Docstoc

The Chemistry of Organic Molecules

Document Sample
The Chemistry of Organic Molecules Powered By Docstoc
					           Chapter 3
The Chemistry of Organic Molecules

            AP Biology
                  Definitions
• Organic Molecules
  – Bonding of H, O, N, and other molecules to
    carbon.
  – Characterize the structure and function of living
    things
• Inorganic Molecules
  – Do not contain C and H together
  – Nonliving matter; however they play important
    roles in living things
             Functional Groups
• Functional groups are the parts of
  molecules involved in chemical reactions
• Give organic molecules distinctive chemical
  properties (ex. Polarity, hydophobic/philic,
  acidic, etc.)
• Six functional groups are important in the
  chemistry of life: (see Figure 3.2, pg 35)
  – Hydroxyl
  – Carbonyl
  – Carboxyl
  – Amino
  – Sulfhydryl
  – Phosphate
                   Isomers
• Isomers are
  molecules with the
  same molecular
  formula but
  different structures
  (different functional
  groups) and
  properties
           Macromolecules
– Are large molecules composed of smaller
  molecules
– Are complex in their structures
     Macromolecules

•Macromolecules are polymers, built from
monomers
• Four classes of life’s organic
   molecules are polymers
    – Carbohydrates
    – Proteins
    – Nucleic acids
    – Lipids
 The Synthesis and Breakdown of Polymers

• Monomers form larger molecules by condensation
  reactions called dehydration synthesis


                      HO     1        2   3    H     HO          H

                            Short polymer            Unlinked monomer

                      Dehydration removes a water
                                                          H 2O
                      molecule, forming a new bond

                            HO    1       2    3     4    H
                                      Longer polymer
         Figure 5.2A (a) Dehydration reaction in the synthesis of a polymer
 The Synthesis and Breakdown of Polymers

• Polymers can disassemble by
  – Hydrolysis (addition of water molecules)

                              HO     1      2     3    4    H



                           Hydrolysis adds a water
                                                            H 2O
                           molecule, breaking a bond




                        HO     1      2     3     H    HO          H

            Figure 5.2B (b) Hydrolysis of a polymer
                    Carbohydrates
• Monosaccharides
   – Glucose
   – Fructose
   – Ribose/Deoxyribose
• Disaccharides
   – Lactose
   – Maltose
   – Sucrose
• Polysaccharides
   –   Starch
   –   Glycogen
   –   Cellulose
   –   Chitin
                    Lipids
• Lipids are a diverse group of hydrophobic
  molecules (nonpolar and insoluble)
• Lipids
  – Are the one class of large biological molecules
    that do not consist of polymers
  – Provide energy storage
  – Act as cell messengers
                         Fats
– Are constructed from two types of smaller molecules, a
  single glycerol and usually three fatty acids
– Vary in the length and number and locations of double
  bonds they contain
• Saturated fatty acids
  – Have the maximum number of hydrogen
    atoms possible
  – Have no double bonds




                                                         Stearic acid




              Figure 5.12 Saturated fat and fatty acid
                        (a)
• Unsaturated fatty acids
  – Have one or more double bonds




                                                                         Oleic acid




                                                           cis double bond
          Figure 5.12 (b) Unsaturated fat and fatty acid   causes bending
                    Waxes
• Chains of fatty acids bonded to an alcohol
  chain.
• Solid
• Protective
• Phospholipids
  – Have only two fatty acids
  – Have a phosphate group instead of a third
    fatty acid
    • Phospholipid structure
       – Consists of a hydrophilic “head” and
         hydrophobic “tails”
                                      CH2        +
                                                 N(CH3)3   Choline
                                      CH2
                                      O
                                  O   P     O–
                                                           Phosphate
                                      O
                      CH2     CH      CH2
                                                           Glycerol
                      O      O
                      C     O C       O




                                                           Fatty acids

                                                                                                         Hydrophilic
                                                                                                           head
                                                                                                         Hydrophobic
                                                                                                          tails


                                                                                                 (c) Phospholipid
                                                                       (b) Space-filling model
Figure 5.13   (a) Structural formula                                                                  symbol
• The structure of phospholipids
   – Results in a bilayer arrangement found in cell
     membranes

                               WATER
               Hydrophilic
               head




                               WATER
               Hydrophobic
               tail
 Figure 5.14
                    Steroids
• Steroids
  – Are lipids characterized by a carbon skeleton
    consisting of four fused rings
  – Differ with functional groups
• One steroid, cholesterol
   – Is found in cell membranes
   – Is a precursor for some hormones
                            H 3C        CH3


