Biomolecules: NEET notes

1. How to analyse chemical composition

NCERT §9.1

• An elemental analysis of living tissue and of a sample of the earth's crust gives similar lists: every element found in the crust is also found in living tissue.
• The difference is in proportion. Carbon and hydrogen are far more abundant, relative to other elements, in living matter than in the crust. By weight, carbon is 18.5% of the human body but 0.03% of the crust; hydrogen is 9.5% against 0.14%.
• To find the organic compounds, a living tissue (a vegetable or a piece of liver) is ground in trichloroacetic acid (Cl3CCOOH) with a mortar and pestle, and the slurry is strained through cheesecloth or cotton.
• This gives two fractions. The filtrate is the acid-soluble pool, in which thousands of organic compounds have been found. The retentate is the acid-insoluble fraction.
• A single compound is identified by extracting it, separating it from everything else until it is pure, and then using analytical techniques to work out its molecular formula and probable structure.
• All the carbon compounds obtained from living tissue can be called biomolecules.
• Inorganic content is found by a destructive test. A weighed piece of fresh tissue (wet weight) is dried to remove all water (dry weight) and then burnt fully. The carbon compounds leave as CO2 and water vapour, and what remains is ash, which contains inorganic elements such as calcium and magnesium.
• Inorganic compounds such as sulphate and phosphate also appear in the acid-soluble fraction. Elemental analysis gives the elements; analysis for compounds gives the organic and inorganic compounds present.

2. Amino acids

NCERT §9.1

• From a biological point of view, the small organic compounds in tissue are grouped as amino acids, nucleotide bases, fatty acids and so on, rather than by chemical functional groups.
• An amino acid carries an amino group and an acidic (carboxyl) group on the same carbon, the alpha carbon, so these are called alpha-amino acids.
• They are substituted methanes: the four valencies of the alpha carbon hold a hydrogen, a carboxyl group, an amino group and a variable R group.
• Many amino acids exist, but only twenty types occur in proteins. When R is a hydrogen the amino acid is glycine; a methyl group gives alanine; a hydroxy methyl group gives serine.
• Their chemical and physical properties come from the amino, carboxyl and R groups. By the number of amino and carboxyl groups they are acidic (glutamic acid), basic (lysine) or neutral (valine). Tyrosine, phenylalanine and tryptophan are aromatic amino acids.
• The –NH2 and –COOH groups can ionise, so the structure of an amino acid changes with the pH of the solution. The form carrying both a positive and a negative charge is the zwitterionic form.

3. Lipids, nucleotides and sugars

NCERT §9.1

• Lipids are generally insoluble in water. The simplest are fatty acids: a carboxyl group attached to an R group, which may be a methyl, an ethyl or a longer chain of –CH2 groups (1 to 19 carbons).
• Palmitic acid has 16 carbons and arachidonic acid 20, counting the carboxyl carbon in both.
• Fatty acids are saturated when they have no double bond and unsaturated when they have one or more C=C double bonds.
• Glycerol, trihydroxy propane, is another simple lipid. Fatty acids esterified with glycerol give monoglycerides, diglycerides and triglycerides.
• Glycerides are called fats or oils depending on their melting point. Oils melt at a lower temperature, so an oil such as gingelly oil stays liquid in winter.
• Phospholipids contain phosphorus and a phosphorylated organic compound. They are found in cell membranes; lecithin is an example. Neural tissue has lipids of more complex structure.
• Some carbon compounds contain heterocyclic rings, such as the nitrogen bases adenine, guanine, cytosine, uracil and thymine.
• A base attached to a sugar is a nucleoside (adenosine, guanosine, thymidine, uridine, cytidine). If a phosphate is also esterified to the sugar, it is a nucleotide (adenylic, guanylic, thymidylic, uridylic and cytidylic acid).
• DNA and RNA are made of nucleotides only, and they act as genetic material. Sugars such as glucose (C6H12O6) and ribose (C5H10O5) are also among the small biomolecules.

