Biomolecules | CBSE Class 11 Biology Notes

This note covers NCERT Class 11 Biology Chapter 9, Biomolecules: how the chemical composition of living tissue is analysed, the small biomolecules (amino acids, lipids, nitrogen bases, nucleosides and nucleotides), primary and secondary metabolites, the biomacromolecules (proteins, polysaccharides and nucleic acids), the four levels of protein structure, and enzymes, including how they work, what affects them, how they are classified and their co-factors.

How is the chemical composition of living tissue analysed?

An elemental analysis of a plant tissue, an animal tissue or a microbial paste gives a list of elements such as carbon, hydrogen and oxygen, with their content per unit mass. The same analysis of a piece of the earth's crust gives a similar list. In absolute terms, all the elements present in a sample of the earth's crust are also present in a sample of living tissue. The difference is in relative abundance: carbon and hydrogen are relatively more abundant in any living organism than in the earth's crust.

Separating organic compounds

1. Any living tissue, such as a vegetable or a piece of liver, is ground in trichloroacetic acid (Cl₃CCOOH) with a mortar and pestle, giving a thick slurry.
2. The slurry is strained through cheesecloth or cotton, giving two fractions.
3. The filtrate is called the acid-soluble pool. Scientists have found thousands of organic compounds in it.
4. The retentate is called the acid-insoluble fraction.

To identify a compound, one extracts the compounds, separates them until one compound is isolated and purified, and then applies analytical techniques that give its molecular formula and probable structure. All the carbon compounds obtained from living tissues can be called biomolecules.

Finding the inorganic constituents

1. A small amount of living tissue, such as a leaf or liver, is weighed. This is the wet weight.
2. The tissue is dried. All the water evaporates, and the remaining material gives the dry weight.
3. The tissue is fully burnt. All the carbon compounds are oxidised to gaseous forms (CO₂ and water vapour) and removed.
4. What remains is the ash, which contains inorganic elements such as calcium and magnesium.

Inorganic compounds such as sulphate and phosphate are also seen in the acid-soluble fraction. NCERT's list of representative inorganic constituents of living tissues includes sodium (Na⁺), potassium (K⁺), calcium (Ca²⁺), magnesium (Mg²⁺), water (H₂O), and compounds such as NaCl, CaCO₃, phosphate and sulphate.

What are the small biomolecules found in living tissues?

From a biological point of view, the organic compounds are classified into amino acids, nucleotide bases, fatty acids and so on.

Amino acids

Amino acids are organic compounds containing an amino group and an acidic group as substituents on the same carbon, the α-carbon, so they are called α-amino acids. They are substituted methanes: the four valency positions are occupied by hydrogen, a carboxyl group, an amino group and a variable group called the R group. Based on the nature of the R group there are many amino acids, but those which occur in proteins are only of twenty types.

The chemical and physical properties of amino acids are essentially those of the amino, carboxyl and R functional groups. A particular property is the ionizable nature of the –NH₂ and –COOH groups, so the structure of amino acids changes in solutions of different pH. The form in which both groups are ionised is called the zwitterionic form.

Lipids

Lipids are generally water insoluble.

• A fatty acid has a carboxyl group attached to an R group, which could be a methyl (–CH₃), an ethyl (–C₂H₅) or a higher number of –CH₂ groups (1 to 19 carbons). Palmitic acid has 16 carbons including the carboxyl carbon, and arachidonic acid has 20.
• Fatty acids may be saturated (without a double bond) or unsaturated (with one or more C=C double bonds).
• Glycerol is a simple lipid: trihydroxy propane.
• Many lipids have both glycerol and fatty acids, with the fatty acids esterified with glycerol: monoglycerides, diglycerides and triglycerides. These are called fats and oils based on melting point. Oils have a lower melting point (for example gingelly oil) and remain as oil in winter.
• Phospholipids have phosphorous and a phosphorylated organic compound in them. They are found in the cell membrane; lecithin is one example.
• Some tissues, especially neural tissues, have lipids with more complex structures.

Nitrogen bases, nucleosides and nucleotides

Nucleic acids like DNA and RNA consist of nucleotides only, and DNA and RNA function as genetic material.

Structural formulae are drawn in groups: sugars (glucose, C₆H₁₂O₆, and ribose, C₅H₁₀O₅); amino acids (glycine, alanine and serine); fats and oils (lipids), which include palmitic acid, glycerol, a triglyceride, the phospholipid lecithin and cholesterol; nitrogen bases (adenine, a purine, and uracil, a pyrimidine); nucleosides (adenosine and uridine); and a nucleotide (adenylic acid).

