Week 2 Notes
Week 2 Notes Bio 208
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This 9 page Class Notes was uploaded by Kylie McLaughlin on Sunday September 6, 2015. The Class Notes belongs to Bio 208 at Northern Illinois University taught by Dr. Ed Draper in Fall 2015. Since its upload, it has received 77 views. For similar materials see Fundamentals of Cell Biology in Biological Sciences at Northern Illinois University.
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Date Created: 09/06/15
Chapter 2 cont Week 2 Notes Enerdv levels of an Atoms Electrons energy e is the capacity to cause change or the ability to do work Potential energy energy that matter possesses because of its location or structure energy is needed absorbed when an electron goes to a higher level energy is lost when an electron goes to a lower level lower levels are and are lled rst as you move farther away from the nucleus levels gain more energy Electron Distribution amp Chemical Properties based on energy level of their electrons it will show how they react with other moleculesatoms the chemical behavior of an atom is determined by the distribution of electrons in the atoms electron shells each electron shell contains electrons at a particular energy level distributed among a speci c number of orbitals of distinctive shapes and orientations Orbital three dimensional space where an electron is found 90 of the time eectrons tend to exist in the lowest available state of potential energy the chemical behavior of an atom depends mostly on the number of electrons in the outermost shell those electrons are called and the outermost shell is called the formula for the number of electrons in a shell is 2nquot2 this is the max number a level can hold n level of the shell EX 21quot2 2 electrons Atomic Stabilitv 3 rules 1 Octet rule lled valence shell usually 8 electrons 2 Electroneutrality number of electrons number of protons Has a net charge of O 3 Electrons are paired all orbits are lled will focus mainly on 1 amp 2 in this course Nobe gases last column on the periodic table meets all 3 rules for atomic stability gtlltgtlltgtlltgtllt all other elements are inherently unstable they can become more stable by interacting with others Covalent Bonds 2 atomselements share one or more pairs of electrons bonds are and bonded atoms cannot bond with any other atoms very strong bonds need lots of energy E to break the bonds ots of energy is released when bonds are formed always display molecular structure same amount of distance of structures water molecule is more stable together than the separate H or O molecules they form to complete their valence shells with same element with different element singe double or triple bonds are possible Eectronegativitw attraction of a particular atom for the electrons of a covalent bond atoms with high electronegativity ON attract electrons more strongly than atoms with lower electronegativity HC Polar easily dissolved in water Nonpolar same af nity for the electron parts of the molecule have 6 and other parts have 5 the bonds between 0 and H gt are and the molecule as a whole is 0nsare charged atoms Cations loss of electron makes it a have a positive charge Anions gain of electron makes it have a negative charge ions have lled valence shells but are not electroneutral lonic Bonds transfer of electrons opposite charges attract each other EX each Na is surrounded by several Cl and vice versa not 11 correspondence of a speci c Na with a speci c Cl atoms have lled valence shells and the is electroneutral NaCl is Hydrogen Bonds noncovalent attraction between a hydrogen and an electronegative atom very weak partia positive charge on a hydrogen atom covalently bonded to an electronegative atoms allows the hydrogen atom to be attracted to a different nearby electronegative atom form 6 and 6 of different molecules attraction of opposite charges can add to chemical properties Van der Waals Interactions if electrons are distributed asymmetrically in molecules or atoms they may accumulate by chance in one part of a molecule van der waals interactions are attractions between molecules that are close together as a result of these changes temporary and weak individually but when all the weak ones are added together they can be strong Chemical Reactions the making and breaking of bonds leading to changes in the composition of matter all chemical reactions are reversible products of the forward reaction become the reactants for the reverse reaction doube arrow does not mean equal amounts it means equal rates Chemical equilibrium is reached when the forward and reverse reactions occur at the same rate at equilibrium the relative concentrations of reactants and products do not change Chapter 3 Water and Life Bonds Polar covalent bonds occur some molecules Hydrogen bonds Hbonds occur polar molecules Physical properties of water Water is sticky High speci c heat high heat of vaporization lce oats Solvent properties Aqueous solutions mole molar wewwe Hydrogen Bonds between Water Molecules Hbonds form between 6 and 6 of different water molecules each water can form up to 4 Hbonds covalent bonds between atoms and hydrogen bonds between H atoms Hbonds are responsible for the physical properties of water Water is Sticky Adhesion water is attracted to Cohesion water sticks to cohesion holds raindrops together and can generate surface tension carbohydrates in the walls of plant waterconducting cells adhere to water which helps water move from root to leaves by transpiration Moderation of Temperature by Water Speci c heat is related to the amount of energy E that is absorbed or lost when the temperature of a substance changes 1 calorie energy needed to increase the temperature of 1 gram of water by 1 C 1000 cal 1 kcal 1 dietetic calorie water has a high speci c heat therefore it resists changes in temperature either up or down when energy is added or removed water is a water has a high heat of much energy is absorbed when water evaporates leading to cooling lce Floats