3.

2: Biological molecule
Biological molecules are any molecules that occur
naturally in living organisms.
- The branch of biology which study of biological
molecules known as molecular biology
Biological molecules can either organic (its main element
is carbon (C) e.g. Carbohydrate, proteins lipids and
nucleic acids) Or in-organic molecules (mainly don’t
contain carbon such as water).
❑ Macromolecule and polymer:
Large organic biological molecules are called
macromolecules (there are four macromolecules
carbohydrates, proteins, nucleic acids, and lipids.)
Objectives of the chapter 5
By the end of this chapter students should be able:
▪ to use and understand the terms macromolecule and polymer
▪ to describe the importance of and basic structure of carbohydrates
(monosaccharides, disaccharides and polysaccharides)
▪ to describe the formation and breaking of a glycosidic bond by
condensation and hydrolysis respectively
▪ to relate the structures of the polysaccharides; starch, glycogen and
cellulose to their functions in living organisms
▪ to describe the structure and formation of the most common type of lipid,
the triglyceride.
▪ to relate the structures of triglycerides and phospholipids to their
functions in living things
▪ to use and understand the terms hydrophobic and hydrophilic,
unsaturated and polysaturated as they apply to lipids.

Polymers are macromolecules that made up of many repeating subunits that are similar or identical to each other.
(Carbohydrates, proteins, and nucleic acids are all polymers because they are made up of many identical repeating subunits.)

The small organic molecules (subunits) joins to form polymer is known as monomers. E.g. monosaccharides, amino acids
and nucleotides.

A chemical reaction by which monomers link to form polymers

known as condensation reaction
During formation of polymers, water is released.
- In this condensation reaction; one monomer released hydroxide
ion (OH -) and the other monomers releases a hydrogen ion (H+)
than hydroxide ion and hydrogen ion combine to form water.
Polymers breakdown into monomers through reverse process
known as hydrolysis
During breakdown of polymers, take in water.
- This water is used to break each bond within the polymers.

❑ Carbohydrates:
Carbohydrates are biological molecule contain the elements carbon, hydrogen and oxygen.
- The ‘hydrate’ part of the name comes from the fact that hydrogen and oxygen atoms are present in the ratio of 2:1, as
they are in water (‘hydrate’ refers to water).
The general formula for a carbohydrate can therefore be written as Cx(H2O)y. ✓ The term “saccharide” derives
There are three types of carbohydrates: from the greek word “sakcharon”,
1. Monosaccharide (Glucose, Galactose and fructose) which means sugar.
2. Disaccharide (maltose, sucrose and lactose)
3. Polysaccharide(starch, glycogen and cellulose)
The main functions of carbohydrate are:
▪ They are an immediate source of energy (glucose).
▪ They provide shape to certain cells (cellulose and chitin in plant and fungi cell walls respectively)
▪ They are the components of mucus, some hormones, many antibiotics, and coenzymes.
▪ They are an essential part of the nucleic acids, DNA and RNA.
▪ They also are components of cell membranes.
 Monosaccharides:
Monosaccharides (also known as simple sugars) are simplest forms of carbohydrates. Its basic subunits (monomers) that
make up complex carbohydrates which are polymers.
- Properties of monosaccharides usually are sweet, soluble in water and colorless.
Monosaccharides have general formula (CH2O) n. where n represents number of carbon atoms and are small integer
(3 up to 10).

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The main types of monosaccharides according the number of carbon atoms in each molecule are:
1. Triose (monosaccharides with 3C e.g. Glyceraldehyde)
- have molecular formula C3H6O3.
2. Pentose (monosaccharides with 5C e.g. deoxyribose and ribose)
- have molecular formula C5H10O5.
3. Hexose (monosaccharides with 6C e.g. Glucose, Galactose and Fructose)
- have molecular formula C6H12O6.

The most common monosaccharides are hexose sugars (mainly glucose.)

One important aspect of the structure of pentoses and hexoses is that the
chain of carbon atoms is long enough to close up on itself and form a more
stable ring structure.

This can be illustrated using glucose as an example. When glucose forms a

ring, carbon atom number1 joins to the oxygen on carbon atom number
5. The ring therefore contains oxygen, and carbon atom number 6 is not
part of the ring.

