Chemistry in Biology
Chapter 6
6.1 Atoms, Elements, and
Compounds
Chemistry: the study
of matter
Atoms: the building
blocks of matter
Atoms
They are soooo small
but they are made up
of even smaller
particles:
neutrons
protons
electrons
Atoms
There is a nucleus at the
center of an atom!
In the nucleus you can
find:
protons: positive
charge
neutrons: no
charge
Outside the nucleus you
find:
electrons: negative
charge
Atoms continued
Electrons orbit around the atoms nucleus.
The attraction between protons and electrons are what
cause the structure of an atom.
There are equal numbers of electrons and protons in an
atom: the overall charge of an atom is zero
Atoms
• The atomic number:
the number of protons
found in the nucleus
of the atom
(therefore, it is also
the number of
electrons found that
orbit around the
nucleus)
• The atomic mass: the
weight of the protons
and the neutrons
combined.
Elements
• Element: pure
substance that can’t be
broken down
further by chemical or
physical means.
• They are made up of
only one type of atom
• There are over 100
known elements
Elements
• Each element
has a unique
symbol and
name
Groups: the
vertical
columns
Periods: the
horizontal
rows
Isotopes
Isotopes: atoms of the same element that have different
numbers of neutrons (so the atomic mass is different)
Radioactive isotopes: less stable nucleus which may decay.
When the nucleus breaks apart it gives off radiation
Carbon-14 used to calculate the age of things (within 50,000
years)
Compounds
Compound: a pure
substance formed when
two or more different
elements combine
Each has a chemical
formula
Each formed from a
specific combination of
elements in a fixed ratio
(like C6H12O6)
compounds
They are chemically and
physically different than the
elements that make them up
for instance: H is a gas,
O is a gas together they
make H20 which is liquid
They can’t be broken down into
simpler compounds or
elements by physical means
but they can by chemical
means
Chemical Bonds
• The force that holds
substances together
are chemical bonds.
The first orbit can hold
2 electrons
The next ring can hold
8 electrons
The outermost ring can
hold 2 electrons
Chemical bonds
• In order for an element to be stable you
must have the outer most energy level
either completely full or completely
empty
• Otherwise it isn’t stable
• Atoms become stable by either losing
electrons to something else or by
attracting more electrons from
something
• Either way, there is energy stored in
the bonds that are made and when
bonds are broken they release energy
Covalent Bonds
Covalent Bond: the
bond that forms when
electrons are shared
Most compounds in living
organisms have
covalent bonds holding
them together.
Molecule
Molecule: a
compound in
which the atoms
are held together
by covalent bonds
Ionic Bonds
Ion: An atom that has lost
or gained one or more
electrons and carries an
electric charge
Ionic bond: an electrical
attraction between two
oppositely charged
atoms or groups of
atoms
ions
•
Substances formed by ionic bonds are
called ionic compounds
– Ions: sodium, potassium, calcium, chloride
and carbonate ions
1. Help to maintain homeostasis
2. Help to transmit signals among cells to see,
taste, hear, feel and smell
ions
• Some atoms tend to donate or accept
electrons more easily than other atoms
• (and when given the opportunity to
choose, will choose certain atoms over
others)
Van der Waals Forces
When molecules are attracted to each other based on positive and negative regions.
Not as strong as covalent or ionic bonds
but determined by the size of the molecule, its shape, and its ability to attract
electrons
Important in water molecules
6.2 Chemical Reactants
Chemical reaction:
when two or more
chemical substances
mix together. They
become new
substances that are
very different than the
original substances.
Chemical reactions
Sometimes substances
change without
involving a chemical
reaction (so they are
still made up of the
same atoms but just
a physical change
happens)
Chemical Equations
• Reactants and products
– Reactants: The starting
substances that go into a
chemical reaction
– Products: The
substances formed at the
end of a reaction (or as a
middle step)
This is a chemical equation!
This shows what goes in and what comes out.
Balanced equations
Matter cannot be created or destroyed
WHAT GOES IN MUST COME OUT (but
it can be rearranged because the
bonds can change and form something
else)
So, you must account for the atoms that
go into a reaction and what comes out
of a reaction
Balancing equations
All chemical equations must
show this balance of mass.
