the essence of life...

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the essence of life...

• biology 1

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outline

• Water the most important molecule in the
  equation of life?
• Inorganics
• Organics

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H2O

• Earth is misnamed - in fact, the earths surface
  is covered by 70 water
• Living cells are 7095 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

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• 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

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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 reactions
• Non-polar molecules tend not to dissolve in
  H2Otermed hydrophobic

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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 bead

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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

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The high heat capacity of H2O

• Hydrogen bonds require extra energy to
  breakthus, 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

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Other inorganics

• Life requires other inorganic molecules and
  elements to mediate biochemical processes
• In some cases they are reactants
• In other cases they are an defining part of an
  organic molecule
• For example, NaCl-, K, Mg, HCO3-

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Organics

• 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

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• Organic molecules are often formed of monomers
  (small, basic units) which may join together to
  form polymers (long chains of monomers).
• 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

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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
  RNAthe cell management)

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Carbohydrates

• 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 example
• Sucrose (Glucose Fructose)
• Maltose (Glucose Glucose)

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• 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 amylopectin)
• Polysaccharides are also structurally important.
  For example,
• Cellulose (D-glucose unbranched chain using b 1-4
  linkages)
• Chitin (in fact an amino sugar)

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Lipids

• 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)
• 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

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• 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
  metabolism

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• 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

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Proteins

• 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 acid
• 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 macromolecules reactivity
• Such a 3-dimensionally shaped polypeptide is
  termed a protein

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• There are only 20 common amino acids
• Proteins are defined by 4 types of structure
• 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

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• 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

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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)

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• 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

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DNA

• 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. Specifically,
• Adenine-Thymine (A-T)
• Guanine-Cytosine (G-C)
• Contains coded information to program all cell
  activity
• Makes up genes, which in turn group into
  chromosones
• Is responsible for the manufacture of mRNA

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RNA

• 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)