Chapter 6: Biomolecules
In the early 1950s, a quiet British biochemist named Frederick Sanger took up a problem that most scientists of his time thought was hopeless. He wanted to find the exact order in which the building blocks of a single protein were joined together. The protein he chose was insulin — the hormone that keeps blood sugar under control.
At that time, nobody knew whether a protein even had a fixed order. Many believed proteins were shapeless, jelly-like masses. Sanger patiently broke insulin into small fragments using acids and enzymes, separated those fragments on sheets of paper, identified each one, and then fitted the overlapping pieces together like a jigsaw puzzle. It took him years.
The answer changed biology. Insulin turned out to be nothing like a shapeless blob. It was two chains of amino acids, arranged in one exact, unchanging order, held together by sulphur bridges. Every insulin molecule in every healthy person carried the same sequence. For this work Sanger received the Nobel Prize in Chemistry in 1958.
Sanger’s result carried a bigger message. The molecules inside a living cell are not a random chemical soup. They are built to a plan — precise, repeatable, and directly linked to what they do. This chapter is about those molecules of life: carbohydrates, lipids, proteins, nucleic acids and the remarkable protein catalysts called enzymes.
Diagram
Fig. 6.0 – A living cell shown at the centre with four arrows leading out to sketches of a starch grain, a fat droplet, a coiled protein chain and a DNA double helix, each labelled with its class of biomolecule.
As you work through this chapter, you will be able to answer each of these questions yourself.
6.1 Introduction
Our planet carries an enormous variety of living organisms. Some of them are unicellular, which means the entire body is made of a single cell — bacteria and yeast are familiar examples. Others are multicellular and are built from many cells working together, as in plants and animals.
You have already learnt that the cell is the basic structural and functional unit of every living organism. Inside each cell lies the protoplasm, the living material of the cell, and this protoplasm holds a very large number of chemical molecules.
These chemical molecules present in living cells are called biomolecules. They are not scattered at random. Each one has a definite composition and a definite job, and together they carry out everything we recognise as “being alive” — growth, movement, energy release, repair and reproduction.
What Biochemistry Studies
Biochemistry is biological chemistry. It gives us the idea of the chemistry of living organisms and explains the molecular basis for the changes taking place in plant cells, animal cells and microbial cells.
Biochemistry develops the foundation for understanding all biological processes. It also explains how communication takes place within a cell and between different cells, and it provides the chemical basis of inheritance and of diseases in animals and plants.
This is a powerful idea, and it is worth pausing on. If life runs on molecules, then a disease is very often a molecule that has gone wrong — a missing enzyme, a faulty protein or a damaged gene. Understanding the molecule is therefore the first step towards understanding, diagnosing and treating the disorder.
Elements That Build Life
Chemical analysis of all living organisms indicates the presence of certain most common elements. These include carbon, hydrogen, nitrogen, oxygen, sulphur, calcium, phosphorus, magnesium and others, each present in its own respective content per unit mass of a living tissue.
Notice in Fig. 6.1 that the inorganic part of the biomolecule chart is arranged according to how much of each element the organism needs.
Diagram
Fig. 6.1 – Classification chart of biomolecules in a living system: Biomolecules branching into Organic (Macromolecules — polysaccharides, polypeptides, polynucleotides with their monomers simple sugar, amino acid, nucleotide; Micromolecules — lipids with fatty acids and glycerol, saturated and unsaturated fatty acids, and secondary metabolites such as alkaloids, phenolics, terpenoids, essential oils, toxins, lectins) and Inorganic (prime elements, macro elements, trace elements with their listed elements).
The prime elements are carbon (C), hydrogen (H) and oxygen (O), and they are present in air and water. The macro elements are nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg) and sulfur (S). The trace elements — boron (B), chlorine (Cl), zinc (Zn), copper (Cu), iron (Fe), sodium (Na), molybdenum (Mo), nickel (Ni), silicon (Si) and cobalt (Co) — are required in extremely small quantities, but the organism cannot manage without them.
Monomers and Macromolecules
Chemically, all living organisms have three basic types of macromolecules. Each of these is a polymer, that is, a very large molecule built by joining together many small repeating subunits. These small repeating subunits are called monomers.
The three polymers and their monomers follow a simple pattern. Polysaccharides (carbohydrates) are polymers of monosaccharides, polypeptides (proteins) are polymers of amino acids, and polynucleotides (nucleic acids) are polymers of nucleotides. This relationship is summarised in FC 6.1.
Flowchart
FC 6.1 – Monomer to polymer relationship in the three classes of macromolecules: monosaccharides → polysaccharides (carbohydrates); amino acids → polypeptides (proteins); nucleotides → polynucleotides (nucleic acids)
Lipids are treated differently in this scheme. They are water insoluble compounds and have a small molecular weight when compared with the macromolecules. For this reason lipids, along with the secondary metabolites, are placed under micromolecules in Fig. 6.1, and not with the macromolecules.
Keep the whole chart of Fig. 6.1 in mind as you read the rest of this chapter, because the sections that follow simply open up one branch of it at a time. Board and NEET questions on this section are usually of the matching or one-line type — matching a monomer to its polymer, or picking out which given element is a trace element and which is a macro element — so the categories themselves are worth learning exactly as they are grouped here.
6.2 Biomolecules in the Cell
We can now open up the chart of Fig. 6.1 one branch at a time. In the sections that follow you will meet the four great classes of organic biomolecules — carbohydrates, lipids, proteins and nucleic acids — followed by the enzymes that control the reactions between them. For each class, keep asking two questions: what is this molecule built from, and what does the cell gain from having it built that way?
6.2.1 Carbohydrates
The word carbohydrate means ‘hydrates of carbon’. Carbohydrates are also called saccharides, a name that comes from the word for sugar.
Carbohydrates are biomolecules made from just three elements: carbon, hydrogen and oxygen. Their general formula is \(C_x(H_2O)_y\). In this formula, \(x\) is the number of carbon atoms and \(y\) is the number of water units the molecule appears to contain.
The name makes sense once you look at the proportions. Carbohydrates contain hydrogen and oxygen in the same ratio as in water, that is \(2:1\) — as though water molecules had simply been attached to a chain of carbon atoms. Carbohydrates can be broken down, that is oxidized, to release energy, which is why they are the cell’s chief fuel.
Based on the number of sugar units they contain, carbohydrates are classified into three types — monosaccharides, disaccharides and polysaccharides. This classification is given in Table 6.2 and is summarised in FC 6.2.
Flowchart
FC 6.2 – Classification of carbohydrates: Carbohydrates → branch 1: Monosaccharides (simple sugars) → triose (3C, e.g. glyceraldehyde) → tetrose (4C, e.g. erythrose) → pentose (5C, e.g. ribose in RNA, deoxyribose in DNA) → hexose (6C, e.g. glucose, fructose, galactose) → heptose (7C, e.g. sedoheptulose); branch 2: Disaccharides (two monosaccharides) → sucrose → glucose + fructose; lactose → glucose + galactose; maltose → glucose + glucose; branch 3: Polysaccharides (polymers of monosaccharides) → homopolysaccharides (one type of monosaccharide: starch, cellulose, glycogen) and heteropolysaccharides (different types of monosaccharides: hyaluronic acid, heparin, blood group substances, chondroitin sulphate)
Monosaccharides: The Simplest Sugars
Monosaccharides are the simplest sugars. They have a crystalline structure, a sweet taste, and are soluble in water. They cannot be further hydrolysed into smaller sugar molecules, which is exactly why they are treated as the starting point of the whole family.
Because they cannot be broken down further, monosaccharides act as the building blocks or monomers of all complex carbohydrates.
They have the general molecular formula \((CH_2O)_n\), where \(n\) can be 3, 4, 5, 6 and 7. According to the number of carbon atoms in one molecule, they are classified as triose, tetrose, pentose, hexose and heptose, as listed in Table 6.2.
A triose has 3 carbons, and glyceraldehyde is its example. A tetrose has 4 carbons, and erythrose is its example. A pentose has 5 carbons — ribose is found in RNA and deoxyribose in DNA. A hexose has 6 carbons — glucose is blood sugar, fructose is fruit sugar and galactose is a product of lactose. A heptose has 7 carbons, and sedoheptulose is its example.
Monosaccharides are also grouped by which chemical group they carry. Monosaccharides containing the aldehyde (-CHO) group are classified as aldoses, for example glucose and xylose. Those with a ketone (-C=O) group are classified as ketoses, for example ribulose and fructose.
The shape of a glucose molecule is shown in Fig. 6.3 — notice that the six carbon atoms close up into a ring, with -OH groups pointing outwards.
Diagram
Fig. 6.3 – Ring structure of glucose, labelling the ring oxygen, the six carbon positions, the -OH groups and the \(CH_2OH\) group.
All monosaccharides are reducing sugars, because of the presence of a free aldehyde or ketone group. These sugars reduce Benedict’s reagent, changing copper from \(Cu^{2+}\) to \(Cu^{+}\), since they are capable of transferring hydrogens (electrons) to other compounds — a process called reduction.
Three hexoses deserve a closer look.
a. Glucose is the most important fuel in living cells. Its concentration in human blood is about 90 mg per 100 ml of blood. The small size of glucose molecules and their solubility in water allow them to pass through the cell membrane into the cell. Energy is released when these molecules are metabolised by cellular respiration.
b. Galactose looks very similar to a glucose molecule. Galactose can also exist in α and β forms. It reacts with glucose to form the disaccharide lactose. However, glucose and galactose cannot be easily converted into one another, and galactose cannot play the same role in respiration as glucose does.
c. Fructose is the fruit sugar. Chemically it is a ketohexose, but it has a five-atom ring rather than a six-atom ring. Fructose reacts with glucose to form sucrose, a disaccharide.
Disaccharides
Monosaccharides are rare in nature. Most sugars found in nature are disaccharides.
A disaccharide is formed when two monosaccharides react by a condensation reaction, releasing a water molecule. This process requires energy. During the reaction a glycosidic bond forms, and it is this bond that holds the two monosaccharide units together.