4. Primary and secondary metabolites

NCERT §9.2

• The thousands of biomolecules in a list of living-tissue compounds, amino acids, sugars and the rest, can be called metabolites.
• Animal tissues contain the classes of compounds shown for small biomolecules. These are primary metabolites, with identifiable functions in normal physiological processes.
• Plant, fungal and microbial cells also hold thousands of further compounds, among them rubber, gums, spices, scents, coloured pigments, essential oils, antibiotics, flavonoids and alkaloids. These are secondary metabolites.
• The roles of many secondary metabolites in the organisms that make them are not yet understood, but many are useful to people (rubber, drugs, spices, scents, pigments), and some have ecological importance.
• Examples by class: pigments (carotenoids, anthocyanins); alkaloids (morphine, codeine); terpenoids (monoterpenes, diterpenes); essential oils (lemon grass oil); toxins (abrin, ricin); lectins (concanavalin A); drugs (vinblastin, curcumin); polymeric substances (rubber, gums, cellulose).

5. Biomacromolecules

NCERT §9.3

• Every compound in the acid-soluble pool has a molecular weight between 18 and about 800 daltons (Da).
• The acid-insoluble fraction holds only four kinds of organic compound: proteins, nucleic acids, polysaccharides and lipids. Except for lipids, these have molecular weights of ten thousand Da and more.
• Biomolecules therefore fall into two groups: micromolecules (or simply biomolecules), under one thousand Da, and macromolecules (biomacromolecules), found in the acid-insoluble fraction.
• Apart from lipids, the molecules of the insoluble fraction are polymers.
• Lipids, whose molecular weights do not go beyond 800 Da, still come down in the insoluble fraction. Grinding breaks the cell membrane and other membranes into pieces that form water-insoluble vesicles, and these separate out with the insoluble pellet. Lipids are not strictly macromolecules.
• The acid-soluble pool roughly represents the composition of the cytoplasm; the macromolecules of the cytoplasm and organelles form the acid-insoluble fraction. Together they are the whole chemical make-up of a tissue.
• Water is the most abundant chemical in living organisms. Average share of total cell mass: water 70–90%, proteins 10–15%, nucleic acids 5–7%, carbohydrates 3%, lipids 2%, ions 1%.

6. Proteins

NCERT §9.4

• Proteins are polypeptides: linear chains of amino acids joined by peptide bonds.
• Since a protein is built from up to 20 types of amino acid, it is a heteropolymer. A homopolymer has only one type of monomer repeated n times.
• Some amino acids are essential: the body cannot make them, so they must come from food, and dietary proteins are their source. Non-essential amino acids are those the body can make.
• Proteins do many jobs: some carry nutrients across the cell membrane, some fight infectious organisms, some are hormones and some are enzymes.
• Examples from NCERT's table: collagen makes up the ground substance between cells, trypsin is an enzyme, insulin is a hormone, antibodies fight infectious agents, receptors sense smell, taste and hormones, and GLUT-4 lets glucose into cells.
• Collagen is the most abundant protein in the animal world. RuBisCO (ribulose bisphosphate carboxylase-oxygenase) is the most abundant protein in the whole biosphere.

7. Polysaccharides

NCERT §9.5

• Polysaccharides (carbohydrates) are another class of macromolecule in the acid-insoluble pellet. They are long chains, or threads, of monosaccharide units.
• Cellulose is made of one type of monosaccharide only, glucose, so it is a homopolymer. Starch is a variant that stores energy in plant tissues; glycogen is the animal variant. Inulin is a polymer of fructose.
• In a polysaccharide chain such as glycogen, the right end is the reducing end and the left end the non-reducing end. Glycogen is branched.
• Starch forms helical secondary structures and can hold I2 molecules inside the helix; the starch-iodine complex is blue. Cellulose has no complex helices, so it cannot hold iodine.
• Plant cell walls are made of cellulose, and paper from plant pulp and cotton fibre is cellulosic.
• More complex polysaccharides are built from amino-sugars and chemically modified sugars such as glucosamine and N-acetyl galactosamine. Chitin, in the exoskeleton of arthropods, is one; these complex polysaccharides are mostly homopolymers.

