Chemistry in Biology
6
The Big Idea
Atoms are the foundation of
biological chemistry and the
building blocks of all living
things.
Section 6.1: Main Idea
Matter is composed of tiny particles
called atoms.
6.1 ATOMS, ELEMENTS, and
COMPOUNDS
I. Chemistry is the study of matter.
A. Matter is anything that takes up space
and has mass.
-Everything in the universe has matter.
-Matter is composed of atoms.
B. Mass is the amount of matter that an
object has.
-Mass and weight are not the same thing.
C. Weight is the pull of gravity on an object
6.1 ATOMS, ELEMENTS, and
COMPOUNDS
II. Composition of Matter
A. Elements—pure substances that cannot be broken down
into simpler kinds of matter
• Made of one type of atom
• More than 100 elements (92 naturally occurring)
• 90% of the mass of an organism is composed of 4 elements
(oxygen, carbon, hydrogen, and nitrogen)
• Each element has a unique chemical symbol
-consists of 1-2 letter
-first letter is always capitalized
-Ex: O, C, F, Al, Ag, Mg
6.1 ATOMS, ELEMENTS, and
COMPOUNDS
B. Atoms—the simplest particle of an element that still
has all the properties of that element
• Atoms are so small that their true structure cannot
be observed. Our understanding of the structure of
atoms is based on scientific models.
6.1 ATOMS, ELEMENTS, and
COMPOUNDS
C. Parts of an atom
•The nucleus of an atom contains two types of
particles:
1. Proton—positively charge
2. Neutron—has no charge, “neutral”
•The nucleus contains most of the mass of the atoms
•All atoms of a given element have the same number of
protons
6.1 ATOMS, ELEMENTS, and
COMPOUNDS
• The third particle of the atom is the electron
which is located outside the nucleus in energy
levels (electron clouds).
-first energy level holds 2 electrons
-second holds 8 electrons
• Electrons have a negative charge.
• Number of protons is balanced by an equal
number of electrons therefore there is no
charge of the atom.
• All atoms have this same basic structure.
Structure of an Atom
6.1 ATOMS, ELEMENTS, and
COMPOUNDS
D. Neutrons
•The number of neutrons varies slightly among
atoms for the same element.
•Atoms of the same element that have different
numbers of neutrons are referred to as isotopes of
that element
6.1 ATOMS, ELEMENTS, and
COMPOUNDS
• Changing the number of neutrons does not change the
overall charge of the atom but can affect the stability of
the nucleus causing it to decay or break apart. Such
isotopes give off radiation and referred to as “radioactive
isotopes.”
6.1 ATOMS, ELEMENTS, and
COMPOUNDS
E. Atomic Mass and Atomic Number
•Protons and neutrons each have a
mass of 1 amu (atomic mass unit)
or Dalton.
•The atomic mass of an element is
equal to the number of protons
plus the number of neutrons in the
nucleus of the atom.
•The atomic number of an element
is equal to the number of protons.
The Periodic Table
6.1 ATOMS, ELEMENTS, and
COMPOUNDS
F. Periodic Table
•The elements are arranged by their atomic
number on the Periodic Table.
•The horizontal rows are called periods and
tell the number of energy levels.
•The vertical groups are called families and
tell the outermost number of electrons.
6.1 ATOMS, ELEMENTS, and
COMPOUNDS
G. Compounds
• Compounds are pure substances formed when two
or more different elements combine.
-Ex: H20, CO2, and C6H12O6
• Compounds are always formed from a specific
combination of elements in a fixed ratio.
• Compounds cannot be broken down into simpler
compounds or elements by physical means.
-can be broken down by chemical means into
simpler compounds or into their original elements
-H2O can be broken down into hydrogen gas and
oxygen gas
6.1 ATOMS, ELEMENTS, and
COMPOUNDS
• Elements can undergo chemical reactions to
combine with other elements in order to
become stable.