Sucrose, lactose and maltose are the examples of disaccharides. Sucrose is a non-reducing sugar, since it lacks a free aldehyde or ketone group. Lactose and maltose are reducing sugars. Lactose also exists in a beta form, which is made from β-galactose and β-glucose.
Disaccharides are soluble in water, but they are too big to pass through the cell membrane by diffusion. They are broken down in the small intestine during digestion. The monosaccharides thus formed then pass into the blood, and through cell membranes into the cells.
This breakdown is a hydrolysis reaction — the reverse of condensation, in which a water molecule is added back to split the glycosidic bond.
\[C_{12}H_{22}O_{11} + H_2O \xrightarrow{\text{hydrolysis}} C_6H_{12}O_6 + C_6H_{12}O_6\]
Here \(C_{12}H_{22}O_{11}\) is the disaccharide, \(H_2O\) is the water molecule used up, and the two molecules of \(C_6H_{12}O_6\) are the monosaccharides released. Read the equation in words as: disaccharide + water → monosaccharide + monosaccharide.
The glycosidic linkage joining two glucose units in maltose can be seen in Fig. 6.4.
Diagram
Fig. 6.4 – Structure of maltose, showing two glucose rings joined through an oxygen bridge, with the glycosidic linkage arrowed and labelled.
Flowchart
FC 6.3 – Fate of a dietary disaccharide: disaccharide in food → small intestine → hydrolysis of glycosidic bond → two monosaccharides → absorbed into blood → cross cell membrane → enter cell → oxidized in cellular respiration → energy released
Monosaccharides are used very quickly by cells. But if a cell is not in need of all the energy released immediately, the sugar may get stored instead. Monosaccharides are converted into disaccharides in the cell by condensation reactions, and these reactions go on to result in the formation of polysaccharides as macromolecules. Being macromolecules, these are too big to escape from the cell — which is precisely what makes them good storage molecules.
Polysaccharides
Monosaccharides can undergo a series of condensation reactions, adding one unit after the other to the chain, till a very large molecule — a polysaccharide — is formed. This process is called polymerization. Polysaccharides are broken down by hydrolysis back into monosaccharides.
The properties of a polysaccharide molecule depend on its length, branching, folding and coiling. This is an important idea: since all three polysaccharides below are built from glucose, it is the way the units are arranged — not the units themselves — that decides whether the product is soft food storage or a rigid wall.
a. Starch is the stored, or reserve, food in plants. It exists in two forms: amylose and amylopectin. Both are made from α-glucose.
Amylose is an unbranched polymer of α-glucose. Its molecules coil into a helical structure, and it forms a colloidal suspension in hot water. Amylopectin is a branched polymer of α-glucose, and it is completely insoluble in water. Both forms are shown in Fig. 6.5.
Diagram
Fig. 6.5 – Starch: an unbranched helically coiled chain of α-glucose units labelled amylose, and a branched chain of α-glucose units labelled amylopectin.
b. Glycogen is amylopectin with very short distances between the branching side-chains. Glycogen is stored in the animal body, particularly in the liver and muscles, from where it is hydrolysed as per need to produce glucose.
c. Cellulose is a polymer made from β-glucose molecules, and its polymer molecules are ‘straight’. Cellulose serves to form the cell walls in plant cells, which are much tougher than cell membranes. This toughness is due to the arrangement of glucose units in the polymer chain and the hydrogen-bonding between neighbouring chains.
Polysaccharides are also classified by whether they use one kind of sugar unit or several. Homopolysaccharides are polymers of one type of monosaccharide — starch, cellulose and glycogen are all of this kind. Heteropolysaccharides are polymers of different types of monosaccharides, for example hyaluronic acid, heparin, blood group substances and chondroitin sulphate.
Biological Significance of Carbohydrates
Carbohydrates supply energy for metabolism. Glucose is the main substrate for ATP synthesis, the molecule in which the cell keeps its usable energy.
Lactose, a disaccharide present in milk, provides energy to lactating babies — a reminder that the first food of every mammal is built around a carbohydrate.
Polysaccharides serve as structural components of the cell membrane and the cell wall, and as reserve food in the form of starch and glycogen.
This section is a favourite for one-mark and matching questions in board and NEET papers: which sugar is reducing and which is not, which polysaccharide is made of α-glucose and which of β-glucose, and which monosaccharides a given disaccharide yields on hydrolysis. Learn these as paired facts rather than as separate lists.
6.2.2 Lipids
Lipids are a group of substances with a greasy consistency, made of a long hydrocarbon chain containing carbon, hydrogen and oxygen. The three elements are the same as in carbohydrates, but the proportions are not.
In lipids, the hydrogen to oxygen ratio is greater than \(2:1\), whereas in carbohydrates it is always \(2:1\). This single difference tells you a great deal: a lipid carries far more hydrogen for every oxygen atom, and hydrogen-rich bonds are exactly the bonds that release large amounts of energy on oxidation.
Lipid is a broader term, used for fatty acids and their derivatives. Lipids are soluble in organic solvents, that is, in non-polar solvents, and not in water. Since the interior of the body is watery, this insolubility is what allows lipids to form barriers and droplets that stay separate from their surroundings.
What Fatty Acids Are
Since lipids are built from fatty acids, we must first understand what a fatty acid is.
Fatty acids are organic acids which are composed of a hydrocarbon chain ending in a carboxyl group (-COOH). The long chain is the greasy, water-hating part, while the carboxyl group at one end is the chemically reactive part that joins to an alcohol.
Fatty acids are of two kinds. Saturated fatty acids have no double bonds between the carbon atoms of the hydrocarbon chain. Palmitic and stearic acids, found in all animal and plant fats, are examples of saturated fatty acids.
Unsaturated fatty acids have one or more double bonds between the carbon atoms of the hydrocarbon chain. Oleic acid, found in nearly all fats, and linoleic acid, found in many seed oils, are examples of unsaturated fatty acids. The difference between the two chains can be seen clearly in Fig. 6.6.
Diagram
Fig. 6.6 – Saturated and unsaturated fatty acid: a straight fully hydrogenated chain ending in -COOH labelled saturated, and a chain with a labelled double bond producing a bend, labelled unsaturated.
These fatty acids are the basic molecules which form different kinds of lipids. On the basis of the groups attached to them, lipids may be classified as simple, compound and derived lipids, as shown in FC 6.4.
Flowchart
FC 6.4 – Classification of lipids: Lipids → Simple lipids (esters of fatty acids with alcohols) → fats (fatty acids + glycerol) and waxes (long chain fatty acids + long chain alcohols); → Compound lipids (esters of fatty acids with an additional group) → phospholipids (with phosphate) and glycolipids (with sugar); → Derived lipids → sterols, e.g. cholesterol
Simple Lipids: Fats and Waxes
Simple lipids are esters of fatty acids with various alcohols. Fats and waxes are simple lipids.
Fats are esters of fatty acids with glycerol, \(CH_2OH-CHOH-CH_2OH\). Glycerol is an alcohol with three -OH groups, and each one of them can hold a fatty acid.
Triglycerides are made of three molecules of fatty acids and one molecule of glycerol. Fig. 6.7 shows this arrangement — a glycerol backbone on the left with three long fatty acid chains extending from it.
Diagram
Fig. 6.7 – Triglyceride: a glycerol backbone with its three carbon atoms on the left, each linked through an oxygen to one of three long fatty acid chains, with the glycerol part and the three fatty acid chains labelled.
Generally, unsaturated fats are liquid at room temperature and are called oils. Unsaturated fatty acids are hydrogenated to produce fats, for example Vanaspati ghee.
Fats are a nutritional source with a high calorific value, which means a given mass of fat yields far more energy than the same mass of carbohydrate. Fats therefore act as reserve food materials.
In plants, fat is stored in seeds to nourish the embryo during germination — the seedling has no leaves yet and cannot make its own food, so a compact, energy-rich store is exactly what it needs.
In animals, fat is stored in the adipocytes of the adipose tissue. Fats deposited in the subcutaneous tissue, that is just below the skin, act as an insulator and minimise the loss of body heat. Fats deposited around the internal organs act as cushions to absorb mechanical shocks.
Wax is another example of a simple lipid. Waxes are esters of long chain fatty acids with long chain alcohols. They are found in blood, gonads and the sebaceous glands of the skin.
Waxes are not as readily hydrolysed as fats and are solid at ordinary temperature. The wax in a beehive, shown in Fig. 6.8, is a familiar example.
Diagram
Fig. 6.8 – Wax in a beehive: a photograph or drawing of a honeycomb with its hexagonal wax cells labelled.
Waxes form a water insoluble coating on hair and skin in animals, and they form an outer coating on stems, leaves and fruits.
Compound Lipids
Compound lipids are esters of fatty acids containing other groups like phosphate, in which case they are called phospholipids, or sugar, in which case they are called glycolipids.
They contain a molecule of glycerol, two molecules of fatty acids, and a phosphate group or a simple sugar. Notice that only two of the three -OH groups of glycerol now carry fatty acids; the third position is taken by the phosphate or sugar. Some phospholipids, such as lecithin, also have a nitrogenous compound attached to the phosphate group.
This arrangement gives a phospholipid a split personality. Phospholipids have both hydrophilic polar groups — the phosphate and nitrogenous group — and hydrophobic non-polar groups, which are the hydrocarbon chains of the fatty acids. Hydrophilic means water-loving and hydrophobic means water-fearing, so one end of the molecule is attracted to water while the other end avoids it.
Because of this, phospholipids contribute to the formation of the cell membrane. Placed in an aqueous medium, they arrange themselves automatically into a double layer, as shown in Fig. 6.9, with the polar heads facing the water on both sides and the non-polar tails tucked away in the middle.
Diagram
Fig. 6.9 – Lipid bilayer in an aqueous medium: two rows of phospholipid molecules with polar head groups facing outwards towards water on both sides and non-polar tails facing each other in the interior; label water, polar head group, non-polar tails and phospholipid molecules.
Glycolipids contain glycerol, fatty acids and simple sugars such as galactose. They are also called cerebrosides. Large amounts of them have been found in the brain white matter and the myelin sheath.
