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Atoms and Molecules:
The Chemical Basis of Life
 Organisms are made of chemicals
 These chemicals behave similarly in
different organisms
 There are even sub disciplines that
study chemistry and physics inside of
organisms
 Organic – carbon based and can be
made of/by organisms
 Inorganic – not carbon based and not
made of/by organisms
Elements and Atoms
 Make up all matter
 Made of only one type of atom
 Can’t be broken down into simpler
substances by ordinary chemical
reactions
 25 are necessary for life
 CHONPS are the most important for
life
 Trace elements are necessary for life
but make up less than 0.01% of your
body
 Each have a unique chemical symbol
 Anything that takes up space and has
mass
 Mass is the measurement of matter
 Everything is made of matter, including
organisms
 Smallest unit of an element that has the
properties of that element
 Atomic nucleus is made of subatomic
particles – protons & neutrons
 Electrons circle the nucleus
 Electrons are attracted to the nucleus
 All atoms of one element have the same
atomic number (# protons)
 Written as subscript in front of symbol
 Atoms may gain or lose electrons when
they react
 Chart of elements listed in order by
atomic number
 1 Atomic Mass Unit (amu) or Dalton is
equal to the mass of one proton or
neutron
 Atomic mass = protons + neutrons
 Written as a superscript with the symbol
 Electron’s mass is only 1/1800 amu
 Therefore ignored when calculating
atomic mass
 Atoms have the same number of protons,
but different numbers of neutrons
 Therefore different atomic mass
 Radioactive isotopes – unstable, tend to
break down, emit radiation when they
decay.
 Orbitals – 3D spaces where electrons
are found around a nucleus
 Contain a max of two electrons
 Electrons found closer to the nucleus
have less energy
 The distance an electron is from the
nucleus is its principal energy level
 Electrons at the same energy level
make up an electron shell
 The most energetic electrons, known as
valence electrons, are found in the
valence shell
 Valence shell electrons
usually determine how
an atom will react
 When the valence shell is
not full, atoms tend to
lose, gain, or share
electrons
Chemical Reactions
 Chemical reactions – chemical bonds
are formed or broken
 Valence electrons (found in the
valence shell) usually determine how
an atom will react
 Atoms are stable when their outer
energy level is full
 Atoms can gain or lose electrons to
become stable
 Consists of atoms of two or more
different elements combined in a fixed
ratio
 Compounds are usually very different
from the elements that make them up
 If only covalent bonds hold atoms
together, it is a molecule
 Chemical formula shows the number and
type of atoms in a molecule
 Simplest Formula gives the smallest
whole-number ratios for the atoms present
(NH2 – 1:2 ratio of nitrogen to hydrogen)
 Molecular Formula indicates the actual
numbers of each type of atom per molecule
(N2H4 – each molecule of hydrazine consists
of two molecules of nitrogen and four
molecules of hydrogen)
 Structural formula shows types and number
of atoms present AND their arrangement.
 Common for complex organic molecules
with different structural formulas to have
same molecular formula
 Sum of the atomic masses of the
component atoms of a single molecule
 Molecular mass of water = [hydrogen
(2) x 1 amu] + [oxygen (16) x 1 amu] =
18 amu
 1 mole of water = 18g
 Each atom is represented by its periodic
table abbreviation
 The number of atoms in a molecule is written
as a subscript after the abbreviation
 The number of molecules is written as a
number in front of the abbreviations
 The number of atoms must be the same
on both sides of the equation
 Reactants enter a reaction
 Products leave a reaction
Chemical Bonds
 Hold atoms together
 Atoms react to become more stable
 Atoms are most stable when the
valence shell level is full
 Bond energy is the amount of energy
needed to break a chemical bonds
 Forms when atoms share electrons
 Atoms can usually only share the
number of electrons needed to fill
their outer energy level
 Atoms held together by covalent
bonds are called molecules
 Can have single, double, and triple
covalent bonds
 Your body recognizes molecules by shape
 Molecules also need the correct shape to
react normally
 The shape is determined by its electrons
 Shape will maximize distance between
electrons
 Orbital hybridization – when valence
electrons rearrange their orbitals after
forming bonds
 Electronegativity – how well an atom can
attract an electron
 If two atoms sharing electrons have equal
electronegativity, a nonpolar bond or
molecule is formed
 Example – H2 or O2
 If they have unequal electronegativity, a
polar bond or molecule is formed
 Molecule formed will have a slight uneven
distribution of charge (still neutral overall)
 Example – H2O
 Ion – charged particle
 Forms due to gaining or losing
electrons
 Cations have a positive charge
 Anions have a negative charge
 Ions usually behave differently than
the neutral atom
 Opposites attract in chemistry
 Cations and anions are attracted to
each other
 Ionic bond – electrons are transferred
 Solvent is what is more common in
solution
 Solute is what there is less of in a
solution
 Ionic compounds usually dissociate
(fall apart) in water
 Process is called Hydration
 Ions don’t interact with each other as
well now
 Weak attraction between polar molecules
 Opposite partial charges attract each other
 Is the weakest bond
 Electrons are not shared or transferred
 Helps some molecules maintain their shape
Redox Reactions
 Type of chemical reaction that moves an
electron from one chemical to another
 Oxidation is when a chemical loses an
electron
 Reduction is when a chemical gains an
electron
 Reduces positive charge
 These always happen together so the
electron has a place to go
 Oxidizing agent accepts electrons
 Reducing agent loses electrons
Water
 Each water molecule can form up to four hydrogen bonds
 Attraction between polar molecules
 Allows for cohesion
 Attraction between like molecules
 Allows for adhesion
 Attraction between different molecules
 Cohesion and adhesion of water allows for capillary action
 Can move up small thin tubes
 Important for plants
 Cohesion allows for surface tension
 Water on surface of body of water is attracted to itself and prevents
small items from sinking
 Water is the almost universal solvent
 Can dissolve anything polar or ionic
 These are hydrophilic
 Many reactions in us only occur if the reactants are dissolved in
water
 Can’t dissolve nonpolar substances
 These are hydrophobic
 Water resists temperature changes
 Due to hydrogen bonds
 Takes change in kinetic energy/heat to break/form hydrogen
bonds
 Allows us to maintain homeostasis easier
 Ex: Evaporative Cooling cools us as we sweat
 Allows for temperature moderation near large bodies of water
 Causes ice to be less dense than liquid water
 Due to needing space for the extra hydrogen bonds
 Allows for soil formation
 Allows for pond mixing
Acids, Bases, and Salts
 Some water in a solution will break down into H+ and OH These will be in equal number in pure water
 Other chemicals in an aqueous solution may release one of
these ions
 Bases release OH Acids release H+
 Measures the concentration of H+ in a solution
 Goes from 0-14
 7 is neutral
 < 7 is acidic
 > 7 is basic
 Each number is 10X change
 pH is critical to most life processes
 Buffers keep pH in the critical range
 They absorb H+ as the pH becomes too acidic and then release
H+ as pH rises
 When acids and bases react, the H+ of the acid combines with
the OH- of the base to form water
 The remainder of the acid and base combine to form a salt
 HCl + NaOH → H2O + NaCl