BIOMOLECULES

Organic and Inorganic

Molecules
1. Elements in living things
 a/ Organic molecules- molecules containing
elements carbon, hydrogen and oxygen.
Examples: carbohydrates, lipids, proteins and
nucleic acids (DNA & RNA)
Proteins and nucleic acids also contain nitrogen.
b/ Inorganic molecules- any compounds that do not
contain carbon
Many inorganic substances are found in living
things and are vital to their structure and
functioning (H2O, NaCl, CO2)
A1.1.1 Water as the medium for life
(a) importance of water
Water makes up 65-75% of human body
weight. A loss of just 4% of total body water
leads to dehydration, and a loss of 15% can be
fatal.
Water is the universal solvent thus excellent
medium for transporting substances.
Water is involved in many chemical
reactions (such as photosynthesis).
 Water can act as a temperature regulator in our body–
for example, blood carries heat from warmer parts of
the body, such as the liver, to cooler parts such as the
feet.
 Water supports cellular structure.
(b) Structure of water
- Water is made up of two hydrogen atoms covalently bonded to an
oxygen atom.
- Water is a polar molecule with unevenly distributed electrical charge:
they have a positive charge on the two hydrogen atoms and a negative charge
on the oxygen atom.
A1.1.2 Hydrogen bonds as a consequence of
the polar covalent bonds within water
molecules
There are weak hydrogen bonds between
the negative charge of one water molecule
and the positive charge of another. This type
of bond is responsible for many of the
properties of water.
Hydrogen bonding is responsible for several properties of water – including
thermal, cohesive and solvent properties.
A large amount of energy is needed to break down these bonds. This gives water a
high specific heat. This is important for maintenance a constant body temperature.
Hydrogen bonds are responsible also for two other properties of
water: Cohesion and adhesion are the "stickiness" that water
molecules have for each other and for other substances.
A1.1.3 Cohesion of water molecules
- Cohesion: a water molecule is able to stick to
other water molecules via the formation of
hydrogen bonds

The hydrogen bonding between water

molecules creates surface tension

Cohesion is responsible for

surface tension, which enables
some small organisms to ‘walk
on water’
A1.1.4 Adhesion of water molecules

Water is also adhesive – a water molecule

is able to stick to other polar molecules via
the formation of polar associations.

A water drop is composed

of water molecules that like
to stick together (cohesion).
In the picture of pine
needles above, the water
droplets are stuck to the end
of the pine needles
(adhesion).
Attraction to polar surfaces (such as cellulose
cell walls) allows water to flow in opposition to
gravitational forces (capillary action)
Capillary action is necessary to allow water
to be transported up plant stems or taking
blood samples using capillary tube.
D2.3.1 Solvation with water as the solvent

Solvation is the process by which solvent

molecules surround and interact with solute
molecules.
Water is the universal solvent due to its
capacity to dissolve a large number of
substances.
Water can dissolve any substance that
contains charged particles (ions) or
electronegative atoms (polarity)
The polar regions of water molecule associate
with molecular surfaces that have an opposing
charge, forming dispersive hydration shells

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 A1.1.6. Physical properties of water
a. Buoyancy
Buoyancy is the upward force applied to
an object in a medium and it depends on the
density of the medium
As water is more dense than air, it applies a
greater upward force which allows objects
to float in water
The capacity of an object to float in water is
determined by its relative weight (heavier
objects will sink)
b. Viscosity
It is a measure of a fluid’s tendency to flow (more
viscous fluids are more resistant to flow)