Derived Lipids: The Sterols
Sterols are derived lipids. They are composed of fused hydrocarbon rings, called the steroid nucleus, together with a long hydrocarbon side chain. Their ring structure sets them apart from the long straight chains of fats and waxes.
One of the most common sterols is cholesterol. It is widely distributed in all cells of the animal body, but particularly in nervous tissue. Cholesterol exists either free or as cholesterol ester.
Cholesterol is also a starting material for making other important molecules. Adrenocorticoids, the sex hormones progesterone and testosterone, and vitamin D are all synthesised from cholesterol.
Cholesterol is not found in plants. In plants, sterols exist chiefly as phytosterols.
The yam plant, Dioscorea, produces a steroid compound called diosgenin. It is used in the manufacture of antifertility pills, that is, birth control pills.
In examinations, lipids are most often tested through comparison and classification — saturated against unsaturated, simple against compound against derived, and which lipid is associated with which structure such as the cell membrane, the myelin sheath or the cell surface of a leaf. Assertion–reason questions here usually turn on the double bond and on the polar head of the phospholipid, so be sure you can explain both.
6.2.3 Proteins
The term ‘protein’ comes from the Greek word proteious, meaning first, or of primary importance. The name was suggested by Berzelius in 1830. Mulder adopted the term protein to refer to the complex organic nitrogenous substances found in the cell of all animals and plants.
The name was well chosen. Proteins are the working molecules of the cell — they build structures, carry oxygen, defend the body and, as you will see later in this chapter, catalyse almost every reaction of life. Notice also the word nitrogenous: unlike carbohydrates and lipids, proteins always contain nitrogen.
Characteristics of Proteins
Proteins are large molecules containing amino acid units, which are their building blocks. The number of amino acid units in a protein ranges from 100 to 3000. Because of this, proteins have high molecular weights.
In proteins, amino acids are linked together by peptide bonds. A peptide bond joins the carboxyl group of one amino acid residue to the amino group of another residue. The formation of this bond is shown in Fig. 6.9a.
Diagram
Fig. 6.9a – Formation of a peptide bond: two amino acids shown with their amino (-NH2) and carboxyl (-COOH) groups joining with the removal of a water molecule, with the resulting -CO-NH- peptide bond circled and labelled.
A protein molecule consists of one or more polypeptide chains. Proteins can contain any or all of the 20 naturally occurring amino acid types.
Levels of Protein Structure
The linear sequence of amino acids in the polypeptide chain of a protein forms its primary structure. This is simply the order of the units, written out from one end of the chain to the other.
Functional proteins, however, do not stay as straight chains. They have a three-dimensional conformation, and it is this shape that lets them do their work. Some proteins, such as keratin of hair, consist of a polypeptide chain arranged like a spiral helix.
Such spirals are in some cases right-handed, called α-helix, and in others left-handed, called β-helix. The spiral configuration is held together by hydrogen bonds.
The sequence of amino acids in the polypeptide chain also determines the location of its bend or fold, and the position of formation of hydrogen bonds between different portions of the chain or between different chains. Due to the formation of hydrogen bonds, peptide chains assume a secondary structure.
In some proteins, two or more peptide chains are linked together by intermolecular hydrogen bonds. Such structures are called pleated sheets. The pleated sheet structure is found in the protein of silk fibres.
In large proteins such as myoglobin and enzymes, peptide chains are much looped, twisted and folded back on themselves, due to the formation of disulphide bonds. Such loops and bends give the protein a tertiary structure.
In haemoglobin, protein subunits are held together to form a quaternary structure. Here more than one complete polypeptide chain comes together to make the finished, functional molecule. The whole ladder of structural levels is shown in Fig. 6.9b and summarised in FC 6.5.
Diagram
Fig. 6.9b – The four levels of protein structure: a straight chain of amino acid beads labelled primary; a coiled helix and a pleated sheet labelled secondary; a folded and looped chain with a disulphide bond marked, labelled tertiary; and several such folded subunits fitted together, labelled quaternary.
Flowchart
FC 6.5 – Levels of protein structure: amino acids joined by peptide bonds → primary structure (linear sequence) → hydrogen bonds form → secondary structure (α-helix, β-helix, pleated sheet) → disulphide bonds with looping and folding → tertiary structure → two or more subunits held together → quaternary structure
Chemical Behaviour of Proteins
Proteins are extremely reactive and highly specific in behaviour.
Proteins are amphoteric in nature, that is, they act as both acids and bases. The behaviour of proteins is strongly influenced by pH.
Like amino acids, proteins are dipolar ions at the isoelectric point. At this point, the sum of the positive charges is equal to the sum of the negative charges, and the net charge on the molecule is zero.
The ionic groups of a protein are contributed by the side chains of the polyfunctional amino acids. In other words, the charge on a protein comes from the side chains that project from the main chain, not from the peptide bonds themselves.
A protein that consists of more basic amino acids, such as lysine and arginine, exists as a cation at the physiological pH of 7.4. Such proteins are called basic proteins. Histones of nucleoproteins are basic proteins.
A protein rich in acidic amino acids exists as an anion at the physiological pH. Such proteins are called acidic proteins. Most of the blood proteins are acidic proteins.
Classification of Proteins
On the basis of structure, proteins are classified into three categories — simple, conjugated and derived proteins, as set out in FC 6.6.
Flowchart
FC 6.6 – Classification of proteins on the basis of structure: Proteins → Simple proteins (yield only amino acids on hydrolysis; e.g. histones, albumins) → Conjugated proteins (simple protein + non-protein prosthetic group) → glycoproteins and mucoproteins (e.g. mucin of saliva, heparin of blood), lipoproteins, nucleoproteins, haemoglobin → Derived proteins (obtained from native proteins by hydrolysis; e.g. metaproteins, peptones)
Simple proteins on hydrolysis yield only amino acids. These are soluble in one or more solvents, and simple proteins may be soluble in water.
Histones of nucleoproteins are soluble in water. The globular molecules of histones are not coagulated by heat. Albumins are also soluble in water, but they get coagulated on heating. Albumins are widely distributed — egg albumin, serum albumin and legumelin of pulses are albumins.
Conjugated proteins consist of a simple protein united with some non-protein substance. The non-protein group is called the prosthetic group.
Haemoglobin is the standard example. In haemoglobin, globin is the protein and the iron containing pigment haem is the prosthetic group. Similarly, nucleoproteins have nucleic acids coupled with histone proteins.
On this basis, proteins are classified as glycoproteins and mucoproteins. Mucoproteins are carbohydrate-protein complexes, for example mucin of saliva and heparin of blood. Lipoproteins are lipid-protein complexes, for example the conjugate protein found in brain, plasma membrane, milk and so on.
Derived proteins are not found in nature as such. These proteins are derived from native protein molecules on hydrolysis. Metaproteins and peptones are derived proteins.
Questions on proteins in board and NEET papers are usually of two kinds: matching a named protein to its structural level or its class — haemoglobin with the quaternary structure and with conjugated proteins, keratin with the helix, silk fibre protein with the pleated sheet — and reasoning questions on why a change in the amino acid sequence changes what the protein can do. Learn each example together with its category, and keep the chain of logic in mind: sequence decides shape, and shape decides function.
6.2.4 Nucleic Acids
Nucleic acids are the information-carrying biomolecules of the cell. Carbohydrates supply fuel, lipids store energy and build membranes, proteins do the work — but it is the nucleic acids that hold the instructions for making those proteins and pass them on to the next generation.
By 1938 it had become evident that nucleic acids are of two types — deoxyribose nucleic acid (DNA) and ribose nucleic acid (RNA). DNA is found in chloroplasts and mitochondria, and DNA is the hereditary material in most of the organisms.
The nucleic acids are among the largest of all molecules found in living beings.
Composition of a Nucleic Acid
Nucleic acids contain three types of molecules: a 5 carbon sugar, phosphoric acid, and nitrogen containing bases. These three join together to form a nucleotide of nucleic acid, and nucleotides are the monomers from which the whole chain is built.
Fuelgen, in 1924, showed that chromosomes contain DNA. He established that nucleic acids contain two pyrimidine bases — cytosine and thymine — and two purine bases — adenine and guanine.
Wilkins and co-workers showed that the purine and pyrimidine bases are placed regularly along the DNA molecules, at a distance of 3.4 Å from one another. This regular spacing was an early clue that DNA is not a random tangle but an orderly, repeating structure.
DNA is composed of the following three components. The sugar molecule is a pentose sugar of the deoxyribose type. The phosphoric acid is also called phosphate when it is in chemical combination. The nitrogen containing bases are nitrogen containing organic ring compounds.
The Nitrogenous Bases
Principally, the bases are of two types: pyrimidine bases and purine bases.
Pyrimidine bases are single ring, that is monocyclic, nitrogenous bases. Cytosine, thymine and uracil are pyrimidines.
Purines are double ring, that is dicyclic, nitrogenous bases. Adenine and guanine are purines. The ring structures of all five bases are shown in Fig. 6.10 — count the rings in each and the difference between the two groups becomes obvious at a glance.
Diagram
Fig. 6.10 – Nitrogen bases in nucleic acid: the double-ringed purines adenine and guanine shown in one panel, and the single-ringed pyrimidines cytosine, uracil and thymine shown in a second panel, each structure labelled.
Erwin Chargaff, in 1950, estimated the relative amounts of the four nitrogenous bases — adenine, thymine, cytosine and guanine — in DNA. He observed that the pyrimidine and purine bases always occur in equal amount in DNA.
He also found that the base ratio A+T / G+C may vary in the DNA of different groups of animals and plants, but that the A+T / G+C ratio remains constant for a particular species.
Structure of DNA
DNA is a very long chain made up of alternate sugar and phosphate groups. The sugar is always deoxyribose, and it is always joined to the phosphate in the same way, so that the long chain is perfectly regular, repeating the same phosphate-sugar sequence over and over again.
Each sugar of the sugar-phosphate chain has a base attached to it, and this base is not always the same. So the backbone is monotonous while the bases along it vary — and it is in that variation that the genetic message is written.
This unit, which consists of a sugar, a phosphate and a base, is called a nucleotide.
