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BIO1140 Textbook Exam Notes.docx

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University of Ottawa
Kathleen Gilmour

BIO1140 Textbook Exam Notes Origins of Life: #1.Cell Theory: -All Organisms are Composed of One or More Cells -The Cell is the Smallest Unit that has Properties of Life ~Theodor Schwann -Cells Arise Only from the Growth and Division of Pre-existing Cells ~Rudolf Virchow, 1855 #2.Central Dogma: DNA RNA Proteins #3.Eukaryotic Cells: -Endomembrane System is Derived from the Plasma Membrane ~ER: Extensive interconnected network of membranous channels and vesicles. +Rough ER: Ribosome studded surface, which synthesize proteins +Smooth ER: Synthesis of lipids which become part of cell membrane. ~Golgi Complex: Receives proteins made in the ER and transported to the Golgi complex by vesicles. Within the Golgi, chemical modifications of proteins occur. Modified proteins are then released in vesicles. +Ex) Golgi Complex creates Lysosomes, performs exocytosis. ~Both the ER and the Golgi complex are abundant in specialized cells for secretion because they are in charge of synthesising and packaging of proteins that are exported from the cell. - The Theory of Endosymbiosis Suggests That Mitochondria and Chloroplast Evolved from Ingested Prokaryotes: ~Mitochondrion were present in cells before chloroplast -Several Lines of Evidence Support the Theory of Endosymbiosis ~Morphology: Shape of mitochondrion and chloroplast is similar to prokaryotic cells ~Reproduction: Mitochondrion and Chloroplast reproduce via binary fission ~Genetic Information: Mitochondrion and Chloroplast contain their own DNA ~Transcription and Translation: M & C contain their own central dogma. ~ETC: M & C can generate energy in the form ofATP through presence of own ETC. -The Cytoskeleton Supports and Moves Cell Structures: ~Cytoskeleton: Interconnected system of protein fibres and tubes that extends throughout the cytoplasm. Helps reinforce the plasma membrane and functions in movement. ~Microtubules: Microscopic hollow tubes +Assembled from individual tubulin subunits. ~Intermediate Filaments: Fibres that occur in parallel fibres which occur singly, in parallel bundles and in interlinked networks, either alone or combination with microtubules, microfilaments, or both. + 8 protein chains wind together to form each subunit. ~Microfilaments: Thin Fibres that consist of two rows of protein subunits wound around each other in a long spiral. +Assembled from two rows of actin proteins, wound around each other in a double helix. +Amoeboid motion, cytoplasmic streaming (directed flow of cytosol) aka motion ~When animal cells divide, both microtubules and microfilaments are active. The chromosomes are divided and moved by microtubules, and the cytoplasm is divided by microfilaments. -Flagella of Eukaryotes and Prokaryotes Are Not Evolutionarily Related (Analogous Structures): ~Structurally different ~Prokaryotes moves like a propeller +Protrudes from cell membrane ~Eukaryotes moves like a whip. +Enclosed by cell membrane ~Eukaryotic Flagellum structure is exactly the same as cilia. Except cilia are shorter and occur in greater numbers. Flagella serve to move cell, cilia acts to move materials over the cells surface. -Size of Eukaryotic and Prokaryotic Cells: (Surface Area: Volume Ratio) ~Eukaryotic Cells: 10-30um ~Prokaryotic Cells: 1-5um ~Eukaryotes are larger because the cell has a larger area of internal membrane structures with specialized functions that can support the larger cell volume (Ex Eukaryotes have mitochondria which create energy, prokaryotes ETC takes place in the cell membrane. -The Evolution of Mutlicellular Eukaryotes: ~Cells specialize and work together for the greater good of the organism #4.Units Relevant to Biology: -1um= 10 m 0.000001 (micrometer) -9 -1nm= 10 -10.000000001 (nanometre) -1A= 10 m 0.0000000001 (Angstrom) #5.Major Structural Features of Eukaryotic Cells: -Non-Membrane Bound Organelles: ~Cytoskeleton: Support/Shape, Internal Organization, movement within and of cell. Made of microfilaments, microtubules, intermediate filaments ~Ribosomes: Protein Synthesis -Membrane bound Organelles: ~Nucleus: Nuclear Envelope, Nuclear pores, Nucleolus, DNA& protein organized into chromosomes (chromatin) ~Endoplasmic Reticulum: Rough ER, Smooth ER, ~Golgi Complex: Sorting, modification and packaging of proteins ~Lysosomes, Peroxisomes: Break down garbage within the cell ~Vacuoles: Temporary Storage, Hydrostatic Pressure/Turgor pressure ~Mitochondirion: Powerhouse of the cell ~Chloroplast: Conversts light energy into chemical energy The Chemistry of Life: #1.Functional Groups:(Use chemistry to help you remember) Chemical Formula Name Properties OH Hydroxyl group Neutral, polar C=O Carbonyl group Neutral, polar SH Sulphhydryl group Neutral, polar COOH Carboxyl Group -ve charge at cellular pH PO 32- Phosphate group -ve charge at cellular pH NH Amino group +ve charge at cellular pH 2 #2.Macromolecules: -Carbohydrates: ~Polymers of monosaccharide’s (i.e. chains of sugar molecules) +Used for Energy Storage and