Chapter 10: Biomolecules (Organic Chemistry)

Glucose and sucrose contain many –OH groups, which form hydrogen bonds with water, so they dissolve readily. Cyclohexane and benzene are non-polar hydrocarbons with no –OH groups; they cannot form hydrogen bonds with water and so are insoluble.

The many –OH groups of the sugars hydrogen-bond with water; the hydrocarbons cannot.

Lactose (milk sugar) is made of β-D-galactose and β-D-glucose. On hydrolysis (dilute acid or the enzyme lactase):

$$\mathrm{C}{}_{12}\mathrm{H}{}_{22}\mathrm{O}{}_{11}+\mathrm{H}{}_2\mathrm{O}\to \mathrm{C}{}_6\mathrm{H}{}_{12}\mathrm{O}{}_6(\mathrm{galactose})+\mathrm{C}{}_6\mathrm{H}{}_{12}\mathrm{O}{}_6(\mathrm{glucose})$$

β-D-Galactose and β-D-glucose.

Glucose pentaacetate does not react with hydroxylamine (no oxime) or with $\mathrm{NaHSO}{}_3$. In the pentaacetate, all five –OH groups are acetylated, including the –OH on C-1 of the cyclic form. With C-1 tied up in the ring as an acetylated hemiacetal, the ring cannot open to give a free –CHO group. This shows glucose exists mainly in a cyclic (hemiacetal) form, not as the open-chain aldehyde.

In the pentaacetate the cyclic C-1 –OH is acetylated, so the ring cannot open to free a –CHO group.

Amino acids exist as zwitterions ($\mathrm{H}{}_3\mathrm{N}{}^{+}-\mathrm{CHR}-\mathrm{COO}{}^{-}$), which are dipolar ionic species held together by strong electrostatic (salt-like) attractions. So they have high melting points, and their ionic nature makes them very soluble in water. Halo acids are ordinary covalent molecules without such ionic attractions.

Amino acids exist as zwitterions with strong ionic attractions, unlike covalent halo acids.

On boiling, the egg proteins are denatured: their globular structure unfolds and the chains coagulate, forming a solid network. The water present is trapped (absorbed and held) within this coagulated protein network, mainly by hydrogen bonding; it does not leave the egg.

It is trapped in the coagulated (denatured) protein network.

Monosaccharides are the simplest carbohydrates, which cannot be hydrolysed into simpler polyhydroxy aldehydes or ketones. Examples: glucose, fructose, ribose. They are classified by the number of carbon atoms and the carbonyl group (aldoses, ketoses).

Carbohydrates that cannot be hydrolysed further, e.g. glucose, fructose, ribose.

Sugars that reduce Fehling's solution and Tollens' reagent are reducing sugars. They have a free aldehyde or ketone group (or a hemiacetal that can open to one). All monosaccharides and disaccharides such as maltose and lactose are reducing sugars; sucrose is not.

Sugars that reduce Fehling's and Tollens' reagents (free carbonyl/hemiacetal group), e.g. glucose, maltose, lactose.

• Structural: cellulose forms the cell walls of plants.
• Storage of energy: starch is the main stored food (energy reserve) in plants.

Cellulose builds cell walls; starch stores energy.

• Monosaccharides: ribose, 2-deoxyribose, galactose, fructose
• Disaccharides: maltose, lactose

Monosaccharides: ribose, 2-deoxyribose, galactose, fructose. Disaccharides: maltose, lactose.

The glycosidic linkage is the oxide (–O–) bond that joins two monosaccharide units, formed with the loss of a water molecule between the hemiacetal –OH of one sugar and an –OH of the other. For example, in maltose the C-1 of one α-D-glucose is joined to C-4 of another glucose through oxygen.

The C–O–C link between two monosaccharide units, formed by loss of water.

Glycogen is the storage carbohydrate of animals (found in liver, muscles and brain); it is called animal starch. Both are polymers of α-D-glucose.

• Starch is a mixture of amylose (unbranched chains, 15–20%) and amylopectin (branched, 80–85%), and it is stored in plants.
• Glycogen is like amylopectin but more highly branched, and it is stored in animals.

Glycogen is animal starch: a more highly branched α-glucose polymer stored in animals, whereas starch (amylose + amylopectin) is stored in plants.

