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CHEM1907/8

Lecture 1. Introduction to Chemistry in Life Science

Lecture Notes (10/03/03)

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).

the interactions between molecules (Intermolecular Forces).

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

Silberberg (3 Edn; Chapter 1; Section 1.1)


Chemistry is the study of matter and its properties, the changes that matter undergoes, and the energy associated with
those changes (pg 3).
A physical change occurs when a substance alters its physical form, not its composition.
A chemical change occurs when a substance is converted (via a chemical reaction) to a different substance.
Define the three states of matter: solid, liquid and gas (Figure 1.2; pg 4).
Solid.
Has a fixed shape that does not conform to the shape of the vessel in which it is contained.
Liquid.
Conforms to the shape of the container; defined volume with a surface.
Gas.
Conforms to the shape of the container, but fills the container and does not have a surface.
Define the three types of matter: elements (as atoms or molecules), compounds and mixtures (Figure 2.1; pg 42).
Element.
The simplest type of matter with unique chemical and physical properties; consists of only one type of
atom. An element may exist as single atoms (e.g., silicon) or as a molecule (e.g., diatomic oxygen), where
a molecule is an independent unit consisting of two or more atoms that are chemically bound together.
Compound. Matter composed of two or more different elements that are chemically bound together (e.g., water). The
properties of a compound differ to the properties of the isolated elements comprising the compound.
Mixture.
The intermingling of two or more substances (elements and/or compounds).

Atoms of an element

Molecules of an element

Molecules of a compound

Mixture of two elements


and one compound

Scientific Units (Table 1.2; pg 17).


Decimal Prefixes (Table 1.3; pg 18).
Prefix
Symbol
Number
Word
Prefix
Symbol
Number
Word
9
2
Hundredth
giga
G
10
Billion
centi
c
10
6
Thousandth
mega
M
10
Million
milli
m
103
3
6
Millionth
kilo
k
10
Thousand
micro

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

Names of Common Polyatomic Ions


Name
Formula
Name

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

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