The nitrogenous base and a sugar of a nucleotide together form a molecule called a nucleoside. Thus, a nucleoside does not contain a phosphate group. Four types of nucleosides are found in a DNA molecule.
In a nucleoside, the nitrogenous base is attached to the first carbon atom (C-1) of the sugar. When a phosphate group gets attached to the carbon (C-5) atom of the sugar molecule, a nucleotide molecule is formed.
Flowchart
FC 6.7 – Building up a DNA molecule: nitrogenous base + pentose sugar (at C-1) → nucleoside → phosphate added at C-5 → nucleotide → many nucleotides joined by phospho-di-ester bonds between C-5 phosphate and C-3 of the sugar above → polynucleotide strand with a 3’ end and a 5’ end → two complementary strands held by hydrogen bonds → double helix
A single strand of DNA consists of several thousands of nucleotides linked one above the other. The phosphate group of the lower nucleotide, attached with the 5th carbon atom of the deoxyribose sugar, forms a phospho-di-ester bond with the 3rd carbon atom of the deoxyribose sugar of the nucleotide placed just above it.
This linking pattern leaves the two ends of the chain chemically different. At one end of the single long chain of polynucleotides, the sugar molecule is not connected with another nucleotide, its C-3 carbon not being connected with a phosphate group. Similarly the other end has the C-5 carbon of the sugar not connected with any more phosphate group. These two ends of the polynucleotide chain are called the 3’ end and the 5’ end respectively.
The single polynucleotide strand of DNA is not straight but helical in shape. The DNA molecule consists of two such helical polynucleotide chains which are complementary to each other.
The two complementary polynucleotide chains of DNA are held together by weak hydrogen bonds. Adenine always pairs with thymine, and guanine with cytosine — in each case a pyrimidine with a purine.
The adenine-thymine pair consists of two hydrogen bonds, and the guanine-cytosine pair consists of three hydrogen bonds. Because the pairing is fixed, if the sequence of bases of one polynucleotide chain is known, that of the other can then be determined.
Notice in Fig. 6.11 how the two chains wind around each other, leaving grooves of two different widths on the outside of the molecule.
Diagram
Fig. 6.11 – Structure of DNA: a double helix with the two sugar-phosphate backbones wound around each other, paired bases joined by hydrogen bonds shown between them, labelling the major groove, the minor groove, the hydrogen bonds and the dimensions marked on the molecule.
The Watson–Crick DNA Model
According to Watson and Crick, the DNA molecule consists of two strands twisted around each other in the form of a double helix.
The two strands, that is the two polynucleotide chains, are supposed to run in opposite directions, and are said to be antiparallel. Because of this, the end of one chain having 3’ lies beside the 5’ end of the other.
The model also gives the measurements of the molecule. One turn of the double helix of DNA measures about 34 Å. It consists of paired nucleotides, and the distance between two neighbouring pairs of nucleotides is 3.4 Å. The diameter of the DNA molecule has been found to be 20 Å.
These three figures fit together neatly. If one complete turn is 34 Å long and each pair of nucleotides is spaced 3.4 Å apart, then one turn of the helix must contain ten pairs of nucleotides.
There are certain organisms, like Bacteriophage φ x 174 and several bacterial viruses, which possess single stranded DNA. The double helix, in other words, is the usual arrangement but not the only one.
Ribonucleic Acid (RNA)
Another nucleic acid found in living organisms is ribose nucleic acid. In most of the organisms it is not found to be the hereditary material, but in certain organisms, like tobacco mosaic virus, it is the hereditary material.
Like DNA, ribose nucleic acid also consists of a polynucleotide chain, with the difference that it consists of a single strand. In some cases, for example Reovirus and wound tumour virus, RNA is double stranded.
The nucleotides of RNA have ribose sugar, instead of the deoxyribose sugar as in the case of DNA. A short length of an RNA chain is shown in Fig. 6.12.
Diagram
Fig. 6.12 – Single strand of RNA: a chain of ribonucleotides showing the ribose sugar, the phosphate links and the attached bases uracil, adenine and cytosine, with one complete ribonucleotide labelled.
In case of RNA, uracil substitutes the thymine of DNA.
Purine and pyrimidine equality is not found in an RNA molecule, because of its single stranded structure. This follows directly from what you have just learnt about pairing: with no partner strand, there is nothing to force the numbers of purines and pyrimidines to match.
An RNA strand is usually found folded upon itself in certain regions, or entirely. These foldings help in the stability of the RNA molecule. Most of the RNA polynucleotide chains start either with adenine or guanine.
Types of Cellular RNA
Three types of cellular RNAs have been distinguished: messenger RNA (mRNA) or template RNA, ribosomal RNA (rRNA), and transfer RNA (tRNA) or soluble RNA.
mRNA carries genetic information for arranging amino acids in a definite sequence. It is a linear polynucleotide, and it accounts for 3% of the total cellular RNA. Its molecular weight is several million.
An mRNA molecule carrying the information to form a complete polypeptide chain is called a cistron. The size of an mRNA is related to the size of the message it contains — a longer protein needs a longer message.
Synthesis of mRNA begins at the 5’ end of the DNA strand and terminates at the 3’ end. The cistron, with its initiation codon at one end and its termination codon at the other, is shown in Fig. 6.13.
Diagram
Fig. 6.13 – The mRNA: a linear strand running from the 5’ end to the 3’ end, with the stretch between marked as the cistron, the initiation codon marked near the 5’ end and the termination codon near the 3’ end.
rRNA forms 50-60% part of ribosomes. It accounts for 80-90% of the cellular RNA, which makes it by far the most abundant RNA in the cell. It is synthesized in the nucleus, and Kurland discovered it in 1960.
rRNA gets coiled here and there due to intrachain complementary base pairing — that is, base pairing between different parts of the same strand, as shown in Fig. 6.14.
Diagram
Fig. 6.14 – The rRNA: a single strand folded back on itself, labelling the sugar-phosphate backbone, the bases and the hydrogen bonds formed between complementary regions of the same chain.
tRNA molecules are much smaller, consisting of 70-80 nucleotides.
tRNA is also single stranded, but it is folded due to a number of complementary base sequences that pair with one another. After this pairing it is shaped like a clover leaf, a structure described by Holley in 1965. Each tRNA can pick up a particular amino acid.
The following four parts can be recognized on a tRNA molecule: the DHU arm, which is the dihydroxyuridine loop or amino acid recognition site; the amino acid binding site; the anticodon loop, which is the codon recognition site; and the ribosome recognition site. These parts are labelled in Fig. 6.15.
Diagram
Fig. 6.15 – The tRNA: the clover-leaf shape with the amino acid attachment site at the 3’ end, the acceptor stem, the D-loop, the T loop, the variable loop, and the anticodon loop with the anticodon marked at its tip.
In the anticodon loop of tRNA, three unpaired nucleotides are present. These are called the anticodon, and they pair with the complementary codon present on the mRNA. The specific amino acid is attached at the 3’ end, in the acceptor stem of the clover leaf of tRNA.
Nucleic acids are heavily tested in both board and NEET papers, most often as differences between DNA and RNA, as identification of a base or a bond in a labelled diagram, and as base-percentage problems built on the pairing rule. Make sure you can move both ways: from a diagram to the name of the bond, and from one base percentage to all four.
6.2.5 Enzymes
Thousands of different chemical reactions take place automatically at a given time in a tiny living cell. What is remarkable is that these reactions take place at the body temperature, without the high heat or strong acids a chemist would need in the laboratory.
The molecules that make this possible are the enzymes. If these enzymes were not present in the cell, either the reactions would not occur at all, or, if they did occur, they would occur at a very very slow rate.
Each enzyme catalyzes a small number of reactions, specifically perhaps only one. The substance upon which an enzyme acts is termed the substrate.
The enzymes which act within the cell in which they are synthesized are known as endo-enzymes, for example the enzymes produced in the chloroplast and mitochondria. If they act outside the cell in which they are synthesized, they are known as exo-enzymes, for example the enzymes released by many fungi — a fungus digests its food outside its body and then absorbs the products.
These enzymes, synthesised by a living cell, retain their catalytic property even when extracted from cells. This is exactly what Buchner’s experiment showed, and it is also what makes it possible to use enzymes in industry.
Nature of Enzymes
On the basis of chemical composition, enzymes can be put into two categories.
The first are purely proteinaceous enzymes, for example the proteases that split protein. The second are conjugated enzymes, which are made up of a protein to which a non-protein prosthetic group is attached.
The prosthetic group is firmly bound to the protein component by chemical bonds and is not removed by hydrolysis. If the prosthetic group is removed, the protein part of the enzyme becomes inactive — the two parts are useless separately and effective only together.
The proteinous part of the enzyme is called the apoenzyme. The apoenzyme together with the prosthetic group forms the holoenzyme.
There are enzymes which require certain organic compounds and inorganic ions for their activity. The organic compounds that are tightly attached to the protein part are called co-enzymes, whereas the inorganic ions which are loosely attached to the protein part are called co-factors.
Some of the organic co-enzymes are nicotinamide-adenine-dinucleotide (NAD) and flavin mononucleotide (FMN).
Inorganic ions of metals which act as co-factors include magnesium, copper, zinc, iron, manganese and others. Iron (\(Fe^{++}\)) is a co-factor of the enzyme catalase, and manganese is a co-factor of peptidases. Often metal co-factors are referred to as enzyme activators.
Properties of Enzymes
Proteinaceous Nature: All enzymes are basically made up of protein, except ribozymes. Because they are proteins, everything you learnt about protein structure in the previous subsection applies to them — their shape, and therefore their working, depends on the amino acid sequence and on the bonds holding the folds in place.
Three-Dimensional Conformation: All enzymes have a specific 3-dimensional conformation. They have one or more active sites to which the substrate, that is the reactant, combines. The points of the active site where the substrate joins with the enzyme are called the substrate-binding site.
Catalytic Property: Enzymes are like inorganic catalysts and influence the speed of biochemical reactions, but themselves remain unchanged. After the completion of the reaction and the release of the product, they remain active and are ready to catalyse again.