See Fig. 9.1 in your NCERT textbook

Note: The three names build on each other. A base alone is a nitrogen base. Base plus sugar is a nucleoside. Base plus sugar plus phosphate is a nucleotide. The nucleoside names end in "-osine" or "-idine", and the nucleotide names end in "-ylic acid".

What are primary and secondary metabolites?

A list of biomolecules would have thousands of organic compounds, including amino acids and sugars. These biomolecules can be called metabolites.

Many secondary metabolites are useful to human welfare, for example rubber, drugs, spices, scents and pigments, and some have ecological importance.

What are biomacromolecules, and why do lipids appear among them?

The molecules in the insoluble fraction, except lipids, are polymeric substances. Lipids have molecular weights that do not exceed 800 Da, so why are they in the acid-insoluble fraction?

1. Lipids are present not only as such, but also arranged into structures like the cell membrane and other membranes.
2. Grinding a tissue disrupts the cell structure, and the membranes are broken into pieces.
3. The pieces form vesicles, which are not water soluble.
4. These membrane fragments separate along with the acid-insoluble pool, and so appear in the macromolecular fraction. Lipids are not strictly macromolecules.

Together, the acid-soluble pool and the acid-insoluble fraction represent the entire chemical composition of living tissues. Water is the most abundant chemical in living organisms.

What are proteins, polysaccharides and nucleic acids?

Proteins

Proteins are polypeptides: linear chains of amino acids linked by peptide bonds. As there are 20 types of amino acids, a protein is a heteropolymer, not a homopolymer. A homopolymer has only one type of monomer repeating n number of times.

Certain amino acids are essential for our health and have to be supplied through the diet, so dietary proteins are the source of essential amino acids. Non-essential amino acids are those which our body can make.

Collagen is the most abundant protein in the animal world, and RuBisCO (ribulose bisphosphate carboxylase-oxygenase) is the most abundant protein in the whole of the biosphere.

Polysaccharides

Polysaccharides are long chains of sugars, with different monosaccharides as building blocks.

In a polysaccharide chain such as glycogen, the right end is called the reducing end and the left end the non-reducing end. The complex polysaccharides are mostly homopolymers.

A cartoon of a chain of sugar rings joined by oxygen links, with a side chain branching off the main chain, showing that glycogen is a branched polysaccharide.

See Fig. 9.2 in your NCERT textbook

Nucleic acids

Nucleic acids are polynucleotides. Together with polysaccharides and polypeptides, they make up the true macromolecular fraction of any living tissue or cell. The building block is a nucleotide, which has three chemically distinct components:

• a heterocyclic compound (a nitrogenous base),
• a monosaccharide, and
• a phosphoric acid or phosphate.

What are the four levels of protein structure?

Structure means different things in different contexts: molecular formulae in inorganic chemistry, a two-dimensional view in organic chemistry, a three-dimensional view in physics. Biologists describe protein structure at four levels.

1. Primary structure: the sequence of amino acids, the positional information in a protein. The protein is imagined as a line: the left end is the first amino acid, called the N-terminal amino acid, and the right end is the last, called the C-terminal amino acid.
2. Secondary structure: the protein thread does not exist as an extended rigid rod. Some portions are folded in the form of a helix, similar to a revolving staircase, and only right-handed helices are observed in proteins. Other regions are folded into other forms.
3. Tertiary structure: the long protein chain is also folded upon itself like a hollow woollen ball. This gives a three-dimensional view of the protein, and it is absolutely necessary for many biological activities of proteins.
4. Quaternary structure: some proteins are an assembly of more than one polypeptide or subunit. The way these folded subunits are arranged with respect to each other, for example as a linear string of spheres or spheres arranged in a cube or plate, is the architecture of the protein.

Adult human haemoglobin consists of 4 subunits: two of α type and two of β type.

(a) Primary: a chain of beads, the amino acids, labelled polypeptide. Arrows lead to (b) Secondary: an alpha-helix and a beta-pleated sheet. Arrows from both lead to (c) Tertiary: the chain folded into a compact globular shape, with a hydrogen bond and a disulphide bond labelled. An arrow leads to (d) Quaternary: several folded chains packed together.

See Fig. 9.3 in your NCERT textbook

What are enzymes, and how do they speed up reactions?

