Tutorial:Basic Chemistry Topics

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='''Substrates'''=
 
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A substrate is a compound that is acted upon by the enzyme. The substrate binds the active site of the enzyme, once bound the enzyme transfers a functional group(s) to the substrate. After the substrate has collected the functional group(s) it is released from the active site. When this occurs the substrate can go on to bind the enzymes compound of interest and transferred the acquired functional groups to it. Once the final transformation occurs the compound is either inhibited or activated by the conformational change. <ref name="substrate">Wikipedia. Wikipedia, 4 Nov. 2012. Web. 7 Nov. 2012. <http://en.wikipedia.org/wiki/Enzyme_substrate_(biology)</ref>
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='''Active Site'''=
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[[Image:Acetylation reconstruction.png| thumb | center | 400px | Acetylation Reaction <ref name="Article" />]]
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The active site of a molecule can be described as a pocket where an interaction between compounds occurs. This interaction will cause a change in structure shape. The conformational change, change in structure shape, can inhibit or activate the physiological/pathological affect. The active site is where the ligand is going to bind. (Ligands are discussed in detail in the next section labeled “Ligands”) The active site can either be inhibited or activated by ligands. Referring back to our article, the active site is where the acetylation is going to occur. In this depiction of the active site you can see the pocked where CoA will aid AAC (2’) in the acetylation of Tobramycin (Toy), the aminoglycoside antibiotic. This acetylation at the active site will cause the antibiotic to be inactive, hence inhibiting the active site. When Tobramycin becomes inactivated it is no longer able to aid in the destruction of bacteria. This is what we call antibiotic resistance.
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From the article summary you know that AAC(2’), an enzyme, has a similar fold to that of the GNAT superfamily. The GNAT fold described in the study has the function of acetylation, the addition of an acetyl group. An acetyl functional group is composed of CH3CO. It is important to note that the discovery of the GNAT fold lead to the understanding of the function of AAC(2’), because of their similar structure. The reaction centered above is the acetylation that occurs to the aminoglycoside antibiotic causing its inactivity. The Acetylation was reconstructed and modified from “Aminoglycoside 2’ –N- Acetyltransferase from Mycobacterium tuberculosis in complex with Coenzyme A and aminoglycoside substrate”, the research article we have been referencing. From this reaction you see the aminoglycoside antibiotic (Ribostamycin) being acted upon by the enzyme AAC(2’). AAC(2’) is adding and acetyl group to the antibiotic. On the right side of the arrow you can see the final product of the acetylation, the antibiotic and acyl group bound. The Acetyl group is circled, so you are able to locate it throughout the reaction. Acetylation is one of the more common reactions that occurs pathologically and physiologically.<ref name="Article" />
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<scene name='Tutorial:Basic_Chemistry_Topics/Active_site/2'>Active Site</scene>
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='''Active Site'''=
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='''Substrates'''=
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The active site of a molecule can be described as a pocket where an interaction between compounds occurs. This interaction will cause a change in structure shape. The conformational change, change in structure shape, can inhibit or activate the physiological/pathological affect. The active site is where the ligand is going to bind. (Ligands are discussed in detail in the next section labeled “Ligands”) The active site can either be inhibited or activated by ligands. Referring back to our article, the active site is where the acetylation is going to occur. In this depiction of the active site you can see the pocked where CoA will aid AAC (2’) in the acetylation of Tobramycin (Toy), the aminoglycoside antibiotic. This acetylation at the active site will cause the antibiotic to be inactive, hence inhibiting the active site. When Tobramycin becomes inactivated it is no longer able to aid in the destruction of bacteria. This is what we call antibiotic resistance.
+
A substrate is a compound that is acted upon by the enzyme. The substrate binds the active site of the enzyme, once bound the enzyme transfers a functional group(s) to the substrate. After the substrate has collected the functional group(s) it is released from the active site. When this occurs the substrate can go on to bind the enzymes compound of interest and transferred the acquired functional groups to it. Once the final transformation occurs the compound is either inhibited or activated by the conformational change. <ref name="substrate">Wikipedia. Wikipedia, 4 Nov. 2012. Web. 7 Nov. 2012. <http://en.wikipedia.org/wiki/Enzyme_substrate_(biology)</ref>
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[[Image:Acetylation reconstruction.png| thumb | center | 600px | Acetylation Reaction <ref name="Article" />]]
 +
 +
 +
From the article summary you know that AAC(2’), an enzyme, has a similar fold to that of the GNAT superfamily. The GNAT fold described in the study has the function of acetylation, the addition of an acetyl group. An acetyl functional group is composed of CH3CO. It is important to note that the discovery of the GNAT fold lead to the understanding of the function of AAC(2’), because of their similar structure. The reaction centered above is the acetylation that occurs to the aminoglycoside antibiotic causing its inactivity. The Acetylation was reconstructed and modified from “Aminoglycoside 2’ –N- Acetyltransferase from Mycobacterium tuberculosis in complex with Coenzyme A and aminoglycoside substrate”, the research article we have been referencing. From this reaction you see the aminoglycoside antibiotic (Ribostamycin) being acted upon by the enzyme AAC(2’). AAC(2’) is adding and acetyl group to the antibiotic. On the right side of the arrow you can see the final product of the acetylation, the antibiotic and acyl group bound. The Acetyl group is circled, so you are able to locate it throughout the reaction. Acetylation is one of the more common reactions that occurs pathologically and physiologically.<ref name="Article" />
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<scene name='Tutorial:Basic_Chemistry_Topics/Active_site/2'>Active Site</scene>
 
