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BIOL 130 (141)


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University of Waterloo
BIOL 130
Heidi Engelhardt

UNIT 1 – INTRODUCTION TO THE CELL Robert Hooke - 1635-1703 - first microscope - viewed slices of cork “cellula” (little rooms) Antoni Van Leeuwenhoek (father of microbiology) - 1632-1723 - worked with glass - huge improvement in quality of lenses - nearly 300x magnification became possible - first to observe: o single-celled organisms  protists from pond water  bacteria from his mouth  blood cells  banded pattern in muscle cells  sperm - progress stalled for a century or so o limited resolving power o emphasis on description rather than explanation - 1830s – compound microscope o improved magnification and resolution o allowed visualization of objects less than 1 um Robert Brown (botanist) - 1833 - noticed that every plant cell contained a round structure - ‘kernel’ nucleus Matthias Schleiden (botanist) - 1838 - all plant tissues are composed of cells - embryonic plant always arose from a single cell Theodor Schwann (zoologist) - 1839 - similar observations in animals - recognition of structural similarities between plants and animals - CELL THEORY formulated by Schwann Cell Theory - all organisms consist of one or more cells - the cell is the basic unit of structure for all organisms - all cells arise only from pre-existing cells Steps in the Scientific Method - make observations - use inductive reasoning to develop tentative explanation (hypothesis) - make predictions based on your hypothesis - make further observations or design and carry out controlled experiments to test your hypothesis - interpret your results to see if they support your hypothesis Electron Microscopy SEM (scanning) – black background, surface TEM (transmission) – white background, slice, looking within Basic Properties of Cells Cells… - are highly complex and organized - atoms  molecules  macromolecules  (organelles ) enclosed in plasma membrane - use the same ‘genetic program’  Central Dogma o DNA (information storage)  RNA (information carrier)  protein (active cell machinery) - are capable of reproducing themselves o must first replicate genetic material - acquire and use energy (bioenergetics) and carry out a variety of chemical reactions (cellular metabolism) - have many processes that are highly conserved at the molecular level o membrane structure, genetic code, ATP synthesizing enzymes, actin filaments, eukaryotic flagella - engage in many mechanical activities o transport of materials in/out, within o assembly and disassembly of structures o motility/movement - respond to environmental signals o move away or toward stimuli o respond to hormones, growth factors, etc - are capable of self-regulation (“homeostasis”) o most evident when control systems break down o defects in DNA replication, DNA repair, cell cycle control Two Classes of Cells - karyon = nucleus - pro = before o prokaryote – no nucleus  eubacteria, archaebacteria - eu = ‘true’ ‘normal’ o eukaryote – true nucleus  protists (single-cell), fungi, plants, animals Generic Prokaryotic Cells - no membrane-bound nucleus - ‘naked’ DNA (fewer proteins), single, circular strand - cell wall in addition to plasma membrane - most diverse cell group (spherical cells, rod-shaped cells, spiral cells) - (eu)bacteria o all have cell walls except mycoplasma o mycoplasma (smallest)  cyanobacteria (most complex, many capable of both carbon and nitrogen fixation) - archaebacteria (archaea) o all have cell walls o best known are extremophiles  halophiles (Great Salt Lake, Dead Sea)  acidophiles  thermophiles Eukaryotes - protists – very diverse group o mostly single cells, but some colonies  includes algae, water molds, slime molds - fungi o single cells (yeasts) and multicellular (mushrooms) o call walls, heterotrophs  dependent on external source of organic compounds - plants o multicellular, cell walls - animals o multicellular, no cell walls, heterotrophs - cytoplasm – everything between plasma membrane and nuclear membrane o includes all membrane-bound organelles (except nucleus) - cytosol – only fluid component - endomembrane system – internal membranes that are either in direct contact or connected via transfer of vesicles (sacs of membrane) o including: nuclear envelope/membrane, endoplasmic reticulum (ER), Golgi apparatus, lysosomes, vacuoles - nucleus – stores genetic information (contains genome) - endomembrane system – creates intracellular compartments with different functions o ER (rough, smooth), Golgi apparatus, Lysosomes - mitochondria – generate energy to power the cell - chloroplasts – capture energy from sunlight, convert to carbohydrate - cytoskeleton – regulates cell shape, movements of materials within the cell, movement of the cell itself - transcription and translation occur in separate compartments in eukaryotes Flow of Traffic within Endomembrane System Rough ER: synthesis or proteins for export (secretion), insertion into membrane, lysosomes Golgi Apparatus: collection, packaging & distribution - rough ER next to membrane, vesicles break off ER and join golgi, golgi breaks apart into vesicle and travel outside of cell, create a protein or create a lysosome Lysosomes and Cellular ‘Digestion’ - cell stomachs have enzymes that can digest all four classes of biological macromolecules o worn-out organelles (mitochondria replaced every 10 days) o material brought into cell by phagocytosis Organelles