Biochemical molecules

2.1 Inorganic and organic molecules

Classification of biochemical molecules

• Biochemical molecules can be inorganic or organic.
• Inorganic molecules do not contain both hydrogen and carbon.
• Organic molecules always contain both carbon and hydrogen.

Which chemical elements are found most

frequently in living organisms?
• An element is a substance that is made of only one kind of atom.
• Most biological molecules are built from carbon, hydrogen, oxygen, nitrogen, sulfur and phosphorus.

Atoms, molecules and compounds

• Atoms are the smallest particles of a chemical element.
• Molecules are groups of two or more atoms of the same element (e.g. O2) or different elements
(e.g. H2O) held together by chemical bonds.

• A compound is a substance made from molecules containing more than one kind of atom in a fixed
ratio.

What is water?
• Water is the most abundant inorganic molecule in living things. It contains two hydrogen atoms
bonded to one oxygen atom.

• Water is a polar molecule. The oxygen and hydrogen atoms share electrons unevenly to form
opposite ends of the molecule, known as dipoles.

• A dipole refers to the separation of charges within a molecule between two covalently bonded atoms
or atoms that share an ionic bond. In a water molecule, the oxygen side of the molecule carries a net
negative charge, while the side with the two hydrogen atoms has a net positive electrical charge.

• Water molecules are interlinked by a hydrogen bond, which joins the oxygen in one water molecule
(the slightly negative part) to the hydrogen in another water molecule (the slightly positive part).

Why is water so important to living things?

Water is important to living things in a number of ways, such as:

• It serves as a habitat for many organisms.

• It is a transport medium in living organisms.
• It is a reactant in many chemical reactions, such as photosynthesis and hydrolysis. Hydrolysis is a
reaction that uses water to split large molecules into smaller ones.

• It is a medium for chemical reactions due to its low viscosity (high flow) and its ability to dissolve
many solutes.

• It is involved in temperature regulation as you lose body heat through sweating.

Properties of water

• It is transparent. This allows light to reach aquatic plants and algae.

• It is a versatile solvent as it can dissolve different kinds of solutes because of its polarity and ability to
form hydrogen bonds easily with polar and charged solutes.

• It has low viscosity. Viscosity is the measure of a fluid's resistance to flow. The low viscosity of water
makes it an ideal medium for chemical reactions because the particles can move around and come
easily into contact with each other.

• It has a high surface tension; the surface of water acts as a thin elastic sheet. This property of water
is due to the strong hydrogen bonding between the water molecules at the surface and the molecules
from the sides of a mass of water. The high surface tension of water enables small animals like water
strides to walk on water easily.

• It has a high specific heat capacity as it takes a lot of energy to heat water up. Water also loses heat
quite slowly. As a result, water stays more or less the same temperature. This is very important to
aquatic organisms as the function of their enzymes is affected by changes in temperature.

• It has a high latent heat of vaporization; it takes a lot of heat to vaporize liquid water. As a result,
water bodies like ponds do not dry up too quickly in hot weather. This property also helps us lose a lot
of body heat while sweating during a hot day.

• Ice is less dense than liquid water. This is because water expands when it freezes.

Organic molecules
• Organic molecules are molecules of carbon and hydrogen. The carbon atoms are covalently bonded
to hydrogen atoms (C-H bonds).

• Many of the organic compounds in living cells are so large that they are known as macromolecules.
• Most macromolecules are formed by a process known as polymerization, a process by which smaller
units, or monomers, join together to form large compounds, or polymers.

• Biologically important groups of organic molecules include carbohydrates, lipids, proteins and nucleic
acids (RNA and DNA).

Carbohydrates
• They contain carbon, hydrogen and oxygen atoms, usually with a hydrogen-oxygen atom ratio of 2:1.
The general formula of carbohydrates is (CH2O)n, where n > 3.

Importance of carbohydrates

• They are the main source of energy for the body. Glucose is the main respiratory substrate of most
organisms.

• They are convenient for storing energy. Starch is the main carbohydrate energy store in plants.
Glycogen is the only carbohydrate energy store in animals.

• Some carbohydrates are used to build structures. Structural carbohydrates include:

⇒⇒ cellulose, which is the main constituent of plant cell wall

⇒⇒ chitin, which occurs in cell walls of fungi and in the exoskeleton of insects
⇒⇒ peptidoglycan, which occurs in bacterial cell wall

Classification of carbohydrates
• Carbohydrates are generally classified into three based on the number of sugar units they are made
from. These are monosaccharides, disaccharides and polysaccharides.

