The Chemical Context of Life

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Matter
• Takes up space
and has mass
• Exists as chemical
elements (pure
form) and in
chemical
combinations
called compounds

2
Elements
• Can’t be broken down into simpler
substances by chemical reaction
• Presented as atoms
• Each element has a unique symbol

3
 Essential Elements
• Are elements that an
organism needs to live a
healthy life and reproduce

• Include 17-25 different

elements, among which
– C, H, O, and N making up
96% of living matter;
– Other elements make up the
remaining 4% of living matter
(some even at trace amount)
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 Essential Elements
• Are elements that an
organism needs to live a
healthy life and reproduce

• Include 17-25
Which different
element is
elements,
toxicamong which
to human?
– C, H, O, and N making up
96% of living matter;
– Other elements make up the
remaining 4% of living matter
(some even at trace amount)
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Deficiencies
• If there is a deficiency of an essential
element, disease results

Nitrogen deficiency in Plants

6
 Trace Elements

• Are required by an
organism in only
minute quantities
(< 0.01%)
• Minerals such as Fe
and Zn are trace
elements Iodine deficiency
(Goiter)

7
Compounds
• Are substances consisting of two or more
elements combined in a fixed ratio
• Have characteristics different from
those of their elements

Sodium Chlorine Sodium Chloride 8

Na Cl NaCl
 Properties of Matter
• An element’s properties
depend on the structure
of its atoms
• Each element consists of
a certain kind of atom
that is different from
those of other elements
• An atom is the smallest
unit of matter that still
retains the properties of
an element
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Sub-atomic Particles
• Atoms of each element Are composed of
even smaller parts called subatomic
particles
– Neutrons, which have no electrical charge
– Protons, which are positively charged
– Electrons, which are negatively charged
• Neutral atoms have equal numbers of protons &
electrons (+ and – charges)
• Atoms of the various elements Differ in their
number of subatomic particles
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Subatomic Particle Location
• Protons and neutrons
– Are found in the atomic
nucleus
• Electrons
– Surround the nucleus in
a “cloud”

• Only electrons involves

in chemical reactions
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https://tex.stackexchange.com
Simplified models of Helium Atom
Cloud of negative Electrons
charge (2 electrons)

Nucleus

(a) This model represents the
electrons as a cloud of
negative charge, as if we had
taken many snapshots of the 2
electrons over time, with each
dot representing an electron‘s
position at one point in time.
(b) In this even more simplified
model, the electrons are
shown as two small blue
spheres on a circle around the
nucleus.

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Atomic Number
❖ The number of protons in the nucleus is
unique for each element = atomic number
•Carbon = 6 Nitrogen = 7 Oxygen = 8

❖ Atomic number is used to arrange atoms on

the Periodic table

❖ All atoms of a particular element have the

same number of protons in the nuclei but
might have different number of neutrons
(called isotopes)

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 Atomic Mass

• Is an approximation of the atomic mass of

an atom
• Atomic mass = The number of protons +
neutrons
• If an element has isotopes, it is the
average of the mass of all isotopes of that
particular element
• Can be used to find the number of neutrons

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15
Question

What’s about number of neutrons in a

Hydrogen atom???

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Isotopes of an element
• Different atomic forms of the same element
• Have the same number of protons, but
different number of neutrons
• Behave identically in chemical reactions
• May be radioactive spontaneously giving off
subatomic particles and energy (i.e. decay)
• May be used for certain purposes
– to date fossils (14C) or
– as medical tracers

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Use of radioactive isotope
– Can be used in medicine to detect tumors
(with high metabolic activity)

Radioactively
labeled
glucose
Cancerous
throat
tissue

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 Energy Levels of Electrons
• Electrons of an atom vary in
the amount of energy they
possess
• Electrons further from the
nucleus have more energy
(higher potential energy)
• Electron can absorb energy
and become “excited”
• Excited electrons gain
energy and move to higher
energy levels or lose energy
and move to lower levels

