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
HOMEOSTASIS-
maintaining 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
(atherosclerosis-
hardening 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)
Chapter 6 Chemistry in Biology

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.
Chapter 6 Chemistry in Biology

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.
Chapter 6 Chemistry in Biology

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Chapter 6 Chemistry in Biology

Chapter Diagnostic
Questions

Which of the following particles is negatively

charged?

A. electron
B. isotope
C. neutron 1. A
2. B
D. proton 3. C
4. D

0% 0% 0% 0%
Chapter 6 Chemistry in Biology

Chapter Diagnostic
Questions

Isotopes are created by a change in the

number of what particle of an atom?

A. electrons
B. neutrons
C. protons 1. A
2. B
D. ions 3. C
4. D

0% 0% 0% 0%
Chapter 6 Chemistry in Biology

Chapter Diagnostic
Questions

Identify the proteins that speed up the rate

of
chemical reactions.
A. substrates
B. enzymes
C. ions 1. A
2. B
D. reactants 3. C
4. D

0% 0% 0% 0%
Chapter 6 Chemistry in Biology

6.1 Formative
Questions

What particles are in an

atom’s nucleus?

A. neutrons and electrons

B. protons and electrons
C. protons and neutrons 1. A
2. B
3. C
0% 0% 0%
Chapter 6 Chemistry in Biology

6.1 Formative
Questions

What causes the overall charge of an atom to

be zero?

A. an equal number of
protons and neutrons
B. an equal number of
1. A
protons and electrons
2. B
C. an equal number of 3. C
neutrons and electrons 0% 0% 0%
Chapter 6 Chemistry in Biology

6.1 Formative
Questions

What type of substance is water?

A. a compound
B. an element
C. an isotope
D. a mixture 1. A
2. B
3. C
4. D

0% 0% 0% 0%
Chapter 6 Chemistry in Biology

6.1 Formative
Questions

What provides the energy for all living

processes?

A. chemical bonds
B. ionic compounds
C. radioactive isotopes 1. A
2. B
D. van der Waals forces 3. C
4. D

0% 0% 0% 0%
Chapter 6 Chemistry in Biology

6.2 Formative
Questions

Which is a chemical reaction?

A. a match burning
B. salt dissolving
C. water boiling
D. gasoline evaporating 1. A
2. B
3. C
4. D

0% 0% 0% 0%
Chapter 6 Chemistry in Biology

6.2 Formative
Questions

Which chemical reaction is endothermic?

A.

B. 1. A
2. B
0% 0%
Chapter 6 Chemistry in Biology

6.2 Formative
Questions

How does an enzyme increase the rate of a

chemical reaction?
A. It acts as a reactant.
B. It reduces the amount

of heat produced. 1. A
2. B

C. It increases the 3.
4.
C
D
amount of product.
0% 0% 0% 0%
D. It lowers the
activation
energy.
Chapter 6 Chemistry in Biology

6.2 Formative
Questions

What occurs at the

active site in the
enzyme substrate
complex?
A. An exothermic chemical
reaction takes place.
B. Chemical bonds are
broken 1. A

and new bonds are 2.

3.
B
C
formed. 4. D

C. The enzyme gets used up

0% 0% 0% 0%

in the reaction.
D. The substrates provide
energy for the enzyme.
Chapter 6 Chemistry in Biology

6.3 Formative
Questions

Why is water able to dissolve a wide variety

of
solutes?
A. It acts as a catalyst.
B. Its pH is neutral.
C. It is a polar molecule. 1. A
2. B
D. It is an ionic compound. 3. C
4. D

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Chapter 6 Chemistry in Biology

6.3 Formative
Questions

What type of bonds attracts water molecules

to each other and to other substances?

A. covalent bonds
B. double bonds
C. hydrogen bonds 1. A
2. B
D. ionic bonds 3. C
4. D

0% 0% 0% 0%
Chapter 6 Chemistry in Biology

6.3 Formative
Questions

Which ion, when released in water, causes a

solution to be basic?

A. Cl–
B. OH–
C. H+ 1. A
2. B
D. Na+ 3. C
4. D

0% 0% 0% 0%
Chapter 6 Chemistry in Biology

6.3 Formative
Questions

What is the name for a substance that keeps

the pH in cells within the 6.5 to 7.5 pH range?

A. alkali
B. antacid
C. buffer 1. A
2. B
D. neutralizer 3. C
4. D

0% 0% 0% 0%
Chapter 6 Chemistry in Biology

6.4 Formative
Questions

Which element do almost all biological

molecules contain?