A small quantity of enzyme can therefore catalyse the transformation of a very large quantity of substrate into an end product. For example, sucrase can hydrolyse 100000 times of sucrose as compared with its own weight.
Specificity of Action: The ability of an enzyme to catalyse one specific reaction and essentially no other is perhaps its most significant property. Each enzyme acts upon a specific substrate or a specific group of substrates.
Enzymes are very sensitive to temperature and pH. Each enzyme exhibits its highest activity at a specific pH, called the optimum pH. Any increase or decrease in pH causes a decline in enzyme activity.
For example, the enzyme pepsin, secreted in the stomach, shows highest activity at an optimum pH of 2, which is acidic. Trypsin, which acts in the duodenum, is most active at an optimum pH of 9.5, which is alkaline. Both these enzymes, pepsin and trypsin, are protein digesting enzymes.
Notice how neatly this fits the body’s plan. Both enzymes digest protein, but each is matched to the chemical conditions of the region where it works — the acidic stomach and the alkaline duodenum — so that protein digestion can continue smoothly as food moves from one to the other.
Temperature: Enzymes are denatured or destroyed at the higher temperature of 60-70°C. Below 4°C temperature they are not destroyed but become inactive. This inactive state is temporary, and the enzyme can become active again at a suitable temperature. Most of the enzymes work at an optimum temperature between 20°C and 35°C.
Nomenclature of Enzymes
There are various ways of naming enzymes.
Enzymes are named by adding the suffix ‘-ase’ to the name of the substrate on which they act, for example protease, sucrase and nuclease, which break up proteins, sucrose and nucleic acids respectively.
The enzymes can also be named according to the type of function they perform. For example, dehydrogenases remove hydrogen, carboxylases add \(CO_2\), decarboxylases remove \(CO_2\), and oxidases help in oxidation.
According to the international code of enzyme nomenclature, the name of each enzyme ends with an -ase and consists of a double name. The first name indicates the nature of the substrate upon which the enzyme acts, and the second name indicates the reaction catalysed.
For example, pyruvic decarboxylase catalyses the removal of \(CO_2\) from the substrate pyruvic acid. Similarly, the enzyme glutamate pyruvate transaminase catalyses the transfer of an amino group from the substrate glutamate to another substrate, pyruvate.
Classification of Enzymes
Oxidoreductases are enzymes catalyzing oxidation and reduction reactions by the transfer of hydrogen and/or oxygen, for example alcohol dehydrogenase.
\[\text{Alcohol} + NAD^+ \xrightarrow{\text{alcohol dehydrogenase}} \text{Aldehyde} + NADH_2\]
Transferases are enzymes which catalyse the transfer of certain groups between two molecules, for example glucokinase.
\[\text{Glucose} + ATP \xrightarrow{\text{glucokinase}} \text{Glu-6-Phosphate} + ADP\]
Hydrolases are enzymes which catalyse hydrolytic reactions. This class includes amylases, proteases, lipases and others, for example sucrase.
\[\text{Sucrose} + H_2O \xrightarrow{\text{sucrase}} \text{Glucose} + \text{Fructose}\]
Lyases are enzymes involved in elimination reactions, resulting in the removal of a group of atoms from the substrate molecule to leave a double bond. This class includes aldolases, decarboxylases and dehydratases, for example fumarate hydratase.
\[\text{Histidine} \xrightarrow{\text{histidine decarboxylase}} \text{Histamine} + CO_2\]
Isomerases are enzymes which catalyze structural rearrangements within a molecule. Their nomenclature is based on the type of isomerism, and thus these enzymes are identified as racemases, epimerases, isomerases and mutases, for example xylose isomerase.
\[\text{Glu-6-Phosphate} \xrightarrow{\text{isomerase}} \text{Fructose-6-Phosphate}\]
Ligases or Synthetases are the enzymes which catalyse the covalent linkage of molecules, utilizing the energy obtained from the hydrolysis of an energy-rich compound like ATP or GTP, for example glutathione synthetase and pyruvate carboxylase.
\[\text{Pyruvate} + CO_2 + ATP \xrightarrow{\text{pyruvate carboxylase}} \text{Oxaloacetate} + ADP + Pi\]
Mechanism of Enzyme Action
The basic mechanism by which enzymes catalyze chemical reactions begins with the binding of the substrate, or substrates, to the active site on the enzyme.
The binding of the substrate to the enzyme causes changes in the distribution of electrons in the chemical bonds of the substrate, and this ultimately causes the reaction that leads to the formation of products.
The products are then released from the enzyme surface, which regenerates the enzyme for another reaction cycle, as shown in Fig. 6.16.
Diagram
Fig. 6.16 – Mechanism of enzyme action: a substrate approaching an enzyme whose active site changes shape to fit it better, forming the enzyme-substrate complex, with the substrate, enzyme and enzyme-substrate complex labelled.
Flowchart
FC 6.8 – Enzyme action cycle: free enzyme (E) + substrate (S) → substrate binds at the active site → enzyme-substrate complex (ES) → redistribution of electrons in the substrate’s bonds → products (P) formed → products released from the enzyme surface → free enzyme (E) regenerated → back to the start for another cycle
There are two models to explain the mechanism of forming the enzyme-substrate complex.
Lock and Key model: The specific action of an enzyme with a single substrate can be explained using a Lock and Key analogy, first postulated in 1894 by Emil Fischer. In this analogy, the lock is the enzyme and the key is the substrate. Only the correctly sized key, that is the substrate, fits into the key hole, that is the active site, of the lock, which is the enzyme. This is illustrated in Fig. 6.17.
Diagram
Fig. 6.17 – Lock and key model: a rigid enzyme with a notch-shaped active site, a sucrose substrate fitting exactly into it to form the enzyme-substrate complex, and the enzyme afterwards releasing the products glucose and fructose.
Induced Fit model (Flexible Model): Koshland, in 1959, proposed the induced fit theory, which states that the approach of a substrate induces a conformational change in the enzyme. It is the more accepted model to understand the mode of action of an enzyme.
Unlike the lock-and-key model, the induced fit model shows that enzymes are rather flexible structures, in which the active site continually reshapes by its interactions with the substrate, until the time the substrate is completely bound to it. This is also the point at which the final form and shape of the enzyme is determined. The sequence is shown in Fig. 6.18.
Diagram
Fig. 6.18 – Complex flexible model: an enzyme whose active site changes shape as the substrate approaches and binds, shown as the sequence E + S → E-S → E + P.
Factors Affecting Enzyme Activity
The following factors affect enzyme activity.
1. Concentration of Substrate: An increase in the substrate concentration gradually increases the velocity of enzyme activity, within a limited range of substrate levels.
A rectangular hyperbola is obtained when velocity is plotted against the substrate concentration, and three distinct phases — A, B and C — of the reaction are observed in the graph. In Graph 6.19, \(V\) is the measured velocity, \(V_{max}\) is the maximum velocity, \(S\) is the substrate concentration and \(K_m\) is the Michaelis-Menten constant.
Diagram
Graph 6.19 – Effect of substrate concentration on enzyme activity: velocity on the y-axis against substrate concentration on the x-axis, giving a rectangular hyperbola with phase A rising steeply, phase B levelling off and phase C flat at \(V_{max}\); mark \(V_{max}\), \(\frac{1}{2}V_{max}\) and the corresponding \(K_m\) on the axes.
\(K_m\), or the Michaelis-Menten constant, is defined as the substrate concentration, expressed in moles/lit, needed to produce half of the maximum velocity in an enzyme catalysed reaction. It indicates that half of the enzyme molecules, that is 50%, are bound with substrate molecules when the substrate concentration equals the \(K_m\) value.
The \(K_m\) value is a constant and a characteristic feature of a given enzyme. It is a representative for measuring the strength of the ES complex. A low \(K_m\) value indicates a strong affinity between enzyme and substrate, whereas a high \(K_m\) value reflects a weak affinity between them. For the majority of enzymes, the \(K_m\) values are in the range of \(10^{-5}\) to \(10^{-2}\) moles.
The reasoning behind this is worth following. If an enzyme binds its substrate strongly, even a little substrate is enough to occupy half the active sites, so \(K_m\) is small. If the binding is weak, a great deal of substrate must be supplied before half the sites are filled, so \(K_m\) is large.
2. Enzyme Concentration: The rate of an enzymatic reaction is directly proportional to the concentration of the substrate. The rate of reaction is also directly proportional to the square root of the concentration of enzymes.
This means that the rate of reaction increases with increasing concentration of enzyme, and that the rate of reaction can also be decreased by decreasing the concentration of enzyme. Graph 6.20 shows this by comparing the product formed over time with no enzyme, with a given amount of enzyme, and with twice that amount.
Diagram
Graph 6.20 – Effect of enzyme concentration: product concentration on the y-axis against time on the x-axis, with three straight lines of increasing slope labelled no enzyme, with 1X enzyme and with 2X enzyme.
3. Temperature: The enzymatic reaction occurs best at or around 37°C, which is the average normal body temperature in homeotherms — animals that maintain a constant body temperature.
The rate of a chemical reaction is increased by a rise in temperature, but this is true only over a limited range of temperature. Enzymes rapidly denature at temperatures above 40°C.
The activity of enzymes is reduced at low temperature. The temperature at which the enzymes show maximum activity is called the optimum temperature, marked at the peak of Graph 6.21.
Diagram
Graph 6.21 – Effect of temperature on enzyme activity: increasing enzyme activity on the y-axis against temperature in °C on the x-axis, showing a curve that rises to a peak at the optimum temperature near 40°C and then falls steeply as the enzyme denatures.
4. Effect of pH: Similar to temperature, there is also a pH at which an enzyme will catalyze the reaction at the maximum rate. Every enzyme has a different optimum pH value, and the enzyme cannot perform its function beyond the range of its pH value. This is shown in Graph 6.22.
Diagram
Graph 6.22 – Effect of pH on enzyme activity: rate of enzyme activity on the y-axis against pH on the x-axis, showing a bell-shaped curve with the peak marked as the optimum pH.