8. Nucleic acids

NCERT §9.6

• Nucleic acids, the remaining macromolecule of the acid-insoluble fraction, are polynucleotides.
• Polysaccharides, polypeptides and polynucleotides together make up the true macromolecular fraction of a tissue or cell.
• The building block is the nucleotide, with three chemically distinct parts: a heterocyclic compound (the nitrogen base), a monosaccharide (the sugar) and phosphoric acid (phosphate).
• Five bases occur: adenine, guanine, cytosine, thymine and uracil. Of these, adenine and guanine are substituted purines, and the other three are substituted pyrimidines.
• The sugar is either ribose or 2' deoxyribose, both pentoses. A nucleic acid with deoxyribose is deoxyribonucleic acid (DNA); one with ribose is ribonucleic acid (RNA).

9. Structure of proteins

NCERT §9.7

• Biologists describe protein structure at four levels.
• Primary structure is the sequence of amino acids, the positional information of which comes first, second and so on. The chain is pictured as a line whose left end is the first amino acid, the N-terminal, and whose right end is the last, the C-terminal.
• A protein thread is not a stiff rod. Parts of it coil into a helix, like a spiral staircase, and only right-handed helices are seen in proteins. Other parts fold in other ways. This is the secondary structure.
• The long chain also folds back on itself like a hollow woollen ball. This is the tertiary structure, the three-dimensional view of a protein, and it is essential for many of a protein's biological activities.
• Some proteins are built from several polypeptide chains, called subunits. How these folded subunits sit relative to one another is the quaternary structure.
• Adult human haemoglobin has 4 subunits: two identical alpha subunits and two identical beta subunits.

10. Enzymes and chemical reactions

NCERT §9.8, §9.8.1

• Almost all enzymes are proteins. Some nucleic acids also act as enzymes; these are ribozymes.
• Like any protein, an enzyme has primary, secondary and tertiary structure. As the chain folds in the tertiary structure it crosses over itself and leaves crevices or pockets. The active site is the pocket into which the substrate fits, and through it the enzyme catalyses reactions at a high rate.
• Inorganic catalysts work best at high temperature and pressure, whereas enzymes are damaged at high temperatures (above about 40°C). Enzymes from organisms of hot vents and sulphur springs (thermophiles) stay stable and active up to 80–90°C.
• A physical change alters shape or state without breaking bonds, such as ice melting or water turning to vapour. A chemical reaction breaks bonds and forms new ones, 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 (δP/δt); with a direction it is called velocity. As a rule of thumb, the rate doubles or halves for every 10°C rise or fall in temperature.
• Catalysed reactions run far faster than uncatalysed ones. CO2 + H2O → H2CO3 forms about 200 molecules of carbonic acid an hour without an enzyme, but about 600,000 every second with carbonic anhydrase, roughly a 10 million-fold speed-up.
• A multistep reaction whose steps are catalysed by one enzyme complex or several enzymes is a metabolic pathway. Glucose becomes pyruvic acid through ten enzyme-catalysed reactions.
• With one or two extra 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.

11. How enzymes speed up reactions

NCERT §9.8.2, §9.8.3

• The chemical an enzyme converts is its substrate (S), and the result is the product (P): S → P.
• The substrate must diffuse to the active site and bind there, so the formation of an enzyme-substrate complex (ES) is obligatory. It lasts only a short time.
• While bound, the substrate takes on a new, unstable transition state structure. Once the bonds are broken or made, the product is released from the active site.
• On a graph of potential energy against the progress of the reaction, the substrate must climb to the higher energy of the transition state before falling to the product. If P lies lower than S the reaction is exothermic and needs no heating.
• Whether the reaction releases energy or needs it, the energy gap between S and the transition state is the activation energy. Enzymes lower this barrier, which makes the change from S to P easier.
• The overall scheme is E + S ⇌ ES → EP → E + P, where EP is the enzyme-product complex. Formation of ES is essential for catalysis.
• The catalytic cycle: the substrate binds to the active site; binding makes the enzyme change shape and fit more tightly around it (induced fit); the active site breaks the substrate's bonds and an enzyme-product complex forms; the enzyme releases the products and is free to bind another substrate molecule.

