Unit 2a Atoms, Chemical Bonds, Carbon

Overview
atoms - neutrons, protons, electrons
- atomic mass, atomic number
electrons orbitals, shells
unpaired electrons and reactivity
chemical bonds covalent (polar, non-polar), non-covalent, ionic
water - polarity, hydrogen bonding
- dissociation, pH scale, acid-base reactions
energy - kinetic, potential
- exergonic and endergonic reactions
- laws of thermodynamics relevance to biology
carbon skeletons, functional groups, macromolecules

What are cells made of?

four types of atoms make up 96% of all matter found in
living organisms
carbon, hydrogen, oxygen, nitrogen (C, H, O, N)
mostly combined in complex macromolecules
also present in simple forms - CO2, H2O
objective of Unit 2a:
What features of these atoms allow them to serve as
biological building blocks?

Parts of an Atom
electron

nucleus
proton
neutron

Hydrogen

Carbon

nucleus dense core in centre of atom consisting of protons and

neutrons
electrons continually orbit the nucleus
# of protons, the atomic number (or proton number), is how we
define an element. Carbon has 6 protons, ALWAYS, if an atom has
7 protons, it is not carbon, it is nitrogen.
Fig 2.1a, Freeman

Parts of an Atom

Fig 2.1a, Freeman

electron

nucleus
proton
neutron

Hydrogen

Carbon

mass number is the # protons and neutrons (for carbon 12, this is
6+6). Since protons and neutrons weigh about the same, and electrons
have a negligible weight, the mass number (i.e. 12) is very close to
the mass of the atom =12.0107 amu (atomic mass units).
Similarly, calcium (Ca) has an atomic number of 20, meaning 20
protons, but also has 20 neutrons, so its mass number is 40, and the
mass of the atom is 40.078 (see preceding periodic table).
by definition, an atom is has a neutral charge if the # protons and
electrons are equal.
5
it is the electrons that determine the reactivity of an atom...

Atomic Mass
mass of a neutron or proton (neutrons are slightly heavier), is
approximated at one atomic mass unit or dalton. Putting the
atomic number is subscript is actually redundant, as the number
of protons is inherent to the atom (i.e. C always has six) so it is
often omitted (i.e. 12C).
mass
number

1
H
1

4
2

He

12
C
6

23
11

Na

atomic
number

Isotopes, while having identical numbers of protons, differ in neutrons.

So while the atomic number stays the same, the mass number
(supercript) can increase with each extra neutron i.e. 12C, 13C, 14C.
6

Atomic Mass
mass
number

1
H
1

4
2

He

12
C
6

23
11

Na

atomic
number

Practice Opportunity:
How many protons does helium (He) have? (2) (Na)? (11)
How many neutrons does hydrogen have? (0) And helium (2)?
Which is the heaviest atom of these four? (Na, 22.98 amu)
There can be very different numbers of protons and neutrons in a nucleus,
simply as an inherent property of the atom i.e. 201
Hg
which has 80 protons and 121 neutrons.
80
7

Electrons travel around atomic nuclei in orbitals.

orbitals are grouped into layers or shells, based on how far the
electrons in that shell travel from the nucleus
max 2 e-

max 8 e-

max 8 e-

Electrons, Shells and Valence

innermost shells fill first
once first shell is filled with a pair of electrons, next
shells fill with 4 singles, then subsequent electrons
form pairs (bus analogy)
outermost valence shell influences an atoms reactivity

electrons in outermost shell are called valence electrons

(valence=available electrons). The valence of an atom refers
to the number of unpaired electrons in its outermost valence
shell
12
C
6
carbon:
4 unpaired electrons,
valence = 4
(can react with 4 atoms
i.e. CCl4, CH4)

35
Cl
17
chlorine:
1 unpaired electrons,
valence = 1

40
Ar
18
argon:
no unpaired electrons,
valence = 0
9

Groups

Group 1 (column 1 above) have a single valence electron, Group 2 has two, (skip transition metals), Group 13
have 3, 14 has 4, 15 has 5, 16 has six, 17 has 7, and 18 (with exception of He, which has 2) have 8 valence
electrons.
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Unpaired Valence Electrons and Reactivity

Blue Square = abundant
elements in biological
systems

- completely filled valence shells non-reactive (stable) e.g. He, Ne, Ar

- those closest to filling valence shell are most reactive e.g. Cl, Fl, O
- atoms with same # valence electrons have similar chemical behaviour
- elements abundant in organisms have at least one unpaired valence
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electron
Fig 2.3

Unpaired Electrons and Biological Reactions

biological reactions are driven by tendency of atoms to
fill outer shells
balance positive and negative charges

How can atoms achieve full valence shells?