The hydroxyl group, –OH, on carbon atom 1 may be above or below the plane of
the ring. If the form of glucose where it is below; the ring is known as α -glucose
(alpha-glucose) and the form where it is above the ring is β -glucose (beta-glucose)

Monosaccharides also can either aldoses or ketoses.

− If the monosaccharides have functional group of aldehydes are called aldoses
− if the monosaccharides have functional group of ketones are called ketoses.
Glucose and fructose are specific examples of an aldohexose and a ketohexose, respectively.
Major functions of monosaccharides are:
▪ They are commonly used as a source of energy in respiration.
▪ They are important as building blocks for larger molecules.
In general; there are two other common ways of
drawing sugar molecules:
 Haworth projections “cyclic structure of
monosaccharides”
 Fischer projections “open chain forms of
monosaccharides”

 Disaccharides:
Disaccharides (double sugars) are composed two monosaccharides joining together. The three most common disaccharides are:
1. Maltose – malt sugar (glucose + glucose): products of digestion of starch.
2. Sucrose - table sugar (glucose + fructose) : found in fruits
3. Lactose – milk sugar (glucose + galactose): found in milk. (All they have same molecular formula “C12H22O11”)
The process or chemical reaction joining of two monosaccharides to form disaccharide known as condensation reaction.
During this reaction; one molecule of water is released and the bond forms between two monosaccharides is called glycosidic
bond. This bond is between carbon atom 1 of one monosaccharide and carbon atom 4 of the other, it’s known as a 1, 4 glycosidic
bond.
When water is added disaccharides break down into its monosaccharides; this reaction known as hydrolysis (its reverse of
condensation). This takes place during the digestion of disaccharides when they are broken down to monosaccharides.

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 During hydrolysis; water breaks down glycosidic bond between disaccharides, one monosaccharide gains its hydroxide ion
and the others gains its hydrogen ion.
The main function of disaccharides is:
▪ They are short term storage energy.
▪ They transport energy.
▪ First carbohydrate new born
mammals consumes.
▪ Joins to form polysaccharides.

Tests for reducing and non-reducing sugars:

All monosaccharides and some disaccharides (Except sucrose) are reducing sugars.
- The testing for reducing sugars are known as the Benedict’s test.
When a reducing sugar is heated with an alkali solution of copper (II) sulphate (Benedict’s reagent); it forms an insoluble
precipitate of copper (I) oxide. The color of precipitate changes from green through yellow, orange, brown and to deep red; depending
on the quantity of reducing sugars present. When sample is heated with Benedict’s reagent; if there is No change (solution remains
blue), then Non- reducing sugars is present.
 Polysaccharides:
Polysaccharides are. Polymer form when many monosaccharides joined together. The monosaccharides are joined by
glycosidic bonds that are formed by condensation reactions. The resulting chain may be varying in length, be branched and be
folded in different ways.
The most important polysaccharides are starch, glycogen and cellulose, all of which are polymers of glucose.
− Polysaccharides are not sugars because large molecules (macromolecules) with no sweet and are insoluble water.
When they are hydrolyzed polysaccharides break down into monosaccharides or disaccharides.
Starch Starch is storage polysaccharides in plants. Plants stores monosaccharides in form of starch.
Starch consists entirely of α-glucose monomers joined by glycosidic bond. Starch can be:
1. Amylose (unbranched starch molecule which contains only α-1,4-glycosidicbond.)
2. Amylopectin (branched starch molecule which contain α-1,4 a glycosidic bond and
α-1,6-glycosidic bond. It branched with every 30 monomers.)
Starch mainly found plant roots and seeds.
Functions of starch:
▪ it’s a primary long-term storage in plants
▪ also its most consumed polysaccharide in human diet.
Glycogen Glycogen is very similar in structure to amylopectin but short chain and is more highly branched and with branched
every 10 and 12 α-glucose. This many branches make it easily break down into its glucose subunits for quick energy
release. Glycogen found in the animal liver and muscles of animals
Function of Glycogen:
▪ It’s used as primary long term energy storage in animals
Cellulose Cellulose is the most abundant organic molecule on the planet, due to its presence in plant cell walls and its slow rate
of breakdown in nature. Cellulose is a polymer of β-glucose monomers, joined by β-1,4- glycosidic bond.
In order to form a glycosidic bond with carbon atom 4, where the –OH
group is below the ring, one glucose molecule must be upside down
(rotated 180 °) relative to the other. Thus, successive glucose units are
linked at 180 ° to each other.
− This orientation of bond prevents the digestive enzymes from
splits cellulose into glucose subunits.
Main function of Cellulose are:
▪ It’s a food of some microbes and also, it’s used as roughage in animals.
▪ Its structural component of plant cells (especially cell wall).
Chitin Chitin is a nitrogen containing polysaccharides. Functions of chitin:
▪ It’s a component of cell walls of fungi. And some protists
▪ Its most important component of the external skeletons of
some animals insects, crabs and spiders.

