in one of two ways 1. Translation completed on free ribosomes  Cytosolic proteins  Peripheral membrane proteins  Proteins targeted to the nucleus, mitochondria, peroxisomes, chloroplasts 2. Translation completed by ribosomes attached to ER membrane (rough ER)  Secreted proteins that leave the cell  Integral membrane  Soluble proteins associated with the lumen of endomembrane system (proteins that function within the ER, Golgi, lysosomes) - Ribosomes are targeted to the ER membrane by a signal sequence in the protein being transla
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