5. Other Substances: The enzyme’s action is also increased or decreased in the presence of some other substances, such as co-enzymes, activators and inhibitors.
Most of the enzymes are a combination of a co-enzyme and an apo-enzyme. Activators are the inorganic substances which increase enzyme activity. An inhibitor is a substance which retards enzyme activity.
Enzymes are among the most heavily tested topics of this chapter. Expect assertion–reason questions on optimum temperature and pH, graph-based questions on Graphs 6.19 and 6.21, matching of enzyme classes to the reactions they catalyse, and the standard trap pairs — apoenzyme against holoenzyme, co-enzyme against co-factor, and lock and key against induced fit.
6.2.6 Concept of Metabolism
Metabolism is the sum of the chemical reactions that take place within each cell of a living organism, and which provide energy for vital processes and for synthesizing new organic material.
Metabolism involves a continuous process of breakdown and synthesis of biomolecules through chemical reactions. Each of the metabolic reactions results in a transformation of biomolecules — one substance is changed into another.
Most of these metabolic reactions do not occur in isolation, but are always linked with some other reactions. The product of one reaction becomes the starting material of the next, so that reactions run in chains called pathways rather than singly.
In living systems, cells are the ‘work centres’ where metabolism takes place, and metabolism involves the two following types of pathways, both of which are shown together in Fig. 6.22.
a. Catabolic pathways lead to the formation of a simpler structure from complex biomolecules.
For example, when we eat wheat, bread or chapati, our gastrointestinal tract digests, that is hydrolyses, the starch to glucose units with the help of enzymes, and releases energy in the form of ATP (Adenosine triphosphate). ATP is the molecule in which the cell keeps energy in a form it can spend immediately.
Flowchart
FC 6.9 – Catabolic pathway: complex biomolecules (carbohydrates such as glycogen and starch, lipids as triglycerides, proteins) → broken down by enzymes → simpler units (glucose; glycerol and fatty acids; amino acids) → oxidized → energy released as ATP → end products \(CO_2\) and \(H_2O\), with nitrogenous wastes also produced from proteins
b. Anabolic pathways are also called biosynthetic pathways. An anabolic pathway involves the formation of a more complex biomolecule from a simpler structure, for example the synthesis of glycogen from glucose, and of protein from amino acids. These pathways consume energy.
Flowchart
FC 6.10 – Anabolic pathway: simple units (glucose; glycerol and fatty acids; amino acids) + energy from ATP → building reactions → complex biomolecules (glycogen; triglycerides; proteins)
Diagram
Fig. 6.22 – Catabolic and anabolic reactions: an upper panel showing carbohydrates (glycogen, starch), lipids (triglycerides) and proteins breaking down into glucose, glycerol and fatty acids, and amino acids respectively, each releasing energy as ATP and ending in \(CO_2\) and \(H_2O\) with nitrogenous wastes; a lower panel showing glucose building into glycogen, glycerol and fatty acids into triglycerides, and amino acids into proteins, each using energy from ATP.
The Metabolic Pool
The metabolic pool is the reservoir of biomolecules in the cell, on which enzymes can act to produce useful products as per the need of the cell.
The concept of the metabolic pool is significant in cell biology because it allows one type of molecule to change into another type. For example, carbohydrates can be converted to fats and fats to carbohydrates.
This flexibility is what allows an organism to survive on varying diets. Whatever the food happens to supply, the products of its digestion enter the same common pool, and from there the cell can build whichever biomolecule it is short of.
The catabolic chemical reactions of glycolysis and the Krebs cycle not only provide ATP, but also make available a metabolic pool of biomolecules that can be utilized for the synthesis of many important cellular components. In other words, a breakdown pathway serves the cell twice — once by yielding energy, and once by yielding useful intermediates.
The metabolites can be added to or withdrawn from this pool according to the need of the cell.
The balance between catabolism and anabolism maintains homeostasis in the cell as well as in the whole body. Homeostasis means the maintenance of a steady internal state, and here it depends on breakdown and build-up going on at matched rates.
In examinations this topic usually appears as short definitions and as classification: given an example such as the synthesis of glycogen from glucose or the digestion of starch, state whether the pathway is catabolic or anabolic, and whether energy is released or consumed. Questions on the metabolic pool almost always ask why the interconversion of one class of biomolecule into another is possible.
6.2.7 Secondary Metabolites
Secondary metabolites (SMs) are small organic molecules produced by organisms that are not essential for their growth, development and reproduction. Several types of bacteria, fungi and plants produce secondary metabolites.
The word ‘secondary’ refers only to their role in the producing organism, and not to their importance to us. Look back at Fig. 6.1 and you will see that secondary metabolites sit on the micromolecule branch of the chart, alongside lipids — separate from the macromolecules that build and run the cell.
Classification of Secondary Metabolites
Secondary metabolites can be classified in several ways: on the basis of chemical structure, for example SMs containing rings or sugar; on the basis of composition, that is with or without nitrogen; on the basis of their solubility in various solvents; or on the basis of the pathway by which they are synthesized, for example the phenylpropanoid pathway, which produces tannins.
A simple way of classifying secondary metabolites includes three main groups, as shown in FC 6.11.
Flowchart
FC 6.11 – Classification of secondary metabolites into three main groups: Secondary metabolites → Terpenes (made from mevalonic acid; mainly carbon and hydrogen) → Phenolics (made from simple sugars; contain benzene rings, hydrogen and oxygen) → Nitrogen-containing compounds (extremely diverse; may also contain sulphur)
1. Terpenes are made from mevalonic acid, and are composed mainly of carbon and hydrogen.
2. Phenolics are made from simple sugars, and contain benzene rings, hydrogen and oxygen.
3. Nitrogen-containing compounds form an extremely diverse class, which may also contain sulphur.
Economic Importance of Secondary Metabolites
Secondary metabolites from natural sources have made a significant contribution for millennia. In modern medicine, drugs developed from secondary metabolites have been used to treat infectious diseases, cancer, hypertension and inflammation.
Morphine was the first alkaloid isolated from the plant Papaver somniferum. It is used as a pain reliever and a cough suppressant.
Secondary metabolites such as the alkaloids nicotine and cocaine, and the terpene cannabinol, are widely used for recreation and stimulation. It should be noted that these compounds are habit-forming, that their long-term use causes serious damage to health, and that their sale and use are controlled by law in most countries.
Flavours of secondary metabolites improve our food preference — much of what we recognise as the taste of a spice, a herb or a fruit comes from these compounds rather than from the sugars or proteins in the food.
The characteristic flavours and aroma of cabbage and its relatives are caused by nitrogen and sulphur-containing chemicals called glucosinolates, and these same chemicals protect these plants from many pests. Here you can see the two roles at once: what we value as flavour, the insect experiences as a deterrent.
Tannins are added to wines and chocolate for improving astringency, that is, the dry, puckering sensation they leave in the mouth.
Since most of the secondary metabolites have antibiotic properties, they are also used as food preservatives. A compound that protects a plant from microorganisms will, for the same chemical reason, slow the spoiling of stored food.
For examination purposes, remember the three groups with what each is made from, the fact that secondary metabolites are not essential for growth, development and reproduction, and the standard examples — morphine from Papaver somniferum, glucosinolates in cabbage, and tannins in wine and chocolate. Matching questions on this topic almost always pair a named compound with its source or its use.
6.3 Summary
The cell is the basic structural and functional unit of every living organism, and its protoplasm holds the chemical molecules called biomolecules.
Biochemistry studies the chemistry of living organisms and the molecular basis of the changes taking place in plant, animal and microbial cells. It underlies all biological processes, cell communication, inheritance and disease.
Chemical analysis of living organisms shows the presence of common elements — carbon, hydrogen, nitrogen, oxygen, sulphur, calcium, phosphorus, magnesium and others. These are grouped as prime elements (C, H, O), macro elements (N, P, K, Ca, Mg, S) and trace elements (B, Cl, Zn, Cu, Fe, Na, Mo, Ni, Si, Co).
Living organisms have three basic types of macromolecules, all of them polymers of small repeating monomers: polysaccharides from monosaccharides, polypeptides from amino acids, and polynucleotides from nucleotides. Lipids are water insoluble and of low molecular weight compared with macromolecules, and are grouped with the micromolecules.
Carbohydrates, or saccharides, are made of carbon, hydrogen and oxygen with the general formula \(C_x(H_2O)_y\), hydrogen and oxygen being present in the \(2:1\) ratio found in water. They are oxidized to release energy.
Based on the number of sugar units, carbohydrates are monosaccharides, disaccharides or polysaccharides.
Monosaccharides have the formula \((CH_2O)_n\) with \(n\) = 3 to 7, and are named triose, tetrose, pentose, hexose and heptose. Those with an aldehyde group are aldoses and those with a ketone group are ketoses. All monosaccharides are reducing sugars and reduce Benedict’s reagent from \(Cu^{2+}\) to \(Cu^{+}\).
Glucose is the chief cellular fuel, present in human blood at about 90 mg per 100 ml. Galactose combines with glucose to give lactose, and fructose combines with glucose to give sucrose.
A disaccharide is formed when two monosaccharides join by condensation, releasing water and forming a glycosidic bond. Sucrose is non-reducing; lactose and maltose are reducing. Disaccharides are hydrolysed in the small intestine before absorption.
Polysaccharides are formed by polymerization and broken down by hydrolysis. Starch (amylose and amylopectin) is the plant reserve, glycogen is the animal reserve, and cellulose, made of β-glucose, forms the plant cell wall. Homopolysaccharides use one type of monosaccharide, heteropolysaccharides use more than one.
Carbohydrates supply energy for metabolism, glucose being the main substrate for ATP synthesis, and polysaccharides serve as structural components and as reserve food.
Lipids are greasy, water insoluble compounds soluble in organic solvents, with a hydrogen to oxygen ratio greater than \(2:1\).
Fatty acids are hydrocarbon chains ending in a carboxyl group. Saturated fatty acids have no double bonds (palmitic, stearic); unsaturated fatty acids have one or more (oleic, linoleic). Unsaturated fats are liquid oils and can be hydrogenated to solid fats such as Vanaspati ghee.
