Chapters 2 & 3:
Biochemistry
Matter: Anything that takes up space
and has weight – can be solid, liquid or
gas
Atom: Smallest particle of matter
Parts of an atom:
•Protons (+)
•Electrons (-)
•Neutrons (0)
•Protons and neutrons are found in the
nucleus
•Electrons orbit energy levels around the
nucleus
•Inner energy level holds two electrons
•Other energy levels holds eight
electrons
•The number of electrons in the outer
energy shell determines the chemical
properties of the atom.
Using the periodic table:
•Atomic number = # of protons
•Atomic mass = # of protons + neutrons
•If number of protons = number of
electrons, atom is neutral (no charge)
•Elements are arranged horizontally in
order of increasing atomic number
•Elements are arranged vertically
according to the number of electrons in
the outer shell
•Isotopes: atoms that differ in their
number of neutrons
•Carbon has 3 isotopes:
•Carbon 12 (most abundant)
•Carbon 13
•Carbon 14 (radioactive - unstable)
•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
•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+
8C
6H2O
3CO2
Structural formula: Shows the
arrangement of atoms within the
molecule
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
•In covalent bonds, atoms share
electrons
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-
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 an acid.
Bases are molecules that either take up
hydrogen ions or give off hydroxide ions in
solution (also called alkaline).
NaOH  Na+ + OH-
•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!!!
Properties of Water
 Water makes up between 60 and 70% of
organisms’ bodies
• 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?
“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-
• Hydrogen bonds form when a
covalently-bonded H+ is attracted to a
negatively-charged atom in a
neighboring molecule (such as oxygen in
neighboring water molecule, or chlorine
in NaCl).
• Hydrogen bonds are relatively weak
bonds.
Cohesion
Because of polarity and hydrogen bonding,
water molecules “stick together.”
Cohesive forces are strong enough to
cause water to act as though it has a thin
“skin” on its surface – surface tension.
Adhesion - the attraction between
water and something else.
Capillarity - adhesion and cohesion
enable water molecules 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
• Examples: carbohydrates, lipids, proteins,
nucleic acids
• Always contain carbon
• 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 chain
•Hydrocarbon chain can
turn back on itself to
form a ring
Carbohydrates
Importance:
• Quick energy and short-term energy
storage
• Make up cell wall in plants
• Help cells to recognize one another
•Monosaccharides (single sugar):
•glucose – blood sugar
•fructose – found in fruit
•galactose – found in milk
•Glucose, fructose, and galactose all have
the 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
•Polysaccharides – contain many glucose
units
•Ex: starch, glycogen, & cellulose
•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 –Fruit, milk, sweets,
sodas, juices
•Starches –
Breads, pasta,
rice, corn,
wheat, cereal,
leafy vegetables,
carrots
Lipids
• Examples:
• Fats - 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
• 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
•Foods they can be found in:
•Butter, foods fried in oil, bacon,
red meat, cheese
Proteins
Importance:
• Build living tissue – hair, nails, tendons,
ligaments, muscle, bone, etc.
• Act as enzymes to speed reactions
• Act as antibodies to fight disease
Proteins are made of amino acids
•
•
•
•
•
Central carbon atom
Hydrogen atom
Amino group (-NH2)
Carboxyl group (-COOH)
“R” group – which differs between amino
acids
Amino acids are joined by peptide bonds
to form polypeptides.
•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
making proteins
•Structure –
made of
nucleotides.
DNA is double-stranded, with complementary
base pairing – A and T, C and G always pair.