Tutorial:Basic Chemistry Topics: Difference between revisions

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An Example of a pH scale is located above. A pH scale ranges from 1-14, 1 being the most acidic and 14 being the most basic. An acidic pH has a value below 7, a basic pH is greater than 7, and a pH of 7 is considered neutral (ex: water). Some common acidic functional groups are alcohols (OH) and carboxylic acids (-COOH). An example of a basic functional group would be an amine (-NH2).  
An Example of a pH scale is located above. A pH scale ranges from 1-14, 1 being the most acidic and 14 being the most basic. An acidic pH has a value below 7, a basic pH is greater than 7, and a pH of 7 is considered neutral (ex: water). Some common acidic functional groups are alcohols (OH) and carboxylic acids (-COOH). An example of a basic functional group would be an amine (-NH2).  


You can predict if an amino acid will be acidic or basic according to its structure. For example, <scene name='Tutorial:Basic_Chemistry_Topics/Glu/1'>glutamic acid</scene> contains a carboxylic acid functional group, which was stated previously to be an acidic functional group that lowers the pH of the amino acid. On the other hand, <scene name='Tutorial:Basic_Chemistry_Topics/Arg/1'>arginine</scene> is classified as a basic amino acid. The functional group of arginine contains a guanidine group. A guanidine group contains amine groups, increasing the pH of the amino acid.  
You can predict if an amino acid will be acidic or basic according to its structure. For example, <scene name='Tutorial:Basic_Chemistry_Topics/Glu/1'>glutamic acid</scene> contains a carboxylic acid functional group, which was stated previously to be an acidic functional group that lowers the pH of the amino acid. On the other hand, <scene name='Tutorial:Basic_Chemistry_Topics/Arg/1'>arginine</scene> is classified as a basic amino acid. The functional group of arginine contains a guanidine group. A guanidine group contains amine groups, which increase the pH of the amino acid.  


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[[Image:Ionic bond.png| thumb | center | 400px | Ionic Bonding<ref>. "File:NaF.gif." Wikipedia. Wikipedia, 17 June 2011. Web. 31 Oct. 2012.<http://en.wikipedia.org/wiki/File:NaF.gif.</ref>]]
[[Image:Ionic bond.png| thumb | center | 400px | Ionic Bonding<ref>. "File:NaF.gif." Wikipedia. Wikipedia, 17 June 2011. Web. 31 Oct. 2012.<http://en.wikipedia.org/wiki/File:NaF.gif.</ref>]]


An ionic bond occurs when an electron(s) is transferred from one atom to another due to the opposite charges of the atoms. The positively charged cation is attracted to the negatively charged anion. In the image to the right, you see an anion, Fluorine (F) and the cation, Sodium (Na). The double-sided arrow between them is representation of their attractive force. Fluorine has a higher electronegativity than sodium. As we discussed previously, when an atom has higher electronegativity it pulls electrons from the lower electronegative atom, in this case sodium. The transfer of the sodium electron (blue) is shown using an arrow.  
An ionic bond occurs when an electron(s) is transferred from one atom to another to become more stable with a full electron shell. The charges result from the transfer of an electron. The positively charged cation is attracted to the negatively charged anion. In the image to the right, you see an anion, Fluoride (F-) and the cation, Sodium (Na+). The double-sided arrow between them is representation of their attractive force. Fluorine has a higher electronegativity than sodium. As we discussed previously, when an atom has higher electronegativity it pulls electrons from the lower electronegative atom, in this case sodium. The transfer of the sodium electron (blue) is shown using an arrow.  


This representation highlights an <scene name='Tutorial:Basic_Chemistry_Topics/New_ionic_bond/1'>ionic interaction</scene> between tobramycin and aspartic acid (Asp). The nitrogen on tobramycin has a (+) positive charge and aspartic acid has a (-) negative charge. The opposing charges are attracted to each other forming an ionic bond, holding the compounds in close proximity.  
Tobramycin and aspartic acid form an <scene name='Tutorial:Basic_Chemistry_Topics/New_ionic_bond/1'>ionic bond</scene> in this representation. The nitrogen on tobramycin has a (+) positive charge and aspartic acid has a (-) negative charge. The opposing charges are attracted to each other forming an ionic bond, holding the compounds in close proximity.  


==Hydrogen Bonds==
==Hydrogen Bonds==
[[Image:3D hydrogen Bonding.jpg | thumb | left | 200px | Hydrogen Bonding<ref>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.</ref>]]
[[Image:3D hydrogen Bonding.jpg | thumb | left | 200px | Hydrogen Bonding<ref>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.</ref>]]


The weakest bond discussed here, the hydrogen bond is an attractive interaction between an electronegative atom and hydrogen. When the electronegative atom pulls the electrons, it leaves the other atom with a slightly positive charge. A common example of this is water. The image to the right demonstrates the hydrogen bonding of water. The highly electronegative oxygen pulls the hydrogen closer by attracting hydrogen’s electrons. When oxygen pulls the electrons, it leaves hydrogen with a slight positive charge. Since oxygen is pulling the hydrogen’s inward, the formation of a water droplet is possible. In this representation the <scene name='Tutorial:Basic_Chemistry_Topics/Hydrogen_bonds/2'>hydrogen bonds</scene> are represented as yellow-dashed lines. The hydrogen bonds are important to the compound used by the study because they offer stability to the secondary structures.  
The weakest bond discussed here, the hydrogen bond is an attractive intermolecular attraction between an electronegative atom and hydrogen. When the electronegative atom pulls the electrons, it leaves the other atom with a slightly positive charge. A common example of this is water. The image to the right demonstrates the hydrogen bonding of water. The highly electronegative oxygen pulls the hydrogen closer by attracting hydrogen’s electrons. When oxygen pulls the electrons, it leaves hydrogen with a slight positive charge. Since oxygen is pulling the hydrogen’s inward, the formation of a water droplet is possible. In this representation the <scene name='Tutorial:Basic_Chemistry_Topics/Hydrogen_bonds/2'>hydrogen bonds</scene> are represented as yellow-dashed lines. The hydrogen bonds are important to the compound used by the study because they offer stability to the secondary structures.  




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