The Chemical Basis of Life
As we have seen in the last chapter, biology is the study of the natural world - the living world around us. Formerly the biologist merely classified plants and animals according to their size, shape ( i.e. anatomy), their physiology and their existence in nature. Scientists later discovered the chemical and physical bases of living things. From their own study they realized that there is a chemical similarity between a plant cell and an animal cell. This leads us to the study of the chemical basis of life

Structural Organization and the Chemical Basis of Life
(A) Introduction

The universe and living bodies are composed of matter which occupies space and possesses mass. Matter can exist in four forms -solid, liquid, gaseous and plasma. Matter is made up of basic substances called elements. There are over a hundred elements recognized by scientists today. An element is made up of identical atoms. Calcium, Carbon, hydrogen, iron, sodium, etc. are some elements.

i) Atoms

Each element is made up of one particular kind of atom. Atoms are the smallest part of an element which do not share the properties of the element. An atom consists of 3 basic particles:

a) Protons, which are positively charged and are present in the nucleus.
b) Electrons, which are negatively charged and which rotate around the nucleus.
c) Neutrons, which are present in the nucleus and which don’t have any electrical charge. A neutron has approximately the same mass as a proton.

In the nucleus of the atom the proton and neutron are firmly attached to each other. The chemistry of the atom is dependent upon the number of protons and electrons in the atom. Protons and electrons are present in the same number in the atom, which leads to a neutral electrical charge in the atom. The nucleus of an atom is surrounded by shells or orbits of electrons. In the first orbit there are a maximum of 2 electrons. From the second shell to the last shell, every shell has a maximum of 8 electrons. When the final orbit of an atom is complete with electrons it becomes a stable atom. When there is a single electron or more missing in the last orbit of the atom, the atom becomes active allowing for a chemical reaction with another atom. During the reaction there is sharing or exchange of electrons. Atoms are most stable when they have a full outer shell. If they can, they will either share one or more electrons with another atom so that both atoms " think " they have full outer shells, or sometimes an atom that " needs " one or two electrons to have a full outer shell will actually take electrons another atom that has only one or two electrons in its outer shell; therefore, both atoms end up with full outer shells.

ii) Molecules

In biology we study molecules as part of molecular biology, molecular interaction, etc. Atoms combine chemically in a specific order to form molecules. For instance, two atoms of hydrogen combine with one atom of oxygen to form a single molecule of water. A molecule is the smallest particle of a substance existing freely yet retaining the characteristics of that substance. A collection of molecules forms a compound. Properties of the compound depend upon molecules and atoms present in the molecule. Consider this example: the molecular weight of the compound, water, is 18. This weight has been calculated taking into account the weight of its molecular components H and O.

H₂O ®H + H + O ® 1 +1+ 16 ® 18

Some molecules are formed from atoms of the same element e.g. oxygen molecule (O₂) is formed from 2 atoms of oxygen; ozone (O₃) is formed from 3 atoms of oxygen. But, oxygen or ozone cannot be called a compound because in a compound we require atoms of different elements.

When the compound is formed it contains different elements. These elements stay together by means of links between them. In scientific terminology this link is called a bond. There are various kinds of bonds. In a compound, when one atom of an element gives away an electron, this exchange creates a bond between these two elements. This is an ionic bond. This bond consists of an electromagnetic force which is formed due to exchange of charge [electron]; the atoms conducting the exchange are called ions. This electromagnetic force attracts two opposite charges: a positive charge in the atom which gives away electrons and a negative charge in the atom which takes up electrons. This attraction force forms the ionic bond.

A second important type of bond is called the covalent bond. Such a bond is formed when two atoms share one or more electrons with one another. For example (fig. 21), in water (H₂O) 2 atoms of hydrogen share 2 electrons with oxygen. In ammonia 3 hydrogen atoms share one electron each with a single nitrogen atom. This leads to the formation of ammonia (NH₃). Between atoms when one pair of electrons is shared, a single covalent bond is formed. When two pairs of electrons are shared a double covalent bond is formed.