That Contain Their Own DNA - mitochondria (all eukaryotic cells) and chloroplasts (plant cells): o contain DNA that encodes some of their own proteins o have unusual double layer of membrane Origin of Eukaryotic Cells: Endosymbiont Theory - early eukaryotes originated as predators o certain organelles (mitochondria, chloroplasts) evolved from smaller prokaryotes engulfed by a larger cell - endo – sym – biosis  within – living – together Symbiosis: Mutual Advantage advantage to host cell: - aerobic respiration (aerobic bacteria  mitochondria) - photosynthesis (cyanobacteria  chloroplasts) advantage to bacteria: - protected environment - supply of carbon compounds from host cell’s other prey Evidence Supporting Endosymbiont Theory mitochondria and chloroplasts ... - are similar size to bacteria, reproduced by fission like bacteria - have double membranes, consistent with engulfing mechanism - have their own ribosomes, which resemble those of prokaryotes rather than eukaryotes in terms of size, composition and sensitivity to antibiotics - have their own genomes, which are organized like those of bacteria - are genetically similar to proposed ‘parent’ bacteria rather than eukaryotic cells Organization within Eukaryotic Cell - cytoskeleton important in: cell shape, cell motility, movement/position of organelles, movement of materials within cell, movement of chromosomes during mitosis Cytoplasm in a living cell is never static… - cytoskeleton is constantly being taken apart and rebuilt - organelles and vesicles are racing back and forth o can cross the cell in ~ 1 second - unattached proteins moving randomly, but rapidly o can visit every corner of the cell within a few seconds - contents of cytosol are in constant thermal motion Recap of Prokaryotes vs Eukaryotes Prokaryotes: - no nucleus o genome is single, circular strand of ‘naked’ DNA - no membrane-bound organelles - cell wall (most) - very small, no need for cytoskeletal transport systems Eukaryotes: - membrane-bound nucleus, containing o multiple, linear strands of DNA packed with histones - organelles, allows specialized compartments o including mitochondria, chloroplasts (plants) - cytoskeleton – involved in transport between compartments - much larger than prokaryotes Model Organisms Organism Major Contribution E. coli DNA replication, gene transcription, translation Saccharomyces cerevisiae cell cycle (yeast) “minimal model eukaryote” Arabidopsis thaliana all flowering plants closely related Drosophila melanogaster/ fruit flies genetics, development C. elegans (“the worm”)/ very first animal genome to be sequenced; location, lineage primitive (1mm long) and fate of every cell in embryo, larva and adult is known Mouse/ the basic mammal ‘model mammal’ genetics well understood UNIT 2 – INTRO TO CELLULAR CHEMISTRY What are Cells Made of? - four types or atoms make up 96% of all matter found in living organisms o carbon, hydrogen, oxygen, nitrogen - mostly combined in complex ‘macromolecules’ - also present in simple forms – CO , 2 O 2 Parts of an Atom nucleus – dense core in center, consists of protons and neutrons electrons – continually orbit the nucleus # of protons – defining feature of an element = atomic number # protons + # neutrons = mass of an atom = mass number - by default, an atom is ‘neutral’, with #protons = # electrons - electrons influence reactivity of an atom Atomic Mass - electrons travel around atomic nuclei in orbitals - mass of a neutron or proton is approximated at one atomic mass unit or Dalton (Da) o masses or electrons tiny  ignored - orbitals are grouped into layers or shells, based on how far the electrons in that shell travel from the nucleus Electrons, Shells and Valence - innermost shells fill first - once first shell filled with pair of electrons, next shells fill with 4 singles then subsequent electrons form pairs - outermost ‘valence’ shell influences an atom’s reactivity o electrons in outermost shell  valence electrons - unpaired valence electrons determine the number of bonds an atom can make Ex. carbon: 4 unpaired electrons, valence = 4 chlorine: 1 unpaired electron, valence = 1 argon: no unpaired electrons, valence = 8 Unpaired Valence Electrons and Reactivity - completely filled valence shells  non-reactive (stable)  eg. He, Ne, Ar - closest to filling valence shell  most reactive  eg. Cl, Fl, O - atoms with same # valence electrons have similar chemical behaviour o Forms basis for ‘periodic’ table - elements abundant in organisms have at least one unpaired valence electron Unpaired Electrons and Biological Reactions - biological reactions are driven by tendency of atoms to fill outer shells and balance +/- charges How can Atoms Achieve Full Valence Shells? - sharing electrons – forming chemical bonds o number of bonds possible depends on how many electrons that atom needs to fill its outer shell - transferring electrons from one atom to another o atoms that are no longer electrically neutral  ions  gain electron  negatively charged  anion  lose electron  positively charged  cation Types of Chemical Bonds - covalent bonds - two or more atoms share pairs of valence electrons (strong bonds of biological systems) - non-covalent bonds, including ionic bonds. hydrogen bonds (H-bonds), hydrophobic interactions - molecule - group of atoms held together by energy in a stable association - compound - molecule composed of two or more different types of atoms - longer bond = weaker bond - shorter bond = stronger bond Types