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  Test for starch:
Iodine solution is brown in colour. Add a drop of iodine solution to the solid or liquid
substance to be tested. A blue-black colour is quickly produced if starch is present.

❑ Lipids:
Lipids are a diverse group of biological molecules. Lipids are insoluble in water
because they are non-polar. Just like carbohydrates, lipids are mainly composed of
carbon, hydrogen, and oxygen. But Lipids generally have very small amounts of
oxygen, compared with the amounts of carbon and hydrogen.

Main functions of lipids are:

▪ Energy source ▪ transports fat soluble vitamins
▪ Energy storage ▪ Provides protection for plants against water loss.
▪ Provide insulation ▪ important component of cell membranes
▪ Protect some organs from physical damage. ▪ provides sex hormones

There are three main types of lipids:

1) Fats, oil and waxes 2) Phospholipids 3) Steroids

 Fats, oil and waxes:

Fats, oil and waxes are similar in structure and all contain three elements; C, H, O.
A fat and oil consist of two kinds of subunits:
 a glycerol(a small organic molecule contain three carbon atoms and have three hydroxyl (OH) groups)
 three fatty acids (small organic molecules consist of a long hydrocarbon chain attached to a carboxyl group)
To make a fat or oil, the hydroxyl groups on the glycerol react with the carboxyl groups of the three fatty acids in
a condensation reaction. This fat or oil forms are known as triglycerides. the new bond forms are known as ester bond.

Fatty acids are different in length or patterns of bonds.

− If there are only single bonds between neighboring carbons in
the hydrocarbon chain, a fatty acid is said to be saturated.
(The thing that fatty acids are saturated with is hydrogen)
− When the hydrocarbon chain has a double bond, the fatty acid
is said to be unsaturated, as it now has fewer hydrogen atoms.
If there is just one double bond in a fatty acid,
its monounsaturated, and while if there are multiple double
bonds, it’s polyunsaturated.

The main difference between fats and oils is that:

 Fats are solid at room temperature (20 – 30℃) because they
contain saturated fatty acids which pack closely together.
 Oils are liquid at room temperature because they contain
unsaturated fatty acids which far to one another (kinks caused
by double bonds in molecules)
The main function of fat and oil:
▪ Its used source energy
▪ Its also used as storage of energy
▪ It protects protects some internal organs from damage.

Waxes are similar to triglycerides; except that glycerol is replaced

by a long chain of alcohol which makes them more complex
structures. They are moresolid than fats at room temperature.
Waxes form water proof layer coating over the surface of the leaves Function of wax:
of the land plants and stem and also as water proofing for ▪ It prevents water loss
mammalian fur and insects exoskeletons ▪ It provides buoyancy for animals
in sea

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  Phospholipids:
Phospholipids are similar oil except that one of the fatty acid molecules is replaced by a phosphate molecule.
Whereas fatty acids repel water and are hydrophobic (water hating) because they
are non-polar; phosphate molecules attract water and are hydrophilic (water
loving) because they are polar. So that; a phospholipid has two contradictory ends.

Phospholipids in plasma membranes form a

double layer, with hydrophilic heads of the
molecules pointing into either the watery
environment outside the cell or inside the cell.
The hydrophobic tails points into middle of the
membrane.
Function of phospholipids:
▪ Its important components of plasma membranes.