Monosaccharides
• Monosaccharides are the simplest carbohydrates that contain only one sugar unit. Examples include
glyceraldehyde, dihydroxyacetone, ribose, deoxyribose, ribulose, glucose, galactose and fructose.

Classification of monosaccharides
• Monosaccharides are classified according to how many carbon atoms are present in the molecule.
These include triose, pentoses and hexoses.

Trioses
• Trioses contain 3 carbon atoms, with the chemical formula C3H6O3.
• The two naturally occurring trioses are glyceraldehyde and dihydroxyacetone. They are important in
cellular respiration.

• Each triose has the same number of each kind of atom, but the atoms are put together in a different
way. They are isomers of each other. Isomers are compounds that have the same chemical formula
but different arrangement of atoms.

Pentoses
• Pentoses have five carbon atoms - C5H10O5. Examples include ribose, deoxyribose and ribulose.
They are isomers of each other. Ribose occurs in RNA, coenzymes and ATP molecules, and
deoxyribose occurs in the DNA molecule.

Hexoses
• Hexoses have six carbon atoms - C6H12O6. Examples include glucose, galactose, mannose and
fructose. They are isomers of each other.

Functional groups of monosaccharides

• There are two functional groups in monosaccharides. These are the aldehyde group, with the formula
(-CHO) and the ketone group, with the formula (C=0). A functional group is a group of atoms
responsible for the reactions of a particular compound.

• Monosaccharides are also classified as aldoses or ketoses based on the functional group that they
possess.

Aldoses
• Aldoses contain an aldehyde functional group. Examples include glyceraldehyde, ribose, glucose and
galactose.

Ketones
• Ketones contain a ketone functional group. Examples include dihydroxyacetone, ribulose and
fructose.

Structures of monosaccharides
• The structures of monosaccharides appear in straight chain and ring forms. The straight chain
structures are often changed into ring forms when they are in solution.
• The straight form of glucose produces two ring forms, namely, a-glucose and b-glucose.

• The straight chain form of fructose produces only one ring form.

Disaccharides
• Disaccharides are carbohydrates which are formed from two monosaccharides joining together.
Examples include maltose, sucrose and lactose.

⇒⇒ Maltose (malt sugar) is formed from two α-glucose molecules.

⇒⇒ Sucrose (table sugar) is formed from an α-glucose molecule and a fructose molecule.
⇒⇒ Lactose (milk sugar) is formed from a β-glucose molecule and a β-galactose molecule.

• Disaccharides are formed from monosaccharides by a type of reaction called condensation.

Condensation is the process in which two small molecules combine to form a large molecule,
producing a smaller molecule (often water) as a by-product. The bond that holds the two
monosaccharide units together is called glycosidic bond.

C6H12O6+C6H12O6⟶C12H22O11+H2OC6H12O6+C6H12O6⟶C12H22O11+H2O

• A molecule of water is formed from a hydroxyl group from one monosaccharide and hydrogen atom
from the other.

Polysaccharides (Complex sugars)

• Polysaccharides are complex and stable carbohydrates whose molecules consist of many hundreds
of monosaccharide molecules bonded together in a condensation reaction. Examples include starch,
glycogen, cellulose and chitin.

Some importance of polysaccharides

• Some are storage molecules. Examples are starch in plants and glycogen in animals.

• Others are structural carbohydrates. These include cellulose, chitin and peptidoglycan.

Starch
• Starch is a plant storage polysaccharide containing two polymers of α-glucose called amylose and
amylopectin.

• Amylose is a straight chain polymer of α-glucose molecules joined by α-1,4-glycosidic bonds. It gives
a blue black color in iodine solution.
• Amylopectin is a branched polymer of α-glucose molecules joined by α-1,4-glycosidic bonds and α-
1,6-glycosidic bonds. The α-1,6-glycosidic linkages cause the branched structure of amylopectin. The
side branches of amylopectin allow it to be quickly hydrolyzed by enzymes.

Glycogen
• Glycogen is a branched, storage polysaccharide in animals having α-1, 4-glycosidic linkages and α-
1,6-glycosidic linkages.

How the structures of starch and glycogen are suited

to their functions
• Starch and glycogen are ideal for storing energy because they are very compact, insoluble and have
side chains that can be quickly hydrolyzed by enzymes.

Cellulose
• Cellulose is a straight chain polymer of β-glucose molecules joined by β-1,4-glycosidic bonds.

• Cellulose microfibrils are formed when many cellulose molecules are bind together by hydrogen
bonds. This fibrous nature of cellulose gives the plant cell walls their strength.

What are lipids?

