CHEMICAL BASIS OF ORGANIZATION I

Matter – Anything that takes up space and has mass

Mass is not equal to weight

Mass – Amount of matter in a given object (Does not vary with position)

Weight – Force with which the object is pulled by gravity (Varies with positions)
 Essential Elements

There are 25 elements are essential for life:

 96% of all living matter (main elements of the human body)

 Carbon (C), Oxygen (O), Hydrogen (H) and Nitrogen (N)
Eg: Carbohydrates, lipids, proteins and nucleic acids

 Remaining 4 %
-Ca, P, K, S, Na, Cl, Mg
-Trace elements (B, Cr, Co, Cu, F, I, Fe, Mn, Mo, Se, Si, Sn, V and Zn)
 ATOMS
-Smallest representative sample of an element with physical and chemical properties
-Different atom types, different properties
(Eg: mass of O is 16 x greater than that of H)
-Atomic structure determines element behaviour

Consist of three subatomic particles:

Subatomic particle Charge Mass (g) Location

 Neuron 0 1.6749286 X 10^-24 Nucleus
 Proton +1 1.6726231 x 10^-24 Nucleus
 Electron -1 9.10993897 x 10^-28 Orbits
 ATOMS
(smallest amount of an element)

 Atomic number (Z)

-The number of protons of a particular atom
-Defines a specific type of atom
(Different atoms, different number of protons)

 Mass number (A)

-Number of protons and neutrons of a particular atom
(can determine the number of neutrons)
-In atomic mass unit (amu)

 Isotopes
-Same number of protons but different number of neutrons
-Have same atomic number but different mass number

 Atomic mass
-The average (mean) mass In amu of the atoms of isotopes of a particular elements that
occurs naturally and stable
 VALENCE ELECTRONS
-Electrons is outermost shell
-Determine the chemical properties of atoms
-Participate in chemical bonds formation
 Octet rule
-An atom tends to gain or lose electrons until its valence (outer) shell has eight
electrons- chemical bonds
-Complete valence shell = Inert or unreactive or stable
 MOLECULES
(Two or more atoms chemically joined)
-Two or more atoms held together by chemical bonds
-Specific ratios to one another:
eg: H2O (2:1) vs H2O2 (2:2)

Molecular elements Molecular compounds

-Composed of two or more atoms of the -Composed of two or more atoms of
same type different types

IONS
(Charged atoms or molecules)
-Atoms or molecules that are electrically charged
-Two types

Cations Anions
-Positive charge (e.g. Na+, Ca2+, NH4+) -Negative charge (e.g. Cl-, O2-, PO43-)
-Removal of one or more electrons -Addition of one or more electrons

Compounds-Two or more atoms different elements chemically joined

 CAUTIONS IN THE BODY

Ions Roles
Ca2+ -Most abundant ions in the body (1.5% of
the total body weight)
-Found in bones and teeth
-Combine with phosphate ions to form
calcium phosphate (increase rigidity and
hardness of bones and teeth)
-Blood clotting, normal muscle contraction
and nerve activity
Na+ -Extracellular fluids
-Transport of water through cells by
osmosis
-Buffer system
K+ -Intracellular fluids
-Transmission of nerve impulses
-Muscle contraction
Mg2+ -Normal functioning of muscle and nerve
tissues
-Bone formation
-Muscle contraction
Cl- -Acid-base balance in food
-Water balance
-Hydrochloric acid in the stomach
-Intracellular and extracellular fluid
PO43- -Formation of bones and teeth
-Buffer in blood
-Muscle contraction and nerve impulses
-Component of coenzymes
-Transfer and storage of energy in ATP
-Components of nucleotides (DNA and
RNA)
 FREE RADICALS
-Atoms, molecules or ions that have one or more unpaired electrons
-Either donate or accept electrons (Reductants or oxidants)
-Unstable and highly reactive (causing chain reaction)

FORMATION OF FREE RADICALS

 UV light
 Ionizing radiation (radiation)
 Smoking
 Air pollution
 Inflammation (White blood cell)
 Metabolism (Mitochondrion)
 LEVEL OF ORGANISATION

Atom > molecule > macromolecule > Organelle > Cell > Tissue > Organ > Organ system > Organism
 CHEMICAL BONDS

Covalent bonds Non-Covalent bonds

-Non-polar -Ionic bonds
-Polar -Hydrophobic interactions
-Van der waals forces (intermolecular
forces)
-Hydrogen bonds (intermolecular forces)
 Covalent bonds
-Formation of bonds releases energy
-Breaking of bonds absorbs energy, 80-100 Kcal/mol of covalent bonds
-The strongest type
 Electronegativity- The power of an atom in a molecule to attract electrons to
itself

Non-polar covalent bonds Polar covalent bonds

-Formed between non-metal atoms
with the same electronegativity
-Symmetric (even) distribution of
electrons
-No change separation
-E.g. H2, Cl2, CH4, Hydrocarbons
-Formed between non-metal atoms
with different electronegativities
-Asymmetric (uneven) distribution of
electrons
-Electron pairs displaced toward the
more electronegative atom > partial
charges (§-, §+)
-Note: Not ions because no excess
protons or electrons
 Non-Covalent bonds
-Do not depend on shared electrons
-Depends on attractive forces between atoms with opposite charges
-Individuals bond is weak, 1.5 Kcal/mol of non- covalent bonds
-Readily irreversible
-Vital molecular interactions in the body
 Ionic bonds

• Electrostatic interactions between fully charged components (ions) – resulted from

electronegativity forces

• Electronegativity difference (ΔEN):

Bond type ΔEN

Non-polar covalent < 0.5

Polar covalent 0.5 – 1.6

Ionic > 2.0

• What about ΔEN 1.6 – 2.0?

-A metal is involved = ionic

-Only non-metals = polar covalent

 Strength of ionic bonds are generally weak (~3 kcal/mol)

 Weak when water is present but strong when water is absent e.g. core of a
protein
 Water molecules inhibit the attraction of oppositely charged ions from
forming ionic bonds
 Hydrophobic interactions

 Hydrophilic (water loving) vs. hydrophobic

 (water fearing)
 Polar molecules – hydrophilic
 Non-polar molecules – hydrophobic (lack of charged regions to attract water
molecules)
 Non-polar molecules mixed with water?
 Aggregate to minimise exposure to polar surroundings → hydrophobic interactions

 Not true bonds – no attraction, only clustering

 Van der Waals forces
 Dipole-dipole forces
 Occur between partially charged molecules
 Attraction between the positive end of one molecule and the
negative end of another (intermolecular)

 London dispersion forces

 Weak attractive forces resulted from instantaneous (temporary) dipole-induced dipole
attractions between non-polar molecules
 Temporary dipole – due to electron movements → unsymmetrical distribution of
electrons
 Weakest intermolecular forces
 Hydrogen bonds

o Electrostatic interaction
o Hydrogen atoms having a ∂+
o Bare hydrogen atoms approach other electronegative atoms (polar
molecules) with unpaired electrons – F, O and N
o weak hydrogen bonds (20× easier to break than covalent bonds)
o 2-5 kcal/mol
 Example: Hydrogen bonds in DNA molecules