Lipids are classified as simple (fats and waxes), compound (phospholipids and glycolipids) and derived (sterols).
A triglyceride has one glycerol and three fatty acids. Fats are high-calorie reserve food, stored in seeds in plants and in adipocytes in animals, and they insulate the body and cushion the internal organs. Waxes coat hair, skin, stems, leaves and fruits.
Phospholipids have hydrophilic polar heads and hydrophobic non-polar tails, and therefore form the lipid bilayer of the cell membrane. Glycolipids, or cerebrosides, are abundant in brain white matter and the myelin sheath.
Cholesterol is the common animal sterol and the starting material for adrenocorticoids, sex hormones and vitamin D. Plants have phytosterols instead; diosgenin from Dioscorea is used to make antifertility pills.
Proteins are nitrogenous macromolecules of 100 to 3000 amino acid units joined by peptide bonds, drawn from the 20 naturally occurring amino acids.
Protein structure has four levels: primary (the amino acid sequence), secondary (α-helix, β-helix and pleated sheet held by hydrogen bonds), tertiary (looping and folding through disulphide bonds) and quaternary (subunits held together, as in haemoglobin).
Proteins are amphoteric and carry no net charge at the isoelectric point. Proteins rich in lysine and arginine are basic proteins (histones); those rich in acidic amino acids are acidic proteins (most blood proteins).
On the basis of structure, proteins are simple (histones, albumins), conjugated (a protein with a prosthetic group, as in haemoglobin, mucoproteins and lipoproteins) or derived (metaproteins, peptones).
Nucleic acids were discovered by Miescher in 1869 and are of two types, DNA and RNA. Each contains a 5 carbon sugar, phosphoric acid and nitrogenous bases.
Purines (adenine, guanine) are double ringed and pyrimidines (cytosine, thymine, uracil) are single ringed. Chargaff showed that purines equal pyrimidines in DNA, and that the A+T / G+C ratio is constant for a species.
Base + sugar = nucleoside; base + sugar + phosphate = nucleotide. Nucleotides are joined by phospho-di-ester bonds between the C-5 phosphate and the C-3 of the sugar above, giving a strand with a 3’ end and a 5’ end.
In the Watson and Crick model, DNA is a double helix of two antiparallel complementary strands. Adenine pairs with thymine by two hydrogen bonds and guanine with cytosine by three. One turn measures about 34 Å, adjacent base pairs are 3.4 Å apart, and the diameter is 20 Å. Bacteriophage φ x 174 and some bacterial viruses have single stranded DNA.
RNA has ribose in place of deoxyribose and uracil in place of thymine, and is usually single stranded, so purine–pyrimidine equality is absent. Reovirus and wound tumour virus have double stranded RNA, and RNA is the hereditary material in tobacco mosaic virus.
The three cellular RNAs are mRNA (3% of cellular RNA; carries the message, one cistron per polypeptide), rRNA (80-90% of cellular RNA; forms 50-60% of the ribosome) and tRNA (70-80 nucleotides; clover-leaf shaped, carries an anticodon and a specific amino acid).
Enzymes are biocatalysts, named by Buchner, which allow the cell’s thousands of reactions to run rapidly at body temperature. Endo-enzymes act inside the cell that made them, exo-enzymes act outside it.
Enzymes are purely proteinaceous or conjugated. In a conjugated enzyme, apoenzyme + prosthetic group = holoenzyme. Co-enzymes are tightly attached organic compounds (NAD, FMN) and co-factors are loosely attached inorganic ions, also called activators.
All enzymes are proteins except ribozymes. They have a specific three-dimensional conformation with an active site, remain unchanged after catalysis, act on a specific substrate, and are sensitive to pH and temperature — pepsin works best at pH 2 and trypsin at pH 9.5.
Enzymes are named after the substrate, the reaction, or the source, and the international code gives each a double name ending in -ase. The six classes are oxidoreductases, transferases, hydrolases, lyases, isomerases and ligases.
Enzyme action begins with the binding of the substrate to the active site to form the enzyme-substrate complex, which yields products and regenerates the enzyme. The lock and key model (Fischer) treats the enzyme as rigid; the more accepted induced fit model (Koshland) treats it as flexible.
Enzyme activity is affected by substrate concentration (giving a rectangular hyperbola, with \(K_m\) the substrate concentration at half of \(V_{max}\); a low \(K_m\) means strong affinity), enzyme concentration, temperature (optimum near 37°C, denaturation above 40°C), pH (each enzyme has its own optimum) and other substances such as activators and inhibitors.
Metabolism is the sum of all chemical reactions in the cells of an organism. Catabolic pathways break complex molecules into simpler ones and release energy as ATP; anabolic pathways build complex molecules from simpler ones and consume energy.
The metabolic pool is the reservoir of biomolecules on which enzymes act as the cell requires, and it allows one class of biomolecule to be converted into another. The balance between catabolism and anabolism maintains homeostasis.
Secondary metabolites are small organic molecules not essential for growth, development and reproduction, produced by bacteria, fungi and plants. The three main groups are terpenes, phenolics and nitrogen-containing compounds.
Secondary metabolites are important as medicines (morphine from Papaver somniferum), as flavours, as protective compounds (glucosinolates of cabbage), as astringents (tannins in wine and chocolate), and as food preservatives because of their antibiotic properties.
Flowchart
FC 6.12 – The chapter at a glance: elements (prime, macro, trace) → biomolecules → organic branch: macromolecules (monosaccharides → polysaccharides; amino acids → polypeptides; nucleotides → polynucleotides) and micromolecules (fatty acids + glycerol → lipids; secondary metabolites) → enzymes (proteins that catalyse reactions) → metabolism: catabolic pathways release energy as ATP and anabolic pathways consume it → metabolic pool → balance of the two → homeostasis
6.4 Points to Ponder
Starch, glycogen and cellulose are all built from glucose alone, yet one feeds a seedling, one fuels a running animal and one holds up a tree. If the units are the same, how much of biology is decided simply by how the units are arranged?
A cell could store its energy as free glucose. Instead it spends energy joining glucose molecules into polysaccharides, and later spends more energy breaking them apart again. What does the cell gain that makes this apparent waste worthwhile?
Water refuses to mix with oil, and a phospholipid has one end that loves water and one that avoids it. Out of this single fact a membrane forms by itself. Where else in living systems might a structure assemble without anything guiding it?
Fats yield far more energy per gram than carbohydrates, yet the body burns carbohydrate first and keeps fat in reserve. What might be the advantage of using the poorer fuel first?
The same 20 amino acids are used by a bacterium, a mango tree and a human being. Does this shared vocabulary tell us something about how living organisms are related to one another?
A single amino acid substitution can change a working protein into one that causes disease, and yet most of the protein remains unchanged. Why should one position in a long chain matter so much more than others?
Enzymes are proteins, and proteins are destroyed by heat. What does this suggest about the temperature range within which life can exist, and how do you explain organisms that live in hot springs?
Pepsin works best at pH 2 and trypsin at pH 9.5, and both digest protein. Why should the body maintain two different chemical environments to carry out what appears to be the same job?
The lock and key model was replaced by the induced fit model, but the older model is still taught and still explains a great deal. When is a scientific model worth keeping even after a better one has been proposed?
An enzyme is not consumed in the reaction it catalyses. If nothing is used up, what actually limits how fast a reaction can go in a cell?
DNA is held together by weak hydrogen bonds rather than strong covalent ones. For a molecule that must last a lifetime and be copied exactly, is weakness here a flaw or an advantage?
Chargaff found that the base ratio stays constant within a species but differs between species. What might this mean for identifying an organism, or for tracing how closely two species are related?
The metabolic pool allows carbohydrate to be converted into fat and fat into carbohydrate. If molecules can be interchanged so freely, what decides which biomolecule a cell builds at a given moment?
Secondary metabolites are described as not essential for growth, development and reproduction — and yet plants make them in large quantities. In what sense is ‘not essential’ a fair description of a molecule that keeps a plant from being eaten?
Nearly every biomolecule you have studied is built and broken by enzymes, and enzymes are themselves biomolecules built under the instructions of nucleic acids. Where, if anywhere, does such a circle begin?
6.5 Check Your Concepts
Carbohydrates are called ‘hydrates of carbon’. Examine the general formula \(C_x(H_2O)_y\) and explain why the name is chemically appropriate, and why it can still be misleading.
Sucrose does not reduce Benedict’s reagent, but the two monosaccharides obtained from it on hydrolysis do. Explain why.
A student is given three unlabelled solutions — glucose, sucrose and starch. Describe how the properties studied in this chapter could be used to identify each one.
Arrange the following in the correct sequence for a dietary disaccharide: absorption into blood, hydrolysis of the glycosidic bond, entry into the cell, oxidation in cellular respiration, arrival in the small intestine.
Amylose and amylopectin are both made from α-glucose and both are starch. Why then does one form a colloidal suspension in hot water while the other is completely insoluble?
What would happen to a plant cell if its cellulose cell wall were replaced by a wall made of amylopectin? Answer with reference to structure and function.
Glycogen is described as amylopectin with very short distances between its branching side-chains. Explain how this structural feature suits the way an animal uses its energy reserve.
Why is a molecule of fat not classified as a macromolecule even though it is much larger than a molecule of glucose?
A phospholipid placed in water arranges itself into a bilayer without anything directing it. Explain this behaviour in terms of the two ends of the molecule.
Draw a labelled diagram of a lipid bilayer in an aqueous medium and mark the polar head group, the non-polar tails and the position of water.
Cholesterol is present in all cells of the animal body, but is absent in plants. Name the class of lipid to which it belongs, and list three substances synthesised from it.
Distinguish between simple, compound and derived lipids, giving one example of each.
All proteins are built from the same 20 amino acids. Explain what makes the protein of one organism different from that of another.
Arrange the four levels of protein organisation in order, and state the type of bond mainly responsible for each level.
Egg albumin coagulates on heating but the globular molecules of histones do not. What does this difference tell you about how heat affects different proteins?
Haemoglobin is given as an example of both a conjugated protein and of quaternary structure. Explain how the same molecule illustrates both ideas.