• (i) Sucrose: α-D-glucose and β-D-fructose
• (ii) Lactose: β-D-galactose and β-D-glucose

(i) Glucose and fructose. (ii) Galactose and glucose.

Starch is made of α-D-glucose units: amylose has C1–C4 α-glycosidic links (unbranched) and amylopectin also has C1–C6 branches. Cellulose is a straight-chain polymer of β-D-glucose units joined by C1–C4 β-glycosidic links.

Starch is built from α-D-glucose (with branching in amylopectin); cellulose is an unbranched chain of β-D-glucose.

• (i) HI (prolonged heating): n-hexane forms, showing the six carbons are in a straight chain: $\mathrm{C}{}_6\mathrm{H}{}_{12}\mathrm{O}{}_6\underset{\mathrm{heat}}{\overset{\mathrm{HI}}{\to }}\mathrm{CH}{}_3\mathrm{CH}{}_2\mathrm{CH}{}_2\mathrm{CH}{}_2\mathrm{CH}{}_2\mathrm{CH}{}_3$
• (ii) Bromine water: the aldehyde group is oxidised to –COOH, giving gluconic acid: $\mathrm{CHO}(\mathrm{CHOH}){}_4\mathrm{CH}{}_2\mathrm{OH}\stackrel{\mathrm{Br}{}_2\mathrm{water}}{\to }\mathrm{COOH}(\mathrm{CHOH}){}_4\mathrm{CH}{}_2\mathrm{OH}$
• (iii) Nitric acid: both ends are oxidised, giving saccharic acid (glucaric acid): $\mathrm{CHO}(\mathrm{CHOH}){}_4\mathrm{CH}{}_2\mathrm{OH}\stackrel{\mathrm{HNO}{}_3}{\to }\mathrm{COOH}(\mathrm{CHOH}){}_4\mathrm{COOH}$

(i) n-Hexane. (ii) Gluconic acid. (iii) Saccharic acid.

• Despite having an aldehyde group, glucose does not give Schiff's test and does not form the hydrogensulphite addition product with $\mathrm{NaHSO}{}_3$.
• Glucose pentaacetate does not react with hydroxylamine, showing no free –CHO group.
• Glucose exists in two crystalline forms, α and β (different melting points and specific rotations), and each changes in solution to an equilibrium mixture (mutarotation).

These are explained by the cyclic (hemiacetal) structure.

No Schiff's test or NaHSO₃ addition, the pentaacetate does not react with NH₂OH, and the existence of α and β forms (mutarotation).

• Essential amino acids: cannot be made in the body and must be supplied in the diet. Examples: valine, leucine (also lysine, isoleucine, phenylalanine).
• Non-essential amino acids: can be synthesised in the body. Examples: glycine, alanine (also glutamic acid, aspartic acid).

Essential (from the diet): valine, leucine. Non-essential (made in the body): glycine, alanine.

• (i) Peptide linkage: the amide bond (–CO–NH–) formed between the –COOH group of one amino acid and the –NH₂ group of another, with loss of water.
• (ii) Primary structure: the specific sequence of amino acids in the polypeptide chain(s) of a protein.
• (iii) Denaturation: the loss of biological activity of a protein when its secondary and tertiary structures are destroyed by heat, change in pH etc.; the hydrogen bonds break and the chains unfold, but the primary structure stays intact (e.g. coagulation of egg white on boiling).

(i) –CO–NH– bond between amino acids. (ii) The amino acid sequence. (iii) Loss of the 2° and 3° structure (and activity) by heat or pH, keeping the 1° structure.

• α-Helix: the chain coils into a right-handed spiral held by hydrogen bonds between –NH of one turn and C=O of the next.
• β-Pleated sheet: chains lie side by side, almost fully extended, and are held by hydrogen bonds between neighbouring chains.

α-Helix and β-pleated sheet.

Intramolecular hydrogen bonding between the –NH group of one amino acid residue and the C=O group of the residue four places along the same chain (the next turn of the helix).

Hydrogen bonds between N–H and C=O groups within the same chain.

Fibrous: thread-like, insoluble, structural (keratin, myosin). Globular: spherical, soluble, functional (insulin, albumin).