 Steroids:
Steroids are another group of lipid molecule which
composed four fused rings.
Common steroids include; cholesterol (found in
cell membranes and helps maintains it fluidity and
also necessary for the manufacture of vitamin D),
testosterone, progesterone and ecdysone (molting
hormone of insects).

High cholesterol levels can lead to clogged arteries that come from a process known as atherosclerosis.
Functions of steroids:
▪ It helps metabolisms such as making Vitamin D.
▪ It also controls the development sexual characteristics.
 Testing for lipids:
One of the testing for lipids is known as emulsion test. Ethanol is added to the unknown substance and mixture is gently
shaken. This allows any lipids in the substance to dissolve in the ethanol. The ethanol is then poured into a tube containing water.
If lipid is present, a cloudy white suspension forms and this kind of mixture is called an emulsion.
By the end of this lesson, students should be able:
❑ Proteins: ▪ to describe the basic structure of amino acids, the
Proteins are polymers that consist of amino acid chains. More than 50% of basic component of proteins.
the dry mass of most cells is proteins. ▪ to describe the formation and importance of the
Proteins have many important functions include: peptide bond.
▪ all enzymes are proteins ▪ to describe the primary structure of
polypeptides and proteins and how it affects their
▪ proteins are essential components of cell membranes
secondary and tertiary structure
▪ some hormones are proteins – for example, insulin and glucagon ▪ to describe the importance of hydrogen bonds,
▪ the oxygen-carrying pigments haemoglobin and myoglobin are proteins disulphide bonds, ionic bonds and hydrophobic
▪ antibodies are proteins which attack and destroy invading microorganisms. interactions in maintaining the three-dimensional
▪ collagen, another protein, adds strength to many animal tissues, such as structure of proteins
bone and the walls of arteries ▪ to describe how the structures of globular (e.g.
▪ hair, nails and the surface layers of skin contain the protein keratin haemoglobin) and fibrous (e.g. collagen) proteins
▪ actin and myosin are the proteins responsible for muscle contraction. are related to their functions
▪ proteins may be storage products – for example, casein in milk and albumin in eggs.
 Amino acids:
Amino acids are the basic structural units of proteins. They all have a
central carbon atom which is bonded to an amine group, –NH2 , and a
carboxylic acid group, –COOH. It is these two groups which give amino
acids their name. The third component that is always bonded to the carbon
atom is a hydrogen atom. The only component in which amino acids differ
from each other is in the remaining, fourth, group of atoms bonded to the
central carbon. This is called the R group.

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 Altogether; there are twenty different amino acids are found naturally in proteins. These twenty amino acids are alphabet
of proteins. Just like the twentysix letters of the Somali alphabets can be used to make infinite number of words, so the
twenty amino acids can be used to make thousands of different kinds of proteins.
− Plants are able to make all the twenty amino acids from carbon dioxide, water and minerals.
− Animals can only make ten out of the twenty amino acids (these are known as non-essential amino acids because does
NOT necessarily for animals to take in diet and are Arginine, Histidine, Isoleucine, Leucine, Lysine, Methionine,
Phenylalanine, Threonine, Tryptophan and Valine) while the other ten amino acids must be obtained from proteins in the diet
(these are known as essential amino acids and are Glycine, Alanine, Glutamic acid, Glutamine, Aspartic acid, Asparagine
Tyrosine Serine Proline and Cysteine).
 Dipeptides and polypeptides:
Amino acids join together to form dipeptides or polypeptides (proteins) by condensation reaction. During this reaction; One
amino acid loses a hydroxyl (–OH) group from its carboxylic acid group, while the other amino acids loses a hydrogen atom
from its amine group. Then a carbon atom of the first amino acid free to bond with the nitrogen atom of the second one. The
hydroxide ions and hydrogen ions removed from the amino acids combines and form a water molecule.
− The bond that forms between the two amino
acids is called a peptide bond.
The new molecule which has been formed, made up
of two linked amino acids, is called a dipeptide.
Any number of extra amino acids could be added to
the chain in a series of condensation reactions.
 A molecule made up of many amino acids
linked together by peptide bonds is called a
polypeptide. (A polypeptide is another
example of a polymer and a macromolecule,
like a polysaccharide.)
A complete protein molecule may contain just
one polypeptide chain, or it may have two or
more chains which interact with each other.
In living cells, ribosomes are the sites of protein synthesis (where amino acids are
joined together to form polypeptides). The reaction is controlled by enzymes.
− Polypeptides or proteins can be broken down to amino acids by breaking the peptide bonds. This is a hydrolysis reaction,
involving the addition of water and happens naturally in the stomach and small intestine during digestion. Here, protein
molecules in food are hydrolysed into amino acids before being absorbed into the blood.

