CHEMICAL BASIS OF LIFE

Lecture Outline

• Matter, atom, element and compound

• Different types of chemical bonds
• Water: The most abundant substance in cells
• Importance of Carbon: Cells formation
What forms
matters?
 Element

• Matter - anything that has mass and occupy

space
• Made of elements
 Substance that cannot be broken down to other
substances by chemical reactions
• Each element has a chemical symbol
Periodic Table of Elements
 Element

• 92 naturally occurring elements

• 25 essential for life
 C, O, H, N  compose 96% of living matters
 Ca, P, K, S, Na, Cl, Mg and trace elements  remaining
4%
 B, Cr, Co, Cu, F, I, Fe, etc  Trace elements (low
quantities, but are essential)
• Atom – the smallest unit of matter that is unique to
a particular element
 Retains the physical and chemical properties of its
element
 Atomic Structure

• Atoms of all elements contain

subatomic particles
• Atoms of the same element share
the same chemical properties
• 3 subatomic particle types:
 Protons
 Neutrons
 Electrons
• Atomic structure determines
behavior of an element
 Subatomic Particle

• Protons
 Found in the nucleus
 Carry a positive charge
 Number of protons = number
of electrons
(normally)
 Numbers do not vary
 Numbers are specific for each
element
 Subatomic Particle

• Neutrons
 Found in the nucleus
 Electrically neutral
 Numbers can vary
 Isotope
 Radioactive isotope
 Isotope

• Isotope of an element has

the same atomic number but
different mass number
 Same number of protons, but
different number of neutrons
• Different isotopes of same
element react chemically in
the same way
 Radioactive Isotope

• An unstable isotope that

spontaneously emits nuclear
particles and/or energy
• Loss of nuclear particles may
transform one element into
another
• Isotopes have half life
 Time for 50% of radioactive
atoms in a sample to decay
 Subatomic Particle

• Electrons
 Orbit the nucleus
 Carry a negative charge
 Number of electrons = number of protons (normally)
 Held in orbits by the electrostatic attraction to
nucleus protons
 Lowest potential energy  Closest to nucleus
 Highest potential energy  Furthest from nucleus
 Not fixed in a single orbit  Move from one energy
level to another  Gain or loss energy
 Subatomic Particle

• Electrons
 Atomic Number

• Designated by the number of

protons in a particular
element
• Eg: sodium has 11 protons
 Nomenclature: 11Na
• In neutral atom, proton and
electron number is equal Sodium
Summary of Atomic Structure
 Valence Shell and Valence Electron

• Electrons in the outermost shell  Determines the

chemical properties of atom
• Octet rule  Valence shell is complete when it
contains eight electrons  inert or unreactive atom
 Eg. Helium, argon, neon
• Atoms without complete valence shell  chemically
reactive
 Responsible for atom’s binding capacity  Interacting
with other atoms
 Results Formation of chemical bonds until 8 electrons
fill valence shell
 Chemical Bonding

• Chemical bonds  Attraction that holds a molecule

together
 Molecule  2 or more atoms
• Chemical formula
 Represents types and numbers of atoms in each molecule
 No indication of bonds arrangement
 Eg. NaCl, H2O
• Structural formula
 Represents the atoms and bonding within a molecule
 Line represents the bond (Eg. H-H)
Chemical Bonding

Chemical
formula: H2O
Structural
formula:
Chemical Bonding
 Chemical Bonding

• Types:
1. Covalent bond
 Formed by sharing pairs of valence electrons
 Strong chemical bond (Eg. H2, O2, N2)
 Single  share a pair of valence electrons
 Double  share 2 pairs of valence electrons
 Triple  share 3 pairs of valence electrons
 Double and triple  rigid bonds and no rotation
allowed
 Chemical Bonding

• Types:
2. Ionic bond
 Formed by electrostatic attraction  Complete
transfer of an electron from a donor atom to an
acceptor
 Forms an ion
 Anion  Atom that has gained 1 or more electrons from
another atom  Negatively charged
 Cation  Atom that has lost 1 or more electrons 
Positively charged
 Strong in crystal form but weak in water
 Chemical Bonding

• Types:
3. Weak chemical bonds
 Temporary associations  Form reversible bonds
briefly  Stabilize tertiary structure of large
molecules
 Hydrogen bonds
 Formed when a hydrogen atom covalently bonded to an
electronegative atom
 20x weaker than covalent bond  Easy to break
 Van der Waals forces
 Occur when molecules are close to each other
 Hydrophobic interactions
 What are the
major
components of
our body?
 Water

