Chemical Principles and Biomolecules(Chapter 2)Lecture MaterialsforAmy Warenda Czura, Ph.D.Suffolk County Community CollegeEastern CampusPrimary Source for figures and content:Tortora, G.J. Microbiology An Introduction 8th, 9th, 10th ed. San Francisco: PearsonBenjamin Cummings, 2004, 2007, 2010.Amy Warenda Czura, Ph.D.1SCCC BIO244 Chapter 2 Lecture SlidesChemistry = the study of atoms and molecules-All matter is composed of atoms-Atoms bond together to form moleculesAtom = smallest unit of matter(Matter = anything with mass &takes up space)-consists of 3 types of subatomic particles:1. protons (p): + charge, in nucleus2. neutrons (n): neutral, in nucleus3. electrons (e`): - charge, around nucleusAmy Warenda Czura, Ph.D.2SCCC BIO244 Chapter 2 Lecture SlidesAtomic number = number of p in the nucleusAtomic Mass = total number of p + nChemical element = all atoms with same # ofprotons that behave the same way.-92 naturally occurring elements-only 26 commonly found in living thingsMost abundant in life:Symbol Atomic # MassHydrogen H 1 1Carbon C 6 12Nitrogen N 7 14Oxygen O 8 16Isotope = atoms with same # of protons butdifferent numbers of neutrons. e.g. oxygen – 3 isotopes in nature.16O (8p, 8n) (99.76% of all)17O (8p, 9n)18O (8p, 10n)Amy Warenda Czura, Ph.D.3SCCC BIO244 Chapter 2 Lecture SlidesElectron Configurations-electrons organized intoshells around the nucleus-shells = regionscorresponding todifferent energy levels-innermost shell can holdup to 2 e`-2nd and 3rd: 8 e` each-4th, 5th, 6th: 18 e` each-shells are filled from inside to outsideAtoms have the same number of electrons asthey do protons (neutral charge)Valence shell = outer most electron shell (atoms “want” this shell to be full)Valence = combining capacity/bonding capacity; the number of extra or missing electrons in the outer most shell2e8e8e18eAmy Warenda Czura, Ph.D.4SCCC BIO244 Chapter 2 Lecture Slidese.g. Mg atomic #12electron shells: 2, 8, 2 2 extra electronsO atomic #8electron shells: 2, 6needs 2 electrons-atoms with outer shells more than half fullwant to take electrons to make a full valence shell-atoms with outer shells more than half emptywant to give away electrons to drop tolower full shell-atoms with full valence shells are inert-a gain/loss of electrons results in the atom nolonger being neutral:Ion = atom with unequal numbers of protonsand electrons-cation = positive charge, more p than e`-anion = negative charge, more e` than pAmy Warenda Czura, Ph.D.5SCCC BIO244 Chapter 2 Lecture SlidesMolecules – any two or more atoms held together by attractive forces called chemical bondsCompound – a molecule that contains at leasttwo different kinds of atoms chemically bondede.g. O2 = moleculeH 2O = molecule and compoundTypes of Chemical Bonds1. Ionic Bonds-electrons are gained or lost, and equal but oppositely charged ions attract each othere.g. Na atomic #11: e` 2:8:1Cl atomic # 17: e` 2:8:7-Na donates 1 e` to Cl-both now have full valence but unequalcharge (Na+ & Cl-)Amy Warenda Czura, Ph.D.6SCCC BIO244 Chapter 2 Lecture Slides-resulting ions attracted forming an ionic bond-create the new molecule NaCl2. Covalent Bonds-atoms share one or more pairs of electrons-these bonds are stronger and more commonin living organisms than ionic bonds-shared e` orbit nuclei of both atoms simultaneouslyAmy Warenda Czura, Ph.D.7SCCC BIO244 Chapter 2 Lecture Slidessingle covalent bond = one pair e` sharede.g. H2 or CH4double covalent bond = 2 pair e` sharede.g. O2triple covalent bond = 3 pair e` sharede.g. N2Nonpolar covalent bond = equal sharing of e`Polar covalent bond = one atom “shares” e` more of the time, causes one side of molecule to be + and other to be - (common with H bonded to O or N)Amy Warenda Czura, Ph.D.8SCCC BIO244 Chapter 2 Lecture Slides3. Hydrogen Bonds-result from polar covalent bonds-when H is bound to a large atom like O or Nthe large atoms takes the electrons more time setting up a slightly positive charge on the hydrogen side of the molecule andnegative on oxygen or nitrogen side.-the + H gets attracted to the - O or N in another molecule creating a weak bond between molecules-H-bonds too weak to form molecules-act as bridges between existing moleculesor within large moleculesAmy Warenda Czura, Ph.D.9SCCC BIO244 Chapter 2 Lecture SlidesChemical Reactions:-making or breaking bondsinput material = reactant (or substrate)resulting material = product-takes energy to make a bond, release energywhen breaking a bondEndergonic reaction – absorbs more energythan it releases (feels cold)Exergonic reaction – releases more energythan it absorbs (feels hot)3 types of reactions common to living cells:1. Synthesis reactions = form new bondsA + B → AB (anabolic reaction)2. Decomposition reactions = break bondsAB → A + B (catabolic reaction)3. Exchange reactions = original bonds arebroken and new bonds are formedAB + CD → AD + BCAmy Warenda Czura, Ph.D.10SCCC BIO244 Chapter 2 Lecture SlidesActivation energy = amount of energy neededto disrupt the stable electron configurationof any molecule or atom so it reactsReaction rate = frequency of interactions containing sufficient energy to bring abouta reaction (can be increased by heat, pressure, or concentration of reactants)Catalyst = substance that can speed a chemicalreaction without being permanently alteredor consumedEnzyme = biological catalyst-acts on a specific substance = substrate-binds substrate at the active site on enzyme-catalyzes only one reactione.g. sucrase: sucrose → glucose + fructose-an enzyme lowers the activation energy of thereaction by orienting the substrate in a wayto increase the probability of a reactionAmy Warenda Czura, Ph.D.11SCCC BIO244 Chapter 2 Lecture Slides*enzymes function to speed up reactions attemperatures compatible with lifeImportant Biological Molecules1. Inorganic molecules:-lack C and H chains-often formed by ionic bonds, but notalwayse.g. H2O, O2, CO2, salts, acids, bases2. Organic molecules-based on C and H chains-structurally complex-typically formed by covalent bondse.g. sugars, amino acids, vitamins, etc.Important Inorganic MoleculesA. Water-most common, most important to life-polar moleculeAmy Warenda Czura, Ph.D.12SCCC BIO244 Chapter 2 Lecture Slides-Water important because of its properties:1. H-bonding resists rapid temp change-each H2O can bond with 4 others-high boiling point-low freezing point-liquid at temps compatible with life2. Good solvent-polar and ionic substances