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An amine group is a nitrogen atom bonded in such a way as to have a pair of nonbonded valence electrons For our purposes, you can think of an amine as a
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B i o p h y s i C s D e mys tifie D
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Secondary amine
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Figure 7-5 An amine group is a nitrogen atom with a pair of nonbonded valence electrons The amines that concern us most are primary and secondary amines which have two and one hydrogen atom, respectively
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nitrogen atom that has three single covalent bonds to three other atoms Typically two of the other atoms are hydrogen, while the third atom is a carbon atom linking the amine group to the rest of the molecule This is called a primary amine, because it has one connection to the rest of the molecule See Fig 7-5 A secondary amine has only one hydrogen atom attached and two covalent bonds to the rest of the molecule Tertiary amines exist but are less common In a tertiary amine the nitrogen has three connections to the rest of the molecule, with no hydrogen atoms directly connected to the nitrogen Amine groups are polar with a slightly negative charge on the nitrogen atom and (for primary and secondary amines) a slightly positive charge on the hydrogen atoms Amines can participate in hydrogen bonding, on either the positive or negative side of the bond One amine group can thus participate in up to three hydrogen bonds at once Amines can form positive ions by covalently binding to an extra hydrogen atom without its electron (ie, by covalently + bonding to a proton) Thus, when ionized, we have NH3 for a primary amine + + ion, NH2 for a secