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Rachel Codd (Wks 1-4): Room 412C, School of Chemistry (phone: X14233; e-mail: r.codd@chem.usyd.edu.au)
Chemists with a Life Science focus study the molecular nature of matter and change in order to better understand
processes associated with human health (e.g., mechanisms of disease and the design of appropriate medical treatments),
agriculture (e.g., the design of improved fertilizers) and the environment (e.g., the use of bacteria with unusual
metabolisms in biomining; green chemistry). An understanding of chemistry is fundamental to understanding theoretical
and practical aspects of Molecular Biology and Genetics, Medical Science and Molecular Biotechnology. The
development of the flu drug, Relenza, for example (which took place over two decades), was based upon an intimate
understanding of the nature of the flu virus itself, how it worked (PDB Code: 2BAT; the flu virus complexed with its natural
substrate) and the use of some clever chemistry to make the invading virus much less efficient at its job (PDB Code:
1NNC; the flu virus complexed with its natural inhibitor).
To achieve a level of understanding of Chemistry in the Life Sciences, we need to consider the following:
the language of chemistry (Nomenclature; from the Latin, nomenclator, a slave who accompanied his master
to tell him the names of people he met).
the accountancy of chemistry (Stoichiometry; stoikheion is Greek for element, metron is Greek for
measure).
what atoms are made of (Atomic Structure) and the similarities and differences among them (Periodic Table).
how atoms are stuck together (Chemical Bonding) and what the final assembly (molecule) looks like in three
dimensional space (The Shapes of Molecules).
we need also to consider the reactivity of molecules, for example, the dissociation of an acid (such as the natural
substrate for the flu virus) in water (Acids and Bases), which may be a useful model for how the molecule
behaves in the human body.
additional aspects relating to the reactivity of molecules, which enables Chemists to make things (one of the great
things about being a Chemist), will be covered later (from Week 5) this semester (Organic Chemistry).
rd
Atoms of an element
Molecules of an element
Molecules of a compound
10
1
9
Tenth
nano
n
Billionth
deci
d
10
10
9
Nanotechnology means technology defined on a 10 m (one nanometer) scale. This is the scale of Chemistry!
Nomenclature
Names of Common Ions
Charge
Formula
Name
+
1+
H
Hydrogen
+
Li
Lithium
+
Na
Sodium
+
K
Potassium
+
Cs
Cesium
+
Ag
Silver
Charge
2+
3+
3+
Formula
2+
Mg
2+
Ca
2+
Sr
2+
Ba
2+
Zn
2+
Cd
Al
Name
Magnesium
Calcium
Strontium
Barium
Zinc
Cadmium
Charge
1
Aluminium
Formula
H
F
Cl
Br
I
2
O
2
S
3
N
Name
Hydride
Fluoride
Chloride
Bromide
Iodide
Oxide
Sulfide
Nitride
the word ion is added to the name of the metal; ie Li is the lithium ion or the lithium cation
Acetate
Hydrogen Carbonate
CH3COO
Cyanide
CN
Chromate
Hydroxide
OH
Dichromate
Hypochlorite
ClO
Peroxide
Chlorite
ClO2
Nitrite
Chlorate
ClO3
Nitrate
Perchlorate
ClO4
Permanganate
Carbonate
Definitions
Melting Point.
Boiling Point.
Vapour Pressure:
Equilibrium:
Density:
Solubility:
Solute:
Formula
HCO3
CrO42
Cr2O72
O22
NO2
NO3
MnO4
CO32
Name
Phosphate
Formula
PO43
Hydrogen Phosphate
HPO42
Dihydrogen Phosphate
H2PO4
Sulfite
SO32
Sulfate
SO42
Hydrogen Sulfate
HSO4
Ammonium
NH4
Hydronium
H3O
+
+
The temperature at which the solid and liquid forms of a substance are at equilibrium.
The temperature at which the vapour pressure of a gas equals the external (atmospheric) pressure.
The pressure exerted by a vapour at equilibrium with its liquid in a closed system.
A system reaches equilibrium where the concentrations of reactants and products do not change,
since the rates of the forward and reverse reactions are equal. At equilibrium, a system remains
dynamic (changeable) at the molecular level, but there are no net changes in one direction (forward
reaction) or the other (reverse reaction).
The ratio of the mass (g) to the volume (mL or cm3) at a defined temperature and pressure.
The maximum amount of solute that dissolves in a fixed quantity of a particular solvent at a specified
temperature when excess solute is present.
The substance that dissolves in the solvent.
Additional Material
The link (www.mhhe.com/physsci/chemistry/silberberg/) takes you to the On Line Learning Centre associated with the
Silberberg text; useful on-line quizzes.
The link (http://www.rcsb.org/pdb/) takes you to the Protein Data Bank (PDB) which houses data relating to the three
dimensional shapes of proteins.
Rachel Codd