Chapter 2: The Chemistry of Life

Corresponds with OpenStax Biology 2e Chapter 2

Chapter 2: The Chemistry of Life
▪ e.g. an iron deficiency = anemia (low red blood cells),
which causes fatigue, impaired immune function, &
eventually death
▪ e.g. a potassium deficiency = muscle cramps,
weakness, eventually the heart will stop beating
▪ e.g. an iodine deficiency = goiters (swollen thyroid
glands, located in the neck),
depression, & eventually
deficits in mental function
– You don’t need to know these examples,
they are just to emphasize the importance
of each element, even if you only need
small amounts.
Figure: [Link]
Chapter 2: The Chemistry of Life
▪ The smallest unit of an
element = an atom
– e.g. one unit of oxygen
is an atom of oxygen
(smallest you can get) A single atom of the element sodium

“Because they are so long lived, atoms really get around. Every
atom you possess has almost certainly passed through several
stars and been part of millions of organisms on its way to
becoming you. We are each so atomically numerous and so
vigorously recycled at death that a significant number of our
atoms – up to a billion for each us, it has been suggested –
probably once belonged to Shakespeare.”
-Bill Bryson in A Short History of Nearly Everything
Figure: [Link]
Chapter 2: The Chemistry of Life
▪ Atoms themselves are all made up of 3 components:
– Protons = positive charge (+) both located
inside the
– Neutrons = no charge
atomic nucleus

– Electrons = negative charge (-)

• orbit around the nucleus within electron shells
• electrons are in constant
motion orbiting the
nucleus - the shells atomic
nucleus
just represent where
they are orbiting
electron
shell

Figure: [Link]
Chapter 2: The Chemistry of Life
▪ Atoms are electrically neutral because the number of
protons (+) is equal to the number of electrons (-)

▪ Other than hydrogen (a special case), a regular

atom also has the same amount of neutrons
– e.g. helium atom = 2 protons, 2 neutrons, 2
electrons

▪ If an atom does not have the

same number of everything, it
will have a special name – we’ll
talk about these soon Helium (He)
Figure: [Link]
Chapter 2: The Chemistry of Life
▪ Protons
– Each element has a unique
number of protons
• e.g. hydrogen ALWAYS has one
• e.g. helium ALWAYS has two Helium (He)
• e.g. carbon ALWAYS has six

– If you change the number of

protons, you change the element
completely
• e.g. if you add a proton to
hydrogen, it becomes helium
Figure: [Link]
Figure: [Link]
Chapter 2: The Chemistry of Life
 ▪ Because an atom of hydrogen always has one
proton no matter what, we can define hydrogen by
this unchanging fact – we call this its atomic number
– Atomic number = the number of protons an atom
has
Hydrogen has an atomic number of 1 Carbon = 6
Helium = 2

Helium (He)
[Link] [Link] [Link]

Chapter 2: The Chemistry of Life

▪ On a periodic table of elements, you’ll always see
the atomic number for each element listed

Figure: [Link]
Chapter 2: The Chemistry of Life
▪ We can also describe an atom by its atomic mass
– Atomic mass = number of protons + neutrons
• Electrons are so light, we usually ignore them
in biology

Atomic mass
of helium = 4

Helium (He)
Figure: [Link]
Figure from OpenStax Biology 2e
Chapter 2: The Chemistry of Life
▪ The atomic number
indicates the number of
Atomic Number
protons in the nucleus.
▪ The chemical symbol is Chemical Symbol
an abbreviation. Element Name
▪ The atomic mass is the
Atomic Mass
number of protons and
neutrons.

Chapter 2: The Chemistry of Life

▪ Identify the atomic structure of each element.

Chapter 2: The Chemistry of Life

▪ Neutrons
– The number of protons never changes, but the
number of neutrons an atom has can change
• A regular helium atom has
2 P+, 2 N, & 2 E-

– An isotope = an atom with

a different number of neutrons
• e.g. helium with
2 P+, 3 N, & 2 E-

Helium (He)
Figure: [Link]
Chapter 2: The Chemistry of Life
▪ Why are isotopes important in biology?