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Bohr atom animation.gif
• Energy: Is defined
as the capacity to
cause change
• Potential
energy: Is the
energy that matter
possesses because
of its location or
structure
• Kinetic Energy:
Is the energy of https://www.quora.com/How-do-hydroelectric-power-plants-produce-
energy-How-much-pollution-do-they-generate

motion
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 Electrons and Energy
• Energy levels are represented by electron shells
• Changes in the potential energy of electrons can
occur only in steps of fixed amounts

(a) A ball bouncing down a flight
of stairs provides an analogy
for energy levels of electrons,
because the ball can only rest
on each step, not between
steps.
(b) An electron can move from one level
to another only if the energy it gains
or loses is exactly equal to the
difference in energy between the two
levels.
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 Electron Configuration and
Chemical Properties
• The chemical behavior of an atom
– Is defined by its electron configuration,
which is the distribution of electrons in the
atom’s electron shells

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 Other information referred from Periodic table

– Shows the electron distribution for all the elements

– Electrons, like all matter, tend to exist in the lowest
available state of potential energy

Hydrogen 2 Atomic number Helium

He 2He
1H 4.00 Element symbol
Atomic mass
First Electron-shell
shell diagram

Lithium Beryllium Boron Carbon Nitrogen Oxygen Fluorine Neon

3Li 4Be 3B 6C 7N 8O 9F 10Ne

Second
shell

Sodium Magnesium Aluminum Silicon Phosphorus Sulfur Chlorine Argon

11Na 12Mg 13Al 14Si 15P 16S 17Cl 18Ar

Third
shell
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 Why do some elements react?
• Valence electrons
– Are those in the outermost shell (valence shell)
– Determine the chemical behavior of an atom (full
valence shell vs incomplete valence shell)
Hydrogen 2 Atomic number Helium
He 2He
1H 4.00 Element symbol
Atomic mass
First Electron-shell
shell diagram

Lithium Beryllium Boron Carbon Nitrogen Oxygen Fluorine Neon

3Li 4Be 3B 6C 7N 8O 9F 10Ne

Second
shell

Sodium Magnesium Aluminum Silicon Phosphorus Sulfur Chlorine Argon

11Na 12Mg 13Al 14Si 15P 16S 17Cl 18Ar

Third
shell 24
Electron Orbitals
• An orbital
– Is the three-dimensional space where an
electron is found 90% of the time

https://www.presentermedia.com/index.php?
target=closeup&maincat=animsp&id=714

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 Electron Orbitals
• Each electron shell
– Consists of a specific number of orbitals
• No more than 2 electrons can occupy a single orbital

Electron orbitals.
Each orbital holds
up to two electrons. x Y

Z
1s orbital 2s orbital Three 2p orbitals 1s, 2s, and 2p orbitals
Electron-shell diagrams.
Each shell is shown with
its maximum number of
electrons, grouped in pairs.

(a) First shell (b) Second shell (c) Neon, with two filled shells
(maximum (maximum (10 electrons)
2 electrons) 8 electrons)

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 Chemical Bonding
• Is a lasting attraction between atoms, ions
or molecules that enables the formation of
chemical compounds

– Strong kinds of chemical bonds: covalent bond

and ionic bond (in dry ionic compounds)
– Weaker kinds of chemical bonds: Hydrogen
bond and Van der Waals

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 Covalent Bonds
• Resulted from Hydrogen atoms (2 H)

the Sharing of a 1 In each hydrogen

pair of valence atom, the single electron

is held in its orbital by
its attraction to the
+ +

electrons proton in the nucleus.

• Participants: 2 When two hydrogen

atoms approach each

unpaired valence other, the electron of

each atom is also + +

electrons
attracted to the proton
in the other nucleus.

• Examples: H2 3 The two electrons

become shared in a
covalent bond,
forming an H2 + +
molecule.

