Biology

Biology – the study of life –

Is founded on the principles of
chemistry and physics

All living organisms are a

collection of atoms and molecules

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 Atoms
• Smallest functional units of matter
• Form all chemical substances and
• Cannot be further broken down into other
substances
Each specific type
of atom is a
chemical element

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 Electrons occupy orbitals
• Scientists initially visualized an atom as
a mini solar system

• Electrons travel within regions

surrounding the nucleus (orbitals) in
which the probability is high of finding
that electron
• Can be depicted as a cloud
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 Atomic shells
• Atoms with progressively more
electrons have orbitals within
electron shells that are at greater and
greater distances from the center of
the nucleus
– 1st shell - 1 spherical orbital (1s) - holds 2 electrons
– 2nd shell - 1 spherical orbital (2s) and 3 dumbbell-
shaped orbitals (2p) – can hold 4 pairs of electrons

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 Nitrogen example
 An atom of nitrogen has seven protons and
seven electrons
• 2 electrons fill 1st shell
• 5 electrons in 2nd shell
2 fill 2s orbital
1 each in the 3 p orbitals

• Outer 2nd shell is not full

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 Atomic Number
• Number of protons in an atom is its
atomic number

• The atomic number is also equal to the

number of electrons in the atom so that
the net charge is zero

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 Periodic table
• Organized by atomic number
• Rows correspond to number of electron shells
• Columns, from left to right, indicate the numbers of
electrons in the outer shell
• Similarities of elements within a column occur
because they have the same number of electrons in
their outer shells, and therefore they have similar
chemical bonding properties

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 Mass Number
• The second number associated with each atom is the

mass number. The mass number expresses the sum

of the masses of the particles in the atom.

proton has a mass number of 1, electron 0, therefore the

mass number indicates the number of proton and neutrons in

the nucleus.

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 Mass Number

• Atomic mass scale indicates an atom’s mass relative

to the mass of other atoms

• Most common form of carbon has six protons and six

neutrons, is assigned an atomic mass of exactly 12

– A hydrogen atom has an atomic mass of 1, indicating that

it has 1/12 the mass of a carbon atom
– A magnesium atom, with an atomic mass of 24, has twice
the mass of a carbon atom

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 Mass or weight?
• Weight is derived from the gravitational pull
on a given mass
• If a man who weighs 154 pounds on earth
were standing on the moon, for example, he
would only weigh about 25 pounds, but he
would weigh 21 trillion pounds if he could
stand on a neutron star. However, his mass is
the same in all locations.

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 Units
• Dalton
–Unit of measurement for atomic mass
–One dalton (d) equals 1/12 the mass of a
carbon atom
–Carbon has an atomic mass of 12 Daltons
• Mole
–1 mole of any element contains the same
number of atoms—6.022 x 1023
–Avogadro’s number 11
 Isotopes
• Multiple forms of an element that differ
in the number of neutrons
• 12C contains 6 protons and 6 neutrons

• 14C contains 6 protons and 8 neutrons

• Atomic masses are averages of the

weights of different isotopes of an
element
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 Hydrogen, oxygen, carbon, and
nitrogen
• Typically make up about 95% of the atoms in living
organisms
– Hydrogen and oxygen occur primarily in water
– Nitrogen is found in proteins
– Carbon is the building block of all living matter

• Mineral elements - less than 1%

• Trace elements - less than 0.01%
– Essential for normal growth and function
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 Chemical bonds and molecules
• Molecule
– 2 or more atoms bonded together

• Molecular formula
– Contains chemical symbols of elements
found in a molecule
– Subscript indicates how many of each
atom are present

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 3 types of bonds
1. Covalent
• Polar covalent

2. Hydrogen
3. Ionic

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 Covalent bonds
• Atoms share a pair of electrons
• Occurs between atoms whose outer electron shells
are not full
• Covalent bonds are often the strongest of all
chemical bonds, because the shared electrons
behave as if they belong to each atom
• Can share …
– 1 pair of electrons – single bond H-F
– 2 pairs of electrons – double bond O=O
– 3 pairs of electrons – triple bond

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 Octet rule
• Atoms are stable when their outer
shell is full
• For many atoms, the outer shell
fills with 8 electrons
• One exception is hydrogen, which
fills its outer shell with 2 electrons