Almost all enzymes are proteins. Some nucleic acids behave like enzymes; these are called ribozymes. Like any protein, an enzyme has primary, secondary and tertiary structures. In the tertiary structure the chain criss-crosses itself and makes many crevices or pockets. One such pocket is the active site: a crevice or pocket into which the substrate fits. Through their active site, enzymes catalyse reactions at a high rate.

Physical change and chemical reaction

• A physical change is a change in shape without breaking of bonds, or a change in state of matter, such as ice melting into water or water becoming vapour.
• A chemical reaction is one in which bonds are broken and new bonds are formed, for example Ba(OH)₂ + H₂SO₄ → BaSO₄ + 2H₂O, or the hydrolysis of starch into glucose.
• The rate of a process is the amount of product formed per unit time. As a rule of thumb, the rate doubles or decreases by half for every 10°C change in either direction.

Worked example: how much faster is carbonic anhydrase?

1. The reaction CO₂ + H₂O → H₂CO₃ without an enzyme forms about 200 molecules of H₂CO₃ in an hour.
2. With carbonic anhydrase it forms about 600,000 molecules every second.
3. In one hour that is 600,000 × 3,600 = 2,160,000,000 molecules.
4. Ratio = 2,160,000,000 ÷ 200 = 10,800,000, that is about 10 million times faster, as NCERT states.

A metabolic pathway is a multistep chemical reaction in which each step is catalysed by the same enzyme complex or by different enzymes. Glucose becomes pyruvic acid through ten different enzyme-catalysed reactions. With one or two additional reactions, the same pathway gives different end products: lactic acid in skeletal muscle under anaerobic conditions, pyruvic acid under normal aerobic conditions, and ethanol in yeast during fermentation.

Activation energy

The substrate (S) has to bind the enzyme at its active site, forming an obligatory, transient ES complex. While the substrate is bound, a new structure of the substrate called the transition state structure is formed. Soon, after the bond breaking and making are completed, the product is released.

Whether a reaction is exothermic (the product P at a lower energy level than S) or endothermic, S has to pass through a much higher energy state, the transition state. The difference in average energy content between S and this transition state is the activation energy. Enzymes bring down this energy barrier, making the transition of S to P easier.

Potential energy is on the y-axis and the progress of reaction on the x-axis. Two curves start at the level of the substrate (S), rise to a peak labelled transition state, and fall to the lower level of the product (P). The taller curve shows the activation energy without enzyme, and the lower curve shows the smaller activation energy with enzyme.

See Fig. 9.4 in your NCERT textbook

How does an enzyme act, and what affects its activity?

Each enzyme (E) has a substrate (S) binding site, so that a highly reactive enzyme-substrate complex (ES) is produced. This complex is short-lived and dissociates into the product(s) P and the unchanged enzyme, with an intermediate formation of the enzyme-product complex (EP): E + S → ES → EP → E + P. The formation of the ES complex is essential for catalysis.

The catalytic cycle

1. The substrate binds to the active site of the enzyme, fitting into the active site.
2. The binding of the substrate induces the enzyme to alter its shape, fitting more tightly around the substrate.
3. The active site, now in close proximity of the substrate, breaks the chemical bonds of the substrate, and the new enzyme-product complex is formed.
4. The enzyme releases the products of the reaction, and the free enzyme is ready to bind to another molecule of the substrate and run through the cycle again.

Factors affecting enzyme activity

Graphs (a) and (b) plot enzyme activity against pH and against temperature; each is a bell-shaped curve with a peak at the optimum. Graph (c) plots the velocity of reaction (V) against substrate concentration [S]: the curve rises steeply and then levels off at Vmax, and a dashed line marks Vmax/2 and the corresponding Km on the x-axis.

See Fig. 9.5 in your NCERT textbook

A competitive inhibitor closely resembles the substrate in its molecular structure. It competes with the substrate for the substrate-binding site, so the substrate cannot bind and the enzyme action declines. For example, malonate, which closely resembles the substrate succinate, inhibits succinic dehydrogenase. Such competitive inhibitors are often used in the control of bacterial pathogens.

How are enzymes classified, and what are co-factors?

Enzymes are divided into 6 classes, each with 4 to 13 subclasses, and are named by a four-digit number.

Co-factors

In many cases non-protein constituents called co-factors are bound to the enzyme to make it catalytically active. The protein portion is then called the apoenzyme.

