Chapter 2
Chemical Principles
part A
LIFE in term of biology
• Life fundamental feature:
– Growth - through metabolism (catabolism and anabolism) - the
set of chemical reactions that occur in living organisms in order
to maintain life
– Reproduction - process by which organisms generate new
individuals of the same kind - heritable genetic information (the
molecular basis for genes is deoxyribonucleic acid (DNA))
• Biochemistry - biological chemistry, is the study of chemical
processes within, and relating to, living organisms
• Chemistry is the study of interactions between atoms and
molecules.
Chemistry
• The atom is the smallest unit of matter that enters into
chemical reactions.
• Atoms interact to form molecules.
The Structure of Atoms
Atoms are composed of:
• Nucleus:
– Protons:
• positively charged particles,
• have a mass about 1.6726×10−27 kg
– Neutrons:
• no charge particles,
• have a mass slightly larger than that of a proton
• Electrons:
• negatively charged particles, mass is approximately 1 / 1836 of that of the
proton
• Electrons are arranged in electron shells corresponding to different
energy levels
• Number of electrons = Number of protons
Electronic Configurations
• Protons and neutrons are in the nucleus
• Electrons move around the nucleus
• Electrons are organized into shells around the nucleus (regions corresponding
to different energy levels)
• The number of missing or extra electrons in outermost shell is the valence.
• Atoms combine to complete the shell.
Table 2.2.1
How Atoms Form Molecules? Chemical Bonds
• Chemical bond - the forces holding atoms in molecules ( the
attraction between atoms)
• A molecule – any two or more atoms held together
O2
H2
• A compound - at least two different kinds of atoms chemically
bonded.
H2O
Bond strength = Bond energy
Types of chemical bonds
• 1. Covalent Bonds
• Covalent bonds form when two atoms share one or more pairs
of electrons.
Carbon atom
Hydrogen atoms
Methane molecule
Figre 2.3a
2. Ionic Bonds
• The number of protons and electrons is equal in an atom.
• Ions are atoms that have gained or lost electrons and are charged.
• Ionic bonds are attractions between ions of opposite charge.
Loss of
electron
Sodium atom
(electron donor)
Sodium ion
(Na+)
Chlorine atom
(electron acceptor)
Chloride ion
(Cl–)
3. Hydrogen Bonds
• Hydrogen bonds
– a weak bond between two molecules (intermolecularly), or within
different parts of a single molecule (intramolecularly)
– resulting from an electrostatic attraction between molecules
– form when a hydrogen atom (H) that is covalently bonded to an O, N, or F
atom is attracted to another N, O or F atom in another molecule
• Weaker than covalent or ionic bonds
Figure 2.4
Chemical Elements
• A chemical element is a type of atom that is distinguished by its
atomic number;
• Atomic number that is the number of protons in its nucleus.
• Atomic mass - the total number of protons and neutrons
(atomic weight)
• Isotopes of an element are atoms with different numbers of
neutrons. Isotopes of oxygen are:
O
8
17
O
8
18
8
16
O
Molecular Weight and Moles
• The sum of the atomic weights in a molecule is the
molecular weight.
• One mole of a substance is its molecular weight in
grams.
H2O
2H
=21
=2
O
= 16
MW
= 18
1 mole weighs 18 g
Chemical Reactions
• Chemical reactions involve the making or breaking of bonds
between atoms.
• A change in chemical energy occurs during a chemical reaction.
– Endergonic reactions absorb energy.
• Synthesis reaction (making bonds)
– Exergonic reactions release energy.
• Decomposition Reactions (breaking bonds)
1. Synthesis Reactions
• Occur when atoms, ions, or molecules combine to form new,
larger molecules
A
Atom, ion,
or molecule A
+
B
Atom, ion,
or molecule B
+ Energy

AB
New molecule
AB
• Anabolism is the synthesis of molecules in a cell – use of energy
2. Decomposition Reactions
• Occur when a molecule is split into smaller molecules, ions, or
atoms.
Breaks
down into
AB
New molecule
AB

A
Atom, ion,
or molecule A
+
B
+ Energy
Atom, ion,
or molecule B
• Catabolism is the decomposition reactions in a cell – release
energy.
3. Exchange Reactions
• Are part synthesis and part decomposition.
NaOH +
HCl  NaCl
+ H2O
4. Reversible Reactions
• Can readily go in either direction.
• Each direction may need special conditions.
Heat
A
+ B
 AB

Water
Table 2.1
Important Biological Molecules
1. Inorganic compounds typically lack carbon and Carbon-Hydrogen
connected.
Carbonic-acid H2CO3
(inorganic)
2. Organic compounds always contain Carbon-Hydrogen connected.
Methane
(organic)
CH4
Inorganic Compounds: Water
• It can be quite correctly argued that life exists on Earth because of
the abundant liquid water
1. Polar molecule
2. Temperature buffer
• Formation of a hydrogen bond between the hydrogen side of one water
molecule and the oxygen side of another water molecule
• Hydrogen bonds absorb heat
• Hydrogen bonding between water molecules makes water a
temperature buffer.
3. Water is Universal Solvent
• A solvent is a liquid or gas that dissolves a solid, liquid, or gaseous
solute, resulting in a solution.
• Water is a good solvent due to its polarity
– Polar substances will mix well and dissolve in water (e.g. salts)
• they are known as hydrophilic ("water-loving") substances,
– Non-polar substances do not mix well with water (e.g. fats and oils),
• are known as hydrophobic ("water-fearing") substances
Figure 2.5
Inorganic Compounds: Acids, Bases, and Salts
• An acid is a substance that dissociates into one or more H+.
HCl  H+ + Cl
• A base is a substance that dissociates into one or more OH.
NaOH  Na+ + OH• A salt is a substance that dissociates into cations and anions,
neither of which is H+ or OH.
NaCl  Na+ + Cl
Figure 2.6a
Acid-Base Balance
• Dissociation
– NaOH  Na+ + OH
– HCl  H+ + Cl
– NaCl  Na+ + Cl
• pH - The concentration of H+ ( [H+] ) in a solution
– Increasing [H+], increases acidity.
– Increasing [OH] increases alkalinity.
– pH = log[H+]
• Most organisms grow best between pH 6.5 and 8.5.
Carbon and Organic Compounds
• Carbon atom
• Carbon can make covalent bonds with another carbon atom
and form long carbon chains and rings.
Organic compounds
• Organic compounds always contain carbon (C) - hydrogen (H)
connected together.
• Carbon has four electrons in outer shell, and can bond with up to four
other atoms (usually H, O, N, or another C).
• Since carbon can make covalent bonds with another carbon atom,
carbon chains and rings that serve as the backbones of organic
molecules are possible.
Organic Compounds
• The chain of carbon
atoms in an organic
molecule is the carbon
skeleton.
H
Methane
H–C–H
H
H
H
Ethane
H–C–C-H
H
H
H
H
H
Propane
H–C–C–C–H
H
H
H
Organic Compounds - Functional groups
Specific groups of atoms within molecules that
are responsible for the chemical properties of
those molecules.
• The same functional group will undergo the same or
similar chemical reaction(s) regardless of the size of
the molecule it is a part of.
• However, its relative reactivity can be modified by
nearby functional groups
Alcohols
Acids
Formic acid
Acetic acid
Propanoic acid
Propionic acid
R
Functional
Group
Learning objectives
• Describe the structure of an atom and its relation
to the chemical properties of elements.
• Define ionic bond, covalent bond, hydrogen bond,
molecular weights, and mole.
• Diagram three basic types of chemical reactions.
• List several properties of water that are important
to living systems.
• Define acid, base, salt, and pH.
• Distinguish between organic and inorganic
compounds.
• Distinguish between alcohol, carboxyl, amino,
methyl, phosphate and sulfhydryl functional
groups.