• Chemical formula?
• Contributes to the ideal environment to
support life
• Living cells composed of 70 – 95% water
• Water covers 75% of earth’s surface
• Can naturally occurs in all 3 physical states
 Solid, liquid, gas
• A polar molecule held together by hydrogen
bonding
 Dissociation of Water
• Hydrogen bonds are continuously broken and formed
 Hydrogen atoms of a water molecule are usually shared in a hydrogen
bond with two other water molecules  Maintains liquidity
• Occasionally, hydrogen atom shifts from one oxygen atom to
another oxygen atom which is hydrogen bonded
 Only proton is transferred, not the electron
 Transferred proton binds to orbital of a second water molecule 
Positively charged  Hydronium ion (H3O+)
 Water molecule that lost a proton  Negatively charged  Hydroxide
ion (OH-)

H2O + H2O H3O+ + OH-

H2O H+ + OH-
 Water as a Solvent

• Many substances dissolve in water (Eg. Dietary sugar)

 Molecules separate from each other and surrounded by water
molecules
• Solution  The mixture formed when a substance dissolved in
a liquid
• Solute  The dissolved substance
• Solvent  The liquid that dissolve the substance (Eg. Water)
 Acids and Bases

• Acid  A substance that, when put into

water, gives up H+
 Donates H+ to a solution
• Base  A substance that, when put into
water, gives up ions (OH-) that will
combine with H+
 Takes H+ out of solution
• At equilibrium (pure water)  [H+] = [OH-]
 Acids and Bases

Solution [H+] ? [OH-]

Neutral [H+] = [OH-]
Acidic [H+] > [OH-]
Basic [H+] < [OH-]
 The pH Scale

• pH scale
 Ranges from 0 – 14
 Neutral pH = 7
 Acidic pH < 7
 Basic pH > 7
• pH of most biological
systems 6 – 8
(except stomach)
 Maintained by a buffer
system
 Resists change in pH
 Cells are Formed from Carbon Compounds

• Besides water, cells are the

major building blocks of
organisms
• Primary cellular
composition  Carbon
• Carbon has the ability to
form large molecules
• Molecules containing
carbon  Organic
molecules
 Carbon

• Carbon is unusual
 Much more versatile than other elements
 Atomic number of 6 and has 4 valence electrons
 Can form as many as 4 bonds with other atoms,
including other C atoms (tetravalent arrangement)
 More or less long chains of carbon atoms can form this way
 C atoms can be joined into rings and other shapes
 C – C combinations introduce
tremendous complexity and
variety into molecular structure
 Carbon Skeleton

• Organic molecules that include a long chain of

carbons covalently bonded together
• May vary in
 Length
 Shape
 Number and location of double bonds
• Hydrocarbons  contain only carbon and hydrogen
elements
Carbon Skeleton
 Functional Groups

• A number of small group of atoms frequently

bound to the carbon skeleton
• Characteristics
 Have specific chemical and physical properties
 Regions of organic molecules that are commonly
chemically reactive
 Number and arrangement determine the unique
chemical properties of organic molecules
 Functional Groups

• Types
1. Hydroxyl group (-OH)  Alcohols
2. Carbonyl group (CO-)  Aldehyde or ketone
3. Carboxyl group (-COOH)  Carboxylic acids
4. Amino group (-NH2)  Amines
5. Sulfhydryl group (-SH)  Thiols
6. Phosphate group (PO43-)  For cellular energy storage
7. Methyl group (-CH3)  For tertiary structure of
macromolecules
 Macromolecules

• Also known as polymers  Large molecules consisting of

many identical or similar subunits/monomers connected
together (40 – 50 various monomers)
• Monomer  A molecule that is able to bond in long chains
• Polymerization
 The process that forms macromolecules
 Condensation reaction that links 2 or more small molecules
through formation of covalent bonds, removing 1 water molecule
per covalent bond formed
• Hydrolysis  The reaction that breaks covalent bonds
between monomers in a macromolecule by addition of
water molecules
 Categories of Organic Compounds

• Four classes of macromolecules

that form the basis of living
matters
1. Carbohydrates
2. Lipids
3. Proteins
4. Nucleic acids