• Stable elements have their outer energy
level filled-meaning they have 8 electrons
6.1 ATOMS, ELEMENTS, and
COMPOUNDS
H. Chemical Formulas
• Subscript after a symbol tell the number of
atoms of each element
• H20 has 2 atoms of hydrogen & 1 atom of
oxygen
• Coefficients before a formula tell the number of
molecules
• 3O2 represents 3 molecules of oxygen or (3x2)
6 atoms of oxygen
6.1 ATOMS, ELEMENTS, and
COMPOUNDS
III. CHEMICAL BONDS
A. The force that holds atoms together is known as a chemical
bond.
• Electrons are directly involved in the formation of chemical
bonds.
-They travel around the nucleus of an atom in areas
called energy levels.
-Each energy levels has a specific number of electrons
that it can hold at any time
-The first energy level which is closest to the nucleus can
hold up to 2 electrons.
-The second energy level can hold 8 electrons.
6.1 ATOMS, ELEMENTS, and
COMPOUNDS
B.Types of Chemical Bonds
1. Covalent bond—forms when atoms share one
or more pairs of electrons
•A molecule is a compound in which the atoms
are held together by covalent bonds.
•Can be a single, double, or triple bond
depending on number of pairs of electrons
shared.
Covalent Bond
6.1 ATOMS, ELEMENTS, and
COMPOUNDS
2. Ionic Bond—forms when atom gives up
electrons and another receives electrons in
order to become stable
• Electrical attraction between two oppositely
charged atoms or groups of atoms called
ions.
• Most ionic compounds are crystalline at
room temperature and have higher melting
points than molecular compounds formed by
covalent bonds.
6.1 ATOMS, ELEMENTS, and
COMPOUNDS
• Sodium and Chlorine
-both atoms are unstable
-to become stable, sodium gives away 1
electron and becomes positive, chlorine
receives 1 electron and becomes negative
6.1 ATOMS, ELEMENTS, and
COMPOUNDS
6.1 ATOMS, ELEMENTS, and
COMPOUNDS
• Some atoms tend to donate or accept
electrons more easily than other atoms.
• The elements identified as metals tend to
donate electrons.
• The elements identified as nonmetals
tend to accept electrons.
6.1 ATOMS, ELEMENTS, and
COMPOUNDS
3. van der Waals Forces
• Defined as the attraction between molecules
• This occurs when molecules come close together,
and the attractive forces between slightly positive
and negative regions pull on the molecules and
hold them together.
• The strength of the attraction depends on the size
of the molecule, its shape, and its ability to attract
electrons
• Important in biological processes.
Section 6.2: Main Idea
Chemical reactions allow living things to
grow, develop, reproduce, and adapt.
6.2 Chemical Reactions
I. Reactants and Products
A. Chemical Reactions
• A chemical reaction is the process by which
atoms or groups of atoms in substances are
reorganized into different substances.
• Clues that a chemical reaction has taken place
include the production of heat or light, and
formation of a gas, liquid, or solid.
• Chemical bonds are broken and formed during
chemical reactions
6.2 Chemical Reactions
B. Chemical Equations
• Chemical formulas describe the substances in the
reaction and arrows indicate the process of
change.
• Reactants are the starting substances, on the left
side of the arrow.
• Products are the substances formed during the
reaction, on the right side of the arrow.
• Reactants
Products
6.2 Chemical Reactions
• Glucose and oxygen react to form carbon
dioxide and water.
• Is this equation written correctly?
6.2 Chemical Reactions
C. Balancing Equations
•The law of conservation of mass states matter
cannot be created or destroyed.
•The number of atoms of each element on the
reactant side must equal the number of atoms of
the same element on the product side.
