Tutorial:Basic Chemistry Topics: Difference between revisions

There are 3 common types of bonds. A hydrogen bond, covalent bonds, or an ionic bond. The strongest bond is a covalent bond followed by the ionic bond, leaving the weakest bond to be the hydrogen bond. Covalent bonds, the strongest type of bond, they involves the sharing of electrons between two molecules. An example of a covalent bond is hydrochloric acid or HCl. The electrons are being shared between the chlorine atom (Cl) and the hydrogen atom (H). An ionic bond is an attraction between two molecules of opposite charge. The opposite charges I am referring to are a positive (+) and a negative charge (-). A positively charged atom is referred to as a cation, and a negatively charged atom is referred to as an anion. Hydrogen Bonds, the weakest of bonds, are attractive interactions (dipole-dipole) between an electronegative atom and hydrogen. Electronegative atoms are atoms that have high electron density. They are strong atoms that pull electrons towards then from weaker/low electron density atoms, such as hydrogen. When the electronegative atom pulls the electrons it leaves the other atom with a slight positive charge.  The most common example of hydrogen bonding is water. The water molecule chemical formula is H2O. The highly electronegative oxygen pulls the hydrogen closer by attracting hydrogen’s electrons allowing the formation of a water droplet. The electronegative atoms allow for the droplet to be held together instead of spreading. The hydrogen bonds in this picture are displayed as yellow dashed lines. The hydrogen bonds in this molecule are important to the secondary structures providing the stability of the atoms orientation.  

Secondary structures are alpha helices and beta sheets. They help contribute to the stability of the molecule. The alpha helices are represented with pink arrows and the beta strands are represented with yellow arrows. This molecule has approximately four alpha helices and two beta strands, when presented as a monomer. Since this structure is represented as a dimer you actually have eight alpha helices and four beta sheets. The concept of a dimer is explained in the "Ligands" section later on in the tutorial. Alpha helices rotate in a clockwise manner and are also oriented in a parallel formation. The parallel alpha helices are held together by hydrogen bond, which we discussed earlier. Beta sheets are often anti-parallel. The structure of the alpha and beta sheets in Tuberculosis/CoA/Tobramycin structure represents the GNAT fold. The folding of a protein is what gives the function. When you have a change in the folding you have a change in the function.  The GNAT fold described in the study has a function of acetylation. Acetylation is the addition of an acyl group. The chemical formula of an acetyl group is COCH3. It is important to note that the discovery of the GNAT fold lead to the understanding of the major function.  

The active site of a molecule can be described as a pocket where interaction between structures causes a desired effect. This is a good representation of the active site. The active site is where the substrate, in this case tobramycin, binds to CoA and the mycobacterium to cause an antibacterial effect. It the study described this is where the acetylation of the mycothiol should be occurring.  

Ligands are molecules or complexes that are within the secondary structures that orient in such a way to contribute the function of the complex as a whole. Ligands can have binding sites on receptors, and when bound can trigger a physiological response. A ligand can be a competitive agonist, allosteric agonist, competitive antagonist, or an allosteric antagonist. An agonist is a ligand that causes a physiological response, activating the active site. An antagonist is a ligand that inhibits a physiological response, not allowing the active site to be activated. When a ligand is competitive that means that the ligand is binding to the same site as the physiological activator, hence it is competing for the same site. When a ligand binds to an allosteric site, the ligand is binding to the same receptor but it is not binding to the active site. The ligands present in the complex used by the research article are coenzyme A, Tobramycin and Phosphate-Adenosine-5'-Diphosphate.

==Coenzyme A==

Amino acids are the building blocks of proteins. There are 20 common amino acids. The contain and amine group (-NH2), a carboxylic acid group (-COOH) and a functional group specific to each amino acid. The functional group determines how the amino acid is classified. They are categorized as either, polar, non-polar, acidic or basic. There are 8 different amino acids present in the <scene name='Sandbox_reserved_392/Original_untouched_molecule/1'>Tobramycin-CoA molecule</scene>. CoA has a combination of 7 amino acids bound to it. The amino acids are two Arginine (basic amino acid), one Glycine (polar amino acid), and  four Valine (non-polar amino acid). PAP has four amino acids bound to it, two Histidine and two tryptophan (non-polar amino acid). Tobramycin also has four amino acids bound to it, two aspartic acid (acidic amino acid)), Serine (polar amino acid) and tryptophan (non-polar amino acid)