the essence of life

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					the essence of life...
biology 1
• Water: the most important molecule in
  the equation of life?
• Inorganics
• Organics
                     H2 O
• Earth is misnamed - in fact, the earth’s
  surface is covered by 70% water
• Living cells are 70–95% water
• Life evolved in water
• Search for life on other planets can be
  simplified as a search for other planets
  containing water
• The vitally important fluid nature of water is
  due to hydrogen bonds, as a result of the
  covalent bonding between H and O2
• The polar nature of the covalent bond
  between hydrogen and oxygen is critical
  in forming the known properties of water
  – Solvency - H2O is the universal solvent
  – Cohesiveness - leads to adhesion,
    capillary action and surface tension
  – Buffer - H2O can mediate processes by
    acting as a buffer
  – Heat capacity - H2O can absorb heat,
    resisting temperature changes
          Solvency of H2O
• Polarity of water causes it to be an
  efficient solvent of ionic compounds,
  termed hydrophylic compounds
  – Most biochemical reactions involve solutes
    dissolved in water
  – Water is an essential medium for transport
    of reactants and products for biochemical
• Non-polar molecules tend not to
  dissolve in H2O—termed hydrophobic
  Cohesion of H2O molecules
• Transient hydrogen bonding causes
  water molecules to ‘stick’ together
• Allows water to ‘stick’ to a substrate
  (adhesion)—e.g., a plant vessel wall
• Cohesion results in capillary action
• Cohesion causes a surface tension at
  air/water interface, causes water to
          H2O as a buffer
• Water can protect cells from
  environments of dangerously high
  chemical concentrations
• By acting as a buffer (e.g., acid/base
  environments), water minimizes
  fluctuations in pH
 The high heat capacity of H2O
• Hydrogen bonds require extra energy to
  break—thus, H2O has an unusually high
  heat capacity
• A large body of H2O can act as a heat
  sink (reducing greenhouse effect?)
• Evaporative cooling is a major mechanism
  in keeping organisms from overheating
• The marine environment has a relatively
  stable temperature
          Other inorganics
• Life requires other inorganic molecules
  and elements to mediate biochemical
  – In some cases they are reactants
  – In other cases they are an defining part of
    an organic molecule
• For example, Na+Cl-, K+, Mg+, HCO3-
• Involve carbon, which has an outer shell
  of 4 electrons, leaving 4 free spaces
• Organic molecules are thus generally
  based on a unit shape of a triangular
  based pyramid
• Organic molecules are generally
  defined by the elements other than
  carbon in them, and by the types of
  bonds they form with carbon
– Organic molecules are often formed of
  monomers (small, basic units) which may join
  together to form polymers (long chains of
– One typical method of polymerization is by the
  condensation reaction (removal of an OH-
  group and an H+ group from two respective
  monomers to form water, leaving a bond
  between the two monomers
– Condensation reactions can be reversed via
  hydrolysis (the addition of water to a bond
  within a polymer
– Condensation and hydrolysis reaction are
  common mechanisms in metabolism
Biologically important organic molecules

