the essence of life...
biology 1
outline
• 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
reactions
• 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
bead
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
processes
– 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-
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
– 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 OHgroup 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”)
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)
• 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)
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
– 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
• 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
– 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 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
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
• 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
DNA only
DNA and RNA
RNA only
Guanine
Adenine
Pyrimidine
Thymine
Cytosine
Uracil
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
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)