Balancing Equations—Practice
1.Fe + Cl2  FeCl3
1. 2Fe + 3Cl2  2FeCl3
2.H2 + O2  H2O
2. 2H2 + O2  2H2O
3.C2H6 + O2  CO2 + H2O
3. 2C2H6+ 7O2 4CO2 + 6H2O
4.CO2 + H2  CH4 + H2O
4. CO2 + 4H2  CH4 + 2 H2O
5.Al + O2  Al2O3
5. 4Al + 3O2  2Al2O3
Bell-Ringer
1. QUIETLY find your seat.
2. Sit down and prepare for the quiz.
3. Clear your desk of everything except a writing utensil.
4. Failure to do so will result in a 10pt deduction on your quiz.
Quiz
1. A ____________is the process by which atoms or groups of atoms in
substances are reorganized into different substances.
2. _____________ is/are the attraction between molecules.
3. _____________ states matter cannot be created nor destroyed.
4. Subscripts tell the number of _____________ per element.
5. Coefficients tell the number of ______________.
6.2 Chemical Reactions
II. ENERGY
A.Energy is defined as the ability to do work or cause a
change.
B.States of Matter:
• Solid—particles are packed tightly and move slowly
• Liquid—particles move freely and take the shape of the
container
• Gas—particles move rapidly and have no definite shape
6.2 Chemical Reactions
C. Energy of Reactions
• The activation
energy is the
minimum amount of
energy needed for
reactants to form
products in a
chemical reaction.
6.2 Chemical Reactions
Exothermic Reaction
Endothermic Reaction
6.2 Chemical Reactions
D. Energy Changes in
Chemical Reactions
• This reaction is exothermic
and released heat energy.
• The energy of the product
is lower than the energy of
the reactants.
6.2 Chemical Reactions
• This reaction is
endothermic and
absorbed heat energy.
• The energy of the
products is higher than
the energy of the
reactants.
6.2 Chemical Reactions
III. ENZYMES
A. An enzyme is a
biochemical catalyst.
• A catalyst is a substance
that lowers the activation
energy needed to start a
chemical reaction.
• It does not increase how
much product is made
and is not used up in the
reaction.
6.2 Chemical Reactions
• The reactants that bind to the enzyme are called
substrates.
• The specific location where a substrate binds on
an enzyme is called the active site.
• The active site changes shape and forms the
enzyme-substrate complex, which helps
chemical bonds in the reactants to be broken
and new bonds to form.
6.2 Chemical Reactions
B. Enzyme Action
1.Enzyme and substrate link together.
2.Chemical reaction occurs
3.Substrate becomes something new and the
enzyme is let go.
4.The enzyme can be reused.
Enzyme Action
6.2 Chemical Reactions
• Factors such as pH, temperature, and
other chemicals affect enzyme activity.
• When enzymes are exposed to one of
these factors, they may become
denatured.
-Denaturing causes the enzyme to not
be as effective or possibly quit working
altogether.
Examples of Biological Enzymes
• http://www.woisd.net/moodle/mod/resou
rce/view.php?id=43
Section 6.3: Main Idea
The properties of water make it well
suited to help maintain homeostasis in an
organism.
6.3 Water and Solutions
I. Water’s Polarity
A. Molecules that have an unequal distribution of charges
are called polar molecules.
• Polar molecules have one side that has a postive
charge and the other has a negative charge.
• Water is a polar molecule.
B. Water molecules are held together by weak
hydrogen bonds.
• A hydrogen bond is a weak interaction involving a
hydrogen atom and a fluorine, oxygen, or nitrogen
atom.
• Hydrogen bonds are important in biological
processes.
6.3 Water and Solutions
6.3 Water and Solutions
II. Properties of Water
1. Cohesion is the attractive force between particles
of the same kind. This property allows water to
bulge from the top of a filled glass without spilling
over.
2. Adhesion is the attractive force between unlike
substances.
•Together these properties make it possible for
water to move upwards against the force of
gravity in a narrow tube.
•This phenomenon is called capillarity.
6.3 Water and Solutions
III. Mixtures with Water
A.Mixture--a combination of two or
more substances in which
each substance retains its individual
characteristics
B.Homogenous mixture--one that has a
uniform composition throughout; a
solution
C.Solvent--a substance in which
another substance is dissolved
(Ex: tea)
D.Solute--the substance that is
dissolved in the solvent (Ex: sugar)
Food coloring dissolved in
water forms a homogenous
mixture.