– Some isotopes are stable, but some are unstable

• Unstable isotopes are radioactive
–They break apart, releasing radiation

radiation

radioactive
isotope
Figure: [Link]
Chapter 2: The Chemistry of Life
▪ How radioactivity / radiation benefits science:
– Harnessed for energy
– Treatment for cancer (more in a future chapter)
– Determining the age of fossils
– Medical imaging (PET scans) Red indicates high
radioactivity, showing
a cancerous tumor
• PET scan = low dose of using a lot of energy
radioactive glucose injected
into patient
– glucose is broken down for
energy, releasing radio-
activity, which we can
measure
Figure: [Link]
Chapter 2: The Chemistry of Life
▪ Too much
exposure to
radiation can
cause:
– cancer
– radiation
sickness
– severe birth
defects
– even death

Figure: [Link]
Chapter 2: The Chemistry of Life
Radiation is dangerous and can cause cancer. Yet,
it’s also used to treat cancer and in medical scans
like PET scans. How do you think it’s possible for
the same thing to be a cause of disease and a tool
for healing?

Chapter 2: The Chemistry of Life

▪ Electrons (-) are distributed around the atomic
nucleus in electron shells, where they are in
constant motion Hydrogen only has 1 electron but 2 can fit in this first shell

– The first electron

shell holds up to
2 electrons
– The second electron
shell holds up to 8
electrons
– The third electron
shell also holds up
to 8 electrons Carbon has 6 electrons, with 2 in the
first shell and the remaining 4 in the
second shell (which could hold up to 8)

Figure: [Link]
Chapter 2: The Chemistry of Life
▪ Electrons are most stable when the outer shell of
the atom is full

– To fill their shells, atoms interact with other

atoms, losing, gaining, or sharing electrons

Hydrogen (H) Helium (He)

- Atomic # = 1 - Atomic # = 2
- Outer shell not filled - Outer shell filled
- Unstable - Stable
- Will interact with - Will NOT interact
other atoms with other atoms
Chapter 2: The Chemistry of Life
 can hold 1 more

can hold 4 more

Figure: [Link]
Chapter 2: The Chemistry of Life
▪ Atoms that lose or gain electrons
to become stable are called ions
Sodium loses an Chloride gains an
electron: cation electron: anion

– An atom that loses an

electron (-) will have a
positive charge = cation
• e.g. carbon with 6 P+, 6 N, & 5 E-

– An atom that gains an electron (-) will have a

negative charge = anion
• e.g. carbon with 6 P+, 6 N, & 7 E-
Figure: [Link]
Figure: [Link] Chapter 2: The Chemistry of Life
cation anion
Figure: [Link]
Chapter 2: The Chemistry of Life
 Atoms link together using
chemical bonds to form molecules
▪ The interaction of atoms can cause them to attach
together through chemical bonds
– 2 or more atoms joined together by
chemical bonds = molecule
• e.g. oxygen joins to 2 hydrogen
atoms through chemical bonds to
make a water molecule

– Remember: life is organized – atoms make up

molecules, which make up cells, which make up us
– Remember: life requires energy & nutrients, which we get
through eating molecules like fats & proteins
Figure: [Link]
Chapter 2: The Chemistry of Life
▪ There are many types of chemical bonds that hold
molecules together
– 3 types are important for biology: they hold
together our bodies & the foods that we eat

Type of Bond Chemical Interaction Strength

Ionic An electron is transferred, creating Moderate –
positive & negative ions that attract breaks easily
one another in water
Covalent Electrons are shared between atoms
- Nonpolar - Equally Strong
- Polar - Unequally
Hydrogen A positive atom within a molecule is
attracted to a negative atom in a Weak
different molecule

Chapter 2: The Chemistry of Life

▪ Ionic Bonds
– The electrical attraction
between cations (+) &
anions (-) pulls atoms cations (+) and anions (-) attract,
forming ionic bonds
together
• similar to magnets

cation anion ionic bond forms between them

Figure: [Link]
Figure: [Link] Chapter 2: The Chemistry of Life
▪ Covalent Bonds
– Two atoms share electrons
• this means each shared electron will orbit its
own atom, but also orbit the other atom

Remember,
electrons are
constantly
orbiting in the
shell.
These are 2
unstable atoms.