 Protein structure:
Proteins can be classified biologically into four levels of structures:
Primary structure Primary structure of protein is a sequence of amino acids a polypeptide chain. Its linear chain because
only has peptide bonds between amino acids.
Secondary structure Secondary structure of protein is most basic level of protein folding. The secondary structures are a
polypeptide chain which coiled into α-helix or folded into β-pleated sheet. It folded or coiled chain
because the hydrogen bond between amino acids in polypeptides and this numerous hydrogen bond makes
a secondary structure stable.
 This secondary structure is due to hydrogen bonding forms between the oxygen of the –CO– group of
one amino acid and the hydrogen of the –NH– group of another amino acid within a single polypeptide.
Tertiary structure When the secondary structure itself is coiled or folded forms three-dimensional folding known as
tertiary structure.
Every protein has a unique tertiary structure
which is responsible for its properties.
This is the result of four possible types of bond
folded proteins in their precise shapes and they are:
▪ Hydrogen bonds can form between a wide variety of R groups.
▪ Disulfide bonds form between two cysteine molecules, which contain sulfur atoms.
▪ Ionic bonds form between R groups containing amine and carboxyl groups.
▪ Hydrophobic interactions occur between R groups which are non-polar, or hydrophobic.
Quaternary structure This structure is found only complex proteins that contain more than one polypeptide chains and also non-
protein groups associated with the molecules.

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  Globular (e.g. haemoglobin) and Fibrous (e.g. collagen) proteins:
A globular protein is a protein whose molecules curl up into a ‘ball’ shape and
− This because their non-polar, hydrophobic R-groups point into the centre of the molecule,
away from their watery surroundings. For example; haemoglobin (The four polypeptide
chains pack closely together, their hydrophobic R groups pointing in towards the centre of the
molecule, and their hydrophilic ones pointing outwards and This outward-pointing
hydrophilic R groups on the surface of the molecule are important in maintaining its
solubility). Enzymes, for example, are globular proteins.
Fibrous proteins are protein molecules do not curl up into a ball, but form long strands.
− This is because they are not usually soluble in water and most have structural roles.
For example, collagen (a collagen molecule consists of three polypeptide chains
with parallel to each other) found in skin, tendons, cartilage, bones, teeth and the
walls of blood vessel.

 Test for proteins:

The most reliable protein test is the biuret test, which detects peptide bonds.
The reagent used for this test is called biuret reagent.
Take a sample of solution contain a protein add some of sodium hydroxide or
potassium hydroxide solution until the suspension clears. Add a few drops of
copper(II) sulfate solution(has blue colour) shaking at each drop. If the colour
changes purple, this indicates the present of proteins.

❑ Water: By the end of this lesson, students should be able:

▪ to explain the properties of water and its
Water is a molecule contains two hydrogen and one oxygen atoms and has
importance in cell biology
formula H2O.
It’s the most abundant chemical compound on earth occupying about two-thirds of its surface.
 Properties of water:
Water has the following properties due to its polarity and hydrogen bond.
Dipolar water molecules Water is made up of two atoms of hydrogen and one of oxygen atom. These atoms form a
triangular shape. Although it has NO overall charge, the distribution of charged electrons
is uneven b/c oxygen atom draws them (electrons) away from the hydrogen atoms.
Therefore; oxygen atoms have slightly negative charge and hydrogen atoms have slightly
positive charge. So that; water is described as dipolar.
− This allows water dissolves only polar substance.
Hydrogen bond Water has different poles. Therefore; the positive pole of one water molecule will be
attracted to the negative pole of another water molecule. This force of attraction between
these opposite charges is called hydrogen bond.
− This causes the water molecules to stick together.
High specific heat capacity Specific heat capacity of water (or simply the specific heat) is the amount of heat energy
required to raise the temperature of 1 kg of water by 1°C. Water has a high specific heat
capacity because water molecules stick together by hydrogen bond.
− This helps to distribute heat around the body and carries excess of heat to skin (water
in blood)