sharing electrons - forming covalent bonds
number of bonds possible depends on
how many electrons that atom needs to fill its outer shell
transferring electrons from one atom to another to form ionic bonds
atoms that are no longer electrically neutral ions
gain electron negatively charged anion
lose electron positively charged cation
12

Types of Chemical Bonds

covalent bonds - two or more atoms share pairs of valence
electrons, forming strong bonds.
2 hydrogen atoms

2 oxygen atoms

one molecule hydrogen gas (H2) one molecule oxygen gas (O2)

H-H

O=O

13

Types of Covalent Bonds

1. electrons shared equally
A non-polar covalent bond can be single (like H2), double (O2)
or even triple (N2), depending on number of electrons shared.
2. electrons not shared equally
A polar covalent bond (i.e. H20) is one where one of the atoms
in a molecule has a stronger pull on the shared electrons than the
other. The oxygen atom in water is quite electronegative.
electronegativity, which produces polar covalent bonds, is the
tendency of an atom to pull electrons towards itself. The more
protons an atom has, the stronger its pull on electrons of other
atoms in the molecule. But, the more electrons an atom has, the
further the valence electrons in other atoms are from the protons
of the electronegative atom, reducing the attraction. The lower
valence shell electrons also act as a shield to reduce the
attraction.
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Polar Covalent Bond: Water

O
H

Electronegativity is not strictly the property of an atom, but of an atom

in a molecule. Water is a polar molecule due to the charge being
unevenly distributed with the oxygen atom being slightly negative, and
the two hydrogens being slightly positive due to the electronegativity
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of the oxygen atom.

Types of Chemical Bonds

Non-Covalent Bonds:
Ionic Bonds - formed by electrostatic attraction between
two oppositely charged ions. Sodium gives up an electron to
give it a stable (noble gas-like)
valence electron configuration,
while fluorine gains an electron
to be similarly satisfied. Their
opposite charges attract to form
an ionic bond.
NaCl (table salt) forms Na+ and
Cl- ions in water as ionic bonds
break.

16

Ionization and Ionic Bonds

Na atom has one

unpaired valence
electron

Na+ has lost electron to Cl atom needs one

form cation; more stable electron to fill valence
shell; very reactive

Cl- gains electron to

form anion; more
stable

The transfer of an electron between

Na and Cl, facilitates the charge
formation leading to the ionic bond.

from Fig 2.6

17

Types of Chemical Bonds

Non-Covalent Bonds:
Hydrogen bonds (H-bonds) occurs when hydrogen is attached
directly to an electronegative element, which causes the hydrogen to
acquire a significant amount of positive charge. This positively
charged hydrogen is so strongly attracted to electrons on other
electronegative atoms (say oxygen) that it is almost as if you were
beginning to form a covalent bond. Hydrogen bonds are about 10 x
weaker than a covalent bond, and are being constantly broken and
reformed between adjacent water
molecules (bonds within a water
molecule are covalent).

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H-Bonding in Pure Water

19

Types of Chemical Bonds

Non-Covalent Bonds:
hydrophobic interactions - tendency of non-polar substances
to aggregate and exclude water. Is an important force driving
protein folding, and the formation of lipid bilayers and
micelles.

Non-polar (hydrophobic)
fatty acid tails

Polar (hydrophilic)
fatty acid heads

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Definitions
molecule a group of at least two atoms held together by bonds i.e.
O2 (two atoms of oxygen), H2O (two atoms of hydrogen and one
of oxygen)
compound - molecule composed of two or more different types of
atoms held together by bonds. All compounds are molecules, but
not all molecules are compounds. So H2O could be considered a
compound (but can equally be called a molecule), while O2 and
N2 would not be considered compounds.
molecules

compounds
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Representations of Molecules (Compounds)

Molecular
formulas:

Methane
CH4

Ammonia
NH3

Water
H2O

Structural
formulas:

Ball-and-stick
models:

Space-filling
models:
from Fig 2.8, 2.10

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Water
water is the most abundant molecule in biological organisms
human body is 70% water
water as a solvent can dissolve more types of molecules than any
other molecule known.
the polarity of water is key to its role in biology

Fig 2.12

hydrogen bonding electrical attraction between electronegative

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oxygen atom and partial positive of hydrogen

Water as a Solvent
polar compounds: e.g. NaCl

hydrophilic affinity for water

water loving

non-polar compounds: e.g. octane C8H18)

hydrophobic no affinity for water

water fearing

All of waters striking properties are a direct result of its ability to form Hbonds.