Now the shells

overlap and each
electron is orbiting
both atoms.
This is now a
stable molecule.
Figure: [Link]
Chapter 2: The Chemistry of Life
 Types of Covalent Bonds

Single Bond Double Bond Triple Bond

One pair of Two pairs of Three pairs of
electrons is shared. electrons are electrons are
shared. shared.

Chapter 2: The Chemistry of Life

▪ Classification of covalent bonds
by bond polarity

– Nonpolar = electrons shared

evenly = uncharged

• No charge builds up on
either side

Same charge on either side (1 positive

proton each), & electrons spend equal
time near each nucleus
So no charge builds up on either side of
this H2 molecule: nonpolar
Figure: [Link]
Chapter 2: The Chemistry of Life
▪ 2 types of covalent bonds:

– Polar = electrons NOT shared evenly = charged

• A charge builds up on either side of the bond

three unstable atoms stable H2O molecule

Figure: [Link]
Chapter 2: The Chemistry of Life
▪ Polar = electrons NOT shared evenly = charged
– Some atoms pull more on electrons than others
(based on “electronegativity,” which is more detail than we will go into)
• Shared electrons now spend more time around
one atom & less time around the other atom
Remember: electrons are in constant orbit but
they’re more often orbiting Oxygen here. That
means the Hydrogen atoms have a positive
proton but no negatives around them most of
the time, so they’re now kind of positive.

In a water molecule
(H2O) the oxygen
pulls more on the
electrons
Figure: [Link] Chapter 2: The Chemistry of Life
▪ Because oxygen pulls more on the electrons (-),
which spend more time around it, it now has a slight
negative charge
▪ The hydrogen atoms don’t have electrons (-) around
them very often, so now they are slightly positive

Figure: [Link] Chapter 2: The Chemistry of Life

▪ Hydrogen Bonds
– Polar covalent bonds (like in H2O) produce
positive & negative regions
• These regions repel
& attract each other,
just like ions (or
magnets)
• Notice the negative
ends attract the
positive ends &
vice versa, so the
entire molecules stick to each other
Figure: [Link]
Chapter 2: The Chemistry of Life
▪ Atoms interact with each other in order to stabilize

– Some chemical reactions cause an atom or

molecule to be stripped of its electrons
• Can be caused by radiation, UV light, some
chemicals & food additives, pesticides,
pollution, cigarette smoke, etc.

– An atom or molecule that has been

stripped of its electrons & is
highly unstable = free radical

Chapter 2: The Chemistry of Life

▪ Free radicals are HIGHLY unstable: grab electrons
from any nearby source to stabilize themselves
– Stealing electrons = new free radicals, plus it
damages the molecules so they can’t do their jobs
in the body anymore

Figure: [Link]
Chapter 2: The Chemistry of Life
Truck driver skin aging after 28 years of sun
exposure.

Chapter 2: The Chemistry of Life

▪ Free radicals are more & more common as
pesticides, pollution, etc. increase in our environment

▪ How can we fight free radicals?