Catalytic activity is lost when the co-factor is removed from the enzyme, which shows that co-factors play a crucial role in catalysis. The essential chemical components of many co-enzymes are vitamins.

Glossary

• Acid-soluble pool — The filtrate obtained when tissue ground in trichloroacetic acid is strained; it contains thousands of small organic compounds.
• Ash — What remains after a dried tissue is fully burnt; it contains inorganic elements such as calcium and magnesium.
• Zwitterionic form — The form of an amino acid in which both the amino and carboxyl groups are ionised.
• Phospholipid — A lipid containing phosphorous and a phosphorylated organic compound, found in cell membranes; lecithin is an example.
• Nucleotide — A nitrogenous base, a sugar and a phosphate joined together; the building block of nucleic acids.
• Secondary metabolites — Compounds such as alkaloids, rubber and essential oils found in plant, fungal and microbial cells, whose roles are not all understood.
• Biomacromolecules — The large molecules of the acid-insoluble fraction: proteins, nucleic acids and polysaccharides, with molecular weights of ten thousand daltons and above.
• Heteropolymer — A polymer made of more than one type of monomer, as a protein is made of 20 types of amino acids.
• Tertiary structure — The folding of a protein chain upon itself like a hollow woollen ball, giving a three-dimensional shape.
• Ribozymes — Nucleic acids that behave like enzymes.
• Active site — The crevice or pocket in an enzyme into which the substrate fits.
• Activation energy — The difference in average energy content between the substrate and the transition state.
• Competitive inhibitor — A chemical that closely resembles the substrate and competes with it for the enzyme's substrate-binding site.
• Apoenzyme — The protein portion of an enzyme that needs a co-factor to be catalytically active.

Common errors and misconceptions

• Misconception: Living tissue contains elements that the earth's crust does not. Correct: All the elements in the earth's crust are also in living tissue. The difference is the higher relative abundance of carbon and hydrogen in living organisms.
• Misconception: Lipids are true macromolecules. Correct: Lipids have molecular weights up to about 800 Da. They appear in the acid-insoluble fraction only because membrane fragments form insoluble vesicles.
• Misconception: A protein is a homopolymer. Correct: A protein is a heteropolymer made of 20 types of amino acids. Cellulose, made only of glucose, is a homopolymer.
• Misconception: Cellulose gives a blue colour with iodine. Correct: Starch forms helices that hold I₂ and give a blue colour. Cellulose has no complex helices and cannot hold I₂.
• Misconception: Collagen is the most abundant protein in the biosphere. Correct: Collagen is the most abundant protein in the animal world. RuBisCO is the most abundant protein in the whole biosphere.
• Misconception: Both left-handed and right-handed helices occur in proteins. Correct: In proteins only right-handed helices are observed.
• Misconception: Low temperature destroys enzymes. Correct: Low temperature keeps an enzyme temporarily inactive. High temperature destroys enzyme activity by denaturing the protein.
• Misconception: A co-enzyme is tightly bound to the enzyme. Correct: Prosthetic groups are tightly bound. Co-enzymes associate with the apoenzyme only transiently.

Exam-style questions with model answers

Q1. Why are lipids found in the acid-insoluble fraction although they are small molecules? [1 mark]

1. Lipids are arranged into cell membranes; grinding breaks the membranes into insoluble vesicles, which separate with the acid-insoluble fraction, so lipids are not strictly macromolecules.

Q2. Distinguish between primary and secondary metabolites, with two examples of each. [2 marks]

1. Primary metabolites have identifiable functions and known roles in normal physiological processes, for example amino acids and sugars.
2. Secondary metabolites are found in plant, fungal and microbial cells, and the roles of all of them are not yet understood, for example alkaloids such as morphine and pigments such as carotenoids.

Q3. What is the difference between a nucleoside and a nucleotide? Give one example of each. [2 marks]

1. A nucleoside is a nitrogen base attached to a sugar, for example adenosine.
2. A nucleotide is a nucleoside with a phosphate group esterified to the sugar, for example adenylic acid.

Q4. Describe the four levels of protein structure. [3 marks]

1. Primary structure is the sequence of amino acids, from the N-terminal to the C-terminal amino acid. Secondary structure is the folding of some portions of the chain into a helix (only right-handed helices occur) and other regions into other forms.
2. Tertiary structure is the folding of the whole chain upon itself like a hollow woollen ball, giving a three-dimensional shape needed for many biological activities.
3. Quaternary structure is the arrangement of more than one folded polypeptide or subunit, as in adult human haemoglobin with two α and two β subunits.

