Workshop: Biology 3 FinalRay ChenLilit HaroyanSpecial Thanks to Dr. Elkerdany for kindly providing his material and support. 1Ion, atom, isotope• Atoms – smallest units that make up the matter– Hydrogen = H– Sodium = Na– Chloride = Cl• Ions – can form when atoms lose or gain electrons– Positive and negative ions are attracted to one another and bond together in ionic bonds– Ex: Na+, Cl-• Isotopes – which have the same numbers of protons and electrons but different numbers of neutron– Ex: C-12, C-13, C-143Atoms• Protons -- (+) charge• Electron -- (-) charge• Neutron -- No charge• Nucleus consists of protons and neutrons• Atomic number = # of proton• Mass number = # of proton+ # of neutrons• # of protons = # of neutrons• # of protons = # of electrons3Example: Carbon# of proton= 6# of nutron= 6# of electron= 6Atomic number= # of proton= 6Mass number = 6+6=12Copyright © 2009 Pearson Education, Inc.126CMass numberAtomic numberChemical symbol5Let’s Practice • Given atom Oxygen: # of proton:__# of electron:__# of neutron:__Atomic number:__Mass number:__56Ionic, covalent, hydrogen bond• Ionic bond: occurs when electron transfer from one to the other. One is losing and one is gaining. (NaCl)• Covalent bond: occurs when two atoms share electron (• Hydrogen bond: Polar water molecules are attracted to one another and can form H-bond.6NaSodium atomTransfer ofelectronClChlorine atomNa+Sodium ionCl–Chloride ionSodium chloride (NaCl)+–Na+Cl–Types of Chemical Bonds• A covalent bond results when two atoms share electrons, thereby completing their valence shells(–)(–)OHH(+) (+)Hydrogen bond11Acid, base, buffer, pH• Acid -- Substance that can release H+ ions- HCl: HCl-->H+ + Cl-• Base -- Substance that can release OH-ions- NaOH: NaOH--> Na++ OH-• Buffer -- is a chemical or combination of chemicals that keeps a pH within a given range• pH -- is a mathematical way of indicating the number of H+ions in a solution11Acidic solutionpH scaleBattery acid012345Lemon juice, gastric juiceGrapefruit juice, soft drink,vinegar, beerTomato juiceRain waterHuman urineSalivaPure water67Human blood,tearsSeawater8910111213Milk of magnesiaHousehold ammoniaHousehold bleachOven cleanerNeutral solutionBasic solutionNEUTRAL[H+]=OH–]Increasingly ACIDIC(Higher concentration of H+)14Increasingly BASIC(Lower concentration of H+)Organic Molecules• Inorganic chemistry - chemistry of the nonliving world• Organic chemistry - chemistry of the living world– Carbon-based molecules are called organic compounds– By sharing electrons (what type of bond?), carbon can bond to four other atoms – By doing so, it can branch in up to four directions • CH4– most simple organic compound14Isomers, hydrocarbon, function group• Hydrocarbon -- Compounds composed of only carbon and hydrogen• Isomer -- different compounds with the same molecular formula can be produced• Functional group --14Carbon skeletons vary in length.Branching. Skeletons may be unbranched or branched. ButaneIsobutanePropaneEthaneDouble bonds.2-ButeneSkeletons may have double bonds,which can vary in location.CyclohexaneLength.1-ButeneBenzeneSkeletons may be arranged in rings.Rings.Hydrophobic vs. hydrophilic• Hydrophobic – afraid of water (hydrocarbons)• Compounds containing functional groups are hydrophilic (water-loving)– carboxyl (COOH), alcohol (-OH), amino (-NH2)17Monomers, polymers• Polymer: Macromolecule- Carbohydrates (Monomer: small sugar)- Lipids (Monomer: fatty acid)- Proteins (Monomer: Amino acid)- Nucleic acids (Monomer: nucleotides)• Monomer: Building block of macromolecule17UnlinkedmonomerShort polymerLonger polymerDehydrationreactionHydrolysis20Mono-and-poly saccharides• Monosaccharides are carbohydrates with a single sugar molecule- Glucose, Deoxyribose, ribose• Polysaccharides are polymers of monosaccharide - Starch, glycogen, cellulose and chitin20Monosaccharides: Ready EnergyPolysaccharides as Energy Storage MoleculesFatty Acids• Two types:– Saturated fatty acids - no double bonds between carbon atoms– Unsaturated fatty acids - at least one double bond between carbon atoms• Oils tend to contain unsaturated fatty acids • Fats like butter tend to contain saturated fatty acidsFatty AcidsFatty AcidsWaterHydrophobictailsHydrophilicheadsWaterFour Levels of Protein StructureAmino acidsPrimary structureAlpha helixHydrogenbondSecondary structurePleated sheetPolypeptide(single subunitof transthyretin)Tertiary structureTransthyretin, withfour identicalpolypeptide subunitsQuaternary structureThe Effect of Osmosis on CellsIsotonic solution(B) Lysed (C) Shriveled(D) Flaccid (E) Turgid(F) ShriveledHypertonic solutionHypotonic solutionPlantcellAnimalcell(A) NormalPlasmamembrane(plasmolyzed)Smooth endoplasmicreticulumRoughendoplasmicreticulumCYTOSKELETON:NUCLEUS:Nuclear envelopeChromosomesNucleolusRibosomesGolgiapparatusPlasma membraneMitochondrionPeroxisomeCentrioleLysosomeMicrotubuleIntermediatefilamentMicrofilamentSmooth endoplasmicreticulumRough endoplasmicreticulumCYTOSKELETON:NUCLEUS:Nuclear envelopeChromosomeNucleolusRibosomesGolgiapparatusPlasma membraneMitochondrionPeroxisomeCell wallCentral vacuoleMicrotubuleIntermediatefilamentMicrofilamentCell wall ofadjacent cellChloroplastPlasmodesmata313 components of cytoskeleton • Microfilaments• Intermediate filaments• Microtubules 31Enzyme availablewith empty activesiteActive site1Enzyme(sucrase)Substrate bindsto enzyme withinduced fit2Substrate(sucrose)Substrate isconverted toproducts3Products arereleased4FructoseGlucoseEnergy of ActivationReactionwithoutenzymeEAwith enzymeReactantsReaction withenzymeEAwithoutenzymeNetchangein energy(the same)ProductsProgress of the reactionLock and Key Model• Enzyme represented rigid• Substrate fits perfectly in the active site region; if doesn’t fit perfectly it will not reactInduced-fit Model• Enzyme structure flexible• Enzyme and active site adjust shape to bind substrate  increases range of substrate specificity363 types of cell transport• Passive transport- Requires no energy- Simple diffusion/Osmosis (diffusion of water) - always from high conc to low conc- always involve small/nonpolar molecules• Active transport- Require energy and membrane protein- always go against its concentration• Bulk transport- Require energy- Endocytosis, Exocytosis36Cellular Respiration– Glucose loses its hydrogen atoms and is ultimately converted to CO2–