Biological Molecules Shazma Hiflan

BIOLOGICAL MOLECULES
1. Water
Water, H2O, is a compound which is liquid at stp. The water molecules are made up of two
hydrogen atoms bound to a highly electronegative oxygen atom (electronegativity is the
tendency of an atom to attract a shared pair of electrons toward itself when covalently
bonded).
The hydrogen atoms are bound to oxygen at an angle of approximately 105 degrees.
The bent shape of the molecule is because the two non bonding pair of electrons exerts a
repulsive force, pushing the hydrogens downwards.
Also, since oxygen has a higher electronegativity (3.44) compared to hydrogen (2.20), when
they form a covalent bond, oxygen pulls the bond pair of electrons towards itself, therefore the
electron pair is more closer to oxygen and not in the middle.
This gives oxygen a sight negative charge and hydrogen becomes slightly positively charged in
comparison. This is called a dipole. Therefore, water is a polar molecule. The dipole nature of
water causes water molecules to be attracted to each other. The δ+ H is attracted to the δ-
oxygen of another molecule. This attractive force is known as a hydrogen bond. It is a relatively
strong bond that gives water its many properties.
Properties of water

 Hydrogen bonding and the polar nature of water makes it an excellent solvent for ions
and polar molecules. This is because water can attract polar molecules and ions and
separate them, thus dissolving the substance in water. Water is an important solvent
because most chemical reactions happen in aqueous solutions. E.g.: NaCl forms Na+ and
Cl- ions.
When they dissolve in water,
(diagram)
The negative solute ion is surrounded by the δ+ hydrogens from water and vise versa,
hence effectively dissolving the substance.
Polar substances like acids, salts, alcohols are soluble in water, while non polar
substances like fats and oils are not. This is because they do not have polar parts
/charges in them, so are said to be hydrophobic (water hating). This makes them clump
together away from water.
 Being a good solvent makes them a good transport medium in the body E.g.:blood,
lymph etc.
 Hydrogen bonding in water gives it a high surface tension, which means it can withstand
more stress before being disrupted because the molecules tend to stick together, giving
it a very high cohesion. This is what makes the water molecules move in unbroken
columns.

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 As hydrogen bonding restricts movement of water molecules, a relatively large amount

of energy is required to raise the temperature of water. Specific heat capacity is the
amount of heat needed to raise 1g of a substance by 1 degree Celsius. Water has a
very high specific heat capacity. Due to this, large water bodies like the oceans would
require large amounts of energy to change temperature, hence making it have a more
or less steady temperature, allowing it to be an ideal habitat for living organisms.
 Latent heat of vaporization is the amount of heat required to change one mol of liquid
under boiling point, to a gas, at stp. Water has a high latent heat of vaporization as
well because its hydrogen bonds need to be broken in order for liquid water to
become steam. The advantage of this is that, as water molecules evaporate, it takes a
lot of heat along with it, cooling the body it evaporated from. This technique is what
happens when we sweat, cooling our body down, allowing maintenance of steady
temperature.

2. Carbohydrates
Carbohydrates are divided in to 3 main groups. They all have the common name ‘saccharide’
which refers to sugar.

• Monosaccharides
• Disaccharides
• Polysaccharides
Monosaccharides
They are monomers, the basic unit of a carbohydrate.
They taste sweet and dissolve in water
Have the general formula (CH2O)n
Examples of monosaccharides include

• Glucose: used in respiration to release energy

• Fructose: fruit sugar
• Galactose: also used to give energy
The above compounds are 6 carbon structures (hexoses) and they form ring structures.

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α-glucose and β-glucose are isomers. Isomers are two forms of the same chemical formula with
different structural formulae.
Monosaccharides have two main functions:

• Used as a source of energy in respiration because a large number of C-H bonds are
present, and these can be broken to release a lot of energy. This energy is transferred to
help convert ADP to ATP.
• It is a monomer which can be used to make polymers like starch, glycogen and cellulose
which are polysaccharides.

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Disaccharides
They are also sweet sugars which are soluble in water.
Maltose -> glucose + glucose (malt sugar)
Sucrose -> glucose + fructose (tea sugar and the transport sugar in plants)
Lactose -> glucose + galactose (milk sugar)
Two monosaccharides join together in a process known as condensation to form a
disaccharide. Two OH groups line up and a water molecule is formed. This is released to leave
an oxygen bridge known as a glycosidic bond. The resulting disaccharide is maltose.