Structure ~Alpha/Beta glucose, Ring/ Linear structure (Ribose) -NucleicAcids: (Phosphodiester bonding of nucleotides forming DNA& RNA) ~Polymers of nucleotides +Nucleotides: Sugar + Nitrogenous Base + Phosphate +Nucleoside: Sugar + Nitrogenous Base ~Nitrogenous Base: +Pyrimidine: CUT +Purine: AG ~Sugar-Phosphate Backbone -Proteins: ~Polymer of amino acids. +Enzymes, Structural (keratin), Motility (actin), transport ~AminoAcids: (~20), Central C atom, carboxyl, amino, R group and an H atom. ~R Groups: Properties of amino acid determined by R group +Non-polar (Just carbons i.e. Me) +Polar, uncharged (OH-CH ) anything with OH 2 +Polar, acidic (negative charge) Carboxyl ion +Polar, basic (positive charge) amine ion +Reactive Functional Groups (SH-CH )2(CH 2C=O(NH ))2 ~N-Terminus: Amide group at end ~C-Terminus: Carboxyl Group at end ~Protein Structure: +Primary +Secondary: Alpha Helix, Beta pleated sheet +Tertiary Structure: Di-sulphide bridges, Fibrous vs. Globular Proteins, Domains +Quaternary: Interactions of subunits to form mutlimeric protein -Lipids: ~Not polymers +Energy Storage, Membrane Structure, Signalling ~Main Types: +FattyAcids: Hydrocarbon chains with carboxyl group, amphipathic. Saturated (no double bonds) Unsaturated (double bonds) +Triglycerids: Glycerol+ 3 fatty acids, energy storage +Phospholipids: Glycerol+ 2 fatty acids+ phosphate with hydrophilic R group. Structural component of membrane,Amphipathic. ~Steroids: +Used as signals, only in eukaryotes, +Sterols: Cholesterol (animals), Phytosterols (plants) #3.Protein Domains: (related to tertiary proteins) -Aprotein domain is a part of protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain. Each domain forms a compact three-dimensional structure and often can be independently stable and folded. Many proteins consist of several structural domains. One domain may appear in a variety of different proteins. ~Shortest domains such as zinc fingers are stabilized by metal ions or disulfide bridges. -Zinc Fingers: Small protein structural motifs that can coordinate one or more zinc ions to help stabilize their folds. They can be classified into several different structural families and typically function as interaction modules that bind DNA, RNA, proteins, or small molecules. #4.Protein Motifs: (Related to secondary proteins) #5.Protein Dimer (Related to quaternary structure of proteins) Membranes and Transport: #1.An Overview of the Structure of Membranes: -Fluid Mosaic Model of Membranes: ~Singer & Nicholson 1972 ~Membrane Structure according to the fluid mosaic model, in which integral membrane proteins suspend individually in a fluid lipid bi-layer. Peripheral proteins are attached to integral proteins or membrane lipids mostly on the cytoplasmic side of the membrane (inner surface). In the plasma membrane, carbohydrate groups of membrane glycoproteins and glycolipids face the exterior of the cell. +This is an example of membrane asymmetry (components of one half of the lipid bilayer are different from those that make up the other half of the bilayer. ~Mosaic of Proteins: Unique complement responsible for specific functions ~Lipid Bi-Layer is ~10nm thick ~Relative proportion of lipid and protein membrane varies considerably depending on the type of membrane: +Ex) Inner Mitochondrion Membrane which needs protein complexes for the ETC is composed of (76% protein and 24% lipid) +Ex)Plasma membrane (49% protein and 51% lipid) +Ex) Myelin which coats and insulates nerve fibres (82% lipid and 18% protein) -Experimental Evidence in Support of the Fluid Mosaic Model: ~The Frye-Edidin Experiment: Tagged human cell membrane proteins with red die, mouse cell membrane proteins with green die. They fused the two cells together. In a range of 40mins the two different coloured membrane proteins were intermixed all around cell membrane ~Fluorescence RecoveryAfter Photo bleaching (FRAP): Tagged the membrane proteins green, bleached a small portion of the green colour to white. The white area of the cell became swarmed with membrane proteins still tagged green. Thus proving membrane fluidity -The Fluid Mosaic Model of Membrane Structure is supported by two major pieces of experimental evidence: ~Membranes are Fluid ~Membrane Asymmetry #2. Functions of the Fluid Lipid Bi-Layer: ~Define Boundaries (selectively permeable barrier) ~Localisation and Organization (scaffold for biochemical activities (enzymes)) ~Regulation of Solute Transport (Active and Passive transport) ~Response to External Signals (Receptors and signal Transduction) ~Cell-to-Cell Communication (Gap Junctions, Recognition, Exchange of Materials) #3.The Lipid Fabric of AMembrane: (Cell membranes are mainly composed of lipid molecules) -Gorter and Grendel, 1925 -Phospholipids are the Dominant Lipids found in the Membrane: ~Phospholipids consist of 2 fatty acid tails linked to one of several types of alcohols or amino acids by a phosphate group. (Amphipathic) ~Each phospholipid contains a region that is hydrophobic and a region that is hydrophilic. ~Fatty acid chains are very hydrophobic (non-polar), the phosphate containing head group