BIOLOGICAL MOLECULES

The 5' cap and the 3' poly-A tail are not translated. Their primary roles are to increase the stability of the mRNA by protecting its ends from ribonucleases, and to facilitate the initiation of translation by interacting with translation initiation factors.

The 2'-OH group in the ribose sugar of RNA is reactive. It can act as a nucleophile and attack the adjacent phosphodiester bond under alkaline conditions, leading to the self-hydrolysis (cleavage) of the RNA strand. DNA, lacking this 2'-OH, is far more chemically stable.

Many enzymes require metal ions (like Mg²⁺, Ca²⁺) as activators or cofactors. EDTA chelates (binds tightly to) these divalent cations, making them unavailable to the enzyme. This effectively inhibits the enzyme's activity. Adding back an excess of the metal ion reverses the inhibition.

Bile salts are amphipathic cholesterol derivatives secreted from the liver. Their hydrophobic side associates with lipid droplets, and their hydrophilic side faces the aqueous intestinal fluid. This coating breaks large globules into smaller ones (micelles), vastly increasing the surface area for lipase action.

With 20 different amino acids as monomers, the number of possible sequences and lengths for a polypeptide is astronomically large. Furthermore, the diverse chemical properties of the 20 R-groups (charged, polar, non-polar, etc.) enable a protein to fold into an immense variety of complex 3D shapes.

The nitrogenous bases in double-stranded DNA are stacked and have a lower absorbance. When the double helix is denatured into two random, single-stranded coils, the bases become unstacked. This unstacking increases their absorbance of UV light at 260 nm, a phenomenon known as the hyperchromic effect.

Specificity is the ability of an enzyme to choose exactly one substrate from a pool of similar molecules. This is due to the exact complementary fit and specific chemical interactions (ionic, H-bonding, hydrophobic) between the substrate and the R-groups lining the active site.

In covalent catalysis, a powerful nucleophilic R-group in the active site (e.g., the -SH of cysteine or -OH of serine) forms a transient covalent bond with the substrate. This acyl-enzyme intermediate is then resolved by another step, releasing the product and regenerating the free enzyme.

Allosteric regulation is mediated by modulator molecules that bind to a site (allosteric site) physically distinct from the active site. This binding causes a conformational change that can either increase (allosteric activator) or decrease (allosteric inhibitor) the activity of the enzyme at its active site.

The definition of competitive inhibition is a "competition" for the active site. At a high enough concentration, the substrate out-competes the inhibitor for the active site, so all enzyme molecules can still bind substrate and reach Vmax. The apparent Km is increased, but Vmax is ultimately unchanged.

The amino-terminal ends of both the light (VL) and heavy (VH) chains form the antigen-binding site. These variable domains have highly diverse amino acid sequences from one antibody clone to another, creating a unique 3D surface that is specific for a single epitope.

Saponification is the base-catalyzed hydrolysis of the ester bonds in a fat or oil. This reaction cleaves the triglyceride, producing glycerol and the salts of the fatty acids (soaps). Lipases perform an analogous enzymatic hydrolysis.

Kinases are a class of transferase enzymes that catalyze the transfer of a γ-phosphate group from a high-energy donor molecule like ATP to a specific substrate. Protein kinases phosphorylate specific serine, threonine, or tyrosine residues on target enzymes, regulating their activity. Phosphatases reverse this.

When glucose forms a ring, carbon 1 becomes an asymmetric carbon (the anomeric carbon). In the α-anomer, the -OH on C1 is below the plane of the ring (trans to the CH2OH at C5). In the β-anomer, the -OH is above the plane of the ring (cis to the CH2OH).

Amylose is a linear polymer of glucose with α-1,4 linkages. Amylopectin is a much larger, branched polymer that has both α-1,4 linkages in the straight chain and α-1,6 glycosidic bonds at the branch points approximately every 24-30 glucose units.

On a double-reciprocal plot, a non-competitive inhibitor produces a line that intersects the control line at the x-axis (Km is unchanged), but has a steeper slope and a higher y-intercept (Vmax is decreased). It reduces the number of functional enzyme molecules.

A competitive inhibitor competes for the active site, effectively making it harder for the enzyme to bind its substrate. More substrate is required to reach half the maximum velocity. Therefore, the apparent Km (substrate concentration at 1/2 Vmax) is increased in the presence of a competitive inhibitor.

tRNA acts as an adaptor, carrying a specific amino acid at its 3' end and recognizing a specific three-nucleotide codon on the mRNA through its complementary anticodon loop. This bridges the genetic code and the amino acid sequence of a protein.

The glycosidic bond in sucrose is formed between the anomeric carbon (C1) of glucose and the anomeric carbon (C2) of fructose. Since neither carbonyl group is free to open into an aldehyde or ketone form, sucrose cannot reduce Cu²⁺ and is thus a non-reducing sugar.