CHAPTER 6--- CHEMISTRY IN
BIOLOGY
Miss Queen
SECTION 6.1
Atoms, Elements, Compounds
COMPOSITION OF MATTER
 Matter
- Everything in
universe is composed of
matter

Matter is anything that occupies
space or has mass
Mass – quantity of
matter an object has
 Weight – pull of
gravity on an object

Atom – the smallest unit of matter “indivisible”
Helium
atom
ATOMS
 The
simplest particle of an
element that retains all
the properties of that
element
 Properties of atoms
determine the structure
and properties of the
matter they compose
 Our understanding of the
structure of atoms based
on scientific models, not
observation
STRUCTURE
NUCLEUS
 Central
OF AN
ATOM--THE
core
 Consists of positive
charged protons and
neutral neutrons
 Positively charged
 Contains most of the
mass of the atom
THE PROTONS
 All
atoms of a given element have the
same number of protons
 Number of protons called the atomic
number
 Number of protons balanced by an equal
number of negatively charged electrons
THE NEUTRONS
 The
number varies slightly among atoms
of the same element
 Different number of neutrons produces
isotopes of the same element
ELEMENTS
 Pure
substances that cannot be broken
down chemically into simpler kinds of
matter
 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 unique chemical
symbol
Consists of 1-2 letters
 First letter is always capitalized

ATOMIC MASS
Protons & neutrons
are found in the
nucleus of an atom
 Protons and neutrons
each have a mass of 1
amu (atomic mass
unit)
 The atomic mass of an
atom is found by
adding the number of
protons & neutrons in
an atom

THE ELECTRONS
 Negatively
charged high energy
particles with little or no mass
 Travel at very high speeds at various
distances (energy levels) from the
nucleus
ENERGY LEVELS
Atoms have 7 energy levels
 The levels are K (closest to the nucleus), L,
M, N, O, P, Q (furthest from the nucleus)
 The K level can only hold 2 electrons
 Levels L – Q can hold 8 electrons (octet rule)

ATOMIC STRUCTURE
Electrons are arranged in Energy Levels or
Shells around the nucleus of an atom.
•
first shell
a maximum of 2 electrons
•
second shell
a maximum of 8 electrons
•
third shell
a maximum of 8 electrons
SUMMARY
1. The Atomic Number of an atom = number of
protons in the nucleus.
2. The Atomic Mass of an atom = number of
Protons + Neutrons in the nucleus.
3.
The number of Protons = Number of Electrons.
4.
Electrons orbit the nucleus in shells.
5.
Each shell can only carry a set number of electrons.
PERIODIC TABLE
Elements are arranged by their atomic number
on the Periodic Table
 The horizontal rows are called Periods & tell
the number of energy levels
 Vertical groups are called Families & tell the
outermost number of electrons

COMPOUNDS
 Most
elements do
not exist by
themselves
 Readily
combine with
other
elements in a
predictable
fashion
A
compound is a pure
substance made up of
atoms of two or more
elements

The proportion of atoms are
always fixed
 Chemical
formula shows
the kind and proportion
of atoms of each element
that occurs in a
particular compound
 Molecules
are the
simplest part of a
substance that
retains all of the
properties of the
substance and
exists in a free
state
 Some molecules
are large and
complex
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) or 6 atoms of
oxygen
PROPERTIES
 The
physical and
chemical
properties of a
compound differ
from the physical
and chemical
properties of the
individual
elements that
compose it

 The
tendency of
elements to combine and
form compounds depends
on the number and
arrangement of
electrons in their
outermost energy level
 Atoms are most stable
when their outer most
energy level is filled
 Most
atoms are not stable
in their natural state
 Tend to react (combine)
with other atoms in order
to become more stable
(undergo chemical
reactions)
 In chemical reactions
bonds are broken; atoms
rearranged and new
chemical bonds are formed
that store energy
COVALENT BONDS
 Formed
when two atoms share one or
more pairs of electrons
IONIC BONDS
 Some
atoms become stable by losing or
gaining electrons
 Atoms that lose electrons are called
positive ions
 Atoms
that gain electrons are called
negative ions
 Because positive and negative electrical
charges attract each other ionic bonds
form
SECTION 6.2
Chemical Reactions, Enzymes
ENERGY AND CHEMICAL REACTIONS
Living things undergo thousands of chemical
reactions as part of the life process
 Chemical reaction is the process by which atoms
or groups of atoms in substances are reorganized
into different substances.

CHEMICAL
 represent
EQUATIONS

chemical reactions
 Reactants are shown on the left side of
the equation
 Products are shown on the right side
The number of each kind
of atom must be the same
on either side of the
arrow (equation must be
balanced)
 Bonds may be broken or
made forming new
compounds
 Activation Energy is the
minimum amount of energy
needed to form products
in a chemical reaction.

 Enzymes
are an important class of
catalysts in living organisms
 Catalyst is a substance that lowers the
activation energy needed to start a
chemical reaction.



Mostly protein
Thousands of different kinds
Each specific for a different chemical reaction
ENZYME STRUCTURE
 Enzymes
work on
substances called
substrates
 Substrates must fit into
a place on an enzyme
called the active site
 Enzymes are reusable!
SECTION 6.3
Water and Solutions
WATER
A
water molecule (H2O), is
made up of three atoms --one oxygen and two hydrogen.
H
H
O
WATER: THE FACTS
Water is possibly the most important compound
in living organisms.
 Water consists of 1 atom of oxygen combined with
2 atoms of hydrogen.
 Water makes up 70 to 95 percent of most
organisms.

