Unit 27: Biochemistry — Short Questions

Glycogen, also called 'animal starch', is a highly branched polysaccharide of glucose (structurally similar to amylopectin but even more branched) that is stored in the liver and muscles. It serves as the body's short-term glucose/energy reserve: when blood glucose is in excess it is converted into glycogen for storage, and when blood glucose falls it is broken down to release glucose for energy, supporting sustained muscular activity.

Glucose is an aldohexose — it carries an aldehyde (–CHO) functional group at C1 and forms a six-membered pyranose ring. Fructose is a ketohexose — it carries a ketone (C=O) functional group at C2 and forms a five-membered furanose ring.

Cellulose is made of long, unbranched chains of glucose units (up to 2500) linked by glycosidic bonds, which hydrogen-bond strongly with each other, making cellulose rigid and water-insoluble — a structural material. Starch is made of two components: amylose, a long unbranched chain, and amylopectin, a compact, highly branched structure; amylopectin is water-soluble while amylose is insoluble, and together they form plants' energy-storage polysaccharide rather than a structural one.

In competitive (reversible) inhibition the inhibitor has a shape resembling the substrate and directly competes with it for binding at the enzyme's active site; its effect can be reduced by increasing substrate concentration. In non-competitive (irreversible) inhibition the inhibitor binds elsewhere on the enzyme and changes the shape of the active site so the substrate can no longer bind at all; this permanently destroys enzymatic activity and is not reversed by adding more substrate.

Glycolipids are lipids with a carbohydrate (sugar) group attached, mostly found in nervous tissue. Lipoproteins are complexes of lipids combined with proteins (not carbohydrates) that transport hydrophobic lipids such as cholesterol and triglycerides in the bloodstream.

The glycosidic linkage (bond C–O–C) occurs in carbohydrates. It is formed by a condensation reaction between the hydroxyl group of one monosaccharide and the hydrogen of another, releasing water, and joins monosaccharide units into disaccharides (e.g. sucrose) and polysaccharides (e.g. starch, cellulose, glycogen), giving these molecules their chain/branch structure.

The peptide linkage occurs in proteins. It is an amide bond formed when the –COO⁻ group of one amino acid reacts with the –NH₃⁺ group of the adjacent amino acid (releasing water), joining amino acids into long polypeptide chains whose sequence (primary structure) ultimately determines the protein's folded shape and function.

The ester linkage occurs in lipids. It forms between the carboxyl group of a fatty acid and the hydroxyl group of an alcohol (e.g. glycerol, or a long-chain alcohol in waxes), joining fatty acids to alcohols to build triglycerides (fats/oils) and waxes, which function as energy stores, insulation and protective coatings.

The phosphodiester linkage occurs in nucleic acids (DNA and RNA). It is a strong covalent bond joining the 3' carbon of one nucleotide's sugar to the phosphate group on the 5' carbon of the next nucleotide's sugar, building the sugar-phosphate backbone of the polynucleotide chain and giving it strength and stability.

The tertiary structure forms when a polypeptide chain (already folded into secondary structures such as α-helices or β-pleated sheets) folds further into an overall three-dimensional shape. This folding is driven by interactions between amino acid side chains (R-groups) — hydrogen bonds, ionic bonds, hydrophobic interactions, and disulphide bridges — causing the chain to twist and bend, often producing a globular protein whose precise shape (e.g. an enzyme's active site) determines its biological function.

Both fats and oils are triglycerides (esters of glycerol with three fatty acids), but fats are made from saturated fatty acids and are solid at room temperature, while oils are made from unsaturated fatty acids (containing one or more double bonds) and are liquid at room temperature.

Steroids are lipid-like compounds (though not formed from fatty acids) built around a steroid nucleus of three fused cyclohexane rings (A, B, C) and one fused cyclopentane ring (D). Many steroids carry an –OH group, placing them in the sterol class (e.g. cholesterol). Cholesterol, as a sterol, is a component of biological membranes and is also the precursor from which the body makes steroid hormones, bile salts and vitamin D — functions reflected in its classification alongside bile salts, vitamin D and steroid hormones as biologically important steroids.

An enzyme has a special region on its surface called the active site. Due to random molecular movement, a substrate molecule enters and binds to the active site, forming a temporary enzyme–substrate complex. Within this complex the substrate is converted into product(s); the product(s) are then released and the enzyme is left unchanged, free to bind another substrate molecule. This is explained by Emil Fischer's 1894 lock-and-key model, in which the enzyme is the lock and the substrate is the key — only a correctly shaped substrate fits into the active site of the enzyme.

Enzymes are highly specific because their active site has a unique three-dimensional shape that allows only a substrate with a matching, complementary shape to fit into it, as in the lock-and-key model. A substrate with a different shape cannot bind at the active site, so the enzyme cannot act on it.

There are three major types of RNA. Messenger RNA (mRNA) carries the genetic blueprint copied from DNA in the nucleus to the ribosomes. Ribosomal RNA (rRNA) helps make up the structure of the ribosome, where protein synthesis occurs. Transfer RNA (tRNA) translates the nucleotide sequence of mRNA into the corresponding sequence of amino acids, delivering the correct amino acid during protein synthesis.

Enzyme inhibitors help regulate biochemical pathways and are widely exploited as medicines and poisons. Competitive (reversible) inhibitors, which resemble the substrate, can be used in medicine to deliberately slow down a specific enzyme's activity in a controlled way. Non-competitive (irreversible) inhibitors permanently block an enzyme's active site and include antibiotics, anti-metabolites, and some drugs and poisons; for example, penicillin irreversibly inhibits the enzyme trans-peptidase, which bacteria need to build their cell wall, so blocking this enzyme kills the bacteria. This shows how understanding inhibition allows the design of antibiotics and other targeted drugs.

Pepsin works in the stomach, where gastric juice (containing HCl) keeps the environment strongly acidic, around pH 2. Since every enzyme has an optimum pH at which its active site retains the correct shape for maximum activity, pepsin's optimum pH matches the naturally acidic environment it operates in; away from pH 2 its structure is disturbed and its activity falls.

Both are condensation (dehydration) reactions that build polymers while releasing a water molecule at each new bond. In sugars, the –OH group of one monosaccharide combines with a hydrogen from another monosaccharide to form a glycosidic bond (C–O–C), releasing H₂O and joining the units into di-/polysaccharides. In amino acids, the –COO⁻ group of one amino acid combines with the –NH₃⁺ group of the next to form a peptide (amide) bond, again releasing H₂O and joining the units into polypeptide chains. In both cases, monomers are linked one after another through loss of water to build a long polymer chain.

Cholesterol is a steroid, and although steroids are not formed from fatty acids like other lipids, they share lipid-like properties: cholesterol is hydrophobic and insoluble in water but soluble in organic solvents, consistent with the general character of lipids. For this reason steroids such as cholesterol are grouped with lipids as 'derived or associated lipids'.

Fats and oils (triglycerides) are esters formed from one molecule of glycerol (which has three –OH groups) and three fatty acid molecules. Each fatty acid attaches to glycerol as an acyl group through an ester bond, so with three acyl groups attached to the glycerol backbone, the molecule is correctly named a triacylglycerol.

Hydrogen bonds between complementary nitrogenous bases on the two polynucleotide strands (2 bonds between A and T, 3 bonds between G and C) hold the two strands of DNA together across the double helix. Although each individual hydrogen bond is weak, the very large number of them along the length of the molecule gives the double helix overall stability, while still being weak enough that the strands can be separated when needed for processes like replication and transcription.

Using complementary base pairing (A pairs with T, G pairs with C), the opposite strand reads: A-T-G-G-C-T.