chapter 3

• 3 types of isomers:

  • structural isomers - differ in covalent partners
  • cis-trans isomers - differ in arrangement about a double bond
  • cis isomer - the 2 Xs are on the same side
  • trans isomer - the 2 Xs are on opposite sides
  • Enantiomers - differ in spatial arrangement around an asymmetric carbon (molecules that are mirror images)
  • can not be superimposed on each other

  
• main chemical groups important for living systems:

  • Hydroxyl
  • Carbonyl
  • Carboxyl
  • Amino
  • Sulfhydryl
  • Phosphate
  • Methyl
• Hydroxyl:

  • -OH
  • Hydrogen atom boded to oxygen atom bonded to carbon skeleton of the organic molecule
  • Alcohols - Ethanol

  
• Carbonyl:

  • >CO
  • Carbon atom joined oxygen atom by double bond
  • Ketones - Acetone
  • Aldehydes - Propanal

  
• Amino:

  • -NH2
  • nitrogen atom bonded to 2 hydrogen atoms and to carbon skeleton
  • Amines - Glycine

  
• Sulfhydryl:

  • -SH
  • sulfur atom bonded to hydrogen atom
  • resembles hydroxyl group in shape
  • Thiols - Cysteine (important sulfur containing amino acid)

  
• Carboxyl:

  • -COOH
  • oxygen atom double bonded to carbon atom bonded to -OH group
  • Carboxyl acid - Acetic acid

  
• 4 ways that carbon skeleton can vary:

  • vary in length
  • may have double bonds, which can vary in location
  • may be unbranched or branched
  • some are arranged rings, in the abbreviated structural formula of a compound, each corner represents a carbon and its attached hydrogen

  
• Phosphate:

  • -OPO3^2-
  • Phosphorus atom bonded to 4 oxygen atoms
  • 1 oxygen bonded to carbon skeleton
  • 2 oxygens carry negative charges
  • organic phosphate - Glycerol phosphate

  
• Methyl:

  • -CH3
  • carbon bonded to 3 hydrogen atoms
  • carbon of methyl group may be attached to a carbon or to a different atom
  • Methylated compounds - 5 methyl cytosine

  
• All living things are built of macromolecules:

  • "macro" - large
  • most macromolecules are polymers
  • lipids
  • carbohydrates
  • nucleic acid
  • proteins
• Macromolecules - dehydration reaction:

  • synthesizing a polymer
  • removes a water molecule, forming a new bond

  
• macromolecules - 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"
  • ATP reacts with H2O ---produce----> 1 inorganic phosphate + ADP + energy

  
• lipids - saturated fats:

  • At room temp, molecules of saturated fat, are packed closely together forming a solid
  • structural formula -

  
• Lipids - unsaturated fats:

  • At room temp, molecules of unsaturated fats can not pack together closely enough to solidify because of the kinks in some of their fatty acid hydrocarbon chains
  • structural formula -

  
• macromolecules - lipids:

  • formation of many macromolecules in the cell is based on reactions similar to this neutralization reaction (acid + base = salt + water)
  • their mechanism is different (dehydration = condensation)

  
• structure of phospholipids:

  • hydrophilic head
  • Hydrophobic tail
  • head consists of
  • Choline
  • Phosphate
  • tail consists of
  • Glycerol
  • fatty acids
• structure of phospholipids:

  • In water, phospholipids spontaneously form a double layer called a membrane
  • hydrophilic head
  • Hydrophobic tail
  • head consists of
  • Choline
  • Phosphate
  • tail consists of
  • Glycerol
  • fatty acids
  • a double bond between 2 of the carbon atoms in 1 of the hydrocarbon (fatty acid)tail causes a slight kink on the molecules, which results in forming space inside of the membrane

  
• composition of cell plasma membrane:

  • Hydrophilic region
  • carbohydrate side chains (sugars)
  • proteins
  • phospholipids heads
  • Hydrophobic region
  • proteins
  • Phospholipids tails

  
• TEM of a plasma membrane:

