Cells & Molecules 2013

Week 1: The chemistry of life

» Chemistry and chemical bonding

» The importance of carbon
» Water

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An element is a pure substance
made up of one kind of atom

» Elements make up all matter.

» An element is a pure substance that cannot be
broken down into simpler substances
» An atom is the smallest particle of an element

Cells & Molecules 2013 R.W. Freeburn

 The properties of elements
depend on atomic structure
» Atoms are composed of
˃ Protons
+ Positively charged particles
+ Located in the nucleus
˃ Neutrons
+ Neutral particles
+ Located in the nucleus
˃ Electrons
+ Negatively charged particles
+ Found in orbitals surrounding the nucleus 3

Cells & Molecules 2013 R.W. Freeburn

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Cells & Molecules 2013 R.W. Freeburn

 Atomic number
» Atomic number = number of protons
˃ Every atom of a particular element has the same
number of protons

• It is used in the periodic table to identify and

organize elements into various groups

Cells & Molecules 2013 R.W. Freeburn

 Atomic mass
» Mass or weight?
˃ Mass – refers to amount of substance
˃ Weight – refers to force gravity exerts on substance

» An element's atomic mass

= number of protons + number of neutrons
(Each proton and neutron has a mass of ~1 dalton)

» Atoms of same element may have same atomic

number but different atomic mass because they
possess different numbers of neutrons
˃ Known as isotopes of a single element 6

Cells & Molecules 2013 R.W. Freeburn

 Electron arrangement
» Rules of atomic structure dictate that electrons
occupy a specific zone beyond the nucleus
˃ these zones comprise the electron orbitals
» Key to the chemical behavior of an atom lies in the
number & arrangement of electrons in their orbitals
» Bohr model – electrons in discrete orbits
» No orbital can contain more than 2 electrons

Cells & Molecules 2013 R.W. Freeburn

Electron arrangement
No orbital can contain
more than 2 electrons

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 Energy levels
» Electrons have potential energy related to their position
 Electrons farther from nucleus have more energy

» Be careful not to confuse energy levels, which are drawn

as rings to indicate an electron’s energy, with orbitals,
which have a variety of three dimensional shapes and
indicate an electron’s most likely location

Cells & Molecules 2013 R.W. Freeburn

Atomic Structure

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 Electrons
Valence shells determine an element's stability and reactivity
» Rules of atomic structure dictate that electrons occupy a specific
zone beyond the nucleus
 electron shell (contains the orbitals)
» Physical laws permit only a set number of electrons in each shell
 2 in the first shell, 8 each in the next two, and so on
» Each shell represents a stable energy level
 When shell has a complete number of electrons, element is stable
 not likely to react with other atoms
» Valence electrons are located in the outermost shell of an atom
 atom's reactivity dependent on whether or not outermost shell is full
 element with a full outer electron shell is a noble gas
»

Cells & Molecules 2013 R.W. Freeburn

 Elements
» Periodic table displays elements according to
valence electrons
» Valence electrons = number of electrons in
outermost energy level
» Inert (nonreactive) elements have all 8 electrons
» Octet rule – atoms tend to establish completely full
outer energy levels

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Cells & Molecules 2013 R.W. Freeburn

Deducing the atomic structure

Atomic number

Atomic mass

Atomic number

Atomic mass

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Cells & Molecules 2013 R.W. Freeburn

Periodic Table of the Elements

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 Textbook Activity

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Principles of Biology
Cells & Molecules 2013 R.W. Freeburn
 Most substances we encounter
in daily life are compounds
» Practically all the materials on Earth are composed of 92
elements which combine in different ways

» Molecules are groups of atoms held together in

a stable association
» Compounds are molecules containing more
than one type of element
» Atoms are held together in molecules or
compounds by chemical bonds

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Cells & Molecules 2013 R.W. Freeburn

 The chemistry of life

» Living systems are based on carbon

 chemical element
» Framework of biological molecules consists primarily of
carbon bonded to
 Carbon
 O, N, S, P or H
» Valency of 4 - forms 4 bonds with other atoms

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Principles of Biology
Cells & Molecules 2013 R.W. Freeburn
 Redox
» During some chemical reactions, electrons can
be transferred from one atom to another
˃ Oxidation = loss of an electron
˃ Reduction = gain of an electron

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 Covalent bonds
» Form when atoms share 2 or more valence electrons
» Results in
˃ no net charge
˃ satisfies octet rule
˃ no unpaired electrons
» Strength of covalent bond depends on the number
of shared electrons
» Many biological compounds composed of more than
2 atoms – may share electrons with 2 or more atoms
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Cells & Molecules 2013 R.W. Freeburn

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 Many elements share electrons, which results in a
strong covalent bond.

