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='''Amino Acids'''=
='''Amino Acids'''=


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)
Amino acids are the building blocks of proteins. There are 20 common amino acids. The basic structure of an amino acid is an 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 categorized. They are categorized as polar, non-polar, acidic or basic. Amino acids are commonly referred to using their three-letter abbreviation. I have provided the three-letter abbreviations along side the amino acids in their category list. When an amino acid is considered polar that means that the charges electronegativity between atoms in the functional group are extremely different. For example, water is considered polar. This is because the electronegativity of oxygen is extremely high and the electronegativity of hydrogen is extremely low. The opposing electronegativity is making water polar. In contrast, non-polar is when the electronegativity of the atoms in the functional group are similar. An amino acid is considered polar when it has an acidic functional group, such as a carboxylic acid (pH~1-6). In correlation, a basic amino acid has a basic functional group, such as an amine group (pH~8-14). An amino acid is neutral when it has a functional group that displays a pH close to physiological pH (~7). A list of the most common amino acids and their categories are as follows for your reference.
Neutral Amino Acids:
Alanine (ala)
Asparagine (asn)
Cysteine (cyc)
Glutamine (gln)
Glycine (gly)
Isoleucine (ile)
Leucine (leu)
Methionine (met)
Phenylalanine (phe)
Proline (pro)
Serine (ser)
Threonine (thr)
Tryptophan (trp)
Tyrosine (tyr)
Valine (val)
Acidic amino acids:
Aspartic acid (asp)
Glutamic acid (glu)
Basic Amino acids:
Arginine (arg)
Histidine (his)
Lysine (lys)
Polar Amino acids:
Arginine (arg)
Asparagine (asn)
Aspartic acid (asp)
Cysteine (cyc)
Glutamic Acid (glu)
Glutamine (gln)
Histidine (his)
Lysine (lys)
Serine (ser)
Threonine (thr)
Tryptophan (trp)
Tyrosine (tyr)
Non-polar amino acids:
Alanine (ala)
Glycine (gly)
Isoleucine (ile)
Leucine (leu)
Methionine (met)
Phenylalanine (phe)
Proline (pro)
Valine (val)
There are 8 different amino acids present in the research article main compound.
 


==CoA Amino Acids==
==CoA Amino Acids==


In this representation it displays the covalent bond between CoA and Arginine 124. Arginine is displayed as the pink molecule and CoA is displayed as the orange and red molecule. Arginine classified as a basic amino acid and is a nonessential alpha amino acid, meaning that can be synthesized by the human body.  
Coenzyme A (CoA) has seven amino acids bound to it. The amino acids consist of two arginine, one glycine, and four valine’s.
Val96 and CoA are bound by a hydrogen bond, clearly displayed in this representation.
Arginine is a basic amino acid and is a nonessential A nonessential amino acid is an amino acid that can be synthesized by the body, so it is not essential that you obtain the amino acid form another source. Glycine is a non-polar, basic amino acid. It is also the smallest common amino acid. The functional group attached is hydrogen. Valine is also categorized as a nonpolar, basic amino acid. Valine is nonpolar and basic because the functional group consists of two methyl groups.
CoA and Arg124
CoA and Gly92
CoA and Val96  
CoA and Val86
CoA and Val94
CoA and Val84
 


==Tobramycin Amino Acids==
==Tobramycin Amino Acids==
Tobramycin has four amino acids bound to it. There are two aspartic acid, a serine, and a tryptophan.
Asp35
Trp181
Ser117
Asp152


==PAP Amino Acids==
==PAP Amino Acids==
PAP has four amino acids bound to it. There are two histidine’s and a tryptophan.
His54
Trp90
His55


This shows His54 bound to  bound through a hydrogen bond.
*References:
The other Amino acid bound to PAP with a hydrogen bond is tcp


<Vetting, M. W., et al. "Aminoglycoside 2'-N-acetyltransferase from Mycobacterium tuberculosis-Complex with Coenzyme A and Tobramycin." RCSB Protien DataBase. N.p., 28 Aug.2002. Web. 13 July 2011. <http://www.rcsb.org/pdb/explore/explore.do?structureId=1M4D>.>


*References:
http://www.elmhurst.edu/~chm/vchembook/561aminostructure.html
<Vetting, M. W., et al. "Aminoglycoside 2'-N-acetyltransferase from Mycobacterium tuberculosis-Complex with Coenzyme A and Tobramycin." RCSB Protien DataBase. N.p., 28 Aug.2002. Web. 13 July 2011. <http://www.rcsb.org/pdb/explore/explore.do?structureId=1M4D>.>
</StructureSection>
</StructureSection>
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