The Chemical Basis of

Life
Biology 1111
Chapter 2 (page 20-34) water stays together
форсфор у добриві- нутриїнт dust (contains p)
when absorbs phosphorus from desert dust

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You are here

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Can you answer these questions?
• What is the difference between an element and an isotope?

• What are atoms comprised of?

• What are the different types of chemical bonds?

• What are the four characteristics of water?

• What is a buffer?

• Can you give an example of a (simple) chemical reaction?

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 At the end of this chapter, you
should be able to:

Define the following terminologies: chemical

element, compound, isotope, ion,
electronegativity, reactivity

Learning Describe the characteristics of the subatomic

Objectives particles and how each relate to the
characteristic of the atom.

for Ch. 2:
Define the atomic number and mass number
given the subatomic particles of an atom.

Describe the role of valence electrons and how

they are determined.

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Differentiate between the different chemical bonds: ionic, polar covalent, non-polar covalent,
double covalent

Discuss the relationship between electronegativity and hydrogen bond formation.

Describe the four characteristics of water and how they are related to hydrogen bonds.

Differentiate between hydrophilic and hydrophobic molecules and give examples.

Define acid, base, buffer, and describe the pH scale.

Define chemical reaction in terms of reactants and products.

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Outline unit 2
• Chemistry of Life
• Life requires ~25 elements
• Atoms: Protons, neutrons, and electrons
• Elements combine to form compounds via chemical bonds
• The Water Molecule
• Hydrogen bonding
• Acids, Bases, and Buffers

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Question:

Why do biologists need to

study chemistry?
 Biological function starts at the
chemical level
The properties of organisms depend on:
• The arrangement
arrangement of atoms in molecules
• The arrangement of molecules in cells
cells

• The chemical between molecules in the cells

chemical interactions between

Examples:
• Why can’t plants walk and animals can?
• Why do all animals on the planet require oxygen but many species
bacteria do not?

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 Biological
function Question:

starts at the Do you think that we can understand all we

need to know about life from looking at
chemical chemical composition of organisms?

level
 Key concept 3: There is a strong
relationship between structure and
function Glucose Galactose Fructose

True for all levels in the hierarchy of life

Examples:
• All three sugars have the same formula
formula
• Slightly different structure
glycogen
• Slightly different utilization (e.g. glycogen
and starch
and starch made only from glucose)

Same formula: C6H12O6

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 Key concept 3: There is a strong
relationship between structure and
function
True for all levels in the hierarchy of life
Examples:
• The arrangement of atoms
atoms in a heme

molecule allows the protein hemoglobin

to bind oxygen
• Found in red blood cells, allows them to
transport
transport oxygen efficiently around the body

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 Life requires about 25 elements

• Organisms are composed

composed
of matter
• Matter is anything that has mass
mass

and takes up space

• All matter
matter is made of chemical

elements

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 Life requires about 25 elements

• A chemical element is a type of

composed
matter composed of only one type
of atom
• The smallest unit that still maintains
the property of the element
• Example:
• The gas oxygen (O2) is comprised
comprised only
of oxygen atoms
element
• Which makes it an element

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 Life requires about 25 elements

• There are ~ 92 naturally

naturalily occurring
elements and few more that occur
in the lab
• Arranged in a table based on their
physical properties
chemical and physical

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 Is glucose a chemical element?
iClicker
question A. Yes
B. No
What are essential elements?
naturally
25 of the 92 naturally occurring
elements are essential
essential for life

• Trace elements are elements

required
required in only minute amounts
(<0.01%, there are 14 trace
elements)

A goiter is the result of an

iodine deficiency that results
in an enlarged thyroid gland.

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 What are essential elements?

Why do you think oxygen, carbon,

hydrogen and nitrogen are so
abundant in our body?
core of most molecules, organic molecules (fat, protein)

This could be a midterm question

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 What are essential elements?

Why do you think trace elements

are found in such small amounts in
our body?
they are toxic, very few molecules require them to function

This could be a midterm question

we require they in small amount because small subset of

molecules need them 18
What is a compound?
• Compound: a substance containing elements
containing at least two elements, in a
fixed ratio!
H2O

What compound is pictured here?

Can you write the chemical formula?

• A compound has properties different(!) from its elements

• Most (but not all!) compounds in living
living things contain at least 4
elements O,H,C,N
• Different arrangements of atoms determines
determine the unique properties
of chemical compounds
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Elements can combine to form compounds

Na Cl2 NaCl

A compound of sodium + chloride in a 1:1 ratio makes an edible

compound from a pure metal and poisonous gas
https://www.youtube.com/watch?v=ODf_sPexS2Q  Na in water
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The secret life of atoms
• Elements consist of unique
unique atoms
• e.g. oxygen consists only of oxygen atoms
• Atoms are the smallest unit of matter
matter that retain the properties of
elements
• Atoms are composed of three subatomic
subatomic particles
• Proton (+ charge)
Nucleus of the atom
• Neutron (no charge)
• Electron (- charge)
• Atoms have a net neutral charge
electrons= number of protons
• Number of electrons

strong nuclear force

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Atomic number vs. atomic mass
Atoms of various elements
elements differ in the
number of subatomic particles
• Atomic number: indicates the number
number of
protons in the nucleus of an element
• Unique to each element
• Atomic mass: of an element is the sum
sum of
protons plus neutrons in the nucleus
• Atoms of an element always have the same number
of protons, but they may differ in the number
number of
neutrons (isotope)
• The elemental table refers only to the most
mostcommon
common
isotope of each element
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 Atomic Number and Atomic Mass
Mass
number 12
Chemical
This is how
you read the Atomic 6
C Symbol for
carbon

number
periodic
table
 A carbon atom has:
 6 protons
 6 neutrons
 6 electrons

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Practice: Atomic Number and Atomic Mass
14 How about nitrogen?
7
N
 The Atomic number is ________
7

 The Mass number is _________

14

Which means….
 A nitrogen atom has:
 __7 protons

 __7 neutrons

 __7 electrons
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Practice: Atomic Number and Atomic Mass
15 How about the nitrogen15 isotope?
7
N
 The Atomic number is ________
7

 The Mass number is _________

15

Which means….
 A nitrogen15 atom has:
 __7 protons

 __8 neutrons

 __7 electrons
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 Stable state- stable isotope
Why should we care about isotopes?
unstable nuclei (too many protone oe neutrone)
• Ever heard of radioactive isotopes?
• Unstable isotopes that we use in medicine, science and to make energy
• What are radioactive isotopes?
https://www.youtube.com/watch?v=cKJMk2Oiod0

• The ratio of an element’s stable isotopes is also useful for science

• For example, the ratio between N14 and N15 can help us understand
migration patterns of early humans as well as animals
https://www.youtube.com/watch?v=T24hdchCVIg

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 The importance of
electrons
• Electrons determine
determine
how an atom
behaves in the presence of other atoms
• Electrons exist in shells that only
accommodate
accommodate a certain number of
electrons

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 The importance of
electrons
• The number
number of rows in the table is number of
possible shells
• First shell/line = up to 2 electrons
• Second shell/line = up to 8 electrons
• Third shell/line = up to 8 electrons and so on
• As we go up the atomic
atomic number
the shell closest to the nucleolus will be
first
filled first

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 Which of the following statements is CORRECT?
A. The second shell can fit at most 8 electrons.

B. The number of neutrons in the atom

determines the atom’s “identity”.
iClicker
C. An atom always has equal numbers of
question protons and neutrons.

D. Carbon is the most abundant element in the

human body by weight.
Electron distribution affects chemical
properties of atoms
• Valence electrons reside in the outermost
outermost or valence
shell
• Chemical properties of atoms are mostly due to valence
velence
electrons
• Atoms with valence shells
shell that are not full tend to be chemically
reactive
• Atoms with full valence shells tend to be chemically inert or
stable
stable (also known as Nobel elements).

• The valence of an element is the number of electrons

electrons to
complete the outer shell of that element

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 What is the valence of these major
elements in organic molecules?

1 16 14
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1 H 8O 7 N 6C
• The closer an atom is to achieving a full valence shell, the more
“electron hungry” it is – Electronegative higher affinity to electrons.
• The emptier it is, the more likely an atom to give up the valance
electrons.
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The number of valence electrons
increases from left to right

Electronegativity

Nobles

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 What are chemical bonds?

• Atoms with incomplete valence

valence shells can share or transfer

valence electrons with other atoms

• Results in a close association between atoms, held by an attraction
= chemical bond
• Chemical bonds are what makes a compound
electro net

• Three types of chemical bonds:

• Ionic bonds Strong
• Covalent bonds (polar
polar or non-polar) interactions
• Hydrogen bonds

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 Ionic bonds are attractions between charged atoms
between
• Ionic bonds are attractions between ions of opposite charge
• Very electronegative atoms strip electrons from their low
electronegative
electrinegative bonding partners

Very low Very

electronegative electronegative 34
 Ionic bonds are attractions between charged atoms
• After the transfer of electrons, both atoms
atoms have a net charge

• Charged atoms (or molecules) are called ions

ions

• Those interactions
interactions are called oxidation-reduction (redox)

reactions

Very low Very

electronegative electronegative 35
Questions:
• Ionic bonds happen mainly between very
electronegative atoms and very low electronegative
atoms. Where would those be found on the table of
elements?

• What will happen if I replace the Na with Mg which

has 2 electrons in its outer shell?

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Covalent bonds
atoms that
• Covalent bonds form between two atoms
share a pair valence electrons
• Shared electrons count
count as part of each
atom’s valence shell
• The number of single covalent bonds an atom
additional
can form is equal to the number of additional
electrons needed to fill its outer shell
• The difference in electronegativity is smaller
smaller
than in ionic bonds

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Covalent bonds
• Double bonds form between atoms sharing
two
two pairs of electrons (stronger than single
covalent bonds!)
molecules are held together by
• Most biological molecules
at least two covalent bonds
Can molecules have a triple or quadruple
covalent bond? N C

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 Polar vs. non-polar covalent bonds
• Covalent bonds are a constant tug-of-
war for the shared
shared valence electrons

• Electronegativity measures an atom’s

affinity for shared electrons
electrons in a bond

• The more electronegative an atom is,

stronger it “pulls” electrons toward
the stronger
itself
• C and H have similar
electronegativity non-polar
• O and N are more electronegative
than C and H (i.e. more “electron-
hungry”) polar
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 Polar vs. non-polar covalent bonds
• Polar covalent bonds, larger difference
difference
between electronegativities
• Electrons pulled closer
closer
to the more
electronegative atom in the bond
• one partial negative atom and partial positive
atom
• Nonpolar covalent bonds,
bonds small
difference in electronegativities
• Electrons shared equally between atoms
in a molecule (e.g. H2, O2, CH4)

Two poles 40
 Question:

Which of these
molecules is held
together by polar
covalent bonds?
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 Why is CO2 not polar?
CO is a polar molecule, why is CO2 not?
• The explanation is beyond the scope of
this course
• The short answer is the geometry
geometry of the
molecule matters

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The Chemistry of Water
not a dry subject
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 Why is water so important for life?
• All living things require water
more than any other
substance
substance
• Most cells are surrounded
surrounded by
water and cells are 70-95%
water
• The abundance of water is
the main reason the Earth
Earth is
habitable
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 The water molecule

Water is made up of two atoms

atoms

with differing electronegativity

• Oxygen is more electronegative
electronegativity

than hydrogen

neatoshop.com

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 Water is a polar molecule
• Water has a net neutral
neutral charge

• Within the molecule,

molecule there are partial positive and
partial negative charges
• These partial charges make water a polar molecule
• The polarity of water
water leads to hydrogen bonding
and other unusual properties
• Hydrogen bonds form between the partial negative
charge on the oxygen
oxygen of one water molecule and the
partial positive charge on the hydrogen
hydrogen atoms of
other water molecules

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Would you expect to see water molecules
lined up like this?

A) Yes
B) No

Explain:

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The emergent properties of water

• Four emergent properties of water contribute

to the ability of Earth to sustain life
life

• All these properties

properties are related to hydrogen-
bonding:
1. Cohesion
2. heat capacity
High specific heat
3. freezing anomality of water
Expansion upon freezing
4. Versatility as a solvent

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Properties of water: cohesion
• Cohesion is the tendency of molecules
molecules to stick together
• Hydrogen bonds
bonds provide water with its unique cohesive
behavior
• Responsible for surface tension

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Why should we care about cohesion?

• Cohesion along with

adhesion allows water
water to
travel up trees
• Cohesion slows down the
water
evaporation rate of water
• Less polar liquids evaporate
faster –chloroform as an
example
https://www.reddit.com/r/ANormalDayInRussia/comment
s/d8o3tc/chloroform_are_for_weaklings/

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 Properties of water: high specific heat
capacity
• Specific heat capacity is the amount of
temperature
energy required to raise the temperature
of a given mass of a substance
1 calorie = +1*C
• Water can absorb
absorb or release a large
amount of heat with minimal
minimal change to its
own temperature

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 Properties of water: high specific heat
capacity

• Allows water to moderate

moderate temperature
inside and outside of biological systems
• On Earth’s surface, water absorbs
absorb heat

from warmer air and releases

releases stored heat
to cooler air
• That’s why costal areas see moderate
moderate
fluctuations in temperature
warming at twice the
• That’s why the arctic is warming
global rate

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 • Heat measures the total energy transfer
transfer
between molecules
• Temperature measures the intensity of heat heat
due to the average kinetic energy of
What is the molecules
difference • Heat is a transfer
transfer of energy caused by a
difference in temperature between
between heat molecules.
and Temperature:
temperature? How “hot” or
“cold” and
object is

Heat:
Transferred to
object (e.g. stove
heats pan) 53
How does water moderate temperature?
• When water is heated, energy first disrupts H-bonds
H-bonds and
molecules move faster
• Heat must be absorbed
absorbed to break H-bonds (energy required!)