Water is more viscous than air as it can form

hydrogen bonds which increase the friction of flowing
molecules

Additionally,water can dissolve many solutes and

these solutes can increase the viscosity of the solution
c. Thermal Conductivity

Thermal conductivity is a measure of a

medium’s ability to move heat across a
temperature gradient
Water absorbs and transfers heat more
readily than air because water particles are
packed more tightly together
d. Specific Heat Capacity
Specific heat capacity describes the amount of
energy required to raise the temperature of 1g of
substance by 1ºC
Water has a higher specific heat capacity than air
(highest of any liquid) as its hydrogen bonds require
additional energy to break
The high specific heat capacity of water makes it an
effective coolant in sweat (sweat absorbs a lot of
thermal energy in order to vaporize)
B1.1.1 Organic compounds
 An organic compound is a compound that
contains carbon and is found in living things.
 Carbon forms the basis of all organic
compounds due to its ability to form large
and complex molecules via covalent
bonding.
 Types of Carbon Compounds
 There are four main groups of organic
compounds that contribute to the
structure and function of a cell
B1.1.2 Monomers and polymers
1. Monomers
Organic compounds are composed of
recurring subunits (monomers)
The monomeric subunit of carbohydrates is a
monosaccharide.
Nucleic acids are composed of repeating
nucleotides
Proteins consist of chains of amino acids
Lipids do not contain monomers but they are
composed of distinct subunits (fatty acids)
2. Polymers
Polymers are large macromolecules
composed of smaller repeating subunits (called
monomers) via condensation reactions
 B.1.1.2-1.1.5 Carbohydrates
1. Characteristics
- The simplest biomolecules
- Contain 3 elements: Carbon, Hydrogen
Oxygen
- The word carbohydrate comes from the fact that
these compounds have many carbon atoms bonded to
hydroxide (OH) groups.
2. Functions:
- They are source of chemical energy for cells in
many living things.
- They are part of the structural material of
plants such as cellulose in the cell wall
 B1.1.4 Monosaccharides and
disaccharides
 Carbohydrates are made of C, H and O
(‘carbo’ – contains carbon ; ‘hydrate’ –
contains H and O)
 Carbohydrates are composed of
monomers called monosaccharides
(‘mono’ – single ; 'saccharide’ – sugar)
 Monosaccharides typically form ring
structures
 Types of Monosaccharides
 They have a single carbon ring.
 Most monosaccharides have either 5 carbons
(pentose sugars) or 6 carbons (hexose sugars).
The name describes the number of carbons.
 Simple sugars are soluble in water.

 An example of a pentose sugar is ribose

 An example of a hexose sugar is glucose
Ribose Glucose
C5H10O5 C6H12O6
 Disaccharides
 Two monosaccharide monomers may be
joined via a glycosidic linkage to form a
disaccharide. A glycosidic linkage is a
covalent connection between a
carbohydrate molecule and another
group (another carbohydrate or not).
Types of Disaccharides
- Havetwo carbon rings in their molecules.
- Soluble in water.
B1.1.2 Polysaccharides
 Polysaccharides are carbohydrate
polymers comprised of hundreds to
thousands monosaccharide monomers
 Three key polymers made from glucose
monosaccharides – cellulose, starch
(in plants) and glycogen (in animals)
 The type of polymer depends on the
monosaccharide subunits involved and
the bonding arrangement between them
 Polysaccharides are insoluble in
water.
B1.1.9 Lipids
 Unlike other biological macromolecules,
lipids are not polymers as they do not
contain monomers
(recurring subunits)

 However, most types of lipids

(excluding steroids) contain at least one
fatty acid chain in their structure
 B1.1.8 Hydrophobic properties
of lipids
 Lipids are a class of organic molecule
composed primarily of hydrocarbon chains
(fatty acids) or rings (steroids)

 Hydrocarbons are non-polar and will not

dissolve in polar substances like water
 Hence lipids are considered to be
hydrophobic molecules (water-repelling)
 The hydrophobic properties of lipids have many
biological consequences:
 Waxes are used to prevent water loss from leaves
 Birds coat their feathers with oil to become waterproof
 Phospholipids provide a structural framework for cells in
aqueous solutions
 Lipids in foods help the body to absorb certain fat-soluble
micronutrients, such as vitamins A and D


 Certain lipids have polar components, becoming
amphipathic (having both hydrophobic and
hydrophilic regions)

 Phospholipids possess a polar phosphate head,

cholesterol has a polar hydroxyl group

 These molecules have a limited capacity to interact

with water, helping them maintaining membrane
integrity
B1.1.9 Types of lipids

1. Formation of triglycerides and

phospholipids by condensation
reactions
 Unlike other biological macromolecules,
lipids are not polymers as they do not
contain monomers (recurring subunits)
 However, most types of lipids
(excluding steroids) contain at least one
fatty acid chain in their structure
Triglycerides are composed of three fatty
acid chains linked to a single glycerol molecule
Phospholipids
are amphipathic
(double-charged)
molecules
composed of one
glycerol molecule,
one phosphate
group, and two
fatty acid units.
 2. Main Classes of Lipids:
 a. Simple Lipids
 Simple lipids include esters of fatty acids
and alcohol (e.g. glycerol)

 Waxes consist of a fatty acid chain linked

to a long chain alcohol group and are used
to create waterproof surfaces
 Triglycerides consist of three fatty acid
chains linked to a glycerol molecule and
are used for energy storage and insulation

 b. Compound Lipids
 Compound lipids include esters of fatty acids and
alcohol linked to an additional group
 Phospholipids consist of a glycerol molecule
linked to two fatty acid chains and one phosphate
group – they are a component of cell membranes
 Glycolipids consist of a carbohydrate linked to
an ester of fatty acids and alcohol – they function
to facilitate cell-cell interactions
 c. Derived Lipids
 Derived lipids are substances produced from the
hydrolysis of simple or compound lipids
 They include signaling molecules such as steroids (a
group of hormones derived from cholesterol that act as
chemical messengers in the body) and prostaglandins
( hormone-like substances that affect several body
functions such as inflammation and pain)