When the reverse happens, to break down a maltose molecule in to two glucose molecules, a
hydrolysis reaction happens. Here the glycosidic bonds break and a water molecule is added.
This happens in digestion.
Polysaccharides
They are made of long chains of many small monomers joined together through a condensation
reaction, bound together by glycosidic bonds. The most important polysaccharides are starch,
glycogen and cellulose. They are all polymers of glucose. Cellulose is the structural
carbohydrate in plant cell walls. Starch is the storage carbohydrate in plants and glycogen is the
storage carbohydrate in animals. They are ideal for storage because, unlike its monomer
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glucose, the polymer is insoluble, has no osmotic effect and less reactive so therefore does not
affect the normal cell chemistry. They have a compact structure as well.

 Starch:
Made of two substances, amylose and amylopectin. Amylose is made up of a long,
unbranched chain of α-glucose molecules joined together by only 1,4-glycosidic bonds.
They coil up to make a compact structure for storage.
Amylopectin is made up of long chains of glucose joined by 1,4-glycosidic bonds and
shorter side chains of glucose bound by 1,6-glycosidic bonds. The 1,6-glycosidic branch
can easily be broken down to release energy when needed.
These are found in starch grains, commonly present inside chloroplasts. They are only
found in plant cells.

 Glycogen:
It is made up of long chains of glucose which are more branched than amylopectin,
consisting of both 1,4- and 1,6- glycosidic bonds. They are found in liver and muscles.
These branches can easily be broken down to release energy when needed.

 Cellulose:
A plant cell wall is made up of long chains of β-glucose to make the polysaccharide
cellulose. It is insoluble and provides a good structural support to plant cells.
When two β-glucose molecules come together, they form 1,4-glycosidic bonds. However
since β-glucose cannot line up their OH groups to form a bond (since the OH group in β-
glucose carbon 4 is below and carbon 1 is above the ring) one glucose molecule is
inverted upside down.
Hydrogen bonds are formed between the H+ of the hydroxyl groups and the O- oxygen
atoms in other parts of the glucose molecules. This cross linking holds the neighboring
chains firmly together, to form cellulose microfibrils. Several fibrils are held together in
bundles to make a cellulose fiber that has a very high tensile strength. They are laid in a
plant cell walls in different directions to enhance the strength while being a freely
permeable membrane.
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3. Lipids
Triglycerides are the most common type of fats. They can be either fats (solid) or oils (liquid) at
room temperature and pressure (rtp).
Triglycerides are made by joining three fatty acid molecules to 1 glycerol molecule. Fatty acids
and glycerol are the basic units of lipids.
Fatty acid: an organic molecule with a COOH (carboxylic acid group) attached to a long
hydrocarbon tail.
Glycerol: An alcohol with OH groups
Each fatty acid is joined to glycerol by a condensation reaction known as esterification to form a
glyceride. When 3 fatty acids join, it comes a triglyceride.

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The esterification reaction:

At the end of esterification, the glycerol and fatty acids are bound by ester bonds. -O-C=O
They are non-polar and hydrophobic and also does not dissolve in polar liquids like alcohol, water,
chloroform etc. This is because of the long hydrocarbon tails of fatty acids do not have any
uneven charge distribution.
Function of triglycerides in living organisms
The main function of triglycerides is to store fat and provide living organisms with energy for
metabolism. They are stored in fat cells.
When our body requires energy, the hormone glucagon is secreted by the pancreas. They signal
the breakdown of triglycerides to fatty acids and glycerol. Fatty acids are broken to CO2 and
water plus energy. The glycerol component is later converted to glucose through a process known
as gluconeogenesis.
The cell membranes of our cells are made up of phospholipids, which has a lipid tail and a polar
phosphate head (discussed in detail in cell membranes and transport).
Saturated and unsaturated lipids
Saturated lipids/fatty acids do not have double bonds in the carbon chain. All carbon atoms are
completely occupied by hydrogen. They are less reactive and does not melt easily. E.g.: Animal
fats.
Unaturated lipids have double bonds in the carbon chain. If there is more than one double bond
it is said to be polyunsaturated.
They are more reactive and melts easily. Most plant oils are unsaturated.