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 Polar covalent bonds
• When two atoms with different electronegativities
form a covalent bond, the shared electrons are
more likely to be in the outer shell of the atom of
higher electronegativity rather than the atom of
lower electronegativity

• Polar covalent bonds occur because the

distribution of electrons around the atoms creates
a polarity, or difference in electric charge, across
the molecule
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 Water
• Classic example of polar covalent
bonds
• Electrons tend to be in the more
electronegative oxygen atom rather
than either of the less electronegative
hydrogen atoms
• Molecule has partial negative charge
region and a partial positive charge
region 19
 Hydrogen bonds
• Weak polar covalent bonds
• Represented as dashed or dotted lines
• Collectively, can form strong bond overall
– Holds DNA strands together
• Individually, weak bonds can form and break
easily
– Substrate and enzyme bonding

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 Ionic bonds
• An ion is an atom or molecule that has gained
or lost one or more electrons
• It now has a net electric charge
• Cations- net positive charge
• Anions- net negative charge
• Ionic bond occurs when a cation binds to an
anion

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 Chemical Reactions
• Occurs when one or more substances are
changed into other substances
– Reactants → products
• Share many properties
– All require a source of energy
– Reactions in living organisms often require a
catalyst (enzymes)
– Tend to proceed in a particular direction but will
eventually reach equilibrium
– Occur in liquid environment - water

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 Properties of water
• A solution is made up of the
– Solvent- liquid
– Solutes- substances dissolved in solvent
• Aqueous solution- water is the solvent
• Ions and molecules that contain polar
covalent bonds will dissolve in water

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• Hydrophillic- “water-loving”
– Readily dissolve in water
– Ions and molecules that contain polar covalent bonds
• Hydrophobic- “water-fearing”
– Do not readily dissolve in water
– Nonpolar molecules like hydrocarbon
• Amphipathic molecule
– Have both polar or ionized regions at one or more sites
and nonpolar regions at other sites
– May form micelles in water
• Polar (hydrophilic) regions at the surface of the micelle and
nonpolar (hydrophobic) ends are oriented toward the interior of
the micelle

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 Solutions
• Concentration
– Amount of a solute dissolved in a unit volume of solution
– 1 gram of NaCl was dissolved in 1 liter of water = 1 g/L
• Molarity
– Number of moles of a solute dissolved in 1 L of water
– 1 mole of a substance is the amount of the substance in
grams equal to its atomic or molecular mass

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 H2O in 3 states of matter
• Solid (ice), liquid (water), and gas (water
vapor)
• Changes in state, such as changes between
the solid, liquid, and gas states of H2O, involve
an input or release of energy
• Water is extremely stable as a liquid

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 Colligative properties of water
• Depend strictly on the concentration of dissolved
solute particles and not on the specific type of
particle
• Addition of solutes to water lowers its freezing point
below 0°C and raises its boiling point above 100°C
• Some animals produce antifreeze molecules that
dissolve in their body fluids, thereby lowering the
freezing point of the fluids and preventing their
blood and cells from freezing in the extreme cold

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 Not just a solvent
• Water has many important functions in living
organisms
– Participates in chemical reactions
• Hydrolysis or dehydration
– Provides force or support
– Remove toxic waste components
– Evaporative cooling
– Cohesion and adhesion

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 Acids and Bases
• Pure water has the ability to ionize to a very
small extent into hydrogen ions (H+) and
hydroxide ions (OH-)
• In pure water
[H+][OH-] = [10-7 M][10-7 M] 10-14 M

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• Acids are molecules that release hydrogen
ions in solution
– A strong acid releases more H+ than a weak acid
• Bases lower the H+ concentration
– Some release OH-
– Others bind H+

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 pH
• pH = log10 [H+]
• Acidic solutions are pH 6 or below
• pH 7 is neutral
• Alkaline solutions are pH 8 or above

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• The pH of a solution can affect
– The shapes and functions of molecules
– The rates of many chemical reactions
– The ability of two molecules to bind to each other
– The ability of ions or molecules to dissolve in
water

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 Buffers
• Organisms usually tolerate only small changes
in pH
• Buffers help to keep a constant pH
• An acid-base buffer system can shift to
generate or release H+ to adjust for changes in
pH

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