Chapter 3 Chemistry of Organic Molecules by hcj


									                          Organic    1
Chapter 3 Chemistry of   Chemistry
Organic Molecules
                                 Organic    2

Organic vs Inorganic
Functional Groups and Isomers
 Nucleic Acids
                                          Organic    3
      Organic Molecules
Inorganic – Chemistry of elements other than carbon
Organic – Carbon-based chemistry
        Inorganic                  Organic
       Usually w/              Always contain
       + & ­ ions                 C and H
         Usually                  Always
      ionic bonding           covalent bonding
       Always w/             Often quite large, w/
       few atoms                 many atoms
   Often associated w/      Usually associated w/
    nonliving matter           living systems
                          Organic    4
     Carbon Atom

Carbon atoms:
6 protons
6 electrons
Mass # = 12.011
How many neutrons?
Carbon to carbon bonds
Octane & Cyclohexane   5
                                 Organic    6
     The carbon skeleton &      Chemistry
     functional groups

Skeleton or backbone:
Functional groups:
  hydrophilic vs. hydrophobic
                                    Organic    7

Isomers - organic molecules that have:
                                             Organic    8
         4 Classes of Organic               Chemistry
         Molecules in Living Things

Some molecules called macromolecules because of
 their large size

Polymer vs. Monomer

Category        Example        Subunit(s)
Lipids          Fat            Glycerol & fatty acids
Carbohydrates Polysaccharide   Monosaccharide
Proteins        Polypeptide    Amino acid
Nucleic Acids   DNA, RNA       Nucleotide
Common Foods   9
                                         Organic    10
     Four Classes of Organics:          Chemistry
     1 - Carbohydrates

A. Monosaccharides: “simple sugar”
     Backbone of 3-7 cabons
  Glucose – C6H12O6 (Hexose)
     isoforms: fructose and galactose
  Ribose and Deoxyribose (Pentose)
     found in nucleic acids
                                       Organic    11
     Four Classes of Organics:        Chemistry
     1 - Carbohydrates

B. Disaccharides:
 Contain 2 monosccharides
   Joined by what type of reaction?
      Dehydration Reaction
 Maltose – 2 glucose molecules
 Sucrose – (Sugar) Glucose + Fructose
 Lactose – Glucose + Galactose
                                          Organic    12
     Four Classes of Organics:           Chemistry
     1 - Carbohydrates

C. Polysaccharides: polymers
   short term energy storage molecules
   helical shape

 Starch: how plants store glucose
  1) Amylose – nonbranched
  2) Amylopectin – branched
      No main C chain new chains occur every
      6th carbon
    Starch      13
Structure and
                                    Organic    14
     Four Classes of Organics:     Chemistry
     1 - Carbohydrates

C. Polysaccharides:
 Glycogen – how animals store glucose
  Stored in liver
  Glycogen      15
Structure and
                                             Organic    16
     Four Classes of Organics:              Chemistry
     1 - Carbohydrates

Structural Carbohydrates
 Cellulose: Most abundant carb and most
  abundant organic molecule on Earth
   ­ Monomer: Glucose
   ­ Humans DO NOT digest cellulose

 Chitin: fungal cell walls and exoskeletons
   ­ monomer has attached amino group
   ­ Cannot be digested by animals
   ­ has antibacterial and antiviral properties
     Used   in wound dressings and suture material
                                       Organic    17
     Four Classes of Organics:        Chemistry
     1 - Carbohydrates

Structural Carbohydrates
 Peptidoglycan – Structural molecule in bacteria
   ­ Monomer has amino acid chain
  Cellulose     18
Structure and
                                                       Organic    19
       Four Classes of Organics:                      Chemistry
       2 - Lipids
Insoluble in water

Types of Lipids

Type            Organismal Uses                 Human Uses
                Long­term energy storage &
Fats            thermal insulation in animals   Butter, lard
                Long­term energy storage in
Oils            plants and their seeds          Cooking oils
                Component of plasma
Phospholipids   membrane                        No­stick pan spray
                Component of plasma
Steroids        membrane; hormones              Medicines

Waxes           Wear resistance; retain water   Candles, polishes
Blubber   20
                                          Organic    21
     Types of Lipids:                    Chemistry
1) Fats
  a) Trigylcerides – 3 fatty acid chains with -COOH
     » ~ 16 – 18 Cabons (some shorter)
  b) Saturated fatty acids – NO DBL bonds
     »can pack tightly
  c) Unsaturated fatty acids – have DBL bonds
     »melt at lower temp
     »cannot pack tightly

 In general:
  Solid @ room temp – animal origin
  Liquid @ room temp – plant origin
Types of Lipids:   22
                                        Organic    23
     Types of Lipids:                  Chemistry

2) Phospholipids

   ­ part of the cell membrane

   ­ Contains a phosphate polar head group & 2
     nonpolar fatty acid tails

   ­ Cell membrane – phospholipid bilayer
Phospholipids Form   24
                                         Organic    25
     Types of Lipids:                   Chemistry
     Steroids & Waxes

3) Steroids – skeleton of 4 fused rings
 Cholesterol, testosterone, estrogen
4) Waxes
 Long-chain fatty acid bonded to a long-chain
   ­ High melting point; solid @ room temp
   ­ Waterproof
   ­ Resistant to degradation
Steroid Diversity   26
                                   Organic    27
     Four Classes of Organics:    Chemistry
     3 –Proteins (polypeptides)

   Support –
   Enzymes –
   Transport –
   Defense –
   Hormones –
   Motion –
                                           Organic    28
     Protein Subunits:                    Chemistry
     The Amino Acids
Amino acids (aa’s)
Shapes of proteins:
 1) primary (1o) - long chain aa's
 2) secondary (2o) - coils or folds
    examples: alpha helix, beta sheet
    H-bonding b/w every 4th amino acid = helix
 3) tertiary (3o) - 3D shape (globular proteins)
    H-bonds, ionic bonds, and covalent bonds
 4) quaternary (4o) - More than 1 polypeptide
    Hemoglobin – 4 polypeptides
          Structural Formulas for   29
              20 Amino Acids

Essential vs.
Levels of Protein   30
Examples of Fibrous   31
                                      Organic    32
     Protein Subunits:               Chemistry
     The Amino Acids

Denatured – when a protein loses its natural
Chaperone Proteins – helps new formed
 proteins fold into normal shape
    might even correct misfolding!
Protein Folding Diseases:
 Cystic Fibroses
 Alzheimers Disease
 Transmissble Spongioform Encephalopathies –
     Prions – misfolded proteins
                                   Organic    33
     Four Classes of Organics:    Chemistry
     4 -Nucleic Acids

Polymers of nucleotides
Nucleotide: sugar + phosphate grp + base
Complementary Base Pairing

DNA (deoxyribonucleic acid)

RNA (ribonucleic acid)
Nucleotide   34
DNA Structure   35
RNA Structure   36
                                                   Organic    37
        Comparison of DNA & RNA

Table 3.4
Feature    DNA                        RNA
Sugar      Deoxyribose              Ribose
           Cytosine, guanine;       Cytosine, guanine;
Bases      adenine, thymine         adenine, uracil
Strands    Pairing across strands   Mostly single stranded

Helix      Yes                      No
           Heredity; cellular control Interprets genetic info;
Function   center                     protein synthesis
           Chromosomes of cell
Where      nucleus                    Cell nucleus and cytoplasm
                                      Organic    38
     Other Nucleic Acids

ATP (adenosine triphosphate)
 composed of adenine, ribose, and three
In cells, one phosphate bond is broken –
 Energy for processes of the cell
ATP   39

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