A. carbon
B. nitrogen
C. phosphorus 1. A
2. B
D. sodium 3. C
4. D

0% 0% 0% 0%
Chapter 6 Chemistry in Biology

6.4 Formative
Questions

How many covalent bonds can

carbon form with other atoms?

A. 1
B. 2
C. 4 1. A
2. B
D. 8 3. C
4. D

0% 0% 0% 0%
Chapter 6 Chemistry in Biology

6.4 Formative
Questions

What type of biological molecule is an

enzyme?

A. hormone
B. nucleic acid
C. protein 1. A
2. B
D. steroid 3. C
4. D

0% 0% 0% 0%
Chapter 6 Chemistry in Biology

6.4 Formative
Questions

What are fats, oils, and waxes composed

of?
A. lipids
B. nucleotides
C. polypeptides
D. sugars 1. A
2. B
3. C
4. D

0% 0% 0% 0%
Chapter 6 Chemistry in Biology

6.4 Formative
Questions

What are the monomers that make up

proteins?

A. amino acids
B. fatty acids
C. glycerols 1. A
2. B
D. nucleotides 3. C
4. D

0% 0% 0% 0%
Chapter 6 Chemistry in Biology

6.4 Formative
Questions

Which biological molecule transports

substances between cells?

A. carbohydrate
B. lipid
C. nucleic acid 1. A
2. B
D. protein 3. C
4. D

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Chapter 6 Chemistry in Biology

Chapter Assessment
Questions

Look at the following figure. ?

Determine what the upward
curve represents.

A. activation energy
B. reactants 1. A

C. products 2.
3.
B
C

D. enzymes 4. D

0% 0% 0% 0%
Chapter 6 Chemistry in Biology

Chapter Assessment
Questions

Look at the energy levels in the

atom. What is the maximum
number of electrons energy
level two can hold?

A. 2
1. A
B. 4 2. B
3. C
C. 6 4. D

D. 8 0% 0% 0% 0%
Chapter 6 Chemistry in Biology

Chapter Assessment
Questions

Explain why chemical equations must be

balanced.

Answer: Chemical reactions require balance

of mass. Therefore, 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.
Chapter 6 Chemistry in Biology

Standardized Test
Practice

Which is a result of van der Waals forces?

A. atoms sharing
electrons
B. table salt dissolving
in water
C. ionic compounds 1.
2.
A
B
forming crystals 3.
4.
C
D

D. water molecules
0% 0% 0% 0%
forming droplets
Chapter 6 Chemistry in Biology

Standardized Test
Practice

What is true of this

chemical reaction?
A. Energy is not needed to
start the chemical reaction.
B. Heat and/or light energy
are released in this reaction.
C. The activation energy is 1. A

greater than the energy 2.

3.
B
C
released. 4. D

D. The energy of the products

and the reactants is the same. 0% 0% 0% 0%
Chapter 6 Chemistry in Biology

Standardized Test
Practice

Which fruit contains

a higher concentration
of hydrogen ions?

A. tomatoes
B. bananas
1. A
2. B
3. C
4. D

0% 0% 0% 0%
Chapter 6 Chemistry in Biology

Standardized Test
Practice

What do cellulose and chitin have in

common?
A. They are energy-
storing polymers.
B. They are found in the
cells of animals.
C. They are structural 1.
2.
A
B
polysaccharides. 3.
4.
C
D

D. They are composed of

0% 0% 0% 0%
repeating sucrose
units.
Chapter 6 Chemistry in Biology

Standardized Test
Practice

Which polysaccharide stores energy in

muscle
and liver tissue?
A. gluten
B. glycogen
C. starch 1. A
2. B
D. sucrolose 3. C
4. D

0% 0% 0% 0%
Chapter 6 Chemistry in Biology

Standardized Test
Practice

What is the function of this

biological macromolecule?
A. communicate signals
between cells
B. produce vitamins
and hormones 1. A

C. provide support 2.
3.
B
C
and protection 4. D

D. store and transmit

genetic information 0% 0% 0% 0%
Chapter 6 Chemistry in Biology

Standardized Test
Practice

Which is a characteristic of all lipids?

A. They are saturated
triglycerides.
B. They do not dissolve
in water.
C. They are liquid at 1.
2.
A
B
room 3. C

temperature. 4. D

D. They store less 0% 0% 0% 0%

energy
than carbohydrates.