                              CH3       CH3




                    CH3




 Figure 5.15   HO
                Proteins
•   Support
•   Enzymes
•   Transport
•   Defense
•   Hormones
•   Motion
• Amino acids
  – Are organic molecules possessing both
    carboxyl (acidic) and amino groups
  – Differ in their properties due to differing side
    chains, called R groups
         Amino Acid Polymers
• Amino acids
  – Are linked by peptide bonds (covalent)
            Protein Structure
• A protein’s specific conformation (shape)
  determines how it functions
    Four Levels of Protein Structure
• Primary structure                +H

                                   Amino
                                        3N
                                                          Gly ProThrGly




                                                       LeuPro
                                                                      Thr



                                                             Cys LysSeu
                                                                       Glu
                                                                            Gly
                                                                                              Amino
                                                                                               acid
                                    end          Met
                                                                                             subunits
   – Is the unique sequence
                                              Val
                                             Lys
                                             Val
                                               Leu
                                                  Asp
                                                     AlaVal ArgGly
                                                                  Ser
                                                                    Pro



     of amino acids in a                                              Ala




     polypeptide
                                                       Glu Lle
                                                                 Asp
                                                                    Thr
                                                                      Lys
                                                                    Ser
                                                           Lys TrpTyr
                                                 Leu Ala
                                              Gly
                                              lle
                                              Ser
                                                 Pro Phe
                                                            His Glu
                                                                      His
                                                                        Ala
                                                                      Glu
                                                                    Val
                                                AlaThrPhe Val
                                             Asn
                                                                            lle
                                                                Thr
                                             Asp             Tyr               Ala
                                                           Arg
                                              Ser       Arg                     Ala
                                                 Gly Pro
                                                                                  Leu
                                                                        Leu
                                                                      Ser
                                                               Tyr Pro
                                                             Ser
                                                    ThrSerTyr
                                               Thr
                                                Ala
                                                    Val                                 o
                                                      Val          Glu            c
                                                        Thr Pro Lys
                                                          Asn                           o–

                          Figure 5.20        Carboxyl end
• Secondary structure
      – Is the folding or coiling of the polypeptide into a
        repeating configuration
      – Includes the  helix and the  pleated sheet

        pleated sheet
                                   O H H                O H H               O H H               O H H
                                                                                            R
 Amino acid                         C C N           R    C C N          R   C C N                C C N
                             C N                   C C N               C C N               C C N           C C
  subunits                                 R                   R                   R               R
                               H                   O H H                OH H                OH H            O

                                               R                   R                   R               R
                                       O               C   O                   O    C        O          H
                                               C    H       H                           H           C
                                                              H                           H
                                       C   N HC N H C N H C N     C                NH C N     C    N HC N
                                           H          H        C                   H   O C         H
                                   C           O  C        O                                           O C
                                                   R            R                           R
                R       H      R       H
                    C              C
    N H     O C    N H       O C
            N H              N H
  O C            O C                        helix
   H C R H C      H C R H C R
               R
     N H O C        N H
                          O C
    O C   N  H    O C      N H
        C               C
       R H            R    H

Figure 5.20
• Tertiary structure
   – Is the overall three-dimensional shape of a
       polypeptide
   – Results from interactions between amino acids
       and R groups
                                                               Hydrophobic
                                                               interactions and
                                                      CH       van der Waals
                                     CH
                                     CH22
                                               H 3C   CH3      interactions
                                      O
                          Hyrdogen    H        H 3C   CH3           Polypeptide
                          bond        O             CH               backbone
                                HO C
                                     CH2        CH2 S S CH2
                                              Disulfide bridge
                                                      O
                                            CH2 NH3+-O C CH2
                                              Ionic bond
• Quaternary structure
  – Results when two or more polypeptide chains
    combine.


                                   Polypeptide
                                   chain




                               Collagen
                                Chains




                                          Iron
                                          Heme
                               Chains
                             Hemoglobin
            Protein Structure
• http://www.stolaf.edu/people/giannini/

• http://www.stolaf.edu/people/giannini/flasha
  nimat/proteins/protein%20structure.swf
•Denaturation is when a protein unravels
and loses its native conformation
(shape)                     Denaturation




           Normal protein                  Denatured protein


    Figure 5.22             Renaturation
                  Nucleic Acids
• Made of nucleotide
  monomers
• Two Types: DNA & RNA
  – Differences in structure
                     ATP
• A nucleotide of ribose and adenine
• 5-C sugar and 3 phosphates
• High energy (bonds)

				
DOCUMENT INFO
Shared By:
Categories:
Tags:
Stats:
views:2
posted:11/11/2011
language:English
pages:32