BIOA01 Module 1 Study notes for midterm.pdf
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Department
Biological Sciences
Course
BIOA01H3
Professor
Ivana Stehlik
Semester
Fall

Description
CHP3 Biology and The Tree of Life September-20-13 7:59 PM Biology is the study of life. Earth is ~ 4.6 Billion years old and lies within the habitable zone around the sun. (this is the position were heat from the sun allows water to exist in liquid state) *Liquid water is the fundamental prerequisite for the development of life* But what is life? In order to be considered alive it must have the 7 characteristics: 1. Display order 2. Harness and utilize energy 3. Reproduce (heritable genetic information) 4. Respond to stimuli 5. Homeostasis 6. Growth and develop 7. Evolve (adapt to change) *Key for diversity* This characteristics are "emergent" (there is a hierarchy of interactions where simpler things do not have the properties found in higher levels) Diversity and unity through evolution How is all life on earth related? • Theory of evolutionthrough natural selection (single common ancestor) Diversity Charles darwin (natural selection, 1859) created a unifying framework Reproduction with potential for errors, errors lead to evolution. Differences enables them to: • Live in diff environments • Adapt to changing environments • Cell theory: cells come from pre-existing cells, all organisms are composed by it. Cells are the basic unit of life How is life on earth unifyied? 1. Cells (Lipid bilayer) 2. Genetic system based on DNA 3. System of information transfer (DNA, RNA, PROTEIN) 4. system of protein assembly using ribosomes and mRNA, tRNA, 5. ATP as source for chemical energy 6. Metabolic pathway to generate ATP 7. Proteins: Major structure and catalytic molecule Taxonomy (classification of life) developed by Linnaeus in 1735 Classifications are made on the basis of share features (structure/function) All organisms have 2 parts for their scientific name (in italics) 1) Genus 2) Species Tree of life (still in progress) Phylogeny (geneological relationship) CHP3 The Origins & Chemical Building Blocks of Life September-20-13 7:59 PM How important molecules for life came to be? Is hypothesized that they came to be in 4 main stages • 1st stage Abioticsynthesis of monomers (NOT SYNTHESIZED BY LIVING ORGANISMS) : 1) Oparin-Haldanehypothesis:reducingatmosphere where molecules in premordial atmosphere contained abundance of electrons and H2, reacting with one another producing larger more complex molecules) Primordial atmosphere contained large quantities of H2, CO2, NH3 (ammonia),CH4 (methane) Because there was no oxygen, there was no ozone layer, therefore, UV light + lighting provided the energy needed for the formation of the molecules Note: Today's atmosphere is considered oxidizingdue to large amounts of oxygen present (because of its affinity it accepts the electrons and reduces chances for complex macromolecules to form) Miller-Ureyexperimentwas the first to demonstrate the abiotic formation of important molecules can be easily produced in the laboratory 2)Deep sea vents: Release superheated nutrient rich water, as well as reduced molecules (CH4,NH3,H2S) which created a geochemical gradient that with the extreme pressures of the environment gave rise to the building macromolecules of life. 3) ExtraterrestrialOrigins (Panspermia):organic molecules tha came from meteorites "Carbon chondrites"- rich in organic molecules • 2nd stage Polymerization Clay hypothesischarged layers of clay allows for molecular adhesion forces to bring monomers together (clay stores potential energy) It also accelerates formation of lipid vesicles FROM MACROMOLECULES TO LIFE • 3rd stage Protobionts(similarto lisosomeswhich are lipid vesicles with lipid bilayer similarto cell membrane) one of the key attributes of a modern cell is that it has a membrane-defined comparment,where it provides a distinction from external environment and the concentration of key molecules within the membrane creates better chances for the formation of more complex molecules. Protobionts are capable of simplereproduction and metabolism all within a selectively permeable membrane. • 4th stage Central Dogma Are the steps from DNA to RNA to ribosomes for the formation of proteins which is aid by enzymes (which are proteins)… but... there