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High latent heat of vapourisation The latent heat of vapourisation is a measure of the heat energy needed to changing a
liquid to a gas. Water has a relatively high latent heat of vapourisation because it needs a
lot of energy to break down hydrogen bonds between water molecules.
− The evaporation of water during sweet production helps to rid the body of excess heat.
Cohesion and adhesion in water The tendency of water molecules to stick together is known as cohesion. The attraction
force between water molecules and walls of vessels or tubes is called adhesion force.
Water has large cohesion and also has large adhesion force.
− This allows water move up within tubes such as xylem vessels in plant.
surface tension in water This tendency of a liquid to hold together at its surface is called surface tension. At the
boundary between water and air, the water molecules form hydrogen bonds with
neighbors to their sides and below them in the liquid. Water has high surface tension
because it is cohesive.
− This allows certain small organisms walk on or skate over its surface such as water strider.
Density and freezing of water Water is an unusual chemical because the solid form, ice, is less dense than its liquid
form. Below 4 °C, the density of water starts to decrease.
− This is increases the chances of life surviving in cold conditions.
Important functions of water to living organisms:
 Water (in metabolism) is used for:
1. to breaking down many complex molecules by hydrolysis.
2. a major raw materials in photosynthesis.
 Water (as solvent) is used for:
3. Transport materials e.g. water in blood. By the end of this lesson, students
4. Removal of wastes, e.g. ammonia and urea. should be able:
5. Secretions, e.g. extracellular enzymes and tears ▪ to describe the functions of some
 Water (as support) is used for : inorganic ions required by living
6. In hydrostatic skeleton to support animals e.g. earth worm. organisms e.g. Ca 2+ , Na+ , K+ ,
7. In amniotic fluid to support foetus. Mg 2+ , Cl -, NO3 -, PO4 3-,
8. Creating turgor pressure to supports the leaves of plants. Fe2+
 Other uses of water:
9. Water is used as lubricant to reduce friction, e.g. synovial fluid in joints.
10. It is transparent; this allows aquatic plants can photosynthesize.
11. its evaporation cools organisms and this allows them to control their temperatures.

❑ In-organic ions:
Living organism also needs in-organic ions which take important part metabolic reactions in the body. The table below shows
inorganic ion and their main functions:
Calcium ions Ca2+ In animals; necessary for: formation of bones, contraction of muscles and blood clotting. In
plants; its major component of middle lamella of the cell wall and also aids for translocation of
carbohydrates and amino acids.
Sodium ion Na + Its important for transmission of nerve impulses, maintains osmotic pressure of the body fluids
and helps reabsorption of water in kidneys. Also its constituent of sap vacuole in plant and so
helps to maintains turgidity.
Potassium ion K + It is important for transmission of nerve impulses, its acts as cofactor of enzymes in
photosynthesis and respiration and its responsible for turgidity of guard cells and controls
opening and closing of stomata.
2+
Magnesium ion Mg It is an important for making chlorophyll and acts as cofactor which activates ATPase. Also its
necessary for formation of bones.
Chloride ionCl - It is important for transmission of nerve impulses and such like sodium ion also help reabsorbs
of water in kidney. Also needs for formation of hydrochloric acids in gastric juice.
3-
Nitrate ion NO Its important for making amino acids, vitamins, nucleotides, coenzymes and ATP. Also some
hormones contain nitrogen.
Phosphate ion PO43- Are important components of ATP, nucleotides and some proteins. also are components of bone.
Iron ion Fe2+ Its necessary for formation of heamoglobin in erythrocytes.
-
Iodide ion I Its necessary for formation of thyroid hormones.

© Abdishakur Ibrahim Abdi 8