This means that the number
of atoms of each element
ON THE REACTANT SIDE
(the left side of the
equation) must equal the
number of atoms of the
same element ON THE
PRODUCT SIDE (the right
side of the equation)
Balancing Equations
• The coefficient (the
number in front) is
used to make the
number of atoms on
each side of the
arrow equal (you do
not use the
subscript for this
Energy of Reactions
There is a minimum
amount of energy
needed to make a
reaction occur. This
is called
ACTIVATION
ENERGY.
The point: allowing
the reactants create
products
Energy Change in Chemical Reactions
When the reaction releases
energy (in the form of heat)
the reaction is
EXOTHERMIC
this means there is
more energy in the
bonds of the
reactant (the stuff on
the left side of the
arrow) compared to the
products(the stuff on
the right side of the
arrow).
Energy Change in Chemical Reactions
When the reaction requires
more energy to happen
than what is released the
reaction is
ENDOTHERMIC
this means there is
more energy in the
bonds of the product
(the stuff on the
right side of the
arrow) compared to
the reactants (the
stuff on the left side of
the arrow).
Enzymes
All living things are
“chemical factories”
driven by chemical
reactions
There has to be an input of
energy in order for
reactions to occur.
Some reactions would
occur incredibly slow if
allowed to occur on their
own.
Enzymes
• In order to reduce the
activation energy
(reduce the amount
of energy needed for
a reaction to occur)
ADDITIONAL
substances are
required.
• This allows the
reaction to happen
more quickly.
Enzymes
• These things are biological catalysts:
– A CATALYST is a substance that lowers the
activation energy needed to start a chemical
reaction.
– It doesn’t change what is made, or how much
is made…only how fast it is made
Enzymes
• A biological catalyst
is an ENZYME
• It is used to speed
up a chemical
reaction
• It is usually specific
to one reaction
• Can be used over
and over
Enzymes
• An enzymes name describes what it does:
– Such as:
• Amylase breaks down amylose
• Maltase breaks down maltose
• Lactase breaks down lactose
(lactose intolerance is when lactose isn’t broken
down by lactase: causing bloating, gas, diarhea)
How enzymes work
• The reactants that bind to the enzyme are
called SUBSTRATES
• Where the SUBSTRATE and the ENZYME
bind together is called the ACTIVE SITE
• The enzyme/active site fit together like
puzzle pieces. Once together the active
site changes shape.
How enzymes work
• Enzymes help
chemical reactions
happen by breaking
bonds and allowing
new ones to form.
• It increases the
speed at which
reactions occur.
6.3 Water and Solutions
• The properties of water
make it well suited to
maintain homeostasis
in an organism
HOMEOSTASIS:
the body’s ability to
regulate its internal
condition by
adjusting cellular
processes
Recall the structure of water
Water is Polar
Meaning- one side of the molecule has a slightly positive
charge while the other side has a slightly negative charge
Water molecules bond to each other with hydrogen bonds
(shown above in the animation). The hydrogen is attracted
to the oxygen.
More Properties of Water
It is the universal
solvent because
many
substances
dissolve in it
Water is cohesive
It has a strong
attraction to
other water
molecules.
Because of this
it has high
surface tension.
This also causes
droplets to form.
Water is Adhesive
It forms hydrogen
bonds with other
molecules on other
surfaces. (think of
tape)
This causes capillary
action.
Acids and Bases
Remember that water is
a universal solvent
because a lot of things
dissolve in it.
Your body is about 70%
water.
When a substance that
contains hydrogen is
dissolved in water it
may release hydrogen
(H+)
Acids
• Substances that
release hydrogen
ions when dissolved
in water are called
ACIDS.
• The more hydrogen
released the more
acidic the solution
becomes
Bases
• Substances that
release hydroxide
ions (OH-) when
dissolved in water are
called BASES.
• The more hydroxide
released the more
basic the solution
becomes
pH Scale
The measure of the concentration
Of hydrogen in a solution is the pH.
The more hydrogen something
Releases the more acidic it is.
HOWEVER, the more acidic it
Is the lower the pH number on
The pH scale.
The more hydroxide (OH-) that
Is released the more basic
Something is.
