Chapter 3

• Four ways carbon skeleton can vary:

  • Length
  • Carbon skeletons vary in length
  • Branching
  • Skeletons may be unbranched or branched
  • Double bond position
  • The skeleton may have double bonds, which can vary in location
  • Presence of rings
  • Some carbon skeletons are arranged in rings
  • In the abbreviated structural formula for each compound, each corner represents a carbon and its attached hydrogens `
• Three types of isomers:

  • Structural isomer
  • Differ in covalent partners
  • Cis-trans isomers
  • Differ in arrangement about a double bond
  • Enantiomers
  • Differ in spatial arrangement around an asymmetric carbon, resulting in molecules that are mirror images
  • Cannot be superimposed on each other
• Main chemical groups important for living systems:

  • Hydroxyl
  • -OH
  • Carbonyl
  • >CO
  • Carboxyl
  • -COOH
  • Amino
  • -NH2
  • Sulfhydryl
  • -SH
  • Phosphate
  • -OPO3^2
  • Methyl
  • -CH3
• Hydroxyl

  • -OH
  • Hydrogen atom bonded to oxygen atom which is bonded to carbon skeleton of organic molecules
  • Alcohols (their names usually end with -ol)
  • Ethanol
• Carbonyl

  • >CO
  • Carbon atom joined to oxygen atom by double bond
  • Ketones: if carbonyl group is within carbon skeleton
  • Acetone
  • Aldehydes: if carbonyl group is at the end of carbon skeleton
  • Propanal
• Carboxyl

  • -COOH
  • Oxygen atom double bonded to carbon atom that is bonded to -OH group
  • Carboxyl acids
  • Acetic acid
• Amino

  • -NH2
  • Nitrogen atom bonded to 2 hydrogen atoms and to carbon skeleton
  • Amines
  • Glycine: both amine and carboxyl acid, because compounds with  both animo group and carboxyl group are called amino acids
• Sulfhydryl

  • -SH
  • Sulfur atoms bonded to hydrogen atom
  • Thiols
  • Cysteine: important sulfur containing amino acid
• Phosphate

  • -OPO3^2-
  • Phosphate atom bonded to 4 oxygen atoms, 1 oxygen bonded to carbon skeleton, 2 oxygen carry negative charges
  • Organic phosphates
  • Glycerol phosphate
• Methyl

  • -CH3
  • Carbon bonded to  3 hydrogen atoms
  • Carbon of a methyl group may be attached to a carbon or to a different atom
  • Methylated compounds
  • 5-methyl cytosine
• All living systems are build of Macromolecules: (Macro = large)

  Most macromolecules are poly = many

  • Lipids
  • Carbohydrates
  • Nucleic acids
  • Proteins
• Dehydration reaction:

  • Synthesizing a polymer
  • Dehydration removes a water molecule, forming a new bond
• Hydrolysis:

  • Breaking down a polymer
  • Hydrolysis adds a water molecule, breaking a bond
• Adenosine triphosphate (ATP):

  • Energy storing molecule
  • Macromolecules are built with energy from ATP and similar compounds
  • ATP can be synthesized in the reverse reaction, so that the molecule is “charged”
• Lipids:

  • fatty acids
  • triacylglycerol
  • saturated fat
  • unsaturated fat
• Fatty acid

  • Glycerol
  • One of the 3 dehydration reactions in the synthesis of a fat
• Triacylglycerol

  • Fat molecules
• Saturated fat

  • At room temp the molecules are packed closely together forming a solid
• Unsaturated fat

  • At room temp the molecules cannot pack together closely enough to solidify because of the kink in some of their fatty acid chairs
• Neutralization reaction:

  • Formation of many macromolecules in the cell is based on reactions similar to this reaction
  • Acid + base = Salt + water
  • This mechanism is different
  • Dehydration = condensation
• Structure of phospholipids:

