Chapter 2: The Molecules of Cells
Matter: Anything that takes up space and
has weight – can be solid, liquid or gas
Atoms:
the building blocks of matter
Element: Substance that cannot be broken
down into substances with different
properties; composed of only 1 type of atom
•Only 92 naturally occurring elements
(others are man-made)
•98% of body weight of organisms
made up of only 6 elements: carbon,
hydrogen, nitrogen, oxygen,
phosphorous, and sulfur
Parts of an atom:
•Protons (+)
•Electrons (-)
•Neutrons (0)
•Protons and neutrons are found in the
nucleus
•Electrons orbit shells around the
nucleus
•Outer energy shell holds eight
electrons
•Inner energy shell holds two
electrons
•The number of electrons in the
outer energy shell determines the
chemical properties of the atom.
•Atom is most stable when the outer shell
is filled
•Ex: Helium – 2 electrons in 1st shell
Neon – 8 electrons in 2nd shell
•Elements in last column of periodic
table have filled outer shells – Noble
gases
•To become stable, atoms form bonds
with other atoms
Using the periodic table:
•Atomic number = # of protons
•Atomic mass = # of protons + neutrons
•If number of protons = number of
electrons, atom is electrically neutral
•Elements are arranged horizontally in
order of increasing atomic number
•Elements are arranged vertically
according to the number of electrons in
the outer shell (valence electrons)
•Isotopes: atoms that differ in their
number of neutrons
•Carbon has 3 isotopes:
•Carbon 12 (most abundant)
•Carbon 13
•Carbon 14 (radioactive - unstable)
•Molecules: Formed when atoms
bond with other atoms; atoms can
be same or different
•Ex: O2 or CO2
•Compound: Formed when atoms
of different elements bond
•Ex: CO2 or C6H12O6
Chemical/molecular formula: shows
kind and proportion of atoms of
element/molecule
Ex: 5HCl
14Fe
C6H12O6
Na+
6O2
8C
6H2O
3CO2
2N2
Cl-
Structural formula: Shows the
arrangement of atoms within the
molecule
The three-dimensional shape of
molecules can be represented in two
ways:
•Space-filling model closer to actual
shape of molecule.
•Shapes of molecules determine how they
function in organisms.
•Ex: HIV binds to certain blood cells
Enzymes fit with substrate to help
digest food
Types of bonds: ionic bonds,
covalent bonds & hydrogen bonds
•In ionic bonds, atoms give up or
accept electrons, resulting in ions.
•Ions with opposite charges (- or +)
are attracted to each other and form
an ionic bond.
Ionic Bonds
Animation
•In covalent bonds, atoms share
electrons
Animation: forward to 0:50
Other ways to represent covalent
bonds:
Single, double, triple covalent bonds:
Single:
Double:
Triple:
:N:::N:
NN N2
Animation
Nitrogen
• Within some molecules, the nuclei of the
atoms within do not attract electrons
equally, resulting in slightly positive and
negative charges within the molecule
• Adjacent molecules with these positive
and negative regions may be attracted and
held together
• These attractions are called van der
Waals forces
• These are not as strong as covalent and
ionic bonds
• Hydrogen bonds (a strong type of van
der Waals force) form when a covalentlybonded H+ is attracted to a negativelycharged atom in a neighboring molecule
(such as oxygen in neighboring water
molecule, or chlorine in NaCl).
• Hydrogen bonds are relatively weak
bonds.
• Without hydrogen bonding between
water molecules, our body fluids would
be gaseous.
•Oxidation is the loss of electrons; hydrogen
atoms are removed from glucose.
•Reduction is the gain of electrons; oxygen
atoms gain electrons.
•Remember OIL RIG (oxidation is loss,
reduction is gain)
Acids and Bases
Water dissociates
and releases
hydrogen ions (H+)
and hydroxide ions
(OH-).
Acids are molecules that release
hydrogen ions in solution.
HCl  H+ + Cl-
**What your book doesn’t tell
you…
When those H+ are released, they
bond to water molecules, forming
H3O+ (hydronium ions).