• Much energy is used to break H-bonds to allow molecules

molecules to move faster,
temperature of water only increases a little with a lot of
meaning the temperature
energy
• When water is cooled, heat is released
released as H-bonds form

• Which is why it takes

takes a long time for water to cool

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 Snowball earth

• A hypothesis that at several

points throughout earth
history, earth was completely
ice covered
• Ice age on steroids
• How could life survive
under such conditions?

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 Properties of water: expansion upon
freezing
• If ice sank, all bodies of water would freeze
freeze solid, making life on
earth impossible
• Ice floats because H-bonds
H-bonds are more ordered in ice than in
liquid water most amount of molecules
• Water achieves the highest density at 4ºC

Somethingscrawlinginmyhair.com
the number of molecules per volum

blanket
crystal
structure

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Ice is less dense than water

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Properties of water: versatile solvent
• A solution is a homogenous
homogenous liquid substance
розчиннят
• A solvent is the dissolving liquid of a solution
• A solute is the substance dissolved in a solution
• Water is the solvent for most of life’s solutions
solution

• The versatility of water

water as a solvent is a result of its polarity

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Hydrophilic vs. hydrophobic
• A hydrophilic substance = • A hydrophobic substance =
“water-loving” “water-fearing”
• A substance
substance that has an affinity • A substance that lacks an
for water affinity for water
affinity

• Oil is hydrophobic
hydrophobic because oil
molecules are relatively
nonpolar

fats(lipid) = polar = don`t interact

with water
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 Which of the following molecules is
HYDROPHOBIC?
A. NaCl (salt)
iClicker B. NH3 (ammonia)
question C. C2H6 (ethane)
D. H2O (water)
Hydrophilicity is
important in nature

One example is the lotus leaf.

• Very hydrophobic
hydrophobic surface that self
cleans.
• Self cleaning windscreens and
windows?!

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Acids and bases
• The chemistry of life is sensitive
sensitive to acidic and basic
conditions
• In aqueous solutions,
solution some water molecules dissociate
dissociate

into H+ (hydrogen cation) and OH- (hydroxyl anion)

H2O  H+ + OH-
• For proper biological function
function to be preserved, the correct
balance of H+ and OH- ions must be maintained
maintained

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 Acids and bases
• Recall: water has a net neutral
neutral charge
• The concentration of H+ and OH- ions is exactly equal in pure water
• Adding solutions called acids or bases disrupts
disrupts the balance of H+

and OH- ions

• Acids donate HH++ ions to solutions
• The higher the acidity of a solution,
solution the higher the [H+]  brackets mean concentration

• Bases accept H+ ions from solutions

• The more basic a solution,
solution the higher the [OH-]

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 What is the pH scale?
• The pH scale measures
measure the acidity of a
solution
most acidic
• Ranges from 0 (most acidic) to 14 (most
basic)
• Acidic
Acidic solutions have a pH less than 7 (high

[H+])
• Basic solutions have a pH greater than
7(high [OH-])

• Most biological fluids

fluids have a pH ~6-8
burn fats
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Buffers are important to biology

• The internal pH of most living cells must remain close to pH 7

• Buffers are substances that minimize

minimize changes in pH
• Maintain a specific
specific balance of [H+] and [OH-]

• Buffers accept H+ ions when they are in excess and donate H+ ions
when there are too little

• Buffers are crucial to living

living things!

carbon dyiox in blood = buffer

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Questions:
Note that buffers don’t necessarily maintain
a pH of 7, buffers can maintain an acidic or
basic pH. acid=release protons
What will happen if you will add a low pH
material to a buffer with pH 10?
accept H+, PH will be maitaned

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 67

Chemical
reactions
rearrange matter
https://gfycat.com/helplessdentalgoldfinc
h
Photo credit: Lawrence Menz (2019)
 Chemical reactions rearrange matter
• Chemical reactions make and break bonds
• The input molecules of chemical reactions are called reactants
reactants

• The output molecules of chemical reactions are called products

products

Reactants Product

The triumph and tragedy of Fritz Haber TONS OF ENERGY

https://www.youtube.com/watch?v=UezB7pJA2tQ 68
Chemical reactions rearrange matter
• Chemical reactions = making
making or breaking chemical bonds

• Some chemical reactions release require

release energy and some require
additional energy

+ ENERGY

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