  • In water phospholipids spontaneously form a double layer called a membrane
• Steroids:

  • Have skeletons of 4 interconnected carbon rings
  • Usually not very water soluble
  • Included in lipids because they are hydrophobic and insoluble in water
  • Cholesterol
  • The precursor of several other steroids
  • Testosterone and estrogen
  • Differ by the functional group attached to the same carbon skeleton
  • Have a profound effect on the body and the sexuality of an animal
• Waxes

  • Long chained fatty acid bonds with a long chain alcohol
  • Secreted onto plant leaves and insect cuticles
  • Very nonpolar and exclude water
  • Provide barrier to water loss
  • High melting point
  • Solid at normal temp
  • Waterproof
  • Resistant to  degradation
  • Structural elements in colonies (bee hives)
• Carbohydrates composed of a single molecule are called monosaccharides (mono = single)

  • Monosaccharides can exist in 2 forms
  • Linear form
  • Circular (ring) form
  • 2 circular monosaccharide molecules can form a disaccharide
• Dehydration reaction in the synthesis of maltose

  • Bonding of 2 glucose units forms maltose
  • The glycosidic linkage joins the number 1 carbon of one glucose to the number 4 carbon of the second glucose
  • Joining the glucose monomers in a different way would result in a different disaccharide
  • Glucose: the major energy-reach molecule in human blood
• Dehydration reaction in the synthesis of sucrose

  • Sucrose is a disaccharide formed from glucose and fructose
  • Fructose forms a 5 sided ring
  • Sucrose: the main product of photosynthesis transported by plant “blood” (sap)
• Starch

  • A plant polysaccharide
  • Chloroplast is the cellular organelle where glucose is made and then stored as starch granules in plant cells
  • Two forms of starch
  • Amylose (unbranched)
  • Amylopectin (branched)
• Glycogen

  • An animal polysaccharide
  • Animal cells stockpile glycogen as dense clusters of granules within liver and muscle cells
  • Mitochondria are cellular organelles that help break down glucose released from glycogen
  • Glycogen is more branched than amylopectin starch
• Many circular monosaccharide molecules can form a polysaccharide

  • Alpha and beta glucose ring structure
  • 2 interconvertible forms of glucose differ in the placement of the hydroxyl group attached to the number 1 carbon
• Starch: 1-4 linkage of alpha glucose monomers

  • All monomers are in the same orientation
  • -OH groups placement differs in starch than cellulose
• Cellulose: 1-4 linkage of beta glucose monomers

  • Every beta glucose monomer in upside down with respect to its neighbors
• Different isomer forms a glucose build polysaccharide with very different properties (starch and cellulose)
• Polysaccharide Chitin

  • Builds cell walls of insects and fungi
  • Also used in surgery for making self dissolving threads
• Polysaccharide: (energy storage molecules)

  • Starch
  • Glycogen
  • Hormones control release and storage of glucose            
• Starch (polysaccharide)

  • Is a mixture of 2 complex carbohydrates
  • Amylose
  • Amylopectin
  • Both are polymers of glucose
  • It is used by plants as a way to store excess glucose
• Glycogen (polysaccharide)

  • Animals store glucose as glycogen (granules in liver)
  • It is a polysaccharide of glucose which functions as the primary short term energy storage in animal cells
• Hormones control release and storage of glucose            

  • Insulin: released from the pancreas promote the storage of the glucose as glycogen
  • Glucagon: hormone released from the pancreas stimulates glycogen breakdown into glucose
• Polysaccharide: (Structural molecules)

  • cellulose
  • Chitin
  • glycosaminoglycan
• Cellulose

  • Most abundant of all the carbohydrates
  • Polymer of beta glucose
  • Cell walls in plants contain cellulose
  • Parallel glucose chains -> cellulose
• Chitin

  • forms the external skeleton of many insects and the cell wall of fungi
  • the sugar monomer of chitin have nitrogen containing groups attached to them