Chapter 2: Biochemistry

Chapter 2:
Elements and Atoms
• 92 natural elements arranged on a periodic table
– cannot be broken down into simpler substances
– represented by 1-2 letter symbols
– C,H,O, and N
• 4 most abundant elements in living organisms
• makes up 96% of the entire mass of the human
Trace Elements
• ex: Fe, I, and Mg
• are present in
very small
• help maintain
healthy cells
• elements are made of atoms
–basic building blocks
–smallest particle of an element
• protons: positive charge
• neutrons: neutral or no charge
• electrons: negative charge
– small
– attracted to the nucleus
– travel around the nucleus in energy levels
• nucleus: consists of protons and neutrons
– the nucleus is always positively charged because of
the positive protons
• energy levels hold a certain amount
of electrons
• 1st energy level only holds 2
electrons (e-)
• 2nd energy level holds 8 electrons
• 3rd energy level holds 18 electrons
• an atom’s identity is based on the number of
protons it has (atomic number)
• most atoms have no overall charge because the
number of protons equals the number of electrons
– ex: Carbon has 6 protons and will have 6
electrons (+6 + -6 = 0)
• ions: charged atoms
– have lost or gained an electron to give the atom
an overall + or – charge
• isotopes: atoms of the same element
– have the same number of protons but different
number of neutrons
– ex: Carbon (normally has 6 protons and 6 neutrons to
equal a mass of 12: C-12)
• C-13: 6 protons + 7 neutrons=13
• C-14: 6 protons + 8 neutrons=14
• Radioactive isotopes: used in science and medicine
– Can be unstable and break apart, giving off radiation
• Compounds:
composed of atoms
of 2 or more different
elements that are
chemically combined
– Ex: NaCl, H20,
Covalent: atoms share electrons (nonmetals with
– H20, C6H12O6 (sugars), fats, and proteins
– Weaker bonds
– Force that holds atoms together
– Molecule: group of atoms held together by covalent
– Has no overall charge
Ionic: atoms transfer electrons (nonmetals with
Gain or lose electrons
Ex: NaCl
Attractive force between 2 ions of opposite charge
Stronger bonds
Many ions are very important in living things
– Na and K: help conduct nerve impulses
– Ca: help with muscle contraction
Bonding Venn Diagram
Chemical Reactions
• Bonds are formed or broken
• Causes substances to recombine
into different substances
• Metabolism: all the reactions that
occur within a living organism
– Break down and build molecules
Chemical Equations
• Reactants (undergo reactions) --------->
Products (formed by reactions)
• Ex: 2H2 + O2 ---------> 2H2O
# of molecules
of each
# of atoms of
Bell Ringer:
1. The nucleus, the center of the atoms, is made
up of ___________ and ____________.
2. The negatively charged particles in atoms are
called __________.
3. Different isotopes of the same element have
different numbers of __________.
4. In a ___________ bond, electrons are
transferred from one atom to another.
5. The process that produces a new set of
chemicals is called a ___________________.
• The most important compound in living organisms
• Makes up 70-95% of most cells
• Water is a polar covalent molecule
– Has an unequal distribution of charge
• Has a positive end and a negative end
• Opposites attract: forms a weak hydrogen bond
• Hydrogen bonds help hold molecules together
– Ex: proteins
Characteristics of Water
• Cohesion: high surface
• Adhesion: able to creep up
tubes (capillary action)
• High heat of vaporization
– Resists changes in
– Ex: sweat cooling
• High specific heat (internal
and external temperature
• Expands when it freezes
(ice floats)
• Great solvent
• Different substances
are not chemically
– Individual
components keep
their own properties
– Ex: sand and sugar
• 1 or more substances are distributed evenly in another
substance (well-mixed)
– Can be a solid, liquid, or gas
– Ex: powdered drink mix (Kool-Aid)
– Important in living things
• Solute: what is getting dissolved
• Solvent: what does the dissolving (what dissolves the
– In greater amounts
• Ex: saltwater
– Concentration of the solution:
• Amount of solute
Amount of solvent
Acids and Bases
• pH: a measure of how acidic or basic a solution
• pH scale: indicates the concentration of H+ ions
in solution
• Ex: stomach juice (pH = 2); blood (ph = 7.2)
• pH below 7 acids (form H ions (H+) in H20)
• pH above 7  bases (form hydroxide ions
(OH-) in H20)
• pH = 7 is neutral (water)
• pH of fluids in humans must be kept
between 6.5 and 7.5 (to maintain
– Higher or lower than this will affect chemical
reactions within cells
• Buffers: weak acids or bases that can react
with strong acids or bases
– Prevents sharp, sudden changes in pH
1. Match the term with appropriate description:
___________ unequal sharing of electrons
___________ lemon juice, pH 1.5
___________ lower concentrations of H+ ions than pure water
___________ ammonia, pH 11.5
___________ a slight negative charge at one end of a molecule, a
slight positive charge at the other end
___________ pH values that are below 7
___________ alkaline solutions
2. A dissolved compound that prevents sharp
swings in pH is called a __________.