 • Carbohydrates (for short term energy)
 • Lipids (for long-term energy and
   membrane structure)
 • Proteins (for membrane and other
   organelle structure
 • Nucleic acids (for the construction of
   DNA and RNA—the cell “management”)
• Monomer form is the monosaccharide (in the
  ratio of CH2O). For example,
  – 6-carbon sugar (hexose): e.g., Glucose (C6H12O6)
  – 5-carbon sugar (pentose): e.g., Ribose
• Two monosaccharides can join together to
  become a disaccharide via a condensation
  reaction that creates a glycosidic linkage. For
  – Sucrose (Glucose + Fructose)
  – Maltose (Glucose + Glucose)
• Many monomers joined together form
  the polymer polysaccharide
  – Polysaccharides are a good source of
    medium term energy. For example,
    • Starch (a helical glucose polymer with a 1-4
      linkages, either unbranched (amylose) or
      branched (amylopectin)
    • Glycogen (highly branched form of
  – Polysaccharides are also structurally
    important. For example,
    • Cellulose (D-glucose unbranched chain using b
      1-4 linkages)
    • Chitin (in fact an amino sugar)
• Typically hydrophobic compounds
• Fats are important for long term energy
  stores, and consist of 3 fatty acid chains
  joined at one end by a molecule of
  glycerol via an ester link
  – Fatty acid chains vary in length, and may
    have double bonds (unsaturated) or not
     • Saturated fats are usually solid at room temp.,
       and are found in animals
     • Unsaturated fats are usually liquid at room
       temp., and are found in plants
– Phospholipids have one of the fatty acids in a
  triglyceride replaced by a phosphate group
  • The fatty acid hydrocarbon tails are hydrophobic
  • The phosphate group (ionic) is hydrophillic
– Phospholipids thus show ambivalent behavior
  to water
– Phospholipids are a major component in the
  structure of a biological membrane
– Biological membranes can be argued to play
  perhaps the most important role in cellular
• A third group of lipids are the Steroids
  – Steroids play an important role in the
    regulation of metabolism. For example,
     • Cholestrol
• All fats have high energy bonds.
  Hydrolysis reactions thus yield high
  energy. Fats are typically broken down
  for their high energy content
– Proteins are made of monomers termed Amino
  Acids which:
   • have both an amine (NH2) and a carboxyl acid
     (COOH) group
   • A third group (given the symbol ‘R’) defines the amino
– Amino acids join together via condensation to
  form polypeptide chains (linked by peptide
  bonds). Components of these chains then
  interact to give a unique 3-dimensional
  structure, vital for the macromolecule’s reactivity
– Such a 3-dimensionally shaped polypeptide is
  termed a protein
• There are only 20 common amino acids
• Proteins are defined by 4 types of
• Primary structure refers to the sequence
  and the types of amino acids linked
  together. Polypeptide chains are
  typically very long)
• Secondary structure refers to linkages
  between carbons within the polypeptide
  backbone (b pleating, a helix coiling) by
  hydrogen bonds
• Tertiary structure refers to linkages
  between R-groups, including
  – Hydrogen bonds
  – Sulphur bridges
  – Others
• Quarternary structure refers to
  incorporation of other polypeptide
  chains. For example,
  – Hemoglobin consists of 4 polypeptide
    chains around Fe
            Nucleic Acid
• Nucleic acids store and transmit
  hereditary information
• This information ultimately is expressed
  through the production of goal-specific
  proteins, including enzymes and
  structural molecules
• There are two types of nucleic acid:
  – DNA (deoxyribonucleic acid)
  – RNA (ribonucleic acid)
• Nucleic acids are polymers, the individual unit
  (monomer) of which is the nucleotide
• Nucleotides have:
  – A “backbone”
     • A pentose sugar
        – Ribose
        – Deoxyribose
     • A Phosphate group
  – A nitrogenous base

                           Purine    Pyrimidine
       DNA only                      Thymine
       DNA and RNA         Guanine   Cytosine
       RNA only                      Uracil
• Is a double stranded helix (model first proposed by
  Watson and Crick). Deoxyribose lacks an OH
  group on the 2nd carbon
  – Nitrogenous bases always pair purine to pyrimidine.
     • Adenine-Thymine (A-T)
     • Guanine-Cytosine (G-C)
• Contains coded information to program all cell
• Makes up genes, which in turn group into
• Is responsible for the manufacture of mRNA
• Is a single stranded nucleic acid that is the
  intermediate agent in production of proteins
• Components of RNA are similar to that of DNA,
  except uracil (U) is substituted for thymine (T)
• There are several kinds of RNA, including
   – Messenger mRNA
   – Transfer tRNA
   – Ribosomal rRNA

• Other uses for nucleotides include chemical transfer
  agents (ATP) and electron transfer agents (NAD)

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