of Covalent Bonds Covalent Bonds – sharing valence electrons - electrons shared ‘equally’ o non-polar covalent bond o can be single (like H ),2double (O ) o2 even triple, depending on number of electrons shared - electrons not shared equally o polar covalent bond o one of the atoms has a stronger pull on the electrons than the other o pull on electrons = electronegativity o eg. H O2 Polar Covalent Bond: Water - water is a polar molecule – charge is unevenly distributed o one part slightly negative, two parts slightly positive Water - water is the most abundant molecule in biological organisms o human body is 70% water - water as a solvent can dissolved more types of molecules than other molecule known - the polarity of water is key to its role in biology hydrogen bonding – electrical attraction between electronegative atom and partial positive of hydrogen Water as a Solvent - polar compound – eg. NaCl - non-polar – eg. oil in water - hydrophilic – affinity for water “watering loving” - hydrophobic – no affinity for water “water fearing” - all of waters striking properties are a direct result of its ability to form H-bonds Dissociation of Water - water is not a completely stable molecule o small amount dissociates (ionize): H2O ↔ H + OH - - hydrogen ions don’t actually exist alone, and usually join with other water molecules Acid-Base Reactions - substance that donates protons  acid (increases H in solution) - substance that accepts protons  base (decreases H in solution) - chemical reaction that involves transfer of protons  acid-base reaction - most molecules act as either an acid or a base o water can be both (both gives up and accept protons) weak acid: very few molecules dissociated (acetic acid, water) strong acid: readily gives up protons (hydrochloric acid) Measuring Acidity: the pH Scale - H can vary by a factor of 100 trillion or more - its concentration is expressed more conveniently via the pH scale o ranges from 0 (acid) to 14 (base) o compresses the range of concentration by emplying logarithms  pH = -log[H+] pK aalues pK a -logK a - When pH = pK speaies is 50% ionized (ionized = non-ionized) - When pH > pK equilibrium lies to right (ionized form dominates) a - When pH < pK equalibrium lies to left (non-ionized form dominates) - pK as a measure of proton binding affinity, it allows us to distinguish between weak and strong acids. low pK = low affinity for protons, binds protons weakly, and gives them up readily, is a strong acid high pK = has high affinity for protons, binds protons strongly, and gives them up reluctantly, is a weak acid - pK af water is 16 What are acid-base reactions important? - transfer of protons changes charge of proton donor and acceptor o change of charge changes their reactivity with respect to H-bonding, other interactions - example: concentration of H in blood is typically very low - if H doubles (still nanomolar), the acid-base reactions triggered would kill you in a few minutes Carbon as the Building Block of Biology - carbon is most important atom in biology o carbon-containing molecules  organic o can form many combinations of single and double bonds o can be linked to form chains, rings Variations in Carbon Skeletons (Pure Hydrocarbons) - carbon has a unique role in the cell because of its ability to form strong covalent bonds with other carbon atoms - carbon atoms give biomolecules their shape but other atoms attached to carbons determine their reactivity o critical H, N, O containing attachments called functional groups - a carbon chain can include double bonds – if these are on alternate carbon atoms, the bonding electrons move within the molecule, stabilizing the structure by a phenomenon called resonance Functional Groups - are the components of organic molecules typically involved in chemical reactions - seemingly minor changes in functional groups can have a dramatic biological effect UNIT 3 – THERMODYNAMICS AND CATALYSIS Thermodynamics – Catalysis – Enzymes Cells need to form complex molecules to function - energetically intensive process - cells must obey same thermodynamic principles as non-living matter Cells must carry out a multitude of chemical reactions - many of these reactions do not occur at rates capable of sustaining life under physiological conditions - cells need a mechanism around this - enzymes – protein (and RNA) based catalysts 1 Law of Thermodynamics - energy can be transferred and transformed, it cannot be created nor destroyed Energy and Chemical Bonds energy = the capacity to do work - to move matter against opposing forces - to rearrange matter kinetic energy (E K = the energy of motion, heat potential energy (E ) = stored energy by location (top of hill), and structure (arrangement of atoms P within molecule) - chemical bonds contain stored energy - cellular chemical reactions can therefore provide a source of useful cellular energy Energy, Electrons and Electron Shells - electrons are a source of potential energy - bond formation is favorable but forming some types of new bonds can free more energy than required to break the old bond; therefore breaking these types of bonds  releases energy 2 ndLaw of Thermodynamics - energy tends to spontaneously disperse, from being localized, ordered to becoming spread out, disordered - entropy = disorder Reactions Cause Disorder 1. Changes of bond energy of the reacting molecules can cause heat to be released, which disorders the environment. 