The Molecules of Life
Chapter 2
Core concepts
1.The atom is the fundamental unit of matter.
2.Atoms can combine to form molecules linked by
chemical bonds.
3.Water is essential for life.
4.Carbon is the backbone of organic molecules.
5.Organic molecules include proteins, nucleic acids,
carbohydrates, and lipids, each of which is built from
simpler units.
6.Life likely originated on Earth through a set of chemical
reactions that gave rise to the molecules of life.
2.1 PROPERTIES OF ATOMS
THE ATOM IS THE FUNDAMENTAL UNIT OF MATTER
Living organisms are structurally and functionally very
diverse
These differences are due to the molecules that build
them
Inspite of the diversity of molecules and their functions
The chemistry of life is based on a few types of
molecules,
these molecules are made up of just a few elements
What are elements?
Elements: Pure substances that can not be broken
down further.
Contain only one type of unique atom
Elements known today – 118
Natural Elements– 94
Artificially created Elements – 24
Element is indicated by its symbol,
For example, Carbon (C), Hydrogen (H), Helium (He)
Nucleus
(6 protons + 6 neutrons)
e–
Carbon Atom
e–
e–
e–
+
+
+
+
+
+
e–
e–
Carbon atom
Proton
Neutron
+
e–
Electron
2.1 PROPERTIES OF ATOMS
Elements are composed of atoms.
Atoms consist of protons, neutrons, and electrons.
Protons are part of atomic nucleus and are positively charged
particles
Neutrons are part of atomic nucleus and do not have any
electrical charge
Electrons move around the nucleus and are negatively
charged particles
Protons and Neutrons together form the atomic nucleus
CARBON ATOM
The number of protons is the atomic
number and specifies the atom as a
particular element.
Atomic number = Number of Protons
(given in periodic table)
For example, an atom with 6 protons is
always a carbon atom.
The number of protons and neutrons
determine the atomic mass.
Atomic mass = Mass of (Protons + Neutrons)
Mass number = Number of(Protons + Neutrons)
Therefore, Number of neutrons = Mass number – Atomic number
CARBON ATOM
Isotopes are atoms of the same elements that have same number
of protons and different numbers of neutrons.
For example, carbon has three isotopes:
6 protons and 6 neutrons , atomic mass 12 (99%)
6 protons and 7 neutrons, atomic mass 13 (1%)
6 protons and 8 neutrons, atomic mass 14 (very small fraction)
Typically, an atom will have the same number of protons and
electrons.
However, an atom that has lost an electron would be a positively
charged ion and
One that has gained an electron would be a negatively charged ion.
ORBITALS AND SHELLS
CARBON ATOM
Electrons move around the nucleus within orbitals—defined
regions of space where an electron is most of the time.
The maximum number of electrons in any orbital is two.
Atoms with more than two electrons have multiple orbitals,
differing in size, shape, and distance from the nucleus.
Orbitals exist in different energy levels, or shells. The first shell
contains one spherical orbital. The second shell has four
orbitals. The first shell can contain up to two electrons. The
second shell can contain up to 8 electrons.
CARBON ATOM
For example, carbon has six electrons.
Two electrons occupy the first orbital in the first shell.
The remaining four electrons are distributed among the four
possible orbitals in the second shell, with no more than two
electrons in each orbital.
PERIODIC TABLE
READING THE PERIODIC TABLE
The periodic table of elements organizes
all chemical elements in terms of their
chemical properties.
Note here the order of increasing atomic
number.
READING THE PERIODIC TABLE
Elements in the same horizontal row have the same number of shells and
therefore have the same number of types of orbitals.
Across a row, electrons fill the outermost shell until a full complement of
eight electrons is reached.
Here, you can see the filling of the shells for the elements in the second
row of the periodic table.
The number of electrons in the outermost shell determines in large part
how elements behave and interact with other elements.
READING THE PERIODIC TABLE
Vertical columns are
called groups, or families.
Members of a group
have the same number
of electrons in their
outermost shell.
For example, carbon and
lead have the same
number of electrons in
their outmost shell.
2.2 MOLECULES AND CHEMICAL BONDS
Atoms can combine with one another to form molecules,
held together by chemical bonds.
The ability of atoms to form molecules explains how a few
type of elements can make many different molecules that
can perform different functions.
CHEMICAL BONDS
Types of chemical bonds,
1) Covalent
2) Polar covalent
3) Hydrogen
4) Ionic
1) COVALENT BOND
A covalent bond is formed when two atoms share electrons.