B1.1.10 Difference between
saturated, monounsaturated
and polyunsaturated fatty acids
 Fatty acids are long hydrocarbon chains
that are found in most types of lipids
(excluding steroids)

 Fatty acids may differ in the length of the

hydrocarbon chain, but most typically
contain between 4 – 24 carbons
1.Types of Fatty Acids
Fatty acids are classified due to the presence or absence
of double bonds between the carbon atoms in the
hydrocarbon chain
Saturated fatty acids possess straight hydrocarbon chains
with no double bonds

Unsaturated fatty acids have double bonds – they can

be:
- mono-unsaturated (1 double bond)
- poly-unsaturated (>1 double bond)
2. Structure of unsaturated fatty acids
a. Cis isomers*: The hydrogen atoms attached
to the carbon double bond are on the same
side, causing the hydrocarbon chain to bend

*An isomer in chemistry is a chemical compound that has the same molecular
formula as another, but it has a different arrangement of atoms in space.
 b.Trans isomers: The hydrogen atoms
attached to the carbon double bond are
on different sides, meaning the
hydrocarbon chain remains straight
 2. Fats versus Oils

a. Fats (Saturated)
 Saturated fatty acids have straight
chains  more tightly packed more
efficient for energy storage

 Tight packaging  higher number of

intermolecular forces between the fatty
acid chains higher melting point 
solid at a room temperature of 25ºC)
 b. Oils (Unsaturated)

 Unsaturated (cis) fatty acids have bended chains 

more loosely packed

 There are fewer intermolecular forces less energy

is required to separate the fatty acids lower melting
point liquid at a room temperature of 25ºC)

B1.1.5 Lipids functions
 1. Energy Storage

 Triglycerides in adipose tissues are used

for long-term energy storage in animals
whereas carbohydrates (glycogen) are more
suitable for short-term energy storage

 Triglycerides can store twice as much

energy per gram as carbohydrates
 2. Thermal Insulation

 Triglycerides have a limited capacity to

conduct heat and are effective thermal
insulators
 Mammals living in cold environments
possess thick layers of subcutaneous
fat to insulate their internal organs
 3. Communication

 Steroid hormones function as

signaling molecules within the body

 Steroid hormones are generally

synthesized from cholesterol in either
the adrenal gland (corticosteroids) or
the gonads (estrogen and testosterone)
 B1.2.1-B1.2.5 Proteins
 B1.2.1 Structure of an amino acid

 Proteins are composed of long chains

of recurring monomers called amino
acids
 There are 20 different amino acids
which are universal to all living
organisms
 Each amino acid contains a central
carbon linked to an amine group,
carboxyl group, a variable side group
and a hydrogen atom
 Each type of amino acid differs in the
composition of their variable group R
 B1.2.3 Dietary requirements for
amino acids
 According to the dietary requirements,
amino acids can be:
 Essential - cannot be produced by the
body and must be present in the diet
 Non-essential amino acids can be
produced by the body and are not required
as part of the diet
 Conditional amino acids can be produced
by the body, but at rates lower than
certain conditional requirements (during
pregnancy)
 B1.2.2 Formation of dipeptides
and chains of amino acids
 Amino acids can be covalently joined together via
condensation reactions

 The created bond is called a peptide bond and forms

between the amine and carboxyl groups of amino acids

 Long chains of covalently bonded amino acids are

called polypeptides
B1.2.4 Variety of peptide chains
 The side groups R have distinct chemical
properties and cause the protein to fold
differently due to its position in the polypeptide
chain

 The way a protein molecule folds plays a critical

role in determining its function

 Most natural polypeptide chains contain

between 50 – 2000 amino acid and organisms
are capable of producing a huge range of
possible polypeptides
 Most natural polypeptide chains contain
between 50 – 2000 amino acid.

 Living organisms are capable of producing

a huge range of possible polypeptides.