6.3 Water and Solutions
E. In a heterogeneous mixture,
the components remain
distinct.
•In a suspension, the
components will eventually
settle to the bottom.
•In a colloid, the particles will
not settle over time.
Examples include fog,
smoke, butter, mayonnaise,
milk, paint, and ink.
6.3 Water and Solutions
F. Concentration—the measure of how much of a
substance is dissolved
G. Saturated solution—one in which nothing else
can dissolve
H. Aqueous solution—water is the solvent
6.3 Water and Solutions
IV. Acids and Bases
A. Substances that release hydrogen ions (H+)
when dissolved in water are called acids.
B. Substances that release hydroxide ions (OH–)
when dissolved in water are called bases.
6.3 Water and Solutions
6.3 Water and Solutions
C. The pH Scale
•The measure of concentration of H+ in a solution
is called pH.
-Ranges from 0-14 with 7 being neutral
•Acidic solutions have pH values lower than 7.
-have a sour taste
•Basic solutions have pH values higher than 7.
-have a bitter taste
•Buffers are mixtures that can react with acids or
bases to keep the pH within a particular range.
-help neutralize a body’s pH level
6.3 Water and Solutions
Section 6.4: Main Idea
Organisms are made up of carbon-based
molecules.
6.4 The Building Blocks of Life
Organic Chemistry
The element carbon is a
component of almost all
biological molecules.
6.4 The Building Blocks of Life
• Carbon has four electrons in its outermost
energy level.
• One carbon atom can form four covalent
bonds with other atoms.
• Carbon compounds can be in the shape of
straight chains, branched chains, and rings.
6.4 The Building Blocks of Life
Macromolecules
• Carbon atoms can be joined to form carbon
molecules.
• Macromolecules are large molecules formed
by joining smaller organic molecules together.
• Polymers are molecules made from repeating
units of identical or nearly identical
compounds linked together by a series of
covalent bonds.
6.4 The Building Blocks of Life
Carbohydrates
• Compounds composed of carbon, hydrogen,
and oxygen in a ratio of one oxygen and two
hydrogen atoms for each carbon atom—
(CH2O)n
6.4 The Building Blocks of Life
• Values of n ranging from three to
seven are called simple sugars, or
monosaccharides.
• Two monosaccharides joined together
form a disaccharide.
• Longer carbohydrate molecules are
called polysaccharides.
6.4 The Building Blocks of Life
Lipids
 Molecules made mostly of carbon and
hydrogen
 A triglyceride is a fat if it is solid at room
temperature and an oil if it is liquid at room
temperature.
6.4 The Building Blocks of Life
• Lipids that have tail chains with only single
bonds between the carbon atoms are called
saturated fats.
• Lipids that have at least one double bond
between carbon atoms in the tail chain are
called unsaturated fats.
• Fats with more than one double bond in the
tail are called polyunsaturated fats.
6.4 The Building Blocks of Life
Proteins
• A compound made of small carbon
compounds called amino acids
• Amino acids are small compounds that are
made of carbon, nitrogen, oxygen, hydrogen,
and sometimes sulfur.
6.4 The Building Blocks of Life
• Amino acids have a central carbon atom.
• One of the four carbon bonds is with
hydrogen.
• The other three bonds are with an amino
group
(–NH2), a carboxyl group (–
COOH), and a variable group (–R).
6.4 The Building Blocks of Life
• The number and the order in which the amino
acids are joined define the protein’s primary
structure.
• After an amino acid chain is formed, it folds into a
unique three-dimensional shape, which is the
protein’s secondary structure, such as a helix or
a pleat.
6.4 The Building Blocks of Life
• Nucleic acids are complex macromolecules
that store and transmit genetic information.
• Nucleic acids are made of smaller repeating
subunits called nucleotides, composed of
carbon, nitrogen, oxygen, phosphorus, and
hydrogen atoms
6.4 The Building Blocks of Life