crystaline ice takes up less space is less dense than liquid water organisms can live in liquid water beneath an ice layer Water The Solvent of Life Solvent water substance using to break apart dissolve another substance Solutes dissolved materials Solution water plus solutes Polar moecues form Hbonds with water they are hydration spheres surround solutes Nonpolar are water can interact with and solvate macromolecules such as proteins positive charges on the protein full or 6 are attracted to the 6 side of H20 negative charges on the protein full or 6 are attracted to the 6 side of H20 Aqueous Solutions Molecules weight sum of atomic mass daltons or AMU s the molecular weight of 1 H20molecule is 18 Da MoleAvogadros number 602 X 10quot23 Grammolecular weight mass of 1 mole of a substance molecular weight of H20 is 18 g Molar number per volume or 1 M 1moe 1 liter Examples from class How many grams of Na2CO3 molecular weight 106 gmol is in 1L of 1M solution 106g1mol X 1 mol1L X 1L 106 g How many grams of Na2CO3 is in 1L of a 2M solution 106g1mol X 2 mol1L X 1L 2X1O6g1 212 g How many garms of Na2CO3 is in 600 mL of a 5 M solution 106g1mol X 5mol1L X 6L 106g X 5 X 6 318 g Ionization of Water H20 hydronium ion H30 hydroxide ion OH in pure water H OH 10quot7 square bracket way to show it s a concentration when it s in a square bracket Acids amp Bases Acid proton donor increases H pH lt 7 Base proton acceptor decreases H pH gt 7 pH is proportional to H pH logH pH of pure water neutral pH og10quot7M 7 if pH increases by one unit eX 4 to 5 1 X H if pH decreases by one unit eX 9 to 8 10 X H III 1 Eiattery add 2 Lemenjuiee Increaaing 3 Vinega Agld Eh CHE I ranl 4 Fiari repreducher affected 5 Nermal range preeipitahen NE Utrai r l39 M39W Normal range CI of stream water 3 Baking soda 9 E eea water Increasmg 1D Mil39lila aeaia H Scale alkalinity 11 A g p 12 mmenia 3 f 14 Ceurteay of Environment Canada httpmrriirwnaee gecai39 Buffers ce activities ex enzyme activity work optimally at a speci c pH In cells and in lab experiments buffers maintain a speci c pH Buffer a chemical that is ionized It if a small amount of acid or base is added the buffer causes pH to resist being changed every buffer has an acid H donor and a base form H acceptor H2CO3carbonic acid H donor HCO3 bicarbonate ion H acceptor H burning fossil fuels adds potentially toxic compounds to the atmosphere which lowers pH and can have severe effects on the health of organisms and ecosystems Chapter 4 Carbon amp Molecular Diversitv of Life organic chemistry is chemistry of life the diversity of carboncontaining molecules isomers functional groups litaism the concept that organic matter possesses a special force or force inherent to things livings for example was discovered in 1799 and was thought to come from living sources such as urine in 1828 Friedrich Wonler synthesized urea from two inorganic substrates and disproved vitalism there is no known biological process that does not agree with the laws of physics and chemistry Atoms form covalent bonds to complete their valence shells Carbon is tetravalent Hydrogen valence shell 1 0 Oxygen valence shell 2 Nitrogen valence shell 3 0 Carbon valence shell 4 Hydrocarbons are rich in hydrogen and carbon atoms nonpolar a Length b Double bond position c Branching d Presence of rings carbon can have single double or triple bonds hydrocarbons from the backbones of biological macromolecules lsomers are molecules that have the different structures have different physical and biological properties 3 types Structural isomers have the same empirical formula both are C5H12 but the rules for the two other types don t apply Cistrans previously geometric isomers must have 1 A CC double bond no rotation around this bond 2 Different substituents on the carbons Cisisomers substituents on the same side of the carbon Transisomer substituents on the opposite side of the carbon Enantiomers are related to each other by An asymmetric or chiral carbon must be present ie carbon with 4 different substituents Laanine and Dalanine are amino acids only Lform is used to make proteins Functional Groups LL Hydroxyl XOH alcohols Carbonyl XCO aldehydes amp ketones Carboxyl XCOOH carboxylic acids ALAmino XNH2 amines Sulfhydryl XSH thiols Phosphate XDO4 organic phosphates x is for the rest of the molecules X may be a simple hydrocarbon Hydroxyl Group OH ethanol the alcohol present in alcoholic beverages poar due to electronegative oxygen forms hydrogen bonds with water compound name alcohol Alcohols speci c names usually end in 0 present in carbohydrates and many other organic compounds Carbonyl Group acetone the simplest ketone When CO is in the middle of the structure propanol an aldehyde sugars with ketone groups are called ketoses those with aldehydes are called aldoses compound name ketone or aldehyde Ketones internal carbonyl C is attached to 2 other C s Aldehyde termina carbonyl C is attached to O or 1 other C present in carbohydrates aldehyde gt aldose Ketone gt ketose poar attracts water molecules gt hydrophilic Carboxvl GrOUD COOH acetic acid which gives vinegar its sour taste ionized form of COOH carboxylate ion found in cells acts as an acid compound name carboxylic acid or organic acid Carboxyic acids or organic acids acidic proton donor weak acids not fully ionized like buffers eg acetic acid ionized XCOO is negatively charged poar attracts water molecules gt hydrophilic Amino Group NH2 gycine an amino acid ionized form of NH2 found in cells acts as a base compound name amine Amines basic proton acceptor ionized form X NH3 is positively charged weak bases not fully ionized eg ammonia NH3 gt NH4 poar attracts water molecules gt hydrophilic Sulfhydryl Group SH may be written as HS cysteine a sulfurcontaining amino acid two SH groups can react forming a quotcrosslink that helps stabilize protein structure compound name thio Thios mercaptans 0r quotsulfur alcohols fou odor rotten eggs skunk scent odorant in natural gas covaent bonding is possible gt poar but less so than acohos