CHEMICALS OF LIFE

 

  1. Chemicals of life - Introduction
    1. Primary atoms :CHNOPS
      1. Carbon is the basis of living chemistry. We say life is 'carbon based'.
      2. Carbon chemistry is called organic chemistry.
      3. One reason carbon is so important is because it forms four covalent bonds which allows for a wide variety of structural possibilities.
      4. One must examine any carbon organic compound in its 3-dimensional structure to identify and distinguish its structure. The structure can be changed by simply switching any two of the groups (stereoisomers) without even changing the overall makeup. (This is only true if each of the four bounds contains something different than each of the other three bonds.)
    2. Primary molecules :
      1. water
      2. ions (H+ OH- Na+ Cl - Mg++ Ca++ PO4-3 )
      3. carbohydrates (monosaccharides-------> polysaccharides)
        1. a polymer is a large molecule made up of many monomer units. In the case of carbohydrates the monosaccharide is the monomer and the polysaccharide is the polymer made up of many monosaccharides.
      4. lipids (usually fatty acids + glycerol------> lipids) fats, oils waxes, phospholipids, cholesterol
      5. nucleotides ------> DNA, RNA, ATP, NAD, cAMP
      6. amino acids -------> polypeptides (proteins)
      7. small molecules (vitamins, heme, etc.)
      8. mixed molecules (e.g. phospholipids, mucopolysaccharides)
  2. The three biologically important chemical bonds:
    1. Dipole-dipole bonds (including hydrogen bonds)
      1. The weakest (8-42 Kcal/mole), but most dynamic, of the three bonds.
      2. These bonds are easily affected by temperature (often breaking above 40oC), and the presence of ions (including pH).
      3. These bonds are involved in weak and strong structure:
        1. water and water solute structures (from liquids to gels).
        2. secondary and tertiary protein structure.
        3. enzyme-substrate interaction; enzyme-controller interaction.
        4. The holding of the double strands of DNA together (point out the importance of coopertivity)
        5. others (microfilaments, RNA, quaternary structure, etc.)
    2. Ionic bonds - charge interactions of ions.
      1. Not fully distinct from dipole-dipole interactions. It is a somewhat stronger bond (70 - 100 Kcal/mole) than hydrogen bonds in water.
      2. Stronger than covalent bonds as solids, but weaker when dissolved.
      3. Involved in structure and dynamic activity:
      4. Tertiary protein structure
      5. Enzyme-substrate interaction; enzyme controller interactions
      6. others.
    3. Covalent bonds - sharing of electrons
      1. The strongest of the three bonds.
        1. The C bond has energy of roughly 80 KCal/mole (C-H:99, C-O:84, C-N:70)
          1. a calorie is the heat it takes to raise the temperature of 1 gram of water 1°C.
        2. Interestingly, the so called high energy covalent bond used in ATP is only 7 Kcal/mole.
      2. Used in structure to hold all atoms together in forming biological molecules. ( The covalent bonds holding together amino acids (peptide bonds) to form proteins, and the covalent bonds holding together nucleotides to form DNA and RNA are particularly well investigated.)
      3. The forming and breaking of covalent bonds (along with oxidation-reduction reactions) involve the prime way of storing, forming, and using energy in living organisms.
        1. Every chemical reaction involves energy
        2. Most biological reactions are under the direction of special proteins called enzymes. These reactions lead to most cellular structural and energetic changes.
    4. Hydrophobic bonds (van der Waals attractions) -
      1. Hydrophobic interactions are usually simply an exclusion because charged and partially charged molecules are interacting and the uncharged guys get left out and together (like oil floating on water).
      2. Van der Waals force is a real attraction (but very weak) and only comes into play when two molecules come very close to each other.
  3. Carbohydrates - approximately : Cn(H2O)n Carbon, hydrogen, and oxygen occur APPROXIMATELY in the ratio of 1:2:1.
    1. Energy
      1. Examples : glucose, fructose, sucrose, glycogen, starch, a variety of sugar+other molecule combinations (e.g. glycoproteins and deoxyribonucleic acid), etc.
      2. Energy function - Useful "biological energy" is stored in the C-H and C-C covalent bonds.

      C6H12O6 + 6 O2 --->--->---> 6 H2O + 6 CO2 + energy (686 Kcal/mole)

    2. Structural function - example: cellulose cell wall in plants, chitin in crustaceans and some insects.
    3. Monosaccharides n=6 (or 5), disaccharides (two monosaccharides covalently bonded together), polysaccharides n=large

    The backbone of a monosaccharide is primarily carbon with several branching hydroxyl groups and a single ketone or aldehyde group in its linear form or an ether group in its ring form.
  4. Lipids - little oxygen; many hydrocarbon groups ( -CH2, -CH3) (usually made up of fatty acids)
    1. Long term energy storage
      1. Energy is again stored in the C-H and C-C bonds.
      2. For a given weight of lipid compared to a given weight of sugar, there is much more energy in the lipid molecule(because there is in fact a higher proportion of C-H and C-C bonds)
    2. Membrane structure (phospholipids)
      1. Usually two hydrophobic (water hating) fatty acid chains attached to a hydrophilic (water loving) head.
      2. Show example transparency
      3. Unsaturated fatty acids have carbon-carbon double bonds (-C=C-) which make them more liquid (lower melting-freezing point).
  5. Nucleotides (C,O,H,N,P)

    1. purine (double ring):

      AMP adenine

      GMP guanine

      pyrimidine (single ring):

      CMP cytosine

      TMP thymine and UMP uracil

      (show transparencies)
    2. Energy related nucleotides (ATP, GTP,FAD,NAD etc.)(show transparencies of structures)

      3. ATP + H2O ----> ADP + H3PO4 + energy (7Kcal/mole)

      The energy is in the covalent bond of the third phosphate.

    3. Control related nucleotides (cyclic AMP, cyclic GMP, etc.) (show comparative transparencies)
      1. Important in controlling internal cellular functions (they have often been referred to as second messengers since they often relay a signal to internal cellular components that a hormone has arrived on the outside of the cell).
      2. The mechanism of action is unknown. In some cases they are known to act by:
        1. turning on or off genes on DNA
        2. activating or deactivating enzymes.
    4. Genetics - make up DNA and RNA
      1. Basic structure DNA (deoxyribose sugar) RNA (ribose sugar)
      2. Basic functions -central dogma involves the two steps of transcription and translation.
        3.

      3. Double helix structure of DNA; role of hydrogen bonding to hold the strands together.

    A-C-A-G-T-A-G-C-T-

    T-G-T-C-A-T-C-G-A-
  6. Proteins - compose more than 1/2 the dry weight of cells. See next lecture for details