is charged and hydrophilic (polar). ~When added to an aqueous solution, phospholipids associate with each other and assemble a lipid bi-layer -Membrane Fluidity: ~2 Factors that influence fluidity: Composition of lipid molecules and temperature. ~Saturated Hydrocarbon tails allow the phospholipids to pack together very tightly. This reduces fluidity of the membrane. (Saturated means maximum # of H atoms on carbons.) ~Unsaturated Hydrocarbon tails does not allow the phospholipids to pack together tightly. This increases fluidity of the membrane (Unsaturated means double bonds) #4.HomeoviscousAdaptation. -Alteration in lipid composition to maintain membrane fluidity at different environmental temperatures. ~Desaturase is a group of enzymes that synthesizes unsaturated fatty acids. +Ex) If the temperature decreases, the transcription of the gene desaturase will be in abundance. This happens because the more desaturase there is the more abundance of unsaturated fatty acids there are. The more fatty acids there are the better the membrane can maintain its fluidity. +Ex) If the temperature increases, the transcription of the gene desaturase will decrease. Less desaturase means less unsaturated fatty acids which means the membrane can become more fluid to accommodate for the increase in heat in the surrounding environment. ~Sterols: The sterols job in the cell membrane of animal cells (cholesterol) is to act as a membrane buffer. +Ex) At high temperatures, cholesterol helps to restrain the movement of lipid molecules, thus reducing the fluidity of the membrane. +Ex) At low temperatures, cholesterol disrupts fatty acids from associating by occupying space between lipid molecules, thus slowing the transition to the non-fluid gel state. #5.Lipid Rafts: -Characterized by lower fluidity -Involved in cell signalling #6.Membrane Proteins: -Key Functions of Membrane Proteins: ~One Protein or protein complex may serve more than one of these functions ~Transport: Many substances cannot freely diffuse through the membrane. Proteins provide channels. ~Enzymatic Activity: Enzymes are membrane proteins. Ex) ETC ~Signal Transduction: Receptor proteins on outer surface bind to specific chemicals such as hormones. On binding receptors trigger changes inside the cell. ~Attachment/ Recognition: Proteins exposed to both internal and external membrane surfaces act as attachment points for a range of cytoskeleton elements, as well as components of cell to cell recognition. ~All membranes can be classified as either integral, peripheral or lipid anchored membrane proteins. -Integral Membrane Protein: (Proteins imbedded in the phospholipid bilayer) ~Transmembrane proteins span from the inside of the cell to the outside. ~Transmembrane proteins can be identified because of the presence of stretches of amino acids that are primarily non-polar. These regions of the protein interact with the hydrophobic regions of the membrane. Usually between 17-20 amino acids are needed to span the membrane once. -Peripheral Membrane Proteins: ~Proteins positioned on the surface of a membrane and do not interact with hydrophobic core. They are held to the surface by non-covalent, hydrogen, and ionic bonds usually by interacting with exposed proteins of integral proteins. ~These structures hold some integral proteins in place ~Made up of a mixture of polar and non-polar amino acids like all amino acids because they do not interact with the hydrophobic region of the cell. -LipidAnchored Membrane Proteins: ~Extracellular orientation ~Can be cleaved by phospholipase C for the reason that it is attached to the cell membrane by a phosphate bond. #7. Passive Membrane Transport -Passive Transport is Based on Diffusion: ~Passive transport: The movement of substances across a membrane without the need to expend chemical energy such asATP ~Diffusion: The net movement of a substance from a region of higher concentration to a region of lower concentrate ion. #8.The Two Types of Passive transport: Simple and Facilitated -Simple Diffusion: ~The size and charge of a molecule affects the rate of diffusion across a membrane ~Driven by diffusion gradient ~Molecules that diffuse readily across the phospholipid-bilayer are: +Hydrophobic molecules (O , CO2, N )2(no2-polar substances) +Small, Uncharged Polar Molecules (H O, g2ycerol) ~Molecules that do not diffuse readily across the phospholipid-bilayer are: +Large, Uncharged Polar Molecules (Glucose, Sucrose) - + + +Ions (Cl , K , Na ) -Facilitated Diffusion: ~Channel proteins: (Forms hydrophilic pathways) +Ions, Water +Highly Selective, Leak vs. Gated (mainly gated, they can be open and closed by changes in voltage across the membrane.) ~Carrier Proteins: (Specific protein binds to a molecule and transports it across the lipid- bilayer. +Ions, larger and/or polar molecules +Highly Selective +Types (Uni-porter, Symporter, Antiporter) -Compared with simple diffusion, facilitated diffusion leads to higher rates of transport and displays saturation kinetics. #9.Types of Facilitated Diffusion -Uni-porter (1 type of molec
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