What is meant by the isoelectric point of a protein? Which part of the protein molecule contributes the charges that are balanced at this point?
Differentiate between a nucleoside and a nucleotide, and state exactly which carbon atoms of the sugar are involved in forming each.
Why must a purine always pair with a pyrimidine in the DNA double helix, and never a purine with a purine?
A stretch of DNA is unusually rich in guanine and cytosine. Would you expect it to separate into two strands more easily or less easily than an adenine-thymine rich stretch? Justify your answer.
Purine–pyrimidine equality holds in DNA but not in RNA. Explain the reason for this difference.
Draw a labelled diagram of a tRNA molecule and mark the acceptor stem, the anticodon loop, the DHU arm and the amino acid attachment site.
What would be the consequence if the anticodon loop of a tRNA molecule were altered but the amino acid attachment site were left unchanged?
An enzyme kept at 2°C shows almost no activity, and an enzyme kept at 65°C also shows almost no activity. Explain why only one of these two enzymes will work again when brought to 30°C.
Pepsin and trypsin both digest protein, yet their optimum pH values are 2 and 9.5. Explain why the body needs two such different enzymes for the same class of food.
Distinguish between an apoenzyme, a prosthetic group and a holoenzyme, and state what happens to activity when the prosthetic group is removed.
Differentiate between a co-enzyme and a co-factor, giving one example of each.
Name the class of enzyme that catalyses each of the following, and give the reason for your choice: (i) removal of \(CO_2\) from a substrate, (ii) conversion of glucose-6-phosphate into fructose-6-phosphate, (iii) hydrolysis of sucrose, (iv) joining of two molecules using energy from ATP.
Compare the lock and key model and the induced fit model of enzyme action, and state why the second is more widely accepted.
Sketch the curve obtained when the velocity of an enzyme reaction is plotted against substrate concentration, mark the three phases A, B and C, and explain what limits the velocity in phase C.
Two enzymes act on the same substrate. One has a low \(K_m\) value and the other a high one. What does this tell you about the strength of the ES complex formed by each?
The graph of enzyme activity against temperature rises gradually but falls steeply after the peak. Explain why the two sides of the curve differ in shape.
Classify each of the following as catabolic or anabolic, and state whether energy is released or consumed: (i) digestion of starch to glucose, (ii) synthesis of glycogen from glucose, (iii) formation of protein from amino acids, (iv) breakdown of triglycerides to glycerol and fatty acids.
A person eats a diet almost free of fat yet gains body fat. Explain this using the concept of the metabolic pool.
Why is the balance between catabolism and anabolism described as necessary for homeostasis?
Secondary metabolites are said to be non-essential for the growth, development and reproduction of the organism that makes them. Give two reasons why a plant would still produce them in large amounts.
Name the three main groups of secondary metabolites, and state what each group is made from.
The glucosinolates of cabbage give it its characteristic flavour and also protect it from pests. Explain how one compound can serve both these ends.
Identify the biomolecule from each description: (i) a polymer of β-glucose, (ii) a lipid with a phosphate group, (iii) a protein with a haem prosthetic group, (iv) the RNA that carries an anticodon, (v) the alkaloid first isolated from the opium poppy, Papaver somniferum.
Observe the following figure and name the type of bond shown by the arrow in the structure.
Diagram
Fig. E6.1 – A short length of double-stranded DNA drawn as two sugar-phosphate backbones with the letters P and S marked along them, the base pairs A–T, G–C, T–A and C–G shown between the strands with their hydrogen bonds represented as dashes, and an arrow pointing upward at the bonds between the last base pair.
What are the building blocks of life?
Explain the peptide bond.
How many types of polysaccharides do you know?
Enlist the significance of carbohydrates.
What is a reducing sugar?
What is the basic difference between a saturated and an unsaturated fatty acid?
Enlist the examples of simple proteins and give their significance.
Explain the secondary structure of protein with examples.
Explain the induced fit model for the mode of enzyme action.
What is RNA? Enlist the types of RNA.
Describe the concept of the metabolic pool.
How are secondary metabolites useful for mankind?
Complete the following chart.
| Protein | Physiological role |
|---|---|
| Collagen | ………………………. |
| ……………………… | Responsible for muscle contraction |
| Immunoglobulin IgG | …………………………. |
| ………………… | Significant in respiration |
| Fibrinogen | ………………………….. |
What are biomolecules? Explain the building blocks of life.
Explain the classes of carbohydrates with examples.
Describe the types of lipids and mention their biological significance.
Explain the chemical nature, structure and role of phospholipids in the biological membrane.
Describe the classes of proteins with their importance.
What are enzymes? How are they classified? Mention an example of each class.
Explain the properties of enzymes.
Describe the factors affecting enzyme action.
What are nucleic acids? Enlist the points of difference between DNA and RNA.
What are the types of RNA? Mention the role of each class of RNA.
What is metabolism? How is the metabolic pool formed in the cell?
The term that describes all the chemical reactions taking place in an organism.
The form in which carbohydrate is transported in a plant.
The reagent used for testing of reducing sugar.
6.6 Practice With Numericals
A sample of double stranded DNA contains 22% adenine. Calculate the percentage of thymine, guanine and cytosine present in it, stating the rule used at each step.
In a double stranded DNA molecule, the amount of guanine is found to be 30%. Work out the value of the ratio \(\frac{A+T}{G+C}\) for this molecule.
One complete turn of the DNA double helix measures about 34 Å, and the distance between two neighbouring base pairs is 3.4 Å. Calculate the number of base pairs present in one complete turn, and then the number of complete turns in a stretch of DNA containing 250 base pairs.
The concentration of glucose in human blood is about 90 mg per 100 ml of blood. Calculate the mass of glucose present in 5 litres of blood.
Sucrase can hydrolyse 100000 times its own weight of sucrose. Calculate the mass of sucrose that could be hydrolysed by 0.5 mg of the enzyme, and express your answer in grams.
Enzyme P has a \(K_m\) value of \(2 \times 10^{-5}\) moles/lit and enzyme Q has a \(K_m\) value of \(5 \times 10^{-3}\) moles/lit for the same substrate. State which enzyme reaches half of its maximum velocity at the lower substrate concentration, and which forms the stronger ES complex.
An enzyme catalysed reaction has a \(V_{max}\) of 40 units. At a certain substrate concentration the measured velocity is 20 units. What does this substrate concentration represent, and what percentage of the enzyme molecules are bound to substrate at this point?
In a cell, rRNA accounts for 85% of the total cellular RNA and mRNA for 3%. If the cell contains 4000 units of total RNA, calculate the number of units of rRNA, of mRNA, and of the remaining RNA.
A polypeptide chain contains 180 amino acid units. Calculate the number of peptide bonds present in it, and the number of water molecules released during its formation.
If double stranded DNA has 14% C (cytosine), what percentage of A (adenine), T (thymine) and G (guanine) would you expect?
6.7 Case-Based Questions
- Answer the questions with reference to the following figure.
- Name the type of bond formed between the two polypeptides.
- Which amino acid is involved in the formation of such a bond?
- Amongst the I, II, III and IV structural levels of protein, which level of structure includes such a bond?
Diagram
Fig. E6.2 – Two polypeptide chains each carrying an -SH group, shown converting by oxidation into a linked S–S structure and back by reduction, with the two polypeptides, the -SH groups, the S–S linkage and the oxidation and reduction arrows labelled.
6.8 Objective Questions
Sugars, amino acids and nucleotides unite with their respective subunits to form ——–
- bioelements b. micromolecules c. macromolecules d. each of these
A glycosidic bond is found in —————
- Disaccharide b. Nucleosides c. Polysaccharide d. each of these
Amino acids in a polypeptide are joined by ————— bond.
- Disulphide b. glycosidic c. hydrogen bond d. none of these
Lipids associated with the cell membrane are ————
- Spingomyelin b. Isoprenoids c. Phospolipids d. Cholesterol
Linoleic, linolenic and ——————– acids are referred to as essential fatty acids, since they cannot be synthesized by the body and hence must be included in the daily diet.
- Arachidonic b. Oleic c. Stearic d. Palmitic
Haemoglobin is a type of ————– protein, which plays an indispensible part in respiration.
- simple b. derived c. conjugated d. complex
When inorganic ions or metallo-organic molecules bind to an apoenzyme, they together form ——
- isoenzyme b. holoenzyme c. denatured enzyme d. none of these
In enzyme kinetics, Km = Vmax/2. If the Km value is lower, it indicates —————-
- Enzyme has less affinity for substrate
- Enzyme has higher affinity towards substrate
- There will be no product formation
- All active sites of enzyme are saturated
Assertion: All monosaccharides give a positive Benedict’s test. Reason: Every monosaccharide carries a free aldehyde or ketone group. State whether the assertion and the reason are true, and whether the reason correctly explains the assertion.
Assertion: Vanaspati ghee is solid at room temperature while the oil from which it is made is liquid. Reason: Hydrogenation removes double bonds from the fatty acid chains. Judge the assertion and the reason.
Assertion: Histones are called basic proteins. Reason: They are rich in lysine and arginine and exist as cations at a physiological pH of 7.4. Judge the assertion and the reason.
Assertion: A boiled piece of potato fails to release oxygen from hydrogen peroxide, but boiled manganese dioxide still does. Reason: An inorganic catalyst is not a protein. Judge the assertion and the reason.
Match the following items given in Column I and Column II.
| Column I | Column II |
|---|---|
| a. RNA | i. Induced fit model |
| b. Yam plant | ii. Flax seeds |
| c. Koshland | iii. Hydrolase |
| d. Omega-3-fatty acid | iv. Uracil |
| e. Sucrase | v. Anti-fertility pills |
- Match the RNA in Column I with the description in Column II.
| Column I | Column II |
|---|---|
| a. mRNA | i. Forms 50-60% of the ribosome |
| b. rRNA | ii. Clover-leaf shaped, 70-80 nucleotides |
| c. tRNA | iii. Accounts for 3% of the cellular RNA |
| d. Cistron | iv. Carries the message for one complete polypeptide chain |