12. Factors affecting enzyme activity

NCERT §9.8.4

• Conditions that alter a protein's tertiary structure change enzyme activity: temperature, pH, substrate concentration, and the binding of specific chemicals that regulate it.
• Enzymes work within a narrow range of temperature and pH. Each shows its highest activity at an optimum temperature and an optimum pH, and activity falls on either side of the optimum.
• Low temperature keeps an enzyme temporarily inactive, while high temperature destroys its activity because heat denatures proteins.
• As substrate concentration rises, reaction velocity rises at first and then levels off at a maximum velocity (Vmax) that more substrate cannot exceed. There are fewer enzyme molecules than substrate molecules, and once all are occupied no free enzyme is left for the extra substrate.
• When a chemical that binds to the enzyme shuts off its activity, the process is inhibition and the chemical is an inhibitor.
• A competitive inhibitor closely resembles the substrate and competes with it for the substrate-binding site, so the substrate cannot bind and activity falls. Malonate inhibits succinic dehydrogenase because it closely resembles the substrate, succinate.
• Competitive inhibitors are often used to control bacterial pathogens.

13. Classification of enzymes and co-factors

NCERT §9.8.5, §9.8.6

• Enzymes are grouped by the type of reaction they catalyse into 6 classes, each with 4–13 subclasses, and are named with a four-digit number.
• Oxidoreductases (dehydrogenases) catalyse oxidoreduction between two substrates. Transferases move a group G, other than hydrogen, from one substrate to another.
• Hydrolases break bonds by adding water: peptide, ester, ether, glycosidic, P–N, C–halide or C–C bonds. Lyases take groups off substrates without hydrolysis, which leaves double bonds behind.
• Isomerases interconvert optical, geometric or positional isomers. Ligases join two compounds, forming bonds such as C–O, C–S, C–N and P–O.
• Many enzymes need a non-protein co-factor bound to them to be catalytically active; the protein part is then called the apoenzyme. The three kinds of co-factor are prosthetic groups, co-enzymes and metal ions.
• Prosthetic groups are organic and tightly bound to the apoenzyme. In peroxidase and catalase, which break hydrogen peroxide into water and oxygen, haem is the prosthetic group and forms part of the active site.
• Co-enzymes are organic too, but they attach only briefly, during catalysis, and serve many different enzymes. Many contain vitamins: NAD and NADP contain the vitamin niacin.
• Metal ions make coordination bonds with the side chains in the active site and with the substrate at the same time; zinc is the co-factor of the protein-digesting enzyme carboxypeptidase.
• Removing the co-factor stops catalysis, which shows how crucial it is.

