Lecture #2

Basic Chemistry
 Chemical Composition of Living
Organisms
• All living things are composed of matter
• Matter always occupies space and has a mass

• Examples: rock, water, grass, animals, human beings

• All matter is composed of elements

• Elements cannot be further broken down chemically

• There are 92 elements that are known to be found in nature

• Examples: carbon, nitrogen, oxygen, hydrogen, gold, copper

• Each element is given a symbol

• Examples: Carbon (C), Oxygen (O), Sodium (Na)
 Chemical Composition of Living
Organisms
• There are 25 elements necessary for human life
• 96% of the bodies weight can be attributed to carbon,
hydrogen, oxygen and nitrogen

• These four elements are the main ingredients of sugars, fats,

proteins and nucleic acids

• The remaining 4% of body weight is comprised of:

• Calcium
• Magnesium
• Chlorine
• Sodium
• Potassium
• Phosphorous
• Sulfur

• Trace elements are essential for life but

are required in very small amounts
 Trace Elements
• Iron is a trace element that accounts for only 0.004% of body mass
• It is absolutely necessary because it is a key component of hemoglobin which
is used to transport oxygen in blood

• Iodine is another trace element

that is required for human life:
• 0.15mg of iodine must be acquired
each day

• Iodine is a key component of hormones

produced by the thyroid gland

• Iodine deficiency leads to an enlargement

of the thyroid gland called a goiter

• To avoid this condition, table salt in many

countries is supplemented with iodine
• Referred to as iodized
 Compounds
• Elements combine to form compounds (molecules):
• A compound is a substance consisting of two or more elements in fixed
proportion

• Much more common than free elements

• Examples: NaCl (sodium chloride), H2O (water)

• Compounds have entirely different properties than the constituent

elements
• Example: Sodium (Na) is a metal, Chlorine (Cl) is a gas, combined they
produce table salt which is edible
 Compounds
• Most compounds found in living organisms contain carbon (C), oxygen
(O), Nitrogen (N) and Hydrogen (H):
• Sugars are composed of carbon, oxygen and hydrogen

• Proteins are composed of carbon, oxygen, hydrogen and nitrogen as well as a

small amount of Sulfur

• Different arrangements and different proportions of these elements provide

proteins and sugars with characteristic properties which are very different
from one another
 Atoms
• Atoms are the smallest units of matter that still display properties of
the element
• Example: a carbon atom is the smallest unit that still has properties of carbon

• Atoms consist of subatomic particles:

• Protons: carry a positive charge and are found in the nucleus
• Neutrons: do not carry any charge and are found in the nucleus
• Electrons: carry a negative charge and are found outside of the nucleus in
orbitals

• The nucleus is the central core of the atom

• The electrons are kept near to the nucleus
because their negative charge is attracted to
the positively charged core (nucleus)
 Atoms
• The main difference between different atoms is the number of sub-
atomic particles
• All atoms of a particular element have the same number of protons within
their nucleus
• The atomic number of the element is the number of protons within the nucleus of
each atom
• Example: Carbon has an atomic number of 6 therefore each carbon atom has
6 protons within the nucleus

• Each atom has an equal number of protons and electrons when it is neutral
therefore the atomic number is also equal to the number of electrons

• The mass number of an atom is equal to the sum

of the protons and the neutrons found within the
nucleus
 Atoms
• Isotopes:
• All atoms of an element always have the same atomic number however the
mass number may differ

• The term isotope refers to an atom that has the exact same number of
protons and electrons as all other atoms of an element but differs from other
atoms in the number of neutrons present within the nucleus
• Since the number of protons and electrons remain unchanged, the isotope has
identical chemical properties to the other atoms of the element

• There are three naturally occurring carbon isotopes

• Carbon-12 accounts for 99% of all carbon found in nature
 Electron Arrangement of an Atom
• Electrons determine the chemical reactivity of an atom
• Different electrons have varying degrees of energy
• The further an electron is from the nucleus the greater the energy it has

• Electrons occur only at certain energy levels referred to

as electron shells
• The number of electron shells surrounding the nucleus varies from
atom to atom depending on the number of electrons
 Electron Arrangement of an Atom
• With some exception outer electron shells can hold 8 electrons
• If the outer shell has fewer than 8 electrons the element is considered
reactive

• The fewer electrons needed to achieve a number of 8 the more reactive the
atoms of the element are

• To achieve a number of 8 electrons in the outer shell atoms form bonds with
other atoms either via:
• Electron sharing: covalent bonds
• Electron Donation: ionic bonds
 Ionic Bonds
• An atom that has only one electron in its outer shell will donate the
electron rather than looking to gain or share 7
• The electron will be donated to an atom that is looking to acquire an electron
because it has 7 electrons in its outer shell
• Example: NaCl
• Sodium has one electron in its outer shell and chlorine has 7 electrons in its outer
shell
• Sodium donates the electron to chlorine so that sodium has 0 electrons in its outer
shell and chlorine has 8 electrons in its outer shell
• This results in the formation of ions (‘ionic’ bonds):
• Sodium lost an electron and was previously neutral (now Na+)
• Chlorine gained an electron and was previously neutral (now Cl-)
• The bond formed is a result of the attraction between the newly formed
positive and negative charges
 Covalent Bonds
• These bonds form when two atoms share electrons
• Molecules are formed when two or more atoms share
electrons