The sharing of electrons occurs in the
outermost orbitals of the atoms.
The electrons found in the outermost
orbitals of an atom are called the
valence electrons.
A molecule is formed when two atoms
share their valence electrons with each
other.
Here, two hydrogen atoms, each with
one electron, combine to form
hydrogen gas.
MOLECULE STABILITY
Molecules tend to be the stable when they share electrons,
to completely occupy the outermost shell.
One carbon atom with four valence electrons combines with four hydrogens, each with one
valence electron, to fill the outer orbital with eight electrons.
Nitrogen has five valence electrons and combines with three hydrogens to form ammonia,
filling the outer shell with eight electrons.
Oxygen, with six valence electrons, combines with two hydrogens to form water and fill the
outer shell with eight electrons.
2) POLAR COVALENT BOND
Polar covalent bond is characterized by unequal sharing of electrons.
In water, the electrons are more likely to be located near the oxygen atom
than the hydrogen atoms. This is due to the property known as
electronegativity—the ability of an atom to attract electrons.
Oxygen is more electronegative than hydrogen and attracts electrons more
than does hydrogen.
In a molecule of water,
Oxygen has a slight negative charge
while the,
two hydrogen atoms have a slight positive
charge.
NON-POLAR COVALENT BOND
A covalent bond between atoms that have the same or nearly the same
electronegativity is a nonpolar covalent bond.
The electrons are shared equally
H
H
H
Hydrogen gas,
H2
H
C
H
H
Methane, CH4
3) HYDROGEN BONDS
A hydrogen bond is an interaction of a hydrogen atom and an
electronegative atom.
For example, hydrogen atoms in water are covalently bound to one
oxygen atom and are attracted to and interact with an oxygen atom of
another water molecule.
Hydrogen bonds are depicted
by
the dashed lines.
than
help
Hydrogen bonds are weaker
covalent bonds, but they do
stabilize biological molecules.
4) IONIC BOND
Ionic bonds are formed due to transfer of electrons between two
oppositely charged ions.
For example, NaCl. The difference in electronegativity between these
two atoms is very large. The chlorine atom has such high
electronegativity that it steals an electron from the sodium atom. This
results in a negative charge on the chlorine atom and a positive charge
on the sodium atom.
When added to water, the two ions are pulled apart and become
surrounded by water molecules and therefore dissolve in water. Once
the water evaporates, the two ions join together and precipitate,
forming salt crystals.
4) IONIC BOND
A CHEMICAL REACTION
Chemical reactions are the breaking and forming of chemical bonds.
Two molecules of hydrogen gas and one molecule of oxygen can react to
form two molecules of water. In this reaction, the numbers of each type of
atom are conserved, but their arrangement is different.
2.3 WATER: THE MEDIUM OF LIFE
Water is the medium of life. When looking for life on other planets in the
1990s, NASA’s strategy was to look for water.
Water naturally exists in three physical states of matter:
solid, liquid, and gas.
All life depends on water.
What makes water so special?
Its properties (functions) because of its structure.
WATER CHEMISTRY
Properties
1) Polar molecule
2) Good solvent
3) pH 7
Structure
WATER CHEMISTRY
We saw earlier that water is a polar molecule with a partial positive charge
at the hydrogens and a partial negative charge at the oxygen.
Water is a versatile solvent due to its polarity,
Solvent – a dissolving agent of a solution
Solute – a substance that is dissolved
Aqueous solution – is one in which water is a solvent
Molecules are classified based on how they react with water:
hydrophilic if they are water-loving and hydrophobic if they are not.
WATER CHEMISTRY
The pH of a solution measures the proton concentration by the following
formula
pH = –log [H+]
In an acidic solution, [H+] is greater than [OH-], and pH < 7
An acid releases [H+]
In a neutral solution, [H+] = [OH-] =10-7 M
In a basic solution, [H+] is less than [OH-], and pH > 7
A base releases [OH-]
WATER CHEMISTRY
For a neutral aqueous solution, [H+] is 10–7 = [OH–] 10–7
[H+] [OH–] = 10–14
pH = –(–7) = 7
pH of solutions can range from 0 to 14,
Pure water has a pH of 7,
which is also the pH of most of our cells.
HYDROGEN BONDING IN WATER
(LIQUID AND SOLID)
Water is characterized by extensive hydrogen bonding.
When water freezes, it expands and becomes less dense. This is unusual
because most solids are typically more dense than their liquid counterparts.
The water molecules when frozen form a highly ordered, open, and
hexagonal structure. As a result, it floats.