  • TEM - transmission electro microscope
  • when using electrons instead of light we get a higher resolution
  • the plasma membrane of a red blood cell appears as a pair of dark bonds separated by a light band

  
• Lipids - Steroids:

  • have skeleton of 4 interconnected carbon rings
  • usually not very water soluble
  • Cholesterol, estrogen, testosterone
  • Backbone of steroids

  
• Cholesterol:

  • the precursor of several other steroids (testosterone and estrogen)

  
• Testosterone and Estrogen:

  • differ only by the functional group attached to the same carbon skeleton
  • has a profound effect on the body and the sexuality of an animal

  
• Waxes:

  • natural wax made of - long-chain fatty acid bonds with a long-chain alcohol
  • secreted onto plant leaves and insect cuticles
  • very nonpolar and exclude water - provide a barrier to water loss
  • high melting point - solid at normal temp
  • waterproof
  • resistant to degradation
  • structural element in colonies (bee hives)
• Carbohydrates:

  • Aldoses (Aldehyde sugars)
  • Ketoses (ketone sugars)
• Aldoses (Aldehyde sugars):

  • Carbonyl group at end of carbon skeleton
  • Trioses - 3 carbon sugars (C3H6O3)
  • Glyceraldehyde - an initial breakdown product of glucose
  • Pentoses - 5 carbon sugars (C5H10O5)
  • Ribose - component of RNA
  • Hexoses - 6 carbon sugars (C6H12O6)
  • Glucose & Galactose - energy source of organisms

  
• Ketoses (Ketone sugars):

  • Carbonyl group within carbon skeleton
  • Trioses - 3 Carbon sugar (C3H6O3)
  • Dihydroxyacetone - an initial breakdown product of glucose
  • Pentoses - 5 carbon sugar (C5H10O5)
  • Ribulose - An intermediate in photosynthesis
  • Hexoses - 6 carbon sugar (C6H12O6)
  • Fructose - An energy source of organisms

  
• Monosaccharides can exist in 2 forms:

  • linear form
  • Circular (ring) form
• Dehydration reaction in the synthesis of maltose:

  • the bonding of two glucose units from maltose
  • Glycosidic linkage joins number 1 carbon of one glucose to number 4 carbon from second glucose
  • joining glucose monomers in a different way would result in a different disaccharide

  
• dehydration reaction in the synthesis or sucrose:

  • disaccharide formed from glucose and fructose
  • fructose forms a 5 sided ring

  
• carbohydrates:

  • 2 circular monosaccharide molecules can form a disaccharide
  • glucose - the major energy-reach molecule in human blood
  • the main production of photosynthesis transported by plant "blood" sap
• polysaccharides:

  • many monosaccharide molecules can form a polysaccharide
  • starch
  • glycogen
• starch:

  • a plant polysaccharide
  • in the chloroplast glucose is made and then stored and starch granules
  • 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
  • NOTE: glycogen is more branched than amylopectin starch

  
• Carbohydrates:

  • alpha and beta glucose and ring structures
  • These 2 interconvertible forms of glucose differ in the placement of the hydroxyl group attached to number 1 carbon

  
• Carbohydrates:

  • different isomer forms of glucose build polysaccharides with very different properties (starch and cellulose)
  • alpha and beta glucose ring structures
  • starch 1-4 linkage of alpha glucose monomers
  • cellulose: 1-4 linkage of beta glucose monomers
• starch:

  • 1-4 linkage of alpha glucose monomers
  • all monomers are in the same orientation
  • position of -OH differs in starch from those in cellulose

  
• Cellulose:

  • 1-4 linkage of beta glucose monomers
  • every beta glucose monomer is upside down with respect to its neighbors

  
• Cellulose microfibrils in a plant cell wall:

  • Microfibril
  • about 80 cellulose molecules associate to form a microfibril
  • main architectural unit of the plant cell wall
  • Cellulose molecules
  • is an unbranched glucose polymer
  • glucose monomer
  • parallel cellulose molecules are help together by hydrogen bond between hydroxyl groups attached to carbon atoms 3 and 6