In water, an amino acid exists as a zwitterion, $\mathrm{H}{}_3\mathrm{N}{}^{+}-\mathrm{CHR}-\mathrm{COO}{}^{-}$, which has both an acidic group ($-\mathrm{NH}{}_3{}^{+}$, can give $\mathrm{H}{}^{+}$) and a basic group ($-\mathrm{COO}-$, can take $\mathrm{H}{}^{+}$). So it reacts with both bases and acids:

• with acid: $\mathrm{H}{}_3\mathrm{N}{}^{+}-\mathrm{CHR}-\mathrm{COO}{}^{-}+\mathrm{H}{}^{+}\to \mathrm{H}{}_3\mathrm{N}{}^{+}-\mathrm{CHR}-\mathrm{COOH}$
• with base: $\mathrm{H}{}_3\mathrm{N}{}^{+}-\mathrm{CHR}-\mathrm{COO}{}^{-}+\mathrm{OH}{}^{-}\to \mathrm{H}{}_2\mathrm{N}-\mathrm{CHR}-\mathrm{COO}{}^{-}+\mathrm{H}{}_2\mathrm{O}$

As zwitterions, amino acids have both a proton-donating (–NH₃⁺) and a proton-accepting (–COO⁻) group.

Enzymes are biological catalysts: mostly globular proteins that speed up specific biochemical reactions in living organisms under mild conditions by lowering the activation energy. They are highly specific; for example, maltase catalyses the hydrolysis of maltose to glucose. Their names usually end in "-ase".

Protein biocatalysts that speed up specific reactions in living organisms.

Denaturation (by heat, change in pH, etc.) breaks the hydrogen bonds and other weak interactions, so the secondary and tertiary structures are destroyed: the globules unfold and helices uncoil. The primary structure (amino acid sequence) remains intact, but the protein loses its biological activity.

The 2° and 3° structures are lost (the protein unfolds and loses activity); the 1° structure stays.

On the basis of solubility:

• Fat-soluble vitamins: A, D, E and K (stored in the liver and fatty tissue)
• Water-soluble vitamins: B-group and C (not stored; must be supplied regularly)

Vitamin K is responsible for the coagulation (clotting) of blood.

Fat-soluble (A, D, E, K) and water-soluble (B, C); vitamin K helps blood clot.

• Vitamin A: needed for healthy eyes and skin; its deficiency causes night blindness and xerophthalmia (hardening of the cornea). Sources: fish liver oil, carrots, butter and milk.
• Vitamin C: needed for healthy gums and skin and for resistance to infection; its deficiency causes scurvy (bleeding gums). Sources: citrus fruits (lemon, orange), amla and green leafy vegetables.

Vitamin A prevents night blindness (fish liver oil, carrots, milk); vitamin C prevents scurvy (citrus fruits, amla, green vegetables).

Nucleic acids are long-chain polymers of nucleotides (polynucleotides), found in the nucleus and cytoplasm: DNA and RNA.

• DNA is the chemical basis of heredity; it stores genetic information and passes it from parents to offspring.
• Nucleic acids (DNA through RNA) direct the synthesis of proteins in the cell.

Polymers of nucleotides (DNA, RNA); they transmit hereditary characters and direct protein synthesis.

• Nucleoside = base + pentose sugar (joined at C-1′ of the sugar).
• Nucleotide = base + pentose sugar + phosphate group (the phosphate is attached to C-5′ of the sugar). Nucleotides are the units of nucleic acids.

Nucleoside: base + sugar. Nucleotide: base + sugar + phosphate.

In the DNA double helix, the bases of the two strands pair by hydrogen bonds in a fixed way: adenine pairs with thymine (two H-bonds) and guanine pairs with cytosine (three H-bonds). So the sequence of one strand decides the sequence of the other: where one strand has A, the other has T, and so on. The two strands are therefore not identical but complementary.

Because of specific base pairing (A with T, G with C), each strand's sequence fixes the other's.

DNA: deoxyribose, thymine, double helix, heredity. RNA: ribose, uracil, single strand, protein synthesis.

• Messenger RNA (m-RNA): carries the genetic code from DNA to the ribosomes.
• Ribosomal RNA (r-RNA): part of the ribosomes, the site of protein synthesis.
• Transfer RNA (t-RNA): brings the specific amino acids to the ribosome during protein synthesis.

m-RNA, r-RNA and t-RNA.