Water is able to resist temperature change more than other substances
because in order for its temperature to increase, hydrogen bonds must
first break. This property is important for living organisms because water
resists temperature variations that would otherwise result from the
numerous biochemical reactions taking place within them.
HYDROGEN BONDING IN WATER
(LIQUID AND SOLID)
Collectively, hydrogen bonds hold water molecules together, a
phenomenon called cohesion
Cohesion helps the transport of water against gravity in plants
Cohesion also results in Surface tension, which is a measure of the
difficulty of breaking the surface of a liquid.
Adhesion is an attraction between different substances, for example,
between water and plant cell walls
HYDROGEN BONDING IN WATER
(LIQUID AND SOLID)
CARBON: LIFE’S CHEMICAL BACKBONE
Human cells consists of mostly
water, but after the removal of water,
the cell’s dry mass is represented in
this graph. The four major elements
are carbon, oxygen, hydrogen, and
nitrogen, making up 94% of the dry
mass.
Carbon is 47% of that dry mass and
is unique because it has the ability to
combine with a wide variety of
molecules. Molecules that contain
carbon are called organic molecules.
CARBON & COVALENT BONDS
A carbon atom behaves as if it has four unpaired electrons, forming a
tetrahedron.
In methane, each of the four valence
electrons of carbon shares a new
molecular orbital with the electron of
one of the hydrogen atoms forming
four covalent bonds. Each of these
bonds can rotate freely about its axis.
All of these bonding properties of
carbon contribute importantly to the
structural diversity of carbon-based
molecules.
DIVERSITY IN CARBON-CONTAINING
MOLECULES
Carbon atoms can also link with one
another to form long chains that can
be branched or form a ring structure.
(a)Two carbon atoms have connected
by a covalent bond.
(b) Multiple carbons have joined to
form a chain or a ring structure.
CARBON DOUBLE BONDS
Adjacent carbons can also share two pairs of electrons, forming a double
bond between them.
The double bond is shorter than a single bond and is not free to rotate, so
two carbon atoms connected by a double bond are in the same plane.
Double bonds can be found in chains and ring structures as well.
ISOMERS
Are molecules with same molecular formula but different structures
and hence different properties (functions)
Butane (C4H10)
vs
Isobutane (C4H10)
Three types of isomers are: a)Structural
b) Geometric
c) Enantiomers
ISOMERS
The arrangement of atoms is also important.
Two molecules with the same chemical formula may arrange differently
to produce different structures and, in turn, molecules with different
functions, making carbon very diverse.
CARBON-BASED MOLECULES AND THEIR
BUILDING BLOCKS
1. Proteins (amino acids)
2. Nucleic acids (nucleotides)
3. Carbohydrates (sugars)
4. Lipids (fatty acids)
Cellular processes depend on a few classes of carbon-based
molecules: proteins, nucleic acids, carbohydrates, and lipids.
AMINO ACID
The general structure of an amino acid: A central carbon atom (alpha carbon)
covalently linked to four groups:
-Carboxyl (COOH)
-Amino (HN2)
-Hydrogen (H)
-R group (side chain)
The R group is what distinguishes
one amino acid from another.
PROTEIN
When amino acids are linked together in a chain, they form a protein.
The carbon of the carboxyl group of one amino acid is linked to the nitrogen
in the adjacent amino acid by a covalent peptide bond.
The carbon atom releases an oxygen atom, and the nitrogen is losing two
hydrogen atoms to form a molecule of water.
NUCLEOTIDES
Nucleotides are composed of three
components:
1.A 5-carbon sugar (ribose or
deoxyribose)
2.A base containing nitrogen
3.And one or more phosphate groups
Note that the sugars only differ by the
OH group or H group at the 2’ carbon.
THE BASES IN NUCLEIC ACIDS
The bases in nucleic acids are
a) single-ring pyrimidines
(T, C, U)
b) double-ring purines
(A, G).
THE BOND IN THE NUCLEIC ACIDS
Adjacent pairs of nucleotides are joined
together by phosphodiester bonds.
The phosphate group of one nucleotide
is joined to the sugar unit in another
nucleotide.
The formation of this bond also results
in the loss of a water molecule.
STRUCTURE OF DNA
DNA consists of two strands of
nucleotides twisted around each
other in the form of a double helix.
The sugar phosphate backbones
wrap around the outside and the
bases form complementary basepairing A-T, G-C.
The base pairing in the middle
results from hydrogen bonding
between the bases.