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Principles of Biology
Cells & Molecules 2013 R.W. Freeburn
 Ionic bonds
» Formed by the attraction of oppositely charged ions
» Gain or loss of electrons forms ions
˃ Na atom loses an electron to become Na+
˃ Cl atom gains an electron to become Cl–
˃ Opposite charges attract so that Na+ and Cl– remain
associated as an ionic compound

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 Ionic bonds

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Principles of Biology
Cells & Molecules 2013 R.W. Freeburn
 Water
» Life is inextricably tied to water
» Single most outstanding chemical property of water
is its ability to form hydrogen bonds
˃ Weak chemical associations that form between the partially negative
O atoms and the partially positive H atoms of two water molecules

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Cells & Molecules 2013 R.W. Freeburn

 Hydrogen Bonding
» covalent bonds within a water molecule give it polarity.
» shared electrons (blue arrows) are found more often on the
oxygen atom than the hydrogen atoms due to oxygen's
higher electronegativity.
» unequal sharing of electrons creates partial positive (δ+) and
partial negative (δ-) poles on the water molecule.

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Cells & Molecules 2013 R.W. Freeburn

 Hydrogen Bonding (cont.)
» Two water molecules form a hydrogen bond.
» A partially positive hydrogen atom on one molecule bonds to
the partially negative oxygen atom on the other

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Cells & Molecules 2013 R.W. Freeburn

 Hydrogen bonds
» Cohesion – polarity of water allows water molecules
to be attracted to one another
» Attraction produces hydrogen bonds
» Each individual bond is weak and transitory
» Cumulative effects are enormous
» Responsible for many of water’s important physical
properties

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Cells & Molecules 2013 R.W. Freeburn

 Water
» Each water molecule forms
4 hydrogen bonds with
surrounding molecules

Cells & Molecules 2013 R.W. Freeburn

 Water
How Water's Properties Sustain Life

The 4 most important properties of water are;

1. its "stickiness"
2. its excellence as a solvent
3. its ability to moderate temperatures
4. the fact that ice floats on liquid water

Cells & Molecules 2013 R.W. Freeburn

 Water
Water is "sticky."

» Cohesion – water molecules » Adhesion – water

stick to other water molecules molecules stick to other
by hydrogen bonding polar molecules by
hydrogen bonding
» cohesion & adhesion play important role in
movement of water through vascular tissue in plants
Cells & Molecules 2013 R.W. Freeburn
 Water

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Principles of Biology
Cells & Molecules 2013 R.W. Freeburn
 Water
Water is an excellent solvent
» many substances dissolve readily in
water
» polarity of water molecules enables
them to attract many different
kinds of substances
» Ionic compounds (e.g. NaCl) are
very soluble in water because the
partially + and - regions of a water
molecule pull apart the positive
and negative ions of the compound
Cells & Molecules 2013 R.W. Freeburn
 Water
Water moderates temperature on large and small scales

» Water has a high specific heat

 large amount of energy required to change temperature of water
 it gives up a lot of heat as it cools
» Water's resistance to temperature change moderates
temperature on a global scale.
 oceans contain so much water that their heat capacity effectively
limits dramatic swings in global temperature

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Cells & Molecules 2013 R.W. Freeburn

 Water
Ice floats on liquid water

» ice expands as it freezes

 unique property among nonmetallic substances
» Water is densest at 4°C
 surface water cooled to this temperature sinks
 explains why water at the surface of a lake or a pond
freezes before water below the surface.
» ice layers on water help insulate the liquid water
below
 allows organisms to survive below the surface when
temperature drops 35

Cells & Molecules 2013 R.W. Freeburn

» Pure water pH
˃ [H+] of 10–7 mol/L
˃ Considered to be neutral
˃ Neither acidic nor basic

» pH is the negative logarithm of hydrogen ion

concentration of solution

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Cells & Molecules 2013 R.W. Freeburn
 Acids & Bases
» Acid
 Any substance that dissociates in water to increase
the [H+] (and lower the pH)
 The stronger an acid is, the more hydrogen ions it
produces and the lower its pH
» Base
 Substance that combines with H+ dissolved in water,
and thus lowers the [H+]

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 The chemistry of life
» Doesn’t tell the whole story!

» Emergent properties define life processes

» What about
Behaviour ?
Emotions ?

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Lot’s to think about in biology !
Cells & Molecules 2013 R.W. Freeburn