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4. Proteins
Proteins are extremely important in living organisms (50% of the dry mass of most cell).
Proteins make up:
- Enzymes (they speed up chemical reactions)
- Present in cell membranes (structural proteins, receptor proteins)
- Hormones (like insulin)
- Haemoglobin
- Antibodies
- Collagen in skin
- Keratin in nails and hair
- Actin and myosin in muscles
The basic unit of proteins are amino acids (monomer). There are 20 different amino acids and
all proteins are made up of different combinations of these joined together. The basic structure
of an amino acid has an amine group (NH2) and a carboxylic acid group (COOH).
(diagram)
H2N – N – CHR – C – OOH
The R group that is attached to the central carbon atom can differ from one amino acid to
another. The most basic amino acid glycine has just one H atom attached.
(diagram)
Other examples of amino acids include serine, valine, cystine etc.
An amino acid joins with another by a peptide bond. The resulting compound is a dipeptide.
This happens in a condensation reaction which involves the removal of a water molecule. A
dipeptide can be broken down in a hydrolysis reaction by the addition of a water molecule.

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(diagram)
The structure of a peptide bond: C=O – NH
Many amino acids join together by peptide bonds to make long polypeptide chains. A complete
protein can be made up of one or more polypeptide chains interacting together. Protein
manufacture in cells occur in the ribosomes.
Proteins can occur in four different structures: Primary, secondary, tertiary and quaternary.
1. Primary structure: a sequence of amino acids joined by peptide bonds to make a long
chain E.g.: enzyme protein ribonuclease
2. Secondary structure: when the primary structure becomes coiled it makes a secondary
structure. This is because amino acids in a chain may have an effect on each other.
There is a polar C=O group and a polar N – H group which can form hydrogen bonds
when they are next to each other.
(diagram)
This can result in a chain to coil to make an α-helix which looks like this
Sometimes the H bonds can make a lose structure called a β – pleated sheets
These structures can easily be broken
down by high temperatures and pH.
3. Tertiary structure: this occurs when
the secondary structure coils and folds
to make a 3D shape. These folds and
coils are held together by cross linkages
like hydrogen bonds, sulfur bridges
(disulfide bonds) and ionic bonds. E.g.:
lysozyme enzyme.
4. Quaternary structure: when a protein molecule is made up of two more tertiary
structures folded and cross linked together it makes a quaternary structure. It can have
multiple polypeptide chains. An example is haemoglobin.

Globular and fibrous proteins

Globular proteins Fibrous proteins

They have compact and round shapes Looser structure with a long narrow shape
Have a folded ball like structure with Have a helical or sheet structure
hydrophobic parts facing inside and
hydrophilic parts facing outside

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Soluble in water, acids and bases Insoluble in water, acids and bases

Involved in metabolic reactions Exists in the secondary structure

Exists in a tertiary structure Have strong intermolecular bonds

Have weaker intermolecular bonds Less sensitive to changes in temperature and
(hydrogen, disulfide) pH
Sensitive to changes in temperature and pH Involved in forming structures
Examples: enzymes, hormones, hemoglobin, Examples: outer layer of skin, hair, nails,
antibodies collagen, elastin, fibrin

Haemoglobin – a globular protein

It is a red pigment which carries oxygen in RBCs and gives blood its red colour. It is made up of
four polypeptide chains interacting together and therefore has a quaternary structure. Each
protein chain is called a globin. Hb is made up of two
types of globin known as α-globin and β-globin. There
are two α chains and β chains with a prosthetic heme
group (a group containing iron) in each chain.
Its 4 polypeptide chains are packed closely together,
with their hydrophobic R groups which are important
in holding its 3D shape.
The outward pointing hydrophilic R groups are
important in maintaining solubility.
Each polypeptide chain of Hb contains a permanent protein molecule called a haem group that
contains an iron atom. This is called a prosthetic group. One oxygen molecule (O2) can bind with
each iron atom. When combined with oxygen, the Hb molecule is called oxyhemoglobin.
Collagen – a fibrous protein
It is the most common protein found in animals. Collagen is insoluble fibrous protein found in
places like skin, tendons, cartilage etc. acting as structural protein.
A collagen molecule contains 3 polypeptide chains, each having the shape of a stretched-out
helix. These three helical polypeptide chains are wound around each other forming a triple helix.
The chains/strands are bound by together by hydrogen bonds. Almost every third polypeptide (3
amino acids per turn) is glycine. This make a collagen molecule.
One collagen molecule can interact with another, making cross linkages, to form fibrils (multiple
triple helices side by side linked by staggered covalent bonds).
(diagram)

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Many fibrils lie alongside each other to make collagen fibres, which is a strong bundle.
This structure gives collagen its properties like very high tensile strength which means it can
withstand large pulling forces without breaking. It is also flexible.

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