The higher the number is on the
pH scale.
• Pure water is neutral and has a pH value of 7.0.
• Acids have a pH number lower than 7
• Bases have a pH number higher than 7
pH Scale
Acids and bases are key
substances in biology.
All the chemical reactions
in the body happen in
certain ideal
temperatures,
environments and pHs
Most chemical reactions
occur between the pH of
6.5 and 7.5
• Maintaining the proper
pH is important for
chemical reactions to
occur.
• This is called
HOMEOSTASISmaintaining the internal
environment.
Buffers
• BUFFERS are
mixtures that can
react with acids or
bases to keep the
Ph within a
particular range.
6.4 The building blocks of life
• Carbon is an element
that is in most
biological molecules.
• It has 4 electrons in
its outermost shell (it
would like 8 electrons
there in order to live
a happy and full life)
• So it likes to make
bonds with other
elements
Organic Chemistry
• Carbon forms covalent bonds with other
elements (they share the electrons)
• Anything with a carbon element in it is
“organic”
Macromolecules
• Macromolecules: large
molecules that are formed by
joining smaller organic
molecules to each other.
• These larger molecules are
also called POLYMERS.
• Polymers: molecules made
from repeating units of
identical or nearly identical
compounds (called monomers)
linked to each other by
covalent bonds.
Biological Macromolecules
• Carbohydrates (sugars,
and starches and
complex things like
cellulose):
– The name “carbo-” means
it has carbon
– The name “hydrate”
means it has water (H2O)
– So For every carbon there
is a water. Looks like this:
(C H2O)n
Carbohydrates
Carbohydrates play a
key role as a source of
energy
Some are a source for
structure (like cellulose
for a cell wall in plants)
Or Chitin which makes
up the exoskeleton of
things like shrimp.
Lipids
• Lipids: molecules
made mostly of carbon
and hydrogen that
make up fats, oils, and
waxes. They are
composed of fatty
acids, glycerol and
other components.
• They are mainly used
to store energy
Saturated fats
Found mostly in animal
fats. Associated with
higher cholesterol
levels (this is bad)
obesity, heart disease
(atherosclerosishardening of the
arteries) etc…
Unsaturated fats
Better for you in small
amounts.
Heart healthy, better
skin, supposedly
some help with
depression and also
keep your cholesterol
down. Some research
suggests it helps in
keeping your brain
healthy!
Saturated and unsaturated fats
Lipids are important
for the phospholipid
bilayer (makes up
cell membrane and
lets things go in/out
of the cell)
Steroids: estrogen,
testosterone and
cholesterol (also,
the bad ones)
Proteins
• Protein: a
compound made
of small carbon
compounds called
amino acids.
• Amino acids:
small compounds
that are made of
carbon, nitrogen,
oxygen,
hydrogen, and
sometimes sulfur.
Amino Acid Structure
Carbon can make four bonds:
One of those is with hydrogen
Another with an amino group that
Contains nitrogen
there is a carboxyl group that has
a carbon
THE 4TH BOND IS WITH A
VARIANT
GROUP (this changes depending
On what kind of amino acid is
Being made)
3D protein structure
Structure of the protein
depends on what
variable group is
attached in the
different amino
acids.
how the amino acids
“line up” determines
the primary structure
of the protein
Protein Structure
After the amino acid chain is formed it folds into
a unique 3D shape. This is its secondary
structure.
3D protein structure
• The Tertiary (3rd) type of structure can be
either globular (like a glob) or they can
form long fibers.
• The Fourth level of structure is when one
strand of protein combines with another
strand of protein.
Protein Function
• Make up about 15% of your body mass
• They make up structures like muscles, skin and
hair.
• They also give other structure, they are used to
transport things, they are used to communicate
signals with in the cell and between cells, they
speed up chemical reactions and control cell
growth.
• This is the cell
(plasma
membrane). It
uses, lipids,
carbohydrates and
proteins to help
maintain
homeostasis in
organisms
Nucleic Acids
• Nucleic Acids: store and transmit genetic
information.
• Made of repeating units of phosphorus,
nitrogen, oxygen, carbon and hydrogen
• A couple types: RNA (ribonucleic acid)
and DNA (deoxyribonucleic acid)