– There are special molecules that can stabilize free
radicals without becoming free radicals themselves
= antioxidants
• break the chain
reaction

Figure: [Link]
Chapter 2: The Chemistry of Life
▪ Antioxidants include vitamins A, E,
& C, flavenoids, carotenoids, etc.
– Found in high amounts in fruits &
vegetables (especially raw)
– Moderate amounts in nuts, tea,
& coffee
– Low amounts in red wine &
dark chocolate
• watch out for milk proteins in
chocolate or coffee though –
bind to & negate antioxidants
[Link] [Link]
[Link] Chapter 2: The Chemistry of Life
Making use of free radicals-Photodynamic therapy
-Increased reactive radicals in cells can lead to cell
death.
-By using photosensitizers to produce radicals upon
light irradiation, PDT could be directed to eliminated
tumors and bacteria for therapeutic applications.

Chapter 2: The Chemistry of Life

Why are molecules of water so important?

Chapter 2: The Chemistry of Life

 Why are molecules of water so important?

▪ Water is essential to life

(as we know it)
– This is why the search for life
on other planets often begins
with a search for water

– Some properties of water that

make it able to support life:
• Water is cohesive
• Many substances dissolve in water
• Water solutions come in a range of pH values
Figure: [Link] Chapter 2: The Chemistry of Life
▪ Water is cohesive
– Cohesion = the 1. Water molecules
are pulled into the
tendency of water atmosphere by
molecules to stick evaporation

together through
2. More water
hydrogen bonds molecules are
pulled up the tree,
• remember following those that
evaporated
hydrogen bonds!
• allows water to 3. More water
move to the top of molecules are pulled
into the tree from the
the tallest trees, root system, following
the previous water due
defying gravity to cohesion
water
Figure: [Link]
Chapter 2: The Chemistry of Life
▪ Water cohesion also allows
organisms to move across it

– Also why belly flops hurt!

[Link]

[Link]

Chapter 2: The Chemistry of Life

▪ Many substances dissolve in water
– Substances that dissolve in water = hydrophilic
• “water-loving”
• e.g. salts, sugars, & electrolytes

–important because we need these things

to move through our blood stream (which
is mostly water) easily

Notice how water molecules

happily surround these salts,
allowing them to move in the
blood stream easily

Figure from OpenStax Biology 2e

Chapter 2: The Chemistry of Life
▪ Many substances dissolve in water – some don’t
– Substances that do NOT dissolve in water =
hydrophobic
• “water-fearing” – clump up in water
• e.g. fats, oils, & cell membranes
–it is important that our cells
do not dissolve when we get
wet, or when they contact
our watery blood stream, so
we use these things to
waterproof ourselves &
form barriers
Figure: [Link]
Chapter 2: The Chemistry of Life
▪ Water solutions come in a range of pH values

– In a solution of water, some molecules become

“ionized” – they break apart & become charged
• H2O → OH– + H+

donated electron

O O
H H H
H

cation anion
Chapter 2: The Chemistry of Life
▪ Solutions where OH– = H+ are neutral (equal)
– pH 7
– e.g. pure water

▪ Solutions where OH– < H+ are acidic (more H+)

– pH 0-6
– e.g. lemon juice & vinegar

▪ Solutions where OH– > H+ are basic (more OH-)

– pH 8-14
– e.g. ammonia & bleach
Chapter 2: The Chemistry of Life
▪ The pH scale is a way of
referring to the acidic, basic, or
neutral quality of a solution

Figure: [Link]
Chapter 2: The Chemistry of Life
 Sweat is effective
at cooling our
bodies due to
this property.

Water has a
high heat
capacity,
meaning a
large amount
of energy is
needed to
raise its
temperature. Chapter 2: The Chemistry of Life
▪ Water will come up over & over as we learn more
about how our cells & bodies work
– We’ll talk about the other molecules that make up
our bodies – how they interact with water will be
important (e.g. hydrophilic vs. hydrophobic)
– We’ll talk about why it’s so important to keep our
blood neutral, & not acidic or basic

▪ Up next: water is essential to life & our bodies contain

a lot of it, but it is not what living things are actually
built of
– So what molecules are we built of?
Chapter 2: The Chemistry of Life