Hydrogen molecule (H2)

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Covalent Bonding
• A molecule
– Consists of two or more atoms held
together by covalent bonds
• A single bond
– Is the sharing of one pair of valence
electrons
• A double bond
– Is the sharing of two pairs of valence
electrons

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Orbitals & Covalent Bonds
• In a covalent bond
– The s and p orbitals may hybridize,
creating specific molecular shapes
Three p orbitals Four hybrid orbitals
Z

s orbital X

Y
Tetrahedron

(a) Hybridization of orbitals. The single s and three p

orbitals of a valence shell involved in covalent bonding
combine to form four teardrop-shaped hybrid orbitals.
These orbitals extend to the four corners of an imaginary
tetrahedron (outlined in pink).
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Orbitals & Covalent Bonds

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Ways of presenting
Bonding
capacity
(atom’s
valence):

To indicate
the number
of covalent
bonds the
atom can
form

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Ways of presenting
Bonding
capacity
(atom’s
valence)

1
Bonding capacity (Atom’s valance)
usually equals the number of unpaired
electrons required to complete the
atom’s outermost shell
2

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Compounds & Covalent Bonds

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Covalent Bonding

• Electronegativity
– Is the attraction of a particular atom in the
molecule for the electrons in a covalent bond
• The more electronegative an atom
– The more strongly it pulls shared electrons
toward itself

35
 Covalent Bonding

• In a nonpolar covalent
bond
– The atoms have similar
electronegativities
– Shares the electron
equally

36
Covalent Bonding
• In a polar covalent bond
– The atoms have differing electronegativities
– Share the electrons unequally
Because oxygen (O) is more electronegative than hydrogen (H),
shared electrons are pulled more toward oxygen.
d–

This results in a
partial negative
charge on the
oxygen and a
partial positive
O charge on
the hydrogens.

H H
d+ d+
H2O
37
 Ions
• In some cases, atoms strip electrons away
from their bonding partners
• Electron transfer between two atoms
creates ions
• Ions: Are atoms with more or fewer electrons
than usual (charged atoms)
* An anion: Is negatively charged
* A cation: Is positively charged
• The term ion also applies to entire molecules
that are electrically charged (e.g. NH4+)
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 Ionic Bonding
• Established by the attraction (electrostatic
force) between anions and cations
1 2 Each resulting ion has a completed
The lone valence electron of a sodium
atom is transferred to join the 7 valence valence shell. An ionic bond can form
electrons of a chlorine atom. between the oppositely charged ions.

+ –

Na Cl Na Cl

Na+ Cl–
Sodium on Chloride ion
Na Cl
(a cation) (an anion)
Sodium atom Chlorine atom
(an uncharged (an uncharged
atom) atom)
Sodium chloride (NaCl)

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 Ionic Substances
• Ionic compounds
– Are often called salts,
which may form crystals
• Unlike a covalent
compound which consists
of molecules having a
definite size and number
of atoms, an ionic
compound does not
consist of molecules
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Weak Chemical Bonds

• Several types of weak chemical bonds

are important in living systems
• Weaker bonds could be formed within
and between molecules
• Can you give examples?

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Weak Bonds
• Weak chemical bonds
– Reinforce the shapes of large molecules
– Help molecules adhere to each other

42
 Molecular Shape and Function
• Structure determines
Function!
• The precise shape of a
molecule
– Is usually very important to
its function in the living cell
– Determines how biological
molecules recognize and
respond to one another with
specificity
– Is determined by the positions
of its atoms’ valence orbitals

43
Hydrogen Bonds
• A hydrogen bond
– Forms when a hydrogen atom covalently
bonded to one electronegative atom is also
attracted to another electronegative atom

d+ 44
Van der Waals Interactions
• Van der Waals interactions
– Occur when transiently
positive and negative regions
of molecules attract each
other

45
Chemical Reactions
• A Chemical reaction
– Is the making and breaking of chemical
bonds
– Leads to changes in the composition of
matter

46
 Chemical Reactions
• Chemical reactions
– Convert reactants to products

2 H2 + O2 2 H2O
Coefficient
indicate the Reaction
number of
Reactants Product
molecules
involved
47
Chemical Reactions
• Photosynthesis
– Is an example of “a chemical reaction” (actually
many chemical reactions take place!)

48
Chemical Reactions
• Chemical equilibrium
– Is reached when the forward and reverse
reaction rates are equal (dynamic
equilibrium)
– The relative concentrations of products
and reactants stop changing

49
 Lecture highlights
• Matter consists of chemical elements in
pure form and in combinations called
compounds
• An element’s properties depend on the
structure of its atoms
• The formation and function of molecules
depend on chemical bonding between atoms
• Chemical reactions make and break
chemical bonds
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