Must-know facts

1. Living and non-living matter contain the same elements; living matter has relatively far more carbon and hydrogen.
2. Tissue ground in trichloroacetic acid and filtered gives the acid-soluble pool (filtrate) and the acid-insoluble fraction (retentate).
3. Wet weight, then dry weight after removing water, then ash after burning; ash holds inorganic elements such as calcium and magnesium.
4. Alpha-amino acids: H, COOH, NH2 and an R group on the alpha carbon; 20 types in proteins; glycine (R = H), alanine (methyl), serine (hydroxy methyl).
5. Acidic glutamic acid, basic lysine, neutral valine; aromatic tyrosine, phenylalanine, tryptophan; zwitterion depends on pH.
6. Palmitic acid 16 C, arachidonic acid 20 C; glycerol is trihydroxy propane; lecithin is a membrane phospholipid.
7. Nucleoside = base + sugar; nucleotide = base + sugar + phosphate.
8. Adenine and guanine are purines; cytosine, thymine and uracil are pyrimidines.
9. Acid-soluble pool: 18 to about 800 Da. Macromolecules except lipids: 10,000 Da and above. Micromolecules: under 1000 Da.
10. Lipids come down in the insoluble fraction as membrane vesicles; they are not strictly macromolecules.
11. Water is the most abundant chemical in cells (70–90% of cell mass); proteins 10–15%.
12. Proteins are heteropolymers joined by peptide bonds; cellulose is a homopolymer of glucose; inulin is a polymer of fructose.
13. Collagen is the most abundant protein in animals; RuBisCO is the most abundant in the biosphere.
14. Starch helices hold iodine (blue); cellulose cannot. Glycogen is branched, reducing end on the right.
15. Chitin of arthropod exoskeletons is a complex polysaccharide of amino-sugars.
16. Four levels of protein structure; only right-handed helices; adult haemoglobin = 2 alpha + 2 beta subunits.
17. Ribozymes are nucleic acids that act as enzymes.
18. Most enzymes are damaged above about 40°C; thermophile enzymes stay active up to 80–90°C.
19. Carbonic anhydrase: about 200 molecules of H2CO3 an hour without it, about 600,000 a second with it (about 10 million times faster).
20. Enzymes lower activation energy; E + S ⇌ ES → EP → E + P.
21. Velocity rises with substrate and plateaus at Vmax when all enzyme is occupied.
22. Malonate competitively inhibits succinic dehydrogenase by resembling succinate.
23. Six enzyme classes: oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases.
24. Co-factors: prosthetic group (haem in peroxidase and catalase), co-enzyme (NAD, NADP contain niacin), metal ion (zinc in carboxypeptidase).

Common traps

Key terms

Acid-soluble pool

The filtrate left when tissue ground in trichloroacetic acid is strained; it holds the small molecules.

Acid-insoluble fraction

The retentate from the same filtration; it holds proteins, nucleic acids, polysaccharides and membrane lipids.

Ash

What remains after dried tissue is fully burnt; it contains inorganic elements such as calcium and magnesium.

Alpha-amino acid

An amino acid whose amino and carboxyl groups are on the same carbon, the alpha carbon.

Zwitterion

The form of an amino acid that carries both a positive and a negative charge at a particular pH.

Triglyceride

Glycerol with three fatty acids esterified to it; a fat or an oil.

Phospholipid

A lipid containing phosphorus and a phosphorylated organic compound, found in cell membranes; lecithin is one.

Nucleoside

A nitrogen base attached to a sugar.

Nucleotide

A nucleoside with a phosphate esterified to its sugar; the building block of nucleic acids.

Secondary metabolite

A compound of plants, fungi or microbes, such as an alkaloid or pigment, whose role in its host is often not fully known.

Heteropolymer

A polymer built from more than one type of monomer, such as a protein.

Homopolymer

A polymer of one type of monomer repeated many times, such as cellulose.

Primary structure

The sequence of amino acids in a protein, from the N-terminal to the C-terminal.

Tertiary structure

The folding of a whole protein chain on itself into a three-dimensional shape.

Quaternary structure

The arrangement of two or more folded polypeptide subunits relative to one another.

Ribozyme

A nucleic acid that acts as an enzyme.

Active site

The crevice or pocket in an enzyme into which the substrate fits.

Activation energy

The difference in energy between the substrate and the transition state; enzymes lower it.

Vmax

The maximum velocity of an enzyme reaction, reached when all enzyme molecules are occupied by substrate.

Competitive inhibitor

A substance resembling the substrate that competes for the active site, like malonate for succinic dehydrogenase.

Apoenzyme

The protein part of an enzyme that needs a co-factor to be active.

Prosthetic group

An organic co-factor tightly bound to the apoenzyme, such as haem in catalase.

Co-enzyme

An organic co-factor that binds only briefly during catalysis and serves many enzymes, such as NAD.