• Lipids are organic molecules made from fatty acids and alcohols. They contain the elements carbon,
hydrogen and oxygen, with much less oxygen than carbohydrates. Examples of lipids include
triglycerides, phospholipids and waxes.

• Lipids are the most efficient energy store in body as they provide over twice as much energy as
carbohydrates.

Importance of lipids

• They store energy, provide insulation and buoyancy, make up cell membranes, provide building
blocks for hormones and form water-repellent layers on leaves and feathers (waxes).

Triglycerides
• A triglyceride molecule is an ester formed from one molecule of glycerol and three fatty acid
molecules. A fatty acid molecule consists of a hydrocarbon chain joined to a carboxyl functional
group.
• Fatty acid molecules can be either saturated (all carbon–carbon bonds are single), monounsaturated
(one carbon–carbon double bond) or polyunsaturated (more than one carbon–carbon double bond).

How are triglycerides formed?

• Triglycerides are formed when three fatty acids are joined to a glycerol molecule in a condensation
reaction. The bond formed between the carboxyl group of a fatty acid and the hydroxyl group of a
glycerol molecule is called ester bond.

Phospholipids
• A phospholipid molecule consists of two fatty acids and a phosphate group bonded to a molecule of
glycerol. The phosphate group gives the molecule a hydrophilic (water-loving) ‘head’ and the fatty
acids give the molecule hydrophobic (water-hating) ‘tails’. Phospholipid bilayers are the basis of
biological membranes.

Waxes
• Waxes are lipids formed from fatty acids and long-chain alcohols in a condensation reaction.

Proteins
• Proteins are polymers of amino acids. They contain carbon, hydrogen, oxygen and nitrogen. Amino
acids have two functional groups – the amino group (–NH2) and the carboxyl group (–COOH), as well
as an '' R'' group, which can be an element or a hydrocarbon chain.

Importance of proteins
• They are structural components of the cell membrane as ion channels, transport proteins and
receptors.
• They are used in the immune system as antigens and antibodies.
• They control the rate of chemical reactions as enzymes.
• They are the structural components of chromosomes. The protein histone covers the DNA molecule.

How are proteins formed?

• Proteins are formed from amino acids when they join together in a condensation reaction. A peptide
bond is a covalent bond formed between two amino acids when the carboxyl group of one amino acid
reacts with the amino group of the other amino acid, releasing a molecule of water ( H2O).

• A polypeptide is a linear polymer consisting of many amino acids bonded together in a long chain.
Structures of proteins
• Proteins have several levels of structure:

⇒⇒ The primary structure is the linear sequence of amino acids in a polypeptide chain.
⇒⇒ The secondary structure is formed by the folding of the primary structure into either an α-helix or a β-
pleated sheet, which are held together by hydrogen bonds.
⇒⇒ The tertiary structure is the three-dimensional folding of the secondary structure into fibrous (string-
like) or globular (ball-like) shape due to further bonding of the side chains or R groups by hydrogen
bonds, disulphide bridges and ionic bonds.
⇒⇒ The quaternary structure is formed when two or more polypeptide chains, each with a tertiary
structure, are bonded together. Examples of proteins with quaternary structures include hemoglobin with
4 polypeptide chains and collagen with 3 polypeptide chains.

• Based on their molecular shapes, proteins can be fibrous or globular. Fibrous proteins like collagen
and keratin have string like shape. Globular proteins like enzymes and receptor proteins have ball like
shape.

Nucleic Acids

• Nucleic acids are biological molecules made from structures called nucleotides. Examples are RNA
and DNA.

• DNA is the genetic material found in the chromosomes. It is a huge molecule that contains the genes
that determine the features of organisms. A gene is a short section of DNA that codes for a specific
protein and, as a result, determines a particular feature.

• DNA has two strands which wound into a double helix.

• RNA is a single-stranded nucleic acid found both in the nucleus and the cytoplasm. It comes in
different types-messenger RNA, transfer RNA and ribosomal RNA.

• RNA carries the genetic code from the DNA in the nucleus to the ribosomes in the cytoplasm and
allows protein synthesis.

• DNA and RNA are polymers of nucleotides.

• A nucleotide contains a phosphate group, a pentose sugar and a nitrogenous base.

Table: The differences between DNA and RNA

Food Test
Iodine test for starch: Starch reacts with a solution of iodine to give a blue-black color.
Test for reducing sugars: Reducing sugars like glucose, fructose, maltose and lactose react with
Benedict’s solution when heated to give a yellow/orange/red precipitate.
Biuret test for protein: Proteins react with Biuret reagent to give a mauve/purple color.
Emulsion test for lipids: It produces a milky-white color in water.