JEE Chemistry Biomolecules Notes Set 02

Amino Acids

Amino acids carry an amino group and a carboxyl group. The proteins of living things are built only from alpha-amino acids, in which both groups sit on the same carbon, and all but glycine are optically active, with the L configuration. There are about 20 of them.

1. Zwitterion: in water the proton of COOH moves to NH₂, giving ⁺NH₃-CHR-COO^-. This is why amino acids have high melting points and are soluble in water.
2. Behaviour with pH: in acid the amino acid is a cation, in base an anion. At the isoelectric point the net charge is zero, the molecule does not move in an electric field and its solubility is least.
3. Neutral amino acids have one NH₂ and one COOH group (glycine, alanine). Acidic ones have more COOH groups (aspartic acid, glutamic acid). Basic ones have more NH₂ (lysine, arginine, histidine). Basic strength order: arginine, lysine, histidine.
4. Essential amino acids cannot be made by the body and must come from food: valine, leucine, isoleucine, lysine, threonine, methionine, phenylalanine, tryptophan (histidine and arginine in children). Non-essential ones, such as glycine, alanine, serine and glutamic acid, are made in the body.
5. Glycine is the simplest amino acid and the only one without optical activity. Proline and tyrosine are other amino acids that often appear in questions.

Peptides and Proteins

The carboxyl group of one amino acid and the amino group of another join with loss of water to form a peptide (amide) bond, -CO-NH-. Many such units form a polypeptide, and a polypeptide with more than about 100 amino acids is a protein. The C-N bond has partial double-bond character, so it is shorter than a normal C-N bond and the group is planar.

1. Fibrous proteins (keratin, collagen, myosin, silk) are long and insoluble in water. Globular proteins (haemoglobin, insulin, albumin, enzymes) are compact and dissolve in water.
2. Denaturation: heat, acids, bases or heavy metals destroy the secondary and tertiary structure but not the primary structure, and biological activity is lost. Boiling an egg and curdling of milk are examples, and both are irreversible.
3. Simple proteins give only amino acids on hydrolysis. Conjugated proteins also have a non-protein part, for example haemoglobin (haem) and casein (phosphate).

Enzymes

1. Enzymes are biological catalysts, almost all proteins. They are highly specific and work under mild conditions by lowering the activation energy.
2. Cofactor is the non-protein part, which can be a metal ion, a coenzyme (loosely bound, often a vitamin derivative) or a prosthetic group (tightly bound). Protein part: apoenzyme. Whole active enzyme: holoenzyme.
3. Competitive inhibitors resemble the substrate and bind at the active site. Non-competitive inhibitors bind elsewhere and change the shape of the active site.
4. Enzyme names usually end in -ase: sucrase (sucrose), maltase (maltose), lactase (lactose), pepsin and trypsin (proteins), amylase (starch).

Nucleic Acids

Nucleic acids are polymers of nucleotides. A nucleotide has a phosphate, a pentose sugar and a nitrogen base. Sugar plus base without phosphate is a nucleoside, joined through an N-glycosidic bond. The phosphate links C-5 of one sugar with C-3 of the next, which gives the chain a 5 to 3 direction.

1. Base pairing: A pairs with T by two hydrogen bonds, and G pairs with C by three. In RNA, A pairs with U.
2. Replication copies DNA to DNA. Transcription makes RNA from a DNA template. Translation makes protein from m-RNA on ribosomes, and a codon is a set of three bases that codes for one amino acid. The code is degenerate: 64 codons for 20 amino acids.
3. A gene is a segment of DNA with the code for one polypeptide.

Vitamins and Hormones

1. Hormones are chemical messengers made by endocrine glands. Peptide hormones: insulin, glucagon, oxytocin. Steroid hormones: testosterone, progesterone, estrogen, cortisone. Amino acid derivatives: thyroxine (contains iodine; deficiency of iodine causes goitre) and adrenaline.
2. Insulin lowers blood glucose by helping cells take up glucose and form glycogen. Glucagon does the opposite. Insulin deficiency causes diabetes.