CEM1000W Recap Notes
CHEMICAL MAKEUP OF ORGANISM
• CHON = 99% of living organisms
o Smallest atoms that can attatin stable e- configurations by sharing 1,2,3,4 e-
respectively
BIO ELEMENTS
• Carbon = versatile bonder
o Forms stable bonds with H,O,N
o Forms CO2
§ Water soluble + stable gas à can circulate carbon between organisms
• Carbon that is exhaled/excreted can be circulated to plamts to be
used in the form of CO2
• Oxygen = water soluble + readily available
o Not extremely water soluble
o Avid electron acceptor
§ Transfer of e- from other molecules to O2 energy (aerobic respiration)
• Phosphorous + Sulfur
o Bonds formed are unstable in H2O
§ Able to release a lot of energy when bonds break
o Molecules containing P and S = energy carriers
o Molecules converted into Coenzyme A form/phosphorylated = more reactive due to
instability of bonds that are easy to break
MONOTOMIC IONS (eg. Na+, K+, Ca2+, Mg2+)
• Maintenance of osmotic balance
• Formation of ionic gradients
• Neutralization of negative charge on macromolecules
• Trace elements = selected for electronic properties
o Fe + Cu form two types of stable ions (2+ à ferrous, cuprous and 3+ àferric and
cupric)
o Fe2+ ions = present in active sites of cytochrome proteins for e- transfer
COVALENT BONDS
• Formed when atoms share electrons
• Covalent bond = sharing of a pair of electrons between two atoms
• Can have polarity = uneven sharing of the pair of e- in the covalent bond
• Non polar = equal sharing
• Polar = unequal sharing
ELECTRONEGATIVITY + BOND POLARITY
• Electronegativity = tendency of an atom to attract e- towards itself
• Difference in electronegativity causes bond polarity à influences chemical reactivity
The structure of water. Two lobes of negative charge formed
by the lone-pair electrons of the oxygen atom lie above and
below the plane of the diagram. This electron density
contributes substantially to the large dipole moment and
polarizability of the water molecule. The dipole moment of
water corresponds to the O—H bonds having 33% ionic
character. Note that the H—O—H angle is 104.3°, not 109°
(the angular value found in molecules with tetrahedral
symmetry, such as CH ). Many of the important properties
4
of water derive from this angular value, such as the
.
decreased density of its crystalline state, ice
, • Hydrogen bonds between water molecules lead to à
o High specific heat
o High surface tension
o Water = universal solvent for many polar molecules
• Electric dipole moment = measure of the separation of positive and negative electrical
charges within a system
• Bond dipole moment = measures the polarity of a bond within a molecule
• Bond energies (amount of energy required to break a chemical bond) of covalently bonded
molecules > non covalently bonded molecules
IONIC BONDS
• Result from electrostatic attractions between two ionized groups of opposite charge
o Eg. COO- and NH3+ groups in proteins à salt bridge
DIPOLE DIPOLE INTERACTIONS
• Hydrogen bonds result from à electrostatic attraction between an electronegative atom (O,
N or F) and a hydrogen atom covalently bonded
NONCOVALENT BONDS
• Van der waals interactions = short range attractive/repulsive forces between chemical
groups in contact
o Weaker than ionic and hydrogen bonds
o Contribute significantly to molecule stability
o Caused by slight charge displacements or momentary dipoles which affect e- distrib.
• Hydrophobic attractions = non polar groups (eg. Hydrocarbon chains) to associate with each
other in aqueous solution
o Primarily responsible for stability of protein molecules + membranes
Biological recognition à results from a 3D structure that allows multiple weak forces between
molecules
• Mediated + governed by weak chemical forces
Biological function à based on structural complementarity + weak chemical interactions between
interacting molecules
Weak forces à restrict organisms to a narrow range of environmental conditions (temp, pH)
à extremes disrupt the forces that are essential to maintaining the structures of macromolecules
NB!! Hydrogen bonds + electrostatic attractions =
associated with interaction of biological molecules
SOLVENT PROPERTIES OF H2O
• Ions = hydrated in water have a
HYDRATION SHELL
• Water forms H-bonds with polar solutes
o H2O molecules orientate so that
the electrical charge on the ion is
sequestered by the water dipole
CHEMICAL MAKEUP OF ORGANISM
• CHON = 99% of living organisms
o Smallest atoms that can attatin stable e- configurations by sharing 1,2,3,4 e-
respectively
BIO ELEMENTS
• Carbon = versatile bonder
o Forms stable bonds with H,O,N
o Forms CO2
§ Water soluble + stable gas à can circulate carbon between organisms
• Carbon that is exhaled/excreted can be circulated to plamts to be
used in the form of CO2
• Oxygen = water soluble + readily available
o Not extremely water soluble
o Avid electron acceptor
§ Transfer of e- from other molecules to O2 energy (aerobic respiration)
• Phosphorous + Sulfur
o Bonds formed are unstable in H2O
§ Able to release a lot of energy when bonds break
o Molecules containing P and S = energy carriers
o Molecules converted into Coenzyme A form/phosphorylated = more reactive due to
instability of bonds that are easy to break
MONOTOMIC IONS (eg. Na+, K+, Ca2+, Mg2+)
• Maintenance of osmotic balance
• Formation of ionic gradients
• Neutralization of negative charge on macromolecules
• Trace elements = selected for electronic properties
o Fe + Cu form two types of stable ions (2+ à ferrous, cuprous and 3+ àferric and
cupric)
o Fe2+ ions = present in active sites of cytochrome proteins for e- transfer
COVALENT BONDS
• Formed when atoms share electrons
• Covalent bond = sharing of a pair of electrons between two atoms
• Can have polarity = uneven sharing of the pair of e- in the covalent bond
• Non polar = equal sharing
• Polar = unequal sharing
ELECTRONEGATIVITY + BOND POLARITY
• Electronegativity = tendency of an atom to attract e- towards itself
• Difference in electronegativity causes bond polarity à influences chemical reactivity
The structure of water. Two lobes of negative charge formed
by the lone-pair electrons of the oxygen atom lie above and
below the plane of the diagram. This electron density
contributes substantially to the large dipole moment and
polarizability of the water molecule. The dipole moment of
water corresponds to the O—H bonds having 33% ionic
character. Note that the H—O—H angle is 104.3°, not 109°
(the angular value found in molecules with tetrahedral
symmetry, such as CH ). Many of the important properties
4
of water derive from this angular value, such as the
.
decreased density of its crystalline state, ice
, • Hydrogen bonds between water molecules lead to à
o High specific heat
o High surface tension
o Water = universal solvent for many polar molecules
• Electric dipole moment = measure of the separation of positive and negative electrical
charges within a system
• Bond dipole moment = measures the polarity of a bond within a molecule
• Bond energies (amount of energy required to break a chemical bond) of covalently bonded
molecules > non covalently bonded molecules
IONIC BONDS
• Result from electrostatic attractions between two ionized groups of opposite charge
o Eg. COO- and NH3+ groups in proteins à salt bridge
DIPOLE DIPOLE INTERACTIONS
• Hydrogen bonds result from à electrostatic attraction between an electronegative atom (O,
N or F) and a hydrogen atom covalently bonded
NONCOVALENT BONDS
• Van der waals interactions = short range attractive/repulsive forces between chemical
groups in contact
o Weaker than ionic and hydrogen bonds
o Contribute significantly to molecule stability
o Caused by slight charge displacements or momentary dipoles which affect e- distrib.
• Hydrophobic attractions = non polar groups (eg. Hydrocarbon chains) to associate with each
other in aqueous solution
o Primarily responsible for stability of protein molecules + membranes
Biological recognition à results from a 3D structure that allows multiple weak forces between
molecules
• Mediated + governed by weak chemical forces
Biological function à based on structural complementarity + weak chemical interactions between
interacting molecules
Weak forces à restrict organisms to a narrow range of environmental conditions (temp, pH)
à extremes disrupt the forces that are essential to maintaining the structures of macromolecules
NB!! Hydrogen bonds + electrostatic attractions =
associated with interaction of biological molecules
SOLVENT PROPERTIES OF H2O
• Ions = hydrated in water have a
HYDRATION SHELL
• Water forms H-bonds with polar solutes
o H2O molecules orientate so that
the electrical charge on the ion is
sequestered by the water dipole