='''Ligand'''=
='''Ligand'''=

Revision as of 03:56, 8 November 2012

This tutorial is designed for High School (ages 14-19)
[1]

Purpose of the Tutorial

  • This tutorial is intended as a beneficial learning/teaching aid for an entry-level chemistry student. Applying general chemistry to a research article will allow the students to see the impact they can have on the research world in the future by applying their knowledge. This tutorial is based on learning, comprehending and applying their knowledge. Various general chemistry topics are discussed in detail for an entry-level student and then shown through various interactive representations of the compound used by the research article.


Summary: Scientific Research Article

This molecule to right is from the article "Aminoglycoside 2'-N-acetyltransferase from Mycobacterium tuberculosis-Complex with Coenzyme A and Tobramycin" published in Nature Structural Biology. [2]. The study focused on aminoglycoside 2’- N- acetyltransferase (AAC (2’)- Ic), an enzyme. An enzyme is a compound that speeds the rate of a reaction.

The scientists involved in the study determined the structure of AAC (2’)-Ic from Mycobacterium tuberculosis, a pathogen. The specific structure, protein fold, of AAC (2’)-Ic, is placed in the GCN5-related N-acetyltransferase (GNAT) superfamily. The GNAT superfamily is a group of enzymes that are similar in structure. The structure, protein fold, is important because it determines the function of a compound. Since the GNAT superfamily and AAC(2’)-Ic have a similar structures, they also have similar functions.[2]

Although the physiological function of AAC(2’)-Ic is not certain, the structure determined by the scientists allowed them to hypothesize the function. The AAC(2’)-Ic enzyme is located within the mycothiol (a component of the pathogen) structure. AAC(2’)-Ic may be capable of acetylating the aminoglycoside antibiotic. An acetylation is the addition of CH3CO group onto a compound, which in this case is the antibiotic. When this occurs the aminoglycoside antibiotic becomes inactive. The basis of this study is important because when pathogens become resistant or inactive to commonly used antibiotics, an infection that used to be easily cured can now become severe and life threatening.[2]


PDB ID 1m4d

Drag the structure with the mouse to rotate

References

  1. ↑ 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
  2. ↑ 2.0 2.1 2.2 2.3 2.4 Vetting, Matthew W., et al. "Aminoglycoside 2'-N-acetyltransferase from Mycobacterium tuberculosis-Complex with Coenzyme A and Tobramycin."Nature Structural Biology 9.9 (2002): 653-58. Print.
  3. ↑ . "File:NaF.gif." Wikipedia. Wikipedia, 17 June 2011. Web. 31 Oct. 2012.<http://en.wikipedia.org/wiki/File:NaF.gif.
  4. ↑ Maňas, Michal, trans. "File:3D model hydrogen bonds in water.jpg." Wikimedia Commons. Wikimedia Commons, 3 Dec. 2007. Web. 31 Oct. 2012 <http://commons.wikimedia.org/wiki/File:3D_model_hydrogen_bonds_in_water.jpg.
  5. ↑ Wikipedia. Wikipedia, 4 Nov. 2012. Web. 7 Nov. 2012. <http://en.wikipedia.org/wiki/Enzyme_substrate_(biology)

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