- water is a polar molecule because oxygen is more electronegative than
hydrogen, and therefore electrons are pulled closer to oxygen.
SOLUTIONS

A solution is a
mixture in which 2 or
more substances are
uniformly
distributed in
another substance
 Solute
is the
substance dissolved
in the solution

Particles may be ions,
atoms, or molecules
 Solvent
is the
substance in which
the solute is
dissolved

Water is the universal
solvent
SOLUTIONS



Solutions can be
composed of varying
proportions of a given
solute in a given
solvent --- vary in
concentration
(measurement of the
amount of solute)
A saturated solution is
one in which no more
solute can be dissolved
Aqueous solution
(water) are universally
important to living
things
ACIDS AND BASES
 One
of the most important aspects of a
living system is the degree of acidity or
alkalinity
ACIDS
 Number
of hydronium ions in solutions is
greater than the number of hydroxide
ions
+
HCl  H + Cl
BASES
 Number
of hydroxide ions in solution is
greater than the number of hydronium
ions
+
NaOH  Na + OH
PH SCALE
 logarithmic scale
for comparing the
relative
concentrations of
hydronium ions and
hydroxide ions in a
solution
 ranges from 0 to
14
 Each pH is 10X stronger than
next
 e.g. ph 1 is 10 times stronger
than ph 2
 the
lower the pH the stronger the acid
 the higher the pH the stronger the base
 pH 7.0 is neutral
BUFFERS
 Control
of pH is very
important
 Most enzymes
function only within a
very narrow pH
 Control is
accomplished with
buffers made by the
body
 Buffers keep a
neutral pH (pH 7)
 Buffers
neutralize
small amounts of
either an acid or
base added to a
solution
 Complex buffering
systems maintain the
pH values of your
body’s many fluids at
normal and safe
levels
ORGANIC COMPOUNDS
Compounds
that contain CARBON
are called organic.
Macromolecules
molecules.
are large organic
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MACROMOLECULES
 Large
organic molecules.
 Also called POLYMERS.
 Made up of smaller “building blocks”
called MONOMERS.
 Examples:
1. Carbohydrates
2. Lipids
3. Proteins
4. Nucleic acids (DNA and RNA)
49
CARBOHYDRATES
Small
sugar molecules to large
sugar molecules.
Examples:
A. monosaccharide
B. disaccharide
C. polysaccharide
50
CARBOHYDRATES
Monosaccharide: one sugar unit
Examples:
glucose
glucose (C6H12O6)
deoxyribose
ribose
Fructose
Galactose
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CARBOHYDRATES
Disaccharide: two sugar unit
Examples:
 Sucrose
(glucose+fructose)
 Lactose (glucose+galactose)
 Maltose (glucose+glucose)
glucose
copyright cmassengale
glucose
52
CARBOHYDRATES
Polysaccharide: many sugar units
Examples: starch (bread, potatoes)
glycogen (beef muscle)
cellulose (lettuce, corn)
glucose
glucose
glucose
glucose
cellulose
glucose
glucose
glucose
glucose
53
LIPIDS
 General
term for compounds which are
not soluble in water.
 Lipids are soluble in hydrophobic solvents.
 Remember: “stores the most energy”
 Examples:
1. Fats
2. Phospholipids
3. Oils
4. Waxes
5. Steroid hormones
6. Triglycerides
54
LIPIDS
Six functions of lipids:
1. Long term energy storage
2. Protection against heat loss
(insulation)
3. Protection against physical shock
4. Protection against water loss
5. Chemical messengers (hormones)
6. Major component of membranes
(phospholipids)
55
LIPIDS
Triglycerides:
composed of 1 glycerol and 3
fatty acids.
H
O
H-C----O C-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH3
O
H-C----O C-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH3
O
fatty acids
H-C----O C-CH -CH -CH -CH
2
2
2
H
glycerol
56
FATTY ACIDS
There are two kinds of fatty acids you may see these on
food labels:
1. Saturated fatty acids: no double bonds (bad)
2.
Unsaturated fatty acids: double bonds (good)
saturated
unsaturated
O
C-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH3
O
C-CH2-CH2-CH2-CH
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PROTEINS (POLYPEPTIDES)
 Amino
acids (20 different kinds of aa) bonded
together by peptide bonds (polypeptides).
 Six
1.
2.
3.
4.
5.
6.
functions of proteins:
Storage:
albumin (egg white)
Transport:
hemoglobin
Regulatory:
hormones
Movement: muscles
Structural: membranes, hair, nails
Enzymes:
cellular reactions
copyright cmassengale
58
PRIMARY STRUCTURE
Amino acids bonded together
by peptide bonds (straight
chains)
Amino Acids (aa)
aa1
aa2
aa3
aa4
aa5
aa6
Peptide Bonds
59
NUCLEIC ACIDS
 Nucleotides
include:
phosphate group
pentose sugar (5-carbon)
nitrogenous bases:
adenine (A)
thymine (T) DNA only
uracil (U) RNA only
cytosine (C)
guanine (G)
60
NUCLEOTIDE
Phosphate
Group
O
O=P-O
O
5
CH2
O
N
C1
C4
Nitrogenous base
(A, G, C, or T)
Sugar
(deoxyribose)
C3
C2
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