• Example: hydrogen (H2) is joined by a covalent bond

• When two electrons are shared, a single bond is

formed
• Example H2 H-H

• When 4 electrons are shared a double bond is

formed
• Example: O2 O=O

• The number of covalent bonds that an atom can

form is equal to the number of electrons needed
to fill its outer shell
• Example: Carbon requires four electrons to
achieve eight electrons in its outer orbital
therefore it can form four covalent bonds
 Unequal Electron Sharing
• Electrons shared in covalent bonds are involved in a ‘tug-of-war’
• The atoms sharing the electrons are both pulling on the electrons involved in
the bond

• Electronegativity is a measure of an atoms attraction for electrons

• The greater the electronegativity of an atom the more it will pull electrons it’s way
 Unequal Electron Sharing
• Molecules of only one atom such as O2 will equally share electrons
• Covalent bonds where electrons are shared equally are called non-polar
covalent bonds

• These bonds form in between atoms of similar electronegativity

• Non-polar covalent bonds can also form in between different atoms that are
of similar electronegativity
• Example: methane (CH4)
 Unequal Electron Sharing
• Covalent bonds that form between atoms of very different
electronegativities result in unequal electron sharing
• These bonds are called polar covalent bonds
• The more electronegative atom pulls the electrons its way more than the less
electronegative atom
• Unequal electron sharing causes a partial positive charge on the less
electronegative atom and a partial negative charge on the more
electronegative atom
• Oxygen is one of the most electronegative elements
• Example: H2O
 Hydrogen Bonds
• Bonds that form between molecules and
within molecules are important for cell
function
• These bonds are non-covalent and weaker
than covalent bonds

• Hydrogen involved in a polar covalent

bond will carry a partial positive charge
• As a consequence the hydrogen will orient
itself near to an atom in an adjacent
molecule that has a partial negative charge

• This weak non-covalent bond is called a

hydrogen bond because the positive
molecule involved is always hydrogen
Hydrogen Bonds and Temperature
• Heat is defined as the amount of energy associated with the
movement of atoms and molecules in an object
• Temperature measures heat intensity: the measurement of the average speed
of molecules

• Heat is required to break hydrogen bonds formed between water

molecules
• Heat is released when these hydrogen bonds form

• Since temperature measures the speed of molecules, heat must be

added to water in order to break hydrogen bonds
• Once these bonds are broken the molecules can move much faster and as a
result the temperature of the water will increase
Hydrogen Bonds and Temperature
• When water is cooled heat is released as hydrogen bonds are
reformed between water molecules
• This results in a decreased speed of the molecules leading to a decrease
in temperature
 Evaporation
• Evaporation of a substance moderates
temperature
• The molecules with the greatest energy
(the hottest) leave the substance

• The remaining liquid is cooler as a result

of this loss

• Example: sweating
• Boiling water
 Hydrogen Bonds and Density
• Water exists in three primary states:
• Solid
• Liquid
• Gas (water vapor)

• Solids are always more dense than gas where

density is the number of particles (molecules)
per unit area
• Exception: water
• Ice has a smaller density than water vapor
• Explains why ice cubes float in water
• Due to hydrogen bonds
• When water freezes each water molecule forms
four bonds with adjacent water molecules result
in the creation of a crystal
• These hydrogen bonds are extremely stable

• In liquid water the hydrogen bonds are less

stable and continually break and reform
 Water as a Solvent
• A solution is a liquid consisting of a uniform mixture of two or more
substances
• The solution consists of a:
• Dissolving agent called a solvent: usually water
• A dissolved substance called a solute: examples include sugar and salt
• When water is the solvent the solution is referred to as an aqueous solution

• Water is such a great solvent because of the polarity of the molecules

• NaCl in water dissociates forming Na+ and Cl- ions
• These ions are then surrounded by
water molecules
• The partial positive charge on water’s
hydrogen interacts with the Cl- ions

• One of the partial negative charges on water’s

oxygen interacts with the Na+ ions
 pH Scale
• Measured on a scale of 0-14

• A solution with a pH of 7 is considered

neutral
• The amount of H+ in solution is equal to the
amount of OH- in solution

• Solutions with a pH of 0-6 are acidic

• pH= 0 is the most acidic
• pH= 6 is the least acidic (near neutral)

• Solutions with a pH of 8-14 are basic

• pH= 8 is the least basic
• pH= 14 is the most basic
 Acids and Bases
• Acids:
• Dissociate when placed in water
• Release H+ ions
• Example: HCl H + + Cl –
• The more HCl that is added to water, the more H + will be present following
dissociation
• The greater the amount (concentration) of H + in the solution, the lower the pH of
the solution
• Lower pH means a greater acidity

• Bases:
• Dissociate in water also
• Release OH – ions
• Example: NaOH Na + + OH –
• The OH - that is generated from the dissociation of NaOH binds to H +
• The greater the amount (concentration) of OH - in the solution, the greater the pH
of the solution
• Higher pH means that the solution is more basic