Q5. What is activation energy, and how do enzymes affect it? [3 marks]

1. In any reaction the substrate has to pass through a much higher energy state called the transition state before it becomes the product.
2. The difference in average energy content between the substrate and this transition state is the activation energy.
3. Enzymes bring down this energy barrier, so that the transition of substrate to product becomes easier and the reaction proceeds much faster.

Q6. Explain competitive inhibition with an example. [3 marks]

1. A competitive inhibitor closely resembles the substrate in its molecular structure.
2. Because of this similarity it competes with the substrate for the substrate-binding site of the enzyme, so the substrate cannot bind and enzyme action declines.
3. For example, malonate, which closely resembles succinate, inhibits succinic dehydrogenase. Such inhibitors are often used in the control of bacterial pathogens.

Q7. Describe the catalytic cycle of an enzyme and the factors that affect enzyme activity. [5 marks]

1. The substrate binds to the active site of the enzyme; the binding induces the enzyme to alter its shape and fit more tightly around the substrate.
2. The active site breaks the chemical bonds of the substrate and an enzyme-product complex forms; the enzyme then releases the products and is free to bind another substrate molecule.
3. Temperature and pH: each enzyme is most active at an optimum temperature and pH; low temperature keeps it temporarily inactive and high temperature denatures it.
4. Substrate concentration: velocity rises at first and then reaches a maximum (Vmax) once all the enzyme molecules are saturated.
5. Specific chemicals: inhibitors shut off enzyme activity, for example a competitive inhibitor that resembles the substrate.

Q8. Name the six classes of enzymes and the three kinds of co-factors, with an example of each co-factor. [5 marks]

1. The six classes are oxidoreductases (dehydrogenases), transferases, hydrolases, lyases, isomerases and ligases.
2. Co-factors are non-protein constituents bound to an enzyme to make it catalytically active; the protein part is then called the apoenzyme.
3. Prosthetic groups are organic compounds tightly bound to the apoenzyme, for example haem in peroxidase and catalase.
4. Co-enzymes are organic compounds associated with the apoenzyme only transiently, for example NAD and NADP, which contain the vitamin niacin.
5. Metal ions form coordination bonds at the active site and with the substrate, for example zinc in carboxypeptidase. Removing the co-factor destroys catalytic activity.

Key takeaways

• Living tissue and the earth's crust contain the same elements, but carbon and hydrogen are relatively more abundant in living organisms.
• Grinding tissue in trichloroacetic acid separates an acid-soluble pool of small molecules from an acid-insoluble fraction of macromolecules.
• Only twenty types of amino acids occur in proteins; fats and oils are fatty acids esterified to glycerol, and phospholipids contain, in addition, a phosphorylated organic compound.
• Proteins, nucleic acids and polysaccharides are true macromolecules; lipids join the insoluble fraction only as membrane vesicles.
• Water is the most abundant chemical in living organisms, making up 70 to 90 per cent of cellular mass.
• Proteins have primary, secondary, tertiary and quaternary structure; RuBisCO is the most abundant protein in the biosphere.
• Enzymes work through an active site, lower the activation energy, and are affected by temperature, pH, substrate concentration and inhibitors.
• Enzymes fall into six classes, and many need co-factors: prosthetic groups, co-enzymes or metal ions.

Test yourself

What are the four substituents on the α-carbon of an amino acid?

The four substituents are hydrogen, a carboxyl group, an amino group and a variable R group.

How many carbon atoms does palmitic acid have?

Palmitic acid has 16 carbon atoms including the carboxyl carbon; arachidonic acid has 20.

Name two alkaloids and two toxins that are secondary metabolites.

Morphine and codeine are alkaloids, and abrin and ricin are toxins.

What range of molecular weight do the compounds of the acid-soluble pool have?

The compounds in the acid-soluble pool have molecular weights ranging from 18 to around 800 daltons.

What is the function of GLUT-4?

GLUT-4 is a protein that enables the transport of glucose into cells.

Which polysaccharide is a polymer of fructose?

Inulin is a polymer of fructose, while cellulose, starch and glycogen are made of glucose.

At what temperatures do enzymes from thermophilic organisms stay active?

Enzymes from organisms of hot vents and sulphur springs retain their catalytic power even at 80° to 90°C.

Which vitamin is part of the co-enzymes NAD and NADP?

The co-enzymes NAD and NADP contain the vitamin niacin.