If the number of hydronium ions is
greater than hydroxide ions, the
solution is acidic.
Bases are molecules that either take up
hydrogen ions or give off hydroxide ions in
solution (also called alkaline).
NaOH  Na+ + OH-
pH in moles/liter:
1 x 10-6 [H+] = pH 6
1 x 10-7 [H+] = pH 7
1 x 10-8 [H+] = pH 8
Pure water contains 10-7 moles per liter
of both hydrogen ions and hydroxide ions,
so it is neutral
Greater the quantity of H+, the more
acidic the solution (greater quantity –
smaller exponent).
•Buffers: substances that help to resist
change in pH – do so by taking up excess
H+ or OH- ions.
•Help maintain pH in blood, stomach
acid, urine, and intestinal fluid –
example of how your body maintains
homeostasis!!!
Example of how buffers work:
•Blood contains combination of bicarbonate ions
and carbonic acid (which can dissociate as seen
below)
•When H+ are added to blood, they combine with
bicarbonate ions
•When OH- are added to blood, it produces
bicarbonate ions and water
•The above 2 reactions keep pH in blood steady
Properties of Water
 Water makes up between 60 and 70% of
organisms’ bodies
Characteristics of water:
1.
2.
3.
4.
5.
6.
Liquid at room temperature
Universal solvent for polar molecules
Water molecules are cohesive
Temperature of water changes slowly
High heat of vaporization
Frozen water is less dense so ice floats
Some of these properties are due to water’s
polarity
•Polarity
 Oxygen atoms are larger than hydrogen, so
electrons spend more time near oxygen,
giving it a slight negative charge, and
hydrogen a slight positive charge.
Why is polarity important?
Makes water a universal solvent
“Like dissolves like” – polar substances are
good at dissolving other polar substances and
substances that are ionic - hydrophilic
Polar substances DO NOT dissolve
substances that are non-polar (without
charged ends) – hydrophobic
Polarity helps chemical reactions to take
place.
Negative ends of water are attracted to Na+
Positive ends of water are attracted to Cl-
Cohesion
Because of polarity and hydrogen bonding,
water molecules “stick together.”
Lizard video
Causes water to form droplets
Cohesive forces are strong enough to
cause water to act as though it has a thin
“skin” on its surface – surface tension.
Polarity affects density
•As water cools, hydrogen bonding becomes
more rigid but also more open – makes ice
less dense than liquid water.
•Water freezes at surface first – insulates life
beneath to survive winter.
•Hydrogen bonding makes water liquid at
room temperature
Adhesion - the attraction between
water and something else; forms
hydrogen bonds between water and
molecules on other surfaces.
Capillary action – adhesion of water
molecules allows water to move
upward through narrow tubes
Ex: water moving through a stem
of a plant, helps blood flow in blood
vessels
Temperature moderation
Because of hydrogen bonds, water can
absorb large amounts of energy
Absorbs lot of heat before it boils
Helps keep cells at an even temperature
despite changes in the environment –
homeostasis again!!
Allows large bodies of water to
maintain a relatively constant
temperature.
Organic Molecules
• Molecules of life: carbohydrates, lipids,
proteins, nucleic acids
• Always contain carbon and hydrogen (often
oxygen as well)
• Why carbon? Carbon has 4 electrons in outer
shell – can form covalent bonds with up to 4
other atoms.
•Carbon can share electrons with other
carbon atoms to form a hydrocarbon
chain
•Hydrocarbon chain can
turn back on itself to
form ring compound
•Organic molecules (carbs, protein, lipid,
nucleic acids) are macromolecules –
molecules joined together.
•Monomers – smaller building block
molecules
•Polymers – when same type of monomers
join together repeatedly
Polymer
carbohydrate
protein
nucleic acid
Monomer
monosaccharides
amino acid
nucleotide
Functional groups – can be attached to
hydrocarbon chains and cause the
macromolecule to behave in a certain
way.