were no proteins! so wth, how did it happen then? Ribozymes:a group of RNA molecules that could themselves act as a catalyst. They are singlestranded molecules that can fold into very specificshapes on intramolecular hydrogen bonding or base pairing. (critical for reacting with substrate molecules) "RNA world" from RNA to RNA, protein to DNA,RNA,PROTEIN From RNA world to DNA world. Why DNA? DNA is more stale, better at storaging information and is double stranded which aids in DNA repair (Base uracil is replaced with thymine). DNA repair (Base uracil is replaced with thymine). From RNA catalyst to Proteins. • more variety (22 diff amino acids, compare to 4 nucleotides) • Aminoacids interact chemically with each other giving rise to many many combinations • grater rate of catalysis (10-100x greater) The model of the origin of life must explain: Membrane defined compartment System to store information way to harness and utilize energy How did life evolve? Early protobionts used molecules present in the environment for growth and replication ○ Heterotrophs(other-feeding)- they obtain carbon from organic molecules and produce C02 ○ Autotrophs(self-feeding) obtain carbon from inorganic molecules (CO2) Anoxygenic photosynthesis, Evolution of oxygenic pho, produce O2. *Primordial heterotrophs did not survive the change in environment and those who did evolved the capacity for aerobic respiration CHP20 *Tree of life- Prokaryotes* September-20-13 9:58 PM Lack of membrane-enclosed organelles • Thrive almos everywhere ○ Including extreme habitats too hostile for most organisms ○ remarkable diversity • Appear simplein structure compared to eukaryotic cells • Have the greates metabolic diversity of all organisms • Classified into two domains that differ in structure, physiology and biochemistry ○ Bacteria ■ Important for food production ■ Some responsiblefor disease, some essential for health ■ most familiar to us ○ Archea ■ Discovered around 40 years ago, not wll known ■ Share some cellular features with bacteria, some with eukaryotes, some unique ■ Live in very extreme condCell structure Internal: Morphology External: • DNA packed into nucleoid • Are unicellular • Cell wall • plasmids • cell membrane • Common shapes: • capsule(layer of • ribosomes ○ Sphere (coccus) polysaccharides • lack of internal membrane ○ Rod (Bacillus) • pili boud organelles ○ Spiral (spirillus) • semblance of cytoskeleton • flagella • Are very small (1 to 10 um) Cell wall (it maintance shape, provides peptoglycon layer (peptide + sugar) protection and prevents from bursting in hypotonic environments ) Primary component is peptidoglycan(polymer of modified sugars cross linked by short polypeptides) Some contain outer membrane (Which contains lopopolysaccharide (LPS) which provides more protection The Gram Stain and immune recognition It differentiate bacterial based on their cellwall cell walls allow to classify constituent. Gram positivebacteria(purple)consist of thick layer of Peptidoglycan, while gram negative (Pink) consistacteria acording to differences of thin layer of Peptidoglycan, and a thick layer of Lipopolysaccharide. Sticky capsule protects many prokaryotic cells. • Layer that lies outside of cell wall which consists of many polysaccharides. • It protects bateria frome external environment ○ Dessication ○ Extreme temperature ○ Extreme temperature ○ Invading viruses* ○ Antibiotics • Considered a virulence factor (helps to evade detection by immune cells) Pili and flagella Pilius (singular)-a hairlike appendage found on the surface of many bacteria • Aids attachment of bacteria to hosts surfaces, required for colonization during infection, • required to initiate formation of biofilm • Conjugative (Sex) pili allow transfer of plasmidsbetween bacteria (one methor for horizontal transfer HGT Flagella(sensory and locomotive)- cell surface appendage -"Whip-like"motion • Primary role in locomotion • sensory to external environment (chemicals and temp) • Prokaryotic and Eukaryotic flagella differin protein composition, structure, and mechanism of propulsion Genome • Ring of DNA (Singlecircular DNA molecule= chromosome) • Packed into nucleoid region • no nucleolus • no nuclear membrane • Small genome May also have smaller rings of DNA called plasmids, which provide resistance to antibiotics, and