• organic substances contain carbon (found in
all living things)
• carbon is the backbone of living things
– has 4 valence electrons
• can bond with other carbon atoms to
form chains, branched chains, or rings
• can form single, double, or triple bonds
• C-CC=C C≡C
• Some compounds have the same molecular
formula but different structural formulas
(called isomers)
– Ex: fructose and glucose- C6H12O6
Macromolecules (polymers)
• Many carbon molecules bond to form long chains
• Ex: proteins and starch
• Condensation reaction: water molecule is
– Dehydration synthesis
– □ + □ = □□
• Hydrolysis: breaking down a polymer
– Adding water to break bonds
– □□  □□ + water  □ + □
Organic Molecules
• basic units
are called
• 4 major types
• Elements: Composed of
C,H, and O
• Monomers: Made up of
simple sugars called
– 2 monosaccharides combine
to make a disaccharide
– many monosaccharides
combine to make a
• Function: Used by cells
to provide energy
• Special features:
examples of
– starch (energy storage
in plants)
– glycogen (energy
storage in animals)
– cellulose (supports cell
walls in plants)
• Examples: breads, pasta,
• Elements: Made of C,H, and O
• Monomer: 3 fatty acids and a
glycerol molecule
• Functions:
Energy storage
Insulation (blubber in some animals)
Important component of the cell
• Special features:
– Insoluble in water
– Structure: May be saturated (C-C) or
unsaturated (C=C)
• Examples: fats, oils, waxes,
• Elements: Composed of C,H,O,N, and sometimes S
• Monomer: Long chains of amino acids (20) joined by
peptide bonds
• Functions:
Structure: hair, nails, hooves, horns, claws, beaks
Contracting muscle tissue
Transport oxygen in blood
Provide immunity
• Special features:
– Basic building material for all living things
– Enzymes increase reactions
• Examples: Insulin, hemoglobin, enzymes, meat, fish
• Proteins that change the rate
of a chemical reaction
• Called a biological catalyst
(lowers the activation energy)
– Energy needed to start a
• Enzyme animation
Nucleic Acids
• Elements: Composed of
C,H,O,N, and P
• Monomer: nucleotides (3
– Nitrogen base (N-base)
– Sugar
– Phosphate group
• Functions:
– Genetic code
• Special features:
– DNA: holds all genetic
– RNA: copies and carries out
instructions from DNA
• Examples: DNA and RNA
How do you test for the presence of
organic compounds?
• Carbohydrates:
– Starches- Iodine test
• Turns starches blue/black
– Sugars- Benedict solution
• Changes from sky blue to
• Lipids:
– Brown paper bag testleaves grease stain
• Proteins:
– Biuret: changes from
lavender to black
Bell Ringer:
1. The two basic kinds of nucleic acids are ______
and ______.
2. Biological catalysts, or enzymes, act by lowering
the _________ required for a reaction.
3. A _______ is a large compound formed by the
joining of small compounds called monomers.
4. Protein monomers are called ________.
5. A ______ stores and transmits genetic