Ex: -COOH (carboxyl group)
Carbohydrates
Importance:
• Quick energy and short-term energy
storage
• Structural role in plants, bacteria, and
insects
• Help cells to recognize one another
•Monomers of carbohydrates are the
monosaccharides (single sugar):
•glucose – blood sugar
•fructose – found in fruit
•galactose – found in milk
•Glucose, fructose, and galactose are all
isomers of one another – same molecular
formula, C6H12O6, but different structural
formulas
Fructose
Galactose
Glucose
•Below are 3 ways to represent glucose:
• Disaccharide - made from linking two
monosaccharides together.
• Examples of disaccharides:
• Maltose = glucose + glucose
• Sucrose = glucose + fructose
• Lactose = glucose + galactose
Sucrose
•When monomers join to form polymers, water
is removed – condensation synthesis
•Also called dehydration synthesis******
•When polymers are broken down, water is
added - hydrolysis
Animation of condensation
synthesis and hydrolysis
Animation
•Polysaccharides – long polymers that
contain many glucose units
•Ex:
Starch can be up
to 4000
glucose units
•Ex: Glycogen
– after eating
starchy foods,
the body
converts
glucose in the
blood into
glycogen –
stored in liver
and released as
needed
•Ex: Cellulose –
found in plant
cell walls.
•Glucose units
joined in such a
way that we
can’t digest it –
passes through as
roughage – may
help prevent
colon cancer
•Foods they can be found in:
•Simple sugars – mono and
disaccharides:
•Fruit, milk, sweets, sodas, juices
•Starches –
polysaccharides:
•Breads, pasta,
rice, corn,
wheat, cereal,
leafy vegetables,
carrots
Lipids
• Examples:
• Fats (triglycerides) - solid at room
temp. – animal origin
• Oils - liquid at room temp. – plant
origin
• Waxes – protective covering on plants
& animals
• Lipids do not dissolve in water - nonpolar
Importance:
•Long-term energy reserves
•Form membranes in cells
•Hormones such as testosterone
and estrogen
•Insulation, nerve impulses
•Repel water – duck feathers
•Structure – 1 glycerol plus 3 fatty acid
molecules
•Fatty acids are long chains of
hydrocarbons ending in - COOH
• Saturated vs. unsaturated fatty acids:
• Saturated – no double covalent bonds
between carbon atoms – makes butter
and lard solids
• Unsaturated – have double bonds
between carbon atoms
• Polyunsaturated – more than 2 double
bonds – makes cooking oil liquid
• Unsaturated and polyunsaturated
are better for you than saturated fats
Phospholipids - form cell membranes
Steroids Examples include cholesterol, and the sex
hormones estrogen and testosterone.
•Foods they can be found in:
•Butter, foods fried in oil, bacon,
red meat, cheese
Proteins
Importance:
• Build living tissue - keratin makes up hair
and nails, collagen supports tendons and
ligaments, hemoglobin to transport
oxygen in blood
• Act as enzymes to speed reactions
• Serve as transport carriers
• Act as antibodies
• Allow materials to cross cell membranes
Proteins are polymers of amino acids –
central carbon atom bonded to a hydrogen
atom, and amino group (-NH2), a carboxyl
group (-COOH), and an R group – which
differs between amino acids
Amino acids are joined by peptide bonds
to form polypeptides.
Levels of organization:
• Shape of protein is related to its function.
• When exposed to extremes in heat or pH,
proteins change their shape – undergo
denaturation – normal bonding between
R groups is disturbed.
• Change cannot be reversed – protein no
longer works.
•Foods they can be found in:
•Meat, eggs, cheese, beans, nuts, soy
Nucleic Acids
• Examples: DNA (deoxyribonucleic
acid) and RNA (ribonucleic acid)
• Importance: molecules of inheritance
– needed for cell reproduction and
activities, and making proteins
•Structure –
polymers of
nucleotides.
DNA is double-stranded, with complementary
base pairing – A and T, C and G always pair.