Chemistry of
Life
Green = IMPORTANT NOTES
How much do
you already
know?
Let’s start small
• Matter: any physical
substance that has mass
and takes up space
• Atom: the basic unit of
matter
o From the Greek word atomos
– unable to be cut
• Protons (+) and Neutrons
(n) are found in the
nucleus in equal amounts
• Electrons (-) are in
constant motion in the
space around the
nucleus
Element: a pure substance that consists
of entirely one type of atom
Atomic Number: #
of protons
Element symbol
Atomic Mass:
# of protons + #
of neutrons
Element name
Periodic Table of Elements
Arranged from left to right by increasing atomic number
Colors indicate similar atomic properties
Elements
Important
to Life
Isotopes
• An isotope is a variation of
chemical element due to a
different number of
neutrons.
• Identify isotopes by the
atomic mass
• Since the number of
electrons remains the same
the chemical properties
remain the same
• Radioactive isotopes have
an unstable nuclei and will
eventually break down
• Used to date fossils, trace
atoms through metabolism,
diagnosis cancer, etc…
Electron Energy Levels
• Valence Electrons are the
outer electrons that can
participate in chemical
bonding
Energy Level
# of electrons
1
2
2
8
3
8
Octet Rule
• Atoms tend to gain,
lose, or share one or
more of their valence
electrons to achieve a
filled outer electron
shell
• Trying to achieve
stability like the Noble
Gases
Compounds
• A compound is composed of 2 or more elements
o Physical and chemical properties are usually very different from
the original individual elements
• This is achieved by chemical bonds
1.
2.
3.
4.
Ionic Bonds
Covalent Bonds
Van der Waals Forces
Hydrogen Bonds (We will get to this later with Water)
Ionic Bonds
• 1 or more electrons
transferred from 1 atom
to another
• Ions: an atom or
molecule that has
gained or lost one or
more of its valence
electrons.
o Gain electron = NEGATIVE
o Lose electron = POSITIVE
• Resulting ions have a
strong attraction for
one another
1 valence
electrons
7 valence
electrons
Covalent Bonds
• Electrons are shared by
2 atoms.
o The electron travels
between the 2 nuclei
1 valence
electrons
1 valence
electrons
Lewis Dot Model
Valence Electrons are represented by dots around the symbol
Ionic Bonds
Covalent Bonds
Van Der Waals Forces
• Intermolecular forces
that are not ionic or
covalent
• Weak attraction
between atoms,
molecules, and
surfaces
Metabolism
• Metabolism: the sum of all chemical reactions within
a living organism
• Anabolism: chemical reaction in which simple
substances are combined to form a more complex
substance
o Need energy = Endergonic
• Catabolism: chemical reaction in which complex
substances are broken down into more simple
substances
o Release energy = Exergonic
Chemical Reactions
Example of Anabolism:
• Dehydration Synthesis: monomers of organic
compounds bind together through a chemical
reaction to form a polymer (with water as a product
of the reaction)
Monomer + Monomer  Polymer +Water
Example of Catabolism:
• Hydrolysis: The reverse of the dehydration reaction
Chemical Reactions
• A chemical reaction is a process that changes or
transforms a set of chemicals into another
CH3COOH + NaHCO3  CO2 + H20 + CH3COONa
Acetic Acid + Sodium Bicarbonate  Carbon dioxide + water + sodium acetate
Reactants
Products
• Chemical reactions involve changes in chemical
bonds that join atoms and compounds
Energy Transformations
• Energy is released or absorbed whenever a
chemical bond is broken or formed
• Exergonic: releases energy – typically spontaneous
• Endergonic: absorbs energy – requires a source of E
o Living organisms obtain their energy from raw materials such as
the sun or other living organisms
Activation Energy:
Energy required to get a reaction started
Higher
Energy
Exergonic
Lower
Energy
Even though this is an energy releasing reaction, a
small amount of activation energy is still needed to
get this reaction started
Endergonic
Higher
Energy
Lower
Energy
A larger amount of activation energy is needed in this
reaction in order to achieve a higher energy state of
the products
Enzymes
• Chemical reactions that are too slow or have a high
activation energy need a helping hand
• Catalysts: substances that speed up the rate of a
chemical reaction
• Enzymes are proteins that act as biological catalysts
o They speed up reactions that take place inside cells
Enzymes
• How do they do this?
