Module 4 - The Chemical Basis of Life

Matter – anything that takes up space and has mass

Greeks believed that matter arises from 4 basic elements: air, water, fire and earth.

Element – is a substance that cannot be broken down to other substances by chemical reactions
-    116 named and unnamed elements to date.
-    92 are naturally occurring and only 25 are known essential to life.

Atom – is the smallest unit of matter that still retains the properties of an element

Sub-atomic particles
1. Neutron – neutral charged particles
2. Proton – positively charged particles
3. Electron – negatively charged particles and form a cloud around the nucleus (proton + neutron)

Compounds – is a substance consisting of two or more different elements combined in a fixed ratio.

Molecule – two or more atoms held together by covalent bonds.

Chemical bonds – attractions that result in atoms staying close together

4 Types of chemical bonds
1. Covalent bonds
2. Ionic bonds
3. Hydrogen bonds
4. Van der Waals Interactions

COVALENT BONDS
- is the sharing of a pair of valence electrons by two atoms with comparable electronegativity
- bond in which two electrons are shared by two atoms

Valence electron – number of electrons in the outermost shell/orbital

Orbital – a region in space about the nucleus where there is a high probability of finding a given electron.

Electronegativity – attraction of an atom for the electrons of a covalent bond.
- ability of an atom to attract toward itself the electrons in a chemical bond.

Types of Covalent Bonding
1. Non-polar – electrons are shared equally.
- ex. O2, H2

2. Polar – one atom is bonded to a more electronegative atom, the electrons of the bond will not be shared equally
- ex. H2O

IONIC BOND
- two atoms are so unequal in their attraction for valence electrons that the more electronegative atom strips an electron completely from its partner
- usually formed between metals and non metals
-atoms with valence electrons = 1, 2, 3 tend to lose electrons to other atoms called CATIONS (positively charged)
- atoms with valence electrons = 5, 6, 7 tend to gain from other atoms called ANIONS (negatively charged)

HYDROGEN BOND
- forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom

VAN DER WAALS INTERACTIONS
- weak attractions between molecules or parts of molecules that are brought about by localized charged fluctuations.

Characteristics of Water
1. The polarity of water molecules results in hydrogen bonding and being a versatile solvent (Water is the solvent of life)
2. Cohesive (Organisms depend on the cohesion of water molecules)
3. High specific heat (Water moderates temperature on Earth)
4. Density (Oceans and lakes don’t freeze solid because ice floats)

TWO TYPES OF COMPOUNDS
1. Inorganic compounds
2. Organic compounds

INORGANIC COMPOUNDS
- usually do not contain carbon
- usually do not contain C-H bonds
- usually contain metal atoms
- exceptions carbon monoxide (CO¬), carbon dioxide (CO2), carbon disulfide (CS2), compounds containing the cyanide (-CN-), carbonate (-CO32-) and bicarbonate (-HCO3-) groups. i.e

4 Categories
1. Ionic Compounds
2. Molecular Compounds
3. Acids and Bases
4. Hydrates

Ionic compounds – formed due to ionic bonding
- made up of cations and anions
- usually formed by metals and nonmetals
Ex. NaCl, KBr (potassium bromide), ZnI2 (zinc iodide)

Molecular compounds – contain discrete molecular units
- usually composed of nonmetallic elements
Ex. HCl (hydrogen chloride), CO2 (carbon dioxide)

Acids – substances that yields hydrogen ions (H+) when dissolved in water
- contain one or more hydrogen atoms as well as an anionic group
Ex. HI (hydroiodic acid; I-, anion), H2SO4 (sulfuric acid; SO4-, anion)

Bases – substance that yields hydroxide ions (OH-) when dissolved in water.
Ex. NaOH (sodium hydroxide), KOH (potassium hydroxide)

Hydrates – compounds that have a specific number of water molecules attached to them.
Ex. CaSO4•2H2O (Gypsum, calcium sulfate dehydrate), MgSO4•7H2O (Epsom salt, Magnesium sulfate heptahydrate)
*the water can be driven off by heating and the resulting compound will then be called anhydrous

ORGANIC COMPOUNDS
 - contain carbon
- usually in a combination with elements such as hydrogen, oxygen, nitrogen and sulfur
- can be classified according to functional groups
- derived from a group of compounds known as hydrocarbons (made up of only hydrogen and carbon)

Functional group – group of atoms that is largely responsible for the chemical behavior of the parent molecule.

2 Main Classes of Organic Compounds
1. Aliphatic Hydrocarbon
2. Aromatic Hydrocarbon

Aliphatic hydrocarbon – do not contain the benzene group or the benzene ring
- simple hydrocarbon chains
- divided into alkanes, alkene and alkynes (cycloalkanes are a type of alkane).

Aromatic hydrocarbon – contain one or more benzene ring
- usually chemically unreactive

Benzene – colorless, flammable liquid obtained chiefly from petroleum and coal tar.
- is relatively inert (unreactive)

Alkane – only single covalent bonds are present
Ex. CH4 (methane) – natural product of the anaerobic bacterial decomposition of vegetable matter under matter; “marsh gas”

Cycloalkanes – carbon atoms are joined in rings

Alkenes – also called olefins
- contain at least one carbon-carbon double bond
Ex. C2H4 (ethylene), used in organic polymers (plastics) and in agricultural purposes.

Alkynes- contain at lease one carbon-carbon triple bond
Ex. C2H2 (ethyne or acetylene), colorless gas and with oxygen used to weld metals

Alcohols – contain the hydroxyl (-OH) groups.
Ex. CH3CH2OH (ethanol, ethyl alcohol)

Ethers – contain the R—O—R’, where R and R’ are a hydrocarbon (aliphatic or aromatic) group.
Ex. CH3OCH3 (diethyl ether), a known anesthetic

Aldehyde – has a carbonyl group (C double bonded to O) and at least has one hydrogen atom is bonded to the carbon in the carbonyl group.
Ex. H2C=O (formaldehyde), preservative for animal specimens

Ketone -  has a carbonyl group (C double bonded to O) and the carbon atom in the carbonyl group is bonded to two hydrocarbon groups
Ex. Acetone as solvent (see below)

Carboxylic Acids – acids that contain the carboxyl group, —COOH.

Ex. HCOOH (Formic Acid) exceted by ants as defense mechanism
 
Ester – R’COOR, where R’ can be H or a hydrocarbon group and R is a hydrocarbon group
- used in the manufacture of perfumes and as flavoring agents in the confectionery and soft-drink industries.

Amines – organic bases with the functional group,  –NH3
- are used mainly in the manufacture of dyes