 There are at least 100,000 proteins in the

human body
 Functions of Proteins
 Structure (collagen, spider silk)
 Hormones (insulin, glucagon)
 Immunity (antibodies)
 Transport (protein channels)
 Sensations (rhodopsin)
 Movement (actin, myosin)
 Enzymes (Rubisco, amylase)
 B1.2.5 Denaturation
 Denaturation is a structural change in
a protein that results in the loss of its
biological properties
 Denaturation of proteins can usually be
caused by two key conditions:

 Temperature:
High temperatures disrupt the
hydrogen bonds that hold the protein
together  the protein starts to unfold
and lose its biological function

Most human proteins function optimally

at body temperature (~37ºC)
 pH:

- Amino acids are neutral molecules (not charged)Changing

the pH alters the charge of the protein  protein solubility
and shape change

- All proteins have an optimal pH which depends on the

environment in which it functions (stomach, mouth, intestine)


A1.2.1- A1.2.10 Nucleic acids
A1.2.2 Nucleotides
Nucleotides are recurring monomers of
nucleic acids
Each nucleotide is composed of a pentose
sugar, a phosphate group and a
nitrogenous base
 A1.2.3 Sugar–phosphate
“backbone” of DNA and RNA
 Nucleotides are linked together into a
single strand via condensation.

 The phosphate group of one nucleotide

attaches to the sugar of another
nucleotide (at the 3’–hydroxyl position)

 This results in a
covalent phosphodiester bond forming
between the two nucleotides
 The sugar and the
phosphate form a
‘backbone’ of the ladder,
while the nitrogenous
bases extend out from
this strand
A1.2.4 Bases in nucleic acids
 Nucleic acids are composed of a
combination of four nitrogenous
bases:
 Guanine and adenine are double-
ringed purine bases

 Cytosine and thymine / uracil are
single-ringed pyrimidine bases
 A1.2.8 Complementary base
pairing
 The nitrogenous bases can pair up (purine
: pyrimidine) via hydrogen bonding to
create a complementary sequence
 Guanine always pairs with cytosine, while
adenine always pairs with thymine (DNA)
or uracil (RNA)
 G-C
 A-T or A-U
 The capacity for nucleic acids to undergo
complementary base pairing is critical
to its function as a genetic code

 It allows for the genetic information to

be replicated (one strand acts as a
template for the synthesis of a new
strand)
A1.2.5 RNA structure
 RNA is a single stranded molecule
produced from a DNA template via
condensation of nucleotide monomers

 The order of the nucleotide monomers is

determined by base pairing
 There are three main types of RNA involved
in the synthesis of proteins:

 Messenger RNA (mRNA) is the transcript

copy of the DNA instructions (it encodes the
protein sequence)


 Transfer RNA (tRNA) carries the
protein subunits (amino acids) to the
mRNA transcript
 Ribosomal RNA (rRNA) provides the
catalytic activity for combining the amino
acids according to the mRNA sequence
A1.2.6 DNA structure

UnlikeRNA, a DNA molecule is

composed of two strands held together
by hydrogen bonding between base
pairs
Adenine pairs with thymine via two
hydrogen bonds, while guanine and
cytosine pair via three hydrogen bonds
 The bases are facing each other and able to pair,
therefore two strands must run in opposite
directions (antiparallel)

 As the antiparallel chains lengthen, the strands will

arrange themselves into the most stable energy
configuration

 This results in the double-stranded DNA forming

a double helix (~10 – 15 bases per twist)
 A1.2.7 Differences between
DNA and RNA
 There are two types of nucleic acids present in
cells – DNA and RNA

 DNA is a more stable molecule that functions as

the master template for all genetic instructions

 RNA is a more versatile molecule and functions

to transfer the genetic information for coding
4. Condensation and hydrolysis
 a/ Condensation reaction (anabolic)
- two molecules can be joined to form a larger
molecule
- the molecules are held together by strong covalent
bonds.
- requires an enzyme to catalyze the process
- produces one molecule of water.
 Polymers can be formed from monomeric
subunits via condensation reactions
 A hydroxyl group (-OH) on one monomer
is combined with a hydrogen atom (-H)
on another monomer
 The two monomers become covalently
bonded and a water molecule is
produced as a by-product
 Condensation reaction-examples:
• The condensation of two monosaccharides
produces a disaccharide.
glucose + galactose → lactose + water
(monosaccharide) (monosaccharide) (disaccharide)

Glycogen consists of compact

molecules made up of branching
chains of glucose.
 Condensation reaction-examples:
• The condensation of two amino acids produces a
dipeptide.
amino acid + amino acid → dipeptide + water

When more than two amino acids are joined in this way,
a polypeptide (protein) is formed.
Condensation reaction-examples:
• Glycerol links to fatty acids to produce triglyceride
lipid molecules.
glycerol + 3 fatty acids → triglyceride lipid + water
a/ Hydrolysis reactions (catabolic)
- breaking down polysaccharides, polypeptides and
triglycerides into the smaller units of which they are
made
- water molecules are used in hydrolysis reactions –
they are the reverse of condensation reactions
- enzymes are required to catalyze the reactions.

https://www.youtube.com/watch?v=WRihqfKemUs