• Catalysts lower the activation energy of a reaction
allowing the reaction to occur quicker and with less
energy
• Enzymes are very specific and generally only
catalyze one reaction
Regular
Reaction
Reaction
with
Catalyst
The activation energy for the reaction with the catalyst is
much smaller than the original activation energy
Enzyme-Substrate
Complex
• In order for a reaction to occur, reactants must
collide together with enough energy to break and
form bonds
• Enzymes provide a site where the reactants can be
brought together.
• The reactants of an enzyme-catalyzed reaction are
known as Substrates.
• The site in which the substrate binds on the enzyme
is called the Active Site.
• The enzyme remains UNCHANGED after a reaction.
This allows one enzyme to catalyze many reactions.
Enzyme-Substrate
Complex
Enzyme-Substrate
Complex
Substrate
Substrate
Active Site
Active Site
Lock and Key Analogy
Organic Compounds
• Organic compounds all contain carbon
• Carbon has 4 valence electrons which allows it to bond
with 4 other elements including itself
• Compounds that make up Organic compounds: C, H,
O, N, P, S
o Or NHCOPS
•
1.
2.
3.
4.
There are 4 types of organic compounds:
Carbohydrates
Lipids
Proteins
Nucleic Acids
Macromolecules
• Macromolecules “giant molecules” are made out
of many small molecules
• Polymerization: large compounds are built by
joining smaller units together
• Monomers “single”
• Polymers “many parts”
Chemical Reactions
• Dehydration Synthesis: monomers of organic
compounds bind together through a chemical
reaction to form a polymer (with water as a product
of the reaction)
Monomer + Monomer  Polymer +Water
• The reverse of this reaction is called Hydrolysis
Carbohydrates
Compounds made of C, H, O
Usually a 1:2:1 ratio
4 calories/gram
Living things use carbohydrates as a main source of
energy and sometimes for structural purposes
• Monomer: Monosaccharide “simple sugars”
•
•
•
•
o Glucose: supplies immediate energy for cells
o Fructose
o Galactose
• Polymer: Polysaccharide “complex sugars”
o Glycogen: Animal storage
o Starch: Plant storage
o Cellulose: Plant structures
Carbohydrates
Glucose
Glycogen
Lipids
Compounds made of C,H, O
Not water soluble
Fats, oils, waxes, steroids
9 calories/gram
Living things use lipids for stored energy sources,
insulation, membrane structure, vitamin and mineral
storage.
• Composed of one glycerol molecule (alcohol) and
3 fatty acids
•
•
•
•
•
Lipids
Triglyceride Molecule: 1 glycerol + 3 Fatty Acids
Phospholipid Bilayer
• Makes up almost all
living organisms cell
membranes
• Barrier that prevents
water soluble
molecules from
diffusing across
• Composed of 2 layers
of phospholipids
• Phospholipids have a
hydrophilic head and 2
hydrophobic tails
Lipids
• Cholesterol: is a steroid
produced by the liver
• It is both fat soluble and
water soluble
• It is an essential
component of the cell
membrane
• Also important in the
manufacturing of other
steroids, bile acids, and
vitamin D
Lipids
• Saturated fats: all single bonds with maximum
number of Hydrogen
o Solid at room temperature
• Monounsaturated fats: 1 double bond
• Polyunsaturated fats: more than one double bond
o Both mono and polyunsaturated fats are liquid at room
temperature
Fat gets a bad rap
• In the 1950s biochemist Ancel Keys conducted “The
Seven Countries Study”
• This study demonstrated a strong positive
correlation between amount of fat consumed and
heart disease
o Although these results were published, the results are actually
inconclusive since Ancel Keys left a number of countries out of his
study.
• From Ancel Key’s Study, the Low Fat Diet/Heart
Healthy Diet was born
Saturated Fats
• Examples:
o Lauric Acid: coconuts, breast milk
o Palmitic Acid: animal products
o Stearic Acid: meat and eggs
• Benefits: improve memory, increase levels of “good
cholesterol”
• High levels of saturated fats in combination with a
poor diet is not recommended, however you do not
need to avoid saturated fats like the plague
Unsaturated Fats
• Examples of Monounsaturated Fats:
o Oleic Acid: olive oil, avocados, nuts
• Benefits of Monounsaturated Fats: antioxidants,
decrease “bad cholesterol”
• Examples of Polyunsaturated Fats:
o The most common types are Omega-3 and Omega-6 fatty acids
o Essential fats: cannot make these in our body
o A 1:1 ratio of Omega-3:Omega-6 is ideal - however, most of
standard American diets do not have this ratio
• Benefits of Polyunsaturated Fats: anti-inflammatory
Trans-fats
• Trans fats are created when a polyunsaturated fat is
transformed into a saturated fat
o Hydrogen atoms are added to the molecule until it becomes a
saturated fat. This process is called hydrogenation.