2. The reactions can decrease the maount of order in the reacting molecules – for example, by breaking apart a long chain of molecules, or by disrupting an interaction that prevents bond rotations. Chemical Reactions - making and breaking or chemical bonds - shifting of atoms or ions from one molecule to another - chemical reactions are ‘spontaneous’ if they occur on their own, without external input (such as added energy) - energy is released – available for use or lost as heat - Exergonic reactions: products of exergonic reactions are less ordered, have lower E P than the reactants (energy released, products contain less energy) - Endergonic reactions: products of endergonic reactions are more ordered, have high EPthan the reactants (energy input required, products contain more energy) Gibbs Free Energy (G) - measures the “useful” work obtainable from a system at a constant temperature and pressure - predicts the spontaneity of reactions - does not predict reaction rates - does not predict chemical equilibria - is additive providing the basis for coupled reactions occurring in biology - allows energetically unfavorable reactions to occur Free Energy From the second law of thermodynamics, we know that the disorder of the universe can only increase. ∆G is negative if the disorder of the universe (reaction plus surroundings) increases. Gproducts– Greactants ∆G < 0 Exergonic: the free energy of Y is greater than the free energy of X. Therefore, ∆G<0, and the disorder of the universe increase durin the reaction X Y. - can occur spontaneously Endergonic: if the reaction X  Y occurred, ∆G would be > 0, and the universe would become more ordered - can occur only if it is coupled to a second, energetically favorable reaction Free Energy and Standard Free Energy ∆G – is dependent on concentration of reactants X ⇄ Y - high concentration of Y drives reaction to left - ∆G becomes more negative for Y  X transition - converse also true - need a standard free energy to compare different reactions, ∆G° - independent of concentration - depends only on intrinsic characteristics of molecules - ideal conditions - concentration of all reactant is 1M Predicting Reaction Direction To predict the outcome of a reaction, we must measure its standard free-energy change (∆G°). This quantity represents the gain or loss of free energy as one moles of reactant is converted to one mole of product under “standard conditions”. Chemical Reactions and Biological Systems - at some point, living organisms have to build more complex molecules out of simple compounds - not likely to be spontaneous chemical evolution: the idea that simple chemical compounds in the ancient atmosphere and oceans combined to form larger, more complex substnaces - starting materials: CO ,2H O2 H , 2 2 - evolutionary proucts (amino acids, nucleic acids) requires endergonic reactions: - non-spontaneous (+ve ∆G°), need energy input to proceed - products more complex (higher E ) thaP reactants Coupling of Reactions – Energetics - reactions can be “coupled” together if they share one or more intermediates - in this case, the overall free-energy change is simply the sum of the individual ∆G° values - a reaction that is unfavorable (positive ∆G°) can be driven by a second, highly favorable reaction - in biology we can synthesize more complex molecules by coupling their synthesis to energetically favorable reactions (exergonic) Energy Recaps - potential energy stored in bonds = chemical energy - chemical reactions can therefore provide a source of useful cellular energy - an exergoic reaction reaults in a net release of energy - thermodynamically favorable; spontanteous - energy can be used or lost as heat - less complex products; loss of order; -ve ∆G° - an endergonic reactions needs energy input to drive it - thermodynamically unfavorable - more complex products; storage of E ; +veP∆G° - due to the additive nature of ∆G° we have the thermodynamic basis for how cells are able to carry out the synthesis of complex, energy-rich molecules Rates of ‘Spontaneous’ Reactions - even if reaction spontaneous, not necessarily fast (iron  rust sugar  CO and H O) 2 2 - both spontaneous but very slow - often one bond has to break before a new one forms - requires the right molecules to collide - odds of collision influenced by: - how fast molecules are moving (temperature) - how crowded they are (concentration) - in a biological system we need a mechanism to have reactions occur quickly enough under physiological conditions of pH, temp, concentration Many Proteins are Enzymes - catalysis of chemical reactions may be the most important role of proteins in the cell - many enzymes have general or common names that indicate what they do (-ase suffix) - hydrolase, nuclease, protease, polymerase, synthase, ATPase - enzymes catalyze reactions by stabilizing/destabilizing particular bonds in the reactants and/or bringing reactants together in proper orientation to make the reaction more likely Enzymes - catalyze thermodynamically favorable reactions - allow them to proceed at rapid rates - living systems use enzymes to accelerate and control the rates of vitally important biochemical reactions - enzymes do not - change equilibrium position of reaction - catalyze non-spontaneous reactions Activation Energy - even exergonic reactions typically need a ‘push’ to get started - burning of cellulose (paper) - explosions - spark plugs in engines - hill analogy: even to roll a boulder downhill sometimes r
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