Fig 2.13

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Dissociation of Water
water is not a completely stable molecule, small amounts
(about 1 in 554 million molecules) dissociate:

H2O H+ + OHhydroxide ion

hydrogen ion

hydrogen ions dont actually exist alone, and usually join

with other water molecules
Technically, the reaction looks like this:

H2O + H2O H3O+ + OHgave up

a proton

accepted
a proton

hydronium ion

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Acid-Base Reactions
substance that gives up (donates) protons acid
(increases [H+] in solution)
substance that accepts protons base
(decreases [H+] in solution)
chemical reaction that involves transfer of protons
acid-base reaction
usually a molecule acts as either an acid or a base
water can be both (both gives up and accepts protons)
weak acid: very few molecules dissociated (acetic acid, water)
strong acid: readily gives up protons (hydrochloric acid)

HCl H+ + Cl26

Measuring acidity: the pH scale

[H+] can vary by a factor of 100 trillion or more
its concentration is expressed more conveniently via the pH scale
ranges from 1 to 14
compresses the range of concentrations by employing logarithms

pH = - log [H+]

[H+] = 1 x 10-7 M = 0.0000001 M

pH = 7

[H+] = 1 x 10-6 M = 0.000001 M

pH = 6

[H+] = 1 x 10-2 M = 0.01 M

pH = 2

Why are acid-base reactions important in biology?

transfer of protons changes the charge of both proton donor
and acceptor, which changes their reactivity with respect to
H-bonding and other interactions.
example:
concentration of H+ in blood typically very low
arterial blood, [H+] = 0.0000000398 M = 3.98 x 10-8 M
= 39.8 nanomoles per L
if [H+] doubles (still nanomolar), the acid-base reactions
triggered would kill you in a few minutes

29

Energy and Chemical Bonds

energy = the capacity to do work
- to move matter against opposing forces
- to rearrange matter
kinetic energy (EK) = the energy of motion, heat
potential energy (EP) = stored energy, as a result of
- location (top of hill, water behind dam), or
- structure (arrangement of atoms within molecule)
chemical bonds contain stored energy
making bonds requires energy (i.e., fixing CO2 to
hydrocarbons requires energy from sunlight)
breaking bonds releases energy (i.e., breaking down
glucose to CO2 in cells provides useful biochemical
energy)

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Energy Transformations
Water molecule at
top has potential
energy due to its
position

Some potential
energy is converted
to kinetic energy as
it falls
When the water molecule
hits the bottom, its kinetic
energy is converted to
mechanical work (abrading
rock etc), heat (friction),
sound (movement of air
molecules).
Fig 2.18

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Energy, Electrons and Electron Shells

electrons also have potential energy
first (innermost) shell lowest potential energy
electrons in outer shells higher potential energy
outside forces acting on an atom can result in:
electrons moving further out from nucleus
gaining energy, getting excited
electrons moving in closer to nucleus
energy lost (usually as heat, but
can be fluoresced as light)

Energy
lost

electrons can only change their position if they absorb or release a

quantity of energy that exactly matches the difference in potential
energy between the two levels
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Thermodynamics
Describes relationships between forms of energy, and transfer of
energy, heat, and work between material bodies or radiation.

1st Law of Thermodynamics

energy can be transferred and transformed, but it cannot be
created or destroyed.

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Energy Transformations

Fig 2.18

Water molecule at
top has potential
energy due to
position

An electron in an outer
shell has a defined
amount of potential energy

Some potential
energy is converted
to kinetic energy as
it falls

As electron falls to
lower energy shell, some of
Its potential energy is
converted to kinetic energy.

When the water molecule

hits the bottom, its kinetic
energy is converted to
mechanical work (abrading
rock etc), heat (friction),
and sound (movement of air
molecules.

Once electron arrives at

lower shell, its kinetic energy
is converted to light or heat.
Light or heat energy released
is equal to the difference in
potential energy between its
former and current shells.
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Chemical Reactions
Are the processes leading to the transformation of one set of
chemical substances to another. Chemical reactions involve the
formation or breaking of bonds, and/or the shifting of atoms or
ions from one molecule to another.

AB + CD

AC + BD

Chemical reactions may be spontaneous (occurring on their own

without external energy inputs), or require energy inputs (nonspontaneous). Spontaneous reactions are usually exergonic, that
is, energy is released.
Products of exergonic reactions are less ordered, and have lower
potential energy than the reactants.

35

Exergonic Reactions
non-biological:

biological:
sugar (glucose)
+ O2

CO2 + H2O
dynamite CO2, water vapour, plus energy!

-in both reactions, the products are less ordered (have lower potential energy
than reactants, which is consistent with the second Law of Thermodynamics.
Fig 2.19, 2.20

36

Thermodynamics
2nd Law of Thermodynamics expresses the tendency of
energy, temperature, and pressure to spontaneously disperse over
time to achieve an equilibrium with the larger system. Anything
energy must be put into to organize or maintain will disperse or
equilibrate on its own.

If left on their own, matter (and your room) are more likely to go from
order to disorder. A pile of bricks are more likely to fall over than to
spontaneously stack neatly. A hot frying pan cools, air shoots out of a
hole in a tire. Changes in energy tend to go from being concentrated, to
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being equally spread out within a system. Order to disorder.