o Examples: Margarine
• Trans fats can lead to heart disease by increasing
blood lipids
Proteins
• Compounds made of C, H, O, N
• 4 calories/gram
• Living things use proteins for growth and repair,
controls rates of chemical reactions (enzymes), cell
membrane, transport, NOT an energy source
• Monomers: Amino Acids
o 20 different amino acids
• Polymers: Polypeptides
o Different structures of polypeptide chains
o Sequence of amino acids is dictated by DNA
Amino Acid
• Amine Group
• Carboxyl Group
• R group
o Accounts for variability and
diversity
Primary Structure:
• Sequence of amino acids
Secondary Structure:
• Alpha-helices
• Beta-sheets
• Held together by H-bonds
Tertiary Structure:
• Secondary structure folded
onto itself
Quaternary Structure:
• 2 or more tertiary structures
combined together.
Nucleic Acids
• Compounds made up of C, H, O, N, P
o NHCOPS
• Nucleic Acids store and transmit heredity or genetic
information (DNA and RNA)
• Monomers: Nucleotides
o Nucleotides composed of: a sugar, triphosphate, and a
nitrogenous base
o 5 nitrogenous bases: Adenine, Guanine, Thymine, Cytosine, Uracil
• Polymers: DNA & RNA
o DNA: deoxyribonucleic acid
o RNA: ribonucleic acid
Nucleic Acids
Nucleotide
DNA
Water
Properties of Water
1. Water is a POLAR
MOLECULE!!!!
• In a covalent bond,
electrons are not
equally shared among
atoms
• This unequal sharing of
electrons causes a
slight positive and slight
negative charge on
the molecule
Properties of Water
2. Water is able to form
many Hydrogen Bonds
• Polar molecules can
attract one another via
the slight charges on
the molecule. These
are very weak bonds.
• This gives water unique
properties
Properties of Water
3. Water can be found in
all 3 phases of matter:
solid, liquid, gas
3. Water molecules
expand when frozen
causing it to be less
dense than in the
liquid state.
Properties of Water
5. Water is cohesive.
• Cohesion is the
attraction between
molecules of the same
substance
• “Like attracts Like”
• Water molecules
“stick” to one another
• This also creates
surface tension
Properties of Water
6. Water is adhesive.
• Adhesion is an
attraction between
molecules of different
substance
• Water can adhere to
the walls of vessels
causing it to move up
the vessel. This is called
Capillary Action.
Properties of Water
7. Water has a high heat
capacity
• Specific Heat: amount
of heat required to
raise the temperature
by 1 degree Celsius
o The specific heat of water is
higher than the specific
heat of land
o This also allows water to
hold heat well.
Properties of Water
8. Water is a universal
solvent.
•It is able to to dissolve
more substances than
any other liquid
•This property allows
water to carry with it
nutrients, chemical, and
minerals
•Water’s polarity allows it
dissolve ionic and polar
compounds
Solutions & Suspensions
• Solvent: Dissolving
substance
• Solute: Substance being
dissolved
• Solution: type of mixture
where all the
components are evenly
distributed
• Suspension: when
materials in a solvent
don’t dissolve but break
into pieces
Acids and Bases
• Water molecules split apart to form ions:
H20
H+ + OH• H+: hydrogen ion
• OH-: hydroxide ion
• The number of positive and negative charges evens
out. Pure water is neutral (pH 7)
• pH: measures the concentration of hydrogen ions
(H+)
Acids, Bases, & Buffers
• Acids are any compounds that form H+ ions in a
solution
• Bases are any compounds that produce OH- ions in
a solution
• Buffers: are weak acids or bases that react with
strong acids or bases to prevent sharp sudden
changes in pH
o pH of most cells is 6.5-7.5
o In order to maintain this balance we use buffers
pH Scale
Acids: H+ > OHBases: H+ < OHEach step is a factor
of 10.
•
A pH of 4 has 10x more
H+ than a pH of 5