that replicate independently of the chromosome (Can be transferred between bacteria via pili) Ribosomes (spreed throughout) • Smaller than eukaryotic ribosomes • Protein synthesis similarto eukaryotes • Archaeal ribosomes shame some similaritieswith eukaruotic ribosomes ○ Bacteria ribosomes sensitiveto antibiotics, archaeal and eukaryotic are not Asexual method of reproduction: Binaryfission Produces exact copies of parent and it can result in rapid population growth 1. Replication 2. Segregation 3. Cytokinesis Promoting genetic diversity 1. Rapid reproduction and mutation 2. Genetic recombination ○ Conjugation(transfer via pilus) ○ Transformation(from surroundings) ○ Transduction(bacteriophages carry gnes from host cell to another) Pathogenic bacteria and antibiotic resistance Antibiotic binds to enzymes. mutations cause binding site of enzyme to change which does not allow antibiotic to work Bio films (communities) attachment of bacteria, growth and divide(Communicate), produce extracellular polymer substance (encapsulates, for protection) , attachment of other organisms. Metabolic diversity Metabolic diversity Autotrophs(Self-feeding)- Energy from inorganic carbon Heterotrophs(other feeding)- energy from organic carbon Organisms are grouped according to source of carbon, also by source of energy Phototrophs(lightas energy source) photoautotrophs & photoheterotrophs Chemotrophs(oxidize inorganic or organic substances) chemoautotrops &chemoheterotrophs Harmful effects They cause about half of all human diseases BUT only a small fraction of bacteria are pathogenic(cause disease by secreting toxins) Exotoxins -Leak from or are secreted (Are proteins) Endotoxins-The lipid A portion of LPS Outer membrane of all gram-negative bacteria Beneficial effects Bacteria cover every inch of the human body Biogeochemicalcycles- ~100 quadrillion bacteria cells Pathway by which a chemical element moves through an ecosystem ex. Bacteria and archea are able to do nitrogen fixation which is the only mechanism of replenishing the nitrogen resources. (all organisms rely on them) CHP2 Eukaryotic cells (I) September-21-13 5:44 PM Origin of endomembrane system Most widely held hypothesis: derived from infolding of a prokaryotic cell plasma membrane, inclosing the DNA Distinguisingfeatures • Separation od DNA and cytoplasm by a nuclear envelope • Presence of membrane-bound compartments with specialized metabolic and synthetic functions Evidence supporting theory of endosymbiosis: 1. Morphology (similarities between shape of bacterium, mitochondrion and chloroplast) 2. Reproduction a. A cell cannot sinthesize a mitochondrion or chloroplast b. Derived only from pre-existing mitochondria and chloroplasts c. Divide by binary fission 3. Genetic information (Contein their own circular DNA) 4. Transcription and translation: Contain complete machinery for transcription and translation- ribosomes similar to bacterial's 5. Electron transport: ○ Have electron transport chains similar to prokaryotic cells ○ Used to generate chemical energy ○ In prokaryotes, ETC in plasma membrane ■ Swallowed up into inner membrane 6. Sequence analysis ○ Ribosomal RNA sequency firmly establishes mitochondria and chloroplasts belong on the bacteria tree of life ○ Chloroplasts RNA most similar to cyanobacteria ○ Mitochondrial RNA most similar to proteobacteria Endosymbiosis and Horizontal Gene Transfer What happened to the genes of human mitochondrial genome? (only 37) • Some genes were lost (redundant with nuclear genes) • Some genes relocated to nucleus through HGT) ○ In order to centralize genetic information ○ 90% of proteins required for mitochondrial and chloroplast function are encoded by genes found in the nucleus Nucleus Why do both mitochondria and chloroplasts still retain a genome? • Gene transfer not yet complete • Retained genes encode for proteins involved in electron transport chain- Tight regulation may be difficult in genes are in the nucleus OVERVIEW OF AN ANIMAL CELL The nucleus • DNA organized into chromosomes (Single DNA molecule+proteins-> Chromatin (the complex combination of DNA, RNA, and protein that makes up chromosomes) • Nucleolus: site of rRNA synthesis • Nuclear envelope is a double membrane(inner, outer + nuclear pore) Pore complex regulates entry and exit (RNA, Proteins, macromolecules) Ribosomes: Protein factories • Free ribosomes in cytosol ○ Proteins which function in cytosol • Ribosomes bound to ER ○ Proteins destined for ■ Insertion in membranes ■ Packaging organeless ■ Export from the cell Endoplasmicreticulum(little net) • Interconnected network of membranous channels and vesicles called cisternae ○ Cisternae formed by a single membrane(enclosed space called ER lumen) Rough ER ○ Ribosomes stud membrane surfaces facing cytoplasm ○ Proteins enter the lumen where they are chemically modified ○ Proteins then delivered to other regions of the cell witin small vesicles BIOA01 Module 1 (revized) página 8 ○ Cisternae formed by a single membrane(enclosed space called ER lumen) Rough ER ○ Ribosomes stud membrane surfaces facing cytoplasm ○ Proteins enter the lumen where they are chemically modified ○ Proteins then delivered to other regions of the cell witin small vesicles Smooth ER ○ Synthesizes lipids ○ Detoxifies drugs and poisons ○ Stores calcium ions The Golgi Complex (sorting machinery) Proteins enter via vesicles at the Cis face and exit via the Trans face ○ Modifies ER products ○ Manufactures certain macromolecules ○ Sorts and packages for transport Lysosomes (Membranous sac of hydrolytic enzymes) • Digest macromelules • Acidic pH Important role in: Phagocytosis (The engulfing and ingestion of bacteria or other foreign bodies by phagocytes) Mitochondria Site of cellular respiration ATP- generating reactions occur in the cristae and matrix BIOA01 Module 1 (revized) página 9 CHP2 Eukaryotic cells (II) September-21-13 10:30 PM The cytoskeletonis composed of three main types of fibres: • Microtubules (biggest) Interior 15nm, exterior 25 nm with +/- ends ○ Tubulin:diameter of an alpha-tubulin and a beta-tubulin. ○ It is a hallow tube, which wall consists of 13 columns of tubulin ○ Functions: ■ Maintain cell shape ■ Cell motility ■ Chromosome movement during cell division ■ Organelle movement. • Intermediate filaments Fibrous proteins coiled and supercoiled into thick cables (Tissue specific proteing composition) 8-12nm, non-polar ○ Functions: ■ Maintain cell shape ■ Anchorage of nucleus and some other organelles ■ Formation on nuclear lamina • Microfilaments (smallest) Two interwined strands of actin(each a polymer of actin subunits) 5-7 nm with +/- ends which provides dynamic change of structure ○ Functions: ■ Maintain cell shape ■ Changes in cell shape ■ Cell motility ■ Cell division ■ (Muscle contraction) The cytoskeleton 1. Provides structural integrity to the cell 2. Drives cell motility (motor protein-driven movement, kinesin molecule *walking*, ATP dependent process) 3. Forms cell surfaces structures which probe the environment ○ Filopodia ○ Microvilli 4. Movement of cargo inside the cell 5. Cell division ○ Separation of chromosomes ○ Cytokinesis Centrioles • Comprise part of the microtubules organizing centre (MTOC) • Involved in microtubule 'spindle' organization during cell division • Flagella and cilia arise from centrioles • It is made up of 9 sets of three microtubules Flagella and cilia • Motile structures extending from cell surface • Similar in structure except cilia usually shorter and often numerous on cells • Dynein motor proteins slide the microtubules over each other to produce movement -Flagella moves in S-waves which propels the cell through watery medium -Cilia beat in oarlike stroke which moves fluids over the cell surface -Cilia beat in oarlike stroke which moves fluids over the cell surface Specialized structures of plant cells • Cell wall (supports and protects) ○ it is composed of cellulose fibres ○ embedded in branched carbohydrate network ○ Perforated by small channels (plasmodesmata)-all ions and small molecules to move between cells • Chloroplast ○ Site of photsynthesis ○ molecules in thylakoid membrane absorb light energy ○ Enzymes in stroma use this energy to make carbohydrates Central vacuole Large vesicles- perfomr specialized functions: organelle 90% of the cell volume may be occupied by one or more central vacoules Surrounded by a tonoplast (membrane)- contains transport proteins to move materian in and out Storage functions Salts Sugars Pigments Waste products Comparison of plant and animal cells • Animals cell ○ Lysosomes ○ Centrosomes (with centrioles) ○ Flagella (present in some plant sperm) • Plant cells ○ Chloroplasts ○ Central vacuole ○ Cell wall ○ Plasmodesmata CHP5 Cell Membranes September-17-13 10:23 PM Importance of membranes for living organisms: 1. Provides internal environment 2. concentration of molecules inside of cells 3. selectively permeable Singer.NicolsonFluid Mosaic Model (1972 Plasma membrane (phospholipidbilayer) in which relatively disperse membrane proteins (not relatively diffuse) could freely diffuse. Proteins not necess. mobile while phospholipidsare. Phospholipd structure • Polar Hydrophilic head (water loving)composed of glycerol, phosphate group + polar unit • Hydrophobic tail (hate) composed of fatty acid chains (Hydrocarbon, it can modify fluidity by ultering saturation) Amphipathic(philic/phobic) This nature enables to self assemble into structures within aqueous env. Hydrophobic effect: Tendency of POLAR molecules to exclude hydrophobic molecules ○ Micelle, single layer ○ Liposome, double layer ○ Planar bilayer Frye-Edidinexperiment Marked membrane proteins of human cells with fluorescent markers. and same with mouse cells. They fuse two cells together to create hybrid cell. At first proteins segregated and then they mixed (moved, fussing). Membrane fluidity is dependent on fatty acid composition and temperature. -All fatty acid are initially sinthesized as saturated molecules (viscous membrane) -Enzymes (desaturases) changes saturation. If unsaturated the membrane becomes more fluid. (increasing spaces between molecules) Organisms can regulate fatty acid saturation by regulating proportion of unsaturated fatty acids by regulation desaturase transcript Bacteria, archea, protist, plants Sterols(act as buffers) influence membrane fluidity Structure: philic(towards aquous env.)/phobic at low tem: disruptfatty acid association at high tem: restrain mov of molecule Plasma membrane proteins Integralmembrane proteinsn(EXPAND): ○ Traverse lipid bilayer ○ distinct domains -Extracellular (sticks out) recognition, it has binding site -Transmembrane(embedded in bilayer) stretch of 17-20 nonpolar aminoacids that form alpha helix in the membrane. alpha helix in the membrane. -Intracellular, comunication within cell for change Peripheralmembrane proteins Associated with outer or inner side. Held to membrane by proteins or lipids Functions 1. transport 2. Enzymatic activity 3. Signal transduction (recognition of signals) 4. Attachment 1. Transport (across plasma membrane) Hydrophobic nature restricts free movement of molecules 02 can diffuse, but many other molecules are not able. Passive: Movement of substance across a membrane without useing energy Diffusion (From high to low concentration, the rate depends on concentration gradient. larger gradient, faster diffusion) a) Simple : movement without involvementof a transporter, rate depends on molecular size and lipid solubility. Osmosis: Diffusion of WATER across selectively permeable membrane from a solution of lesser solute concentration to a solution of greater solute concentration. b) Facilitated: carried out by transmembrane proteins -Channelproteins:Hydrophilic pathways (Molecules are protected from hydrophobic core of bilayer), transport of water and ions • Aquaporin: Very narrow- single filemovement of water. very specific for water. • Voltage-gated channel: Critical movement for most ions from high to low. produced in a change in the 3D shape. Important for nerve conduction and muscle contraction -Carrierproteins(grab and transport) specific substrate that binds to molecule that causes protein to change conformation allowing molecule to be release into intracellular region. From high to low. Both transmembraneprotein* TransportKinetics( chart) : Rate of diffusion dependent on concentration gradient. -For simple diffusion:as long as there is a concentration gradientthe rate of transportcontinues to increase -For facilitated diffusion:concentration differs acrossthe membraneand as the concentrationis increased you reach a plato (flat, saturation)because carrier molecules areused up. Active: require energy, movement against concentration gradient (Low to high) Large proportion of cell ATP goes towards active transport (fundamental for cell activity: uptake of nutrients, removal of waste, maintenance of intracellular concentration of ions) Primary. (protein
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