CARBOHYDRATES (C6H12O6)
Carbohydrates are composed of C, H, and O.
The simplest carbohydrates are
saccharides and can be linear or cyclic
and contain five or six carbons.
Sugars containing an aldehyde group
are aldose sugars, and those
containing a ketone group are called a
ketose sugars.
The three sugars here each have 6
carbons, 12 hydrogens, and 6 oxygens
but differ in their arrangements of the
atoms. They are isomers.
NAMING SUGARS
Monosaccharides  One sugar
Disaccharides  Two sugars linked together
Polysaccharides  Many sugars linked together
Complex carbohydrates  Long, branched chains of monosaccharides
CYCLIC MONOSACCHARIDES
Virtually all monosaccharides
in cells are in ring form.
To form a ring, the carbon in
the aldehyde of a ketone
group forms a covalent bond
with the oxygen of the
hydroxyl group carried by
another carbon in the same
molecule.
GLYCOSIDIC BONDS
Monosaccharides are attached to one another by covalent bonds
called glycosidic bonds.
Again, the formation of these bonds involves the loss of a water
molecule.
LIPIDS
Lipids are defined
by a property—all
are hydrophobic.
They share a
property and not a
structure.
Lipids are a diverse
group of chemicals;
1) Fats
2) Steroids
3) Phospholipids
Fatty Acids
Steroids
Phospholipids
LIPIDS
1) Fats are composed of a glycerol backbone attached to three fattyacids (long chains of carbons).
2) Steroids, like cholesterol here, are composed of many carbon atoms
bonded to form rings.
3) Phospholipids are composed of a glycerol backbone, two fatty-acid
chains, and a phosphate-containing head group.
1) TRIGLYCEROLS(FATS)
Triacylglycerols (fats) are lipids
used for energy storage.
They can contain different types of
fatty acid, but all are hydrophobic
and form oil droplets inside the cell.
By excluding water molecules, a
large number can be packed into a
small volume, making triacylglycerol
a very efficient form of energy
storage.
SATURATED VS. UNSATURATED
Fatty acids are hydrocarbon attached to carboxyl group.
Fatty acids that do not contain double bonds are saturated—saturated with
hydrogen atoms.
Fatty acids with carbon-carbon double bonds are unsaturated.
VAN der WAALS FORCES
Hydrocarbon chains of fatty acids contain no polar
covalent bonds, and are uncharged.
The constant motion of electrons leads to regions
of slight charges, and these charges are attracted
to or repelled by neighboring molecules.
These forces are weaker than hydrogen bonds, but
many act together to stabilize molecules.
• Length of hydrocarbon chains increases these forces.
• Kinks caused by unsaturated (double-bonded) carbons
reduce tightness, causing a lower melting point.
2) STEROIDS
Steroids like cholesterol are a component of animal cell membrane.
They are composed of 20 carbon atoms bonded to form four fused rings
and are hydrophobic.
Cholesterol is the precursor for the synthesis of steroid hormones such as
estrogen
and
testosterone.
HYDROPHOBIC
HYDROPHILI
C
3) PHOSPHOLIPIDS
Choline
Polar head
group
Phosphate
Phospholipids are a major
component of the cell
membrane.
Consist of: 1 Glycerol
2 Fatty acids and
1 Phosphate
Thus, they have hydrophobic
and hydrophilic groups in the
same molecule.
Fatty acid
chains
Glycerol
backbone
COULD THESE BUILDING BLOCKS HAVE BEEN
GENERATED ON EARLY EARTH?
In 1953, Stanley Miller performed an
experiment using gases thought to be
present in early earth (water vapor,
methane, ammonia, and hydrogen gas).
He built an apparatus that would
simulate early Earth and used a spark
to simulate lightning within the
apparatus. This caused a red
substance to develop within the walls of
the flask, and upon analysis of the
substance, there were about 20
different amino acids present.
HOW DID BUILDING BLOCKS FORM
MACROMOLECULES?
Clay minerals that
form from volcanic
rocks can bind
nucleotides on their
surfaces. The clays
provide a surface
that places
nucleotides in
proximity to one
another, making it
possible for them to
join to form chains
or simple strands of
nucleic acid.
In an experiment, Leslie Orgel
placed a short nucleic-acid
sequence into a reaction vessel
and then added individual
chemically modified nucleotides.
The nucleotides spontaneously
joined into a polymer, forming
the sequence complementary to
the nucleic acid already present.
This experiment showed that
nucleic acids can be
synthesized experimentally from
nucleotide building blocks.