Rates of Reactions
Even if a reaction is spontaneous (thermodynamically
favourable), it is not necessarily fast.
iron +O2+moisture slowly forms Fe(OH)3 (rust).
Glucose slowly forms CO2 and H2O
both reactions are spontaneous, but very slow
To initiate a spontaneous reaction, the right molecules need to
collide with sufficient energy to break a bond. The energy for
such a collision is dependent on how fast the molecules are
moving (a function of temperature) and the chance of collision
(how concentrated or crowded the reaction medium is).

38

Non-Spontaneous (Endergonic) Reactions

are thermodynamically unfavourable.
need energy inputs to proceed, but can generate products
more complexity (of higher potential energy) than reactants.
This type of reaction allows simple chemical compounds
(i.e. CO2, H2O, H2, N2) in the presence of energy (lightening,
sunlight etc), to combine to form larger, more complex
substances.

39

Endergonic Reactions
Formaldehyde (H2CO) is a key intermediate in the formation
of more complex molecules in cells
formed from H2 and CO2, but both reactants
have full outer shells, which makes them stable
and non-reactive.

But, photons from sunlight can break molecules apart,

knocking electrons out of orbitals, creating reactive
compounds.

Energy +CO2 + 2 H2 H2CO

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Energy Recaps
potential energy stored in bonds = chemical energy
making chemical bonds requires energy
breaking bonds releases energy
an exergonic reaction results in a net release of energy
themodynamically favourable and spontaneous
energy can be used or lost as heat
results in less complex products; loss of order
an endergonic reaction needs energy input to drive it
thermodynamically unfavourable
results in more complex products storage of potential energy,
often in chemical bonds
combining the two Laws of Thermodynamics:
the quantity of energy is constant, but the form (quality) can vary41

So Why Doesnt the Universe Just Fall Apart if Everything is

Moving From Order to Decay as the Second Law of
Thermodynamics Suggests?

42

Energy From Sun Keeps Restoring Potential Energy to the System

(Earth) as it is Captured by Photosynthetic Plants and Transferred as
Chemical Potential Energy (Food for Heterotrophs)
photons (kinetic energy)
energy from sun

electrons boosted up to next energy level

light energy stored as potential energy

excited electrons jump from molecule to molecule

(mostly as H atoms (i.e. NADH) proton plus electrons)
many highly organized,
regulated transfers of energy

energy stored in chemical bonds (Potential Energy)

energy used to create more complex
molecules from simpler ones

Carbon as the Building Block of Biology

carbon is most important atom in biology,
carbon-containing molecules are considered
organic

12
C
6

Most abundant carbon isotope, 12C (99%) has 6

protons and electrons (as all carbon isotopes do!)
as well as 6 neutrons.
can form many combinations of single and double
bonds, and can be linked to form chains, rings etc

Benzene ring

Hydrocarbon chain

44

Variations in Carbon Skeletons (Pure Hydrocarbons)

carbon atoms give biomolecules their shape but other atoms attached to
carbons to determine their reactivity
critical H, N, O containing attachments are called functional groups

45

hydroxyl (OH) - OH

alcohols
O

carbonyl (CO)

aldehydes

-C

ketones

-Ccarboxyl (COOH)

amino (NH2)

-C

OH

-C

H
-N
H

sulfhydryl (SH)

-N

carboxylic acids
O- (gives up a proton)

H
H
H

- SH

amines (acts as a base,

attracting a proton)
thiols

O
phosphate (PO4)

- O P OO-

organic phosphates

Functional Groups
are the components of organic molecules most involved in
chemical reactions
functional groups behave consistently from one molecule to
another
all functional groups are hydrophilic (polar)
Testosterone

Marked biological differences between an estrogen and an androgen are attributable to

their functional groups.

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Macromolecules
large, organized molecules that are typically created by
polymerization (built using smaller molecules).
biological macromolecules (biomolecules) provide the
structure and carry out the activities of a cell
4 groups of biological macromolecules:
proteins
nucleic acids
carbohydrates
lipids

48

Condensation Reaction used in polymerization

to make the chain

Hydrolysis breaking the chain

49

Overview of Macromolecules
Macromolecule

Subunit (Monomer)

Function

Example

proteins
functional
structural

amino acids

enzymes, transport
support

hemoglobin
hair, silk

nucleic acids
DNA
RNA

nucleotides

encodes genes
gene expression

chromosomes
mRNA

carbohydrates
starch, glycogen
cellulose
chitin

glucose or modified
glucose

energy storage
plant cell walls
support

potatoes
paper, celery
crab shells

glycerol + FAs
glycerol + FAs + PO4
ring structures

energy storage
cell membranes
cell communication

butter, plant oil

lecithin
steroids

lipids
fats
phospholipids
other