Enzyme Reactions and DNA/RNA Structure: A Detailed Analysis

Posted on Dec 20, 2024 in Biology

Enzyme Reactions: Key Processes in Metabolism

Enzyme reactions are chemical conjugates in metabolism, involving very low concentrations and accelerating reactions involved with decreasing activation energy. They are water-soluble globular proteins that are well in the diffusion of organic liquids. They can act at intracellular and extracellular levels (where they are secreted).

Chemical Nature

Enzymes can be shaped by one or more polypeptide chains, denominated solely as protein enzymes, or a part of the polypeptide fraction (apoenzyme) can take a fraction that could not be a prosthetic group (if the union is permanent) or a cofactor (if not). The nature of cofactors is diverse and can be metallic cations (governing the activation of the apoenzyme) or complex organic molecules (coenzyme). The latter enzyme is called a holoenzyme.

Allosteric Enzymes

Allosteric enzymes are those that can take two stable forms: an active conformation of the enzyme and an inactive conformation. These enzymes, besides the active site, have a center to which a regulator can bind a specific substance (ligand). Often, a single conformation presents affinity; in those cases, the presence of the ligand determines the conformation, called allosteric transition. There are two types depending on whether the ligand-induced conformation favors activators or inhibitors.

Watson and Crick Model of DNA

The Watson and Crick model, which supports a set of experimental data on this molecule, shows that the structure of DNA presents the following characteristics:

  1. The DNA molecule forms a double helix of 2nm in diameter, consisting of two chains of polynucleotides wrapped around an imaginary axis.
  2. The nitrogenous bases are inside, in the same plane, and their rings are parallel to each other and perpendicular to the axis of the double helix.
  3. The polynucleotide chains are antiparallel; that is, they are in opposite directions: if one has a 5′ to 3′ position, the other has 3′ to 5′.
  4. The sequence of bases is complementary, as there is a correspondence between the bases of the two chains: A can only be in front of T, and C in front of G. This correspondence causes the chains to have complementary sequences. The union between bases is produced by hydrogen bridges: two in A-T and three in C-G. Therefore, the latter is the strongest link in the chain; hence, DNA with more C-G effects will be more stable to temperature and denaturing.
  5. The winding of the double helix is dextrorotatory and plectonemic; that is, to separate the strings, it is necessary to unwind them.
  6. Each pair of nucleotides is separated from the next by 0.34nm, and each turn consists of 10 pairs of nucleotides; this is a longitude of 3.4 nm per turn.

Differences Between DNA and RNA

The pentose in DNA is deoxyribose, and in RNA, it is ribose. In RNA, there is uracil instead of thymine. DNA has a double-stranded structure, except in some single-stranded viruses. RNA is the opposite. In terms of structural complexity levels, prokaryotes have primary and secondary structures, and eukaryotes also have other complex levels (nucleosome, beads on a string, chromatin fiber, structural domains, rosettes, etc.). mRNA only has a primary structure, and tRNA and rRNA have primary, secondary, and tertiary structures. The function of DNA is to store genetic information, transcription, and replication. The function of the different types of RNA is diverse.

Chemical Nature and Structure of RNA

RNA is composed of ribose, the nucleotide bases guanine, cytosine, adenine, and uracil. These ribonucleotides are linked together by 5′ to 3′ phosphodiester bonds, as in DNA. RNA is almost always single-stranded, except in some viruses where it is double-stranded.

Types and Functions of RNA

  • Messenger RNA (mRNA): Transports genetic information from the nucleus to the cytoplasm for protein synthesis.
  • Ribosomal RNA (rRNA): Forms part of the ribosome structure and contributes to these grooves or ribbed sites capable of housing mRNA and tRNA amino acids bound to participate in the synthesis of an amino acid polypeptide chain.
  • Transfer RNA (tRNA): Transports amino acids from the cytoplasm to the ribosome during the translation process, that is, during protein synthesis. There are many secondary structures of tRNA, but all of them present certain characteristics that are kept in all of them:
    • 5′ end: Contains a guanine nucleotide with a free phosphate.
    • Contains a loop or D-arm; the sequence is recognized in a specific way by one of the 20 enzymes called aminoacyl-tRNA synthetases, in charge of joining each amino acid with its corresponding tRNA molecule.
    • 3′ end: Has a CCA sequence.
    • TΨC loop or arm: Acts as a recognition site for ribosomes.
    • Long arm of the boomerang: Contains a sequence of three bases called the anticodon. Each tRNA with its corresponding amino acid is linked via the anticodon with an mRNA triplet of bases (triplet or codon) in the translation.