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iii) Acids and Bases or Alkali's

If a compound reacts with water and releases hydrogen ions (H+) ions then this compound is called an acid, and is said to be acidic in nature. For example, when hydrogen sulphide is mixed with water it releases hydrogen ions and the solution becomes one of sulphuric acid. Other chemical compounds when dissolved in water attract hydrogen atoms. These substances are called bases or alkali's. For example, when sodium hydroxide (NaOH) is mixed with water, sodium hydroxide attracts hydrogen ions from H₂O, and (OH-) ions remain. So these substances that remove (H+) from water act as bases or alkali's.

Organic Compounds

Many chemical compounds in living organisms are known as organic compounds' which contain C,H and O. In the earlier chapter we have seen that an organism is formed primarily from six elements: C, H, O, N, P, Ca. The study of organic compounds is called organic chemistry.

(A) Carbohydrates

There are plenty of organic compounds present in nature. All living things contain basically four types of organic compounds.Carbohydrates form the first category of organic compounds.

For metabolism the organism requires energy. This energy is provided primarily by carbohydrates. Carbohydrates are basically composed of 3 elements, C, H, and O. The ratio of H to O is 2:1, as in a water molecule (H₂O). There are types of carbohydrates according to the complexity of the carbohydrate molecule. Carbohydrates and usually taste sweet to humans are referred to as sugar. If a carbohydrate is made up from a single molecule it is called monosaccharide. When the carbohydrate is made up of 2 sugar molecules linked together it is referred to as a adisaccharide Carbohydrates which have more than 3 molecules are called polysaccharides. The general formula to represent the carbohydrate is Cx(H₂O)y.

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  Table I : Schematic Representation of Carbohydrates

1) Monosaccharides

They are the simplest soluble sugar. Depending on the number of carbon atoms present, monosaccharides are further classified as:

a) trioses ® (3 carbons) C₃H₆O₃ e.g. glyceraldehyde

b) pentoses ® (5 carbons) C₅H₁₀O₅ e.g. ribose and deoxyribose

c) hexoses ® (6 carbons) C₆H₁₂O₆ e.g. glucose

Glucose C₆H₁₂O₆ is a basic form of fuel in all living things. It is soluble in blood plasma and water and so it is transported by body fluids to all cells in the body. In cells it is metabolized and releases energy. Glucose is also the main product of photosynthesis and also an initiating material for cellular respiration.

Figure 2.2 A molecular representation of glucose

Disaccharides: These carbohydrates contain two monosaccharides linked together and accordingly they are known as: (a) Disaccharide : contains two monosaccharides e.g. lactose, maltose, sucrose
Maltose ® Glucose + Glucose
Sucrose ® Glucose + Fructose
Lactose ® Glucose + Galactose

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(b) trisaccharide: containing 3 monosaccharides. e.g. raffinose
(c) tetrasaccharide: containing 4 monosaccharide e.g stachyose

3) Polysaccharides
General formula n (C₆H₁₀O₅). These complex carbohydrates are formed by chains of at least ten monosaccharides.
They are of two types:

(a) Homoglycans: containing only one type of monosaccharide (e.g. glycogen, starch, cellulose, contain only glucose molecules). Starch is a very important polysaccharide because it is formed through a chain of hundreds or thousands of glucose units. Carbohydrates in plants are stored in the form of starches. Starch contained in energy rich food like rice, corn, and potatoes form part of the staple diet of most people.

Starch
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A second important polysaccharide is glycogen. Glycogen also contains thousands of glucose chains; the difference from starch though is in its branching pattern. Glucose is stored in the human liver in the form of glycogen.

Another important polysaccharide is cellulose. Cellulose is used primarily as a structural carbohydrate. It is also composed of glucose units, linked in a different orientation but the units cannot be released from one another except by a few species of organisms. Wood is formed from cellulose. Even the cell wall of all plants is made up of cellulose. Cotton and paper are also cellulose products.

(b) Heteroglucans: contain more than one type of monosaccharide linked together (e.g. mucilage, gum etc.)

4) Proteins and its derivatives

Proteins are the fundamental chemical compounds of the protoplasm indispensable for vital life processes. They are complex, large molecules each containing thousands of atoms. proteins contain nitrogen in addition to carbon, hydrogen and oxygen; they usually also contain phosphorus and sulfur. These compounds are polymers of unit structures called amino acids, represented chemically as:

amino acid

-NH₂ is an amino group, - COOH is the carboxyl group, ,and R represents the variable chain forming different amino acids. There are 20 diferent of amino acids. The amino acids differ depending on the nature of the R group. Examples of. amino acids are valine, alanine, glutamic acid, tyrosine and histidine.

Two molecules of amino acids are joined by the carboxyl group of one ammino acid with the amino group of the other by loss of one molecule of water. This process is called dehydration synthesis and the bond thus formed between two molecules is referred to as the peptide or peptide bond.

Formation of dipeptide

Click here to enlarge There are 3 types of proteins namely :

(1) Simple proteins: like albumins and globulins formed by group of amino acids only.

(2) Derived proteins: like proteose and peptones which are hydrolytic cleavage products of complex proteins.

(3) Conjugated proteins: like nucleo proteins (Proteins + nucleic acid), lipoproteins (protein + lipid), or glycoproteins (protein + carbohydrates) which are formed by the combination of proteins with some non-protein molecule. This non-protein portion is called Prosthetic group.

All living things require protein for survival. In fact an organism is constructed by means of proteins. All living things then, in any form - liquid, solid, or plasma - contain proteins. Protein is also seen as a supporting tissue with main tissue. Bone, tendons, muscle, cartilage, ligaments are all formed of protein.

Enzymes are a specified class of proteins. Enzymes act as catalysts in chemical reactions of the body. They are not used up by the reaction, rather they remain chemically unchanged and available to catalyze succeeding reactions.

Nucleotides And Nucleic Acid

Every organism reproduces within its life span. This is accomplished through cell divisions and is regulated by many kinds of protiens. The information forsynthesizing unique proteins is located in the nucleus of the cell. It is called the genetic code which is the "blue print" for producing specific sequences of the amino acids in proteins. Thus the genetic code can regulate chemical reaction going on in the cell.

Man’s queries into the nature of cells did not end with its discovery of general structures. In an attempt to understand the chemical make up and functional details of the cell he succeeded in discovering a substance called nucleic acid, made up of long chains of nucleotide units.

(A) Nucleotide
It is the structural unit of nucleic acid. Each nucleotide is composed of:

(1) Pentose sugar

(2) Phosphate group

(3) One of four nitrogen bases attached to the pentose sugar. A nucleotide without a phosphate group is a nucleoside.

(B) Nucleic acids

They are complex, large biomolecules formed of many units called nucleotides.

Nucleic acids are of two types :
(1) DNA - Deoxyribonucleic acid and, (2) RNA - Ribonucleic acid

The DNA of cells contains genetic information in a coded form, and is only present in the nucleus of the cell's formed from DNA, plus a few special organelles. RNA and is present in the cytoplasm and in the nucleus of the cell.

DNA and RNA differ from one another in their components. DNA contains the pentose sugar, deoxyribose, while RNA contains ribose.

There are also small differences in the types of nitrogen bases found in DNA and RNA. (The structure of DNA and its importance in the life of cells will be explained in th"Genes and Molecular genetics

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Lipids

Fats and their derivatives are collectively called lipids. Fats are compounds containing fatty acids and glycerol. They are composed of carbon, hydrogen and oxygen, but less oxygen than that in carbohydrates. Fatty acids are long chains of CH₂ groups with terminal methyl and carboxyl groups with general formula CH₃[CH₂]n-COOH, while glycerol molecule contains a chain of three carbon atoms and has a formula C₃H₆O₃. In the formation of fat, three molecules of fatty acids are combined with three-OH groups on one molecule of glycerol, with removal of 3 molecules of water which is represented as follows :

Formation of Fat molecule
There are mainly three types of lipids . the simple lipids, commonly known as fats and oils, the compound lipids such as phospholipids and glycolipids which on hydrolysis yield not only alcohol and fatty acids but also other compounds and derived lipids such as steroids which include cholesterol, Vitamin D, estrogen , testosterone, cortisol, etc. Lipids are practically insoluble in water but are soluble in organic solvents like chloroform, ether and benzene.

Fats stored in cells are usually clear oil droplets called globules. Because fats do not dissolve in water, animals store fat in large clear globules in the cells of adipose tissue. The enzyme lipose breaks down fats into fatty acids and glycerol which can be further broken down to produce energy.

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