Chapter 2
Chemistry Comes Alive

Introduction
Matter
Chemical elements
 Chemical symbols – C, H, O, N, Ca, Na, K, Cl, Fe, He
 Trace elements- present in tiny amounts- Cr, Co
Cu, Zn
 96% body mass –
C, H, O, N

Structure of Atoms
All chemical elements are made of atoms.
Atoms contain:

 Nucleus: protons (p+) & neutrons (no)
 Electrons (e-) surround the nucleus as a cloud Electrons
Electrons are very small and light
Revolve around the atomic nucleus in orbits or shells
Negatively charged
# of protons = # of electrons
Atoms – electrically neutral

Protons & Neutrons
Protons and neutrons - nucleus of an atom
Neutrons - neutral
Protons - positively-charged particles
Atomic Number = # of protons in nucleus
Mass number (atomic weight) = p + n
Representative atoms: 2311Na,
35

17

Cl, 126C, 11H, 147N, 42He, 168O, 3919K

Isotopes

Isotopes - have same number of protons (or atomic number) i.e. carbon-12 vs. carbon-14
Radioisotopes – unstable isotopes used in research & medicine

Proton
Neutron
Electron

Hydrogen (1H)
(1p+; 0n0; 1e–)

Deuterium (2H)
(1p+; 1n0; 1e–)

Tritium (3H)
(1p+; 2n0; 1e–)

Structure of Atoms

Electron filling rules – 1st shell = 2 e; 2nd shell = 8e; 3rd shell = 18e; 4th shell = 32e
Valence shell/electrons – outermost shell/electrons (determine bond formation)
Full outermost shells = inert atoms (cannot form bonds)
Incomplete shells = reactive atoms (can form bonds) octet rule (rule of eights)
Complete HW- Draw atomic structure of representative atoms in slide #5
Helium (42He)

Ions, Molecules, & Compounds
Ions - atoms that have given up or gained an electron
 Written with its chemical symbol and (+) or (–)

Molecules are formed when atoms share electrons.
 Written as a molecular formula -H2O, O2, CO2, NaCl etc
 What molecule is C6H12O6?
 What molecule is NaHCO3?

Chemical
Bonds:
Ionic
Bond
Ionic bonds- form when an atom loses or gains (transfers) a valence electron.
Ions are formed; Positively and negatively charged ions attract one another.
 Cations are positively charged ions – Na+ , K+ Ca++
 Anions are negatively charged ions – Cl Ionic compounds dissociate - Electrolytes

Chemical Bonds: Covalent bonds
Covalent bonds - formed by sharing electrons.
 Strongest chemical bonds.
 Single, double, or triple covalent bonds are formed by sharing one, two, or three pairs of electrons, respectively.

Chemical Bonds: Covalent bonds
Covalent bonds may be nonpolar or polar.
 Nonpolar covalent bond - atoms share the electrons equally

 Polar covalent bonds - formed by unequal

sharing of electrons between atoms
+

+
+

+

Chemical Bonds: Hydrogen bonds
See movie posted in Angel on Hydrogen bonds
Hydrogen bonds are weak interactions
Intramolecular (covalent) versus Intermolecular bonds (hydrogen bonds)
Hold distant parts of a very large molecule (like proteins) together
Water surface tension

Chemical Reactions
Recall from Ch 1- What is Metabolism? Catabolism? Anabolism?
Review terms – Reactants (substrate), Products
Types of chemical reactions – Synthesis (anabolic), Decomposition (catabolic),
Exchange

An exergonic reaction is catabolic and releases energy
An endergonic reaction is anabolic and absorbs/requires energy

Chemical Reactions: Enzymes

Enzymes- Proteins that serve as biological catalysts
Increase speed of a chemical reaction
Lower activation energy (Activation Energy - energy required to break chemical bonds in the reactant molecules to start a reaction)
See animation: How enzymes work
Specific to a chemical reaction
Unchanged at the end of the reaction
Can be reused several times
Enzyme name typically end in –ase, (Urease, Lactase, Phosphorylase, Oxidase)
Holoenzyme = Apoenzyme (protein) + Cofactor (metal ion)/ Coenzyme
(vitamins)
Define - Active site
WITHOUT ENZYME

WITH ENZYME

Less activation energy required

Energy

Energy

Activation energy required

Reactants

Reactants

Product

Progress of reaction

Progress of reaction

Energy is Water is absorbed; released. bond is