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Notes:
   Animal Body
   Arthropods
   Biochem
   Cell Cycle
   Cell Interactions
   Cell Structure
   Circulation Respiration
   Communities
   Digestion
   DNA
   Ecosystems
   Energy
   Evolution Evidence
   Future of Biosphere
   Genetic Engineering
   Gene Function
   Genetics
   Hormones
   Human Evolution
   Immunity
   Species Interaction
   Kidneys
   Locomotion
   Membranes
   Mollusks
   Mutation
   Nervous
   Non-Coelmic
   Photosynthesis
   Plant Physiology
   Population Genetics
   Population Dynamics
   Cellular Respiration
   Sensory
   Speciation
   Taxonomy
   Vertebrates
   Vertebrate Org
Vocabulary:
   1,2,3,4,5,6,7,8,9,10,
   11,12,13,14,15,
   16,17,18,19,20,
   21,22,23,24,25,
   26,27,28,29,30,
   31,32,33,34,35,
   36,37,38,39,40,
   41,42,43,44,45,
   46,47,48,49,50,
   51,52,53,54

Biochemistry

Ionic Bonds-
Gives up the outer electrons; nonmetal - metal

Covalent-

Shared electrons; nonmetal - nonmetal

Noble gases-
Doesn’t form compounds

Ionization of Water

    Water has the ability to ionize (break spontaneously) into H+ and OH- ions

H2O ~> H+ + OH-

    When a substance dissociates in water to form an excess of H+ (hydronium) ions, it is called an acid. (Can be written as H3O+). Creates an excess of H+ ions, thus acidic solution.

ex. HClH2CO3

    When a substance combines with H+ ions when dissolved in water, it is called a base. This creates a solution which has an excess of OH- (hydroxyl) ions and is therefore alkaline. (basic)

ex. NaOH

    Pure water has equal concentrations of hydronium and hydroxyl ionsDistilled (deionized) water has only water molecules no dissociation occurs.

pH Determination

    pH is based on the [H+] ions in a solution.At 25oC, water has ionization constant of [H+] of 1/10,000,000 or 1x10-7pH (pure water) = -log[H+], then:

pH = -log (1x10-7) = -(-7) = 7

    Note that since this is a logarithmic scale, each change of one on the pH scale is equivalent to a tenfold changeAcid rain caused by pollutants kills fish, plants, causes defects in organisms, and can erode structures. This is caused by conversion of pollutants such as SO2 and NO2 into H2SO4 and HNO3 in the clouds. These then fall to the Earth in precipitation.

Neutralization

    An acid and a base forms water and a salt.

HCl(aq) + NaOH(aq) ~> HOH(aq) + NaCl(aq)

Buffers

    Living systems contain with a pH of round 7.Very sensitive to small changes in pHBlood Acidosis/AlkalosisWe eat and produce acid/bases on a regular basisWe need substances that will counter these acids/bases and help mantain a constant pHCalled Buffers and they act as reservoirs for excess/depleted [H+]These are usually acid/base pairs and can donate/accept H+ ions.

ex. Carbonic acid / Bicarbonate System
H2O + CO2 H2CO3 HCO3 + H+

    Acid (Pepsi) taken in: Bicarbonate acts as a base and removes excess H+ by forming H2CO3, thus maintaining homeostasis
    Determines electronegativity; ability to attract electronsTetrahedronAllows the breakdown of solutes
      Solute = being dissolvedSolution = being dissolved in
     Forms hydrogen bonds; very weak; don’t lastAdhesion: water molecule to anotherCohesion: water molecule to itself
      Capillary ActionTranspiration (evaporation of water from leaves)Surface tension (resistance to being moved apart)
    Specific Heat
      High Specific Heat = 1Allows for gradual increase in temperature
    High heat of Vaporization
      Wouldn’t be able to sweat if it was low
    Universal solventWater dissolves things by ionizationIce floats (less dens         e) because of crystallizationDissociation and ionizationViscosity – high = gooey low = good flowPoor electrical conductorHeat of fusion – heat needed to meltChemically stableLight penetrable
    Molecules
      Macro - cannot fit thru a cell membraneMicro - can fit thru a cell membrane
    Organic Chemistry
      Carbon is basis for Organic Chem.Used to build back bone of all organic moleculesFour Groups:
        CarbohydratesLipids (carboxyl)Nucleic AcidsProteins (amino acids & carboxyl)
    Dehydration Synthesis
      Method used to create all substances in all organisms




      Requires energy to create bonds. This can slow rxn down. Catalysis can overcome this problem. (Use enzymes to speed rx         n) This lowers the activation energy
    Hydrolysis
      Molecule of water is added as subunits are broken apartEnergy is released (catabolism)
    Types of Molecules (Macro; Sugars)
      Carbohydrates
        Contain C,H,O in a ratio of 1:2:1 (monosacharides)Function in energy storage (short term)Empirical formula: CH2OEnergy is provided when bonds are broken
          HydrolysisCatabolismExergonic
        Monosaccharides are simplest formUsually straight chains, but form rings in H2OMost common (primary) six carbon sugar is glucose (C6H12O6Ex. of monosaccharides: fructose (fruit), galactose (milk), glucoseCan form Isomers Isomers have same molecular formula, but different structural formulas, such as fructose, glucose (taste polymers)Monosaccharide Sugar


        Stereo isomers are mirror images of each other
          ex. glucose, galactose


        Disaccharides
          Two monosaccharides joined by dehydration synthesisJoined by oxygen bond
          ex. Maltose (glucose & glucose), sucrose (glucose & fructose), lactose (glucose & galactose)
        Polysaccharides
          aka starchPasta, potatoes, celluloseamylose - animal starchamylopectins - plan starchkhytin - insects exoskeleton
      Lipids
        Three Major Forms
          FatsOilsWaxes
        Chemical Make-Up
          C,H,O in variable ratiosMuch higher ratio of H to O then in CarbosInsoluable in water / soluable in oil
        Types
          Fats ~> 3 fatty acids & glycerol ~> stored energy ~> butter, soap, oilsPhospholipidsSteroidsTerpenesProstaglandins
        Fats
          Non-polar - don’t form H-bonds ; C-H bonds are hydrophobic

i'm st

          Saturated – all single bondsUnsaturated – double bonds
            Mono – 1 doublePoly – many double
          Double bonds cause kinks in the chain
          Hydrogenation – making more solid by adding H
            Ex. Peanut Butter
          Energy Storage
            More C-H bonds than carbos9 kilocalories per gram of fat4 kilocalories per gram of carbos
        Phospholipid
          Glycerol, 2 fatty acids & (PO4) phosphateCauses a hydrophobic and a hydrophilic endCell membranes


        Steroids
          Four carbon ringsImportant in cell membranes, hormonesCholesterol, hormones (reproductiv         e) estrogen & testosterone
        Terpenes

          Very long carbon chains that are branched
          Many pigments (retinal, carotene, chlorophyll)Rubber

        Prostoglandins
          About 20 lipids that are modified fatty acids2 nonpolar tails attached to a 5 carbon ringThey function as chemical messengers in vertebrate systems
      Proteins
        Strings of Amino Acids20 Amino Acids – “8 are essential”
          Body can’t make most of them, get it from diet
        cell membrane, antigens, hormones, toxines, antibodies, muscles, enzymes, fibersMade up of C, H, O, **N**


        Polypeptides (amino acids put together)Held together by peptide bonds5 Classes of Amino Acids – “Radical”
          Non-Polar         ex. –CH2   -CH3Polar, uncharged           ex.  –O-Ionizable          ex.  Acid/BaseAromatic           ex.  Ring w/ alternating single & double bondsSpecial Function           ex.  Proline (kinks), Cysteine (link chains), methionine (initiates)When making a polypeptide, you must have an ionized amino acid (NH4+, COO-)Allowing peptide bonds to occurPeptide bonds are unable to rotate
        Protein Structure
          1950’s – first discovered
            Sanger – first to discover AA sequence of insulinX –ray diffraction (atom position)
          Many proteins are very stiff and have hydrophobic innersEnzymes can also denature (unfold)
        Primary Structure
          Actual AA sequenceSubject to mutationsProteins to 1,000 to 100,000 of AA longThis produces high diversity
            20100  = 1, (130 zeros)
          Based upon genetic sequence
        Secondary Structure
          Initial folding due to side chain interactions
            a-helix = Amino Acids that join with another down the chain

b-sheets = AA join across two chains

These are amino-carboxyl bonds (H-bonds)

          Motifs
            Super secondary structurebab = fold or creaseb barrel = b sheets in a tubea turn a = proteins used to bind to DNA double helix
        Tertiary Structure
          Driven by hydrophobic interactionsNon-polar are moved inside; polar to the outsideDomains
            Super tertiary structureShort sections of exons (good DNA)Functions to bind NAD+ as well as other substratesRope in a knot
        Quaternary Structure
          Two or more chains (sub-uni         t) working together for one function
            Ex. Hemoglobin
      Nucleic Acids
        DNA – Deoxyribonucleic AcidRNA – Ribonucleic AcidDifference
          DNA – double helix; RNA – single helixRNA has urcil in place of thymineRNA is mobile and DNA is stationaryDNA’s five-carbon sugar has one less oxygen



        DNA’s purpose is to store genetic informationRNA’s purpose is to transport that information to ribosomesAdenine always to thymine/UrcilGuanine always to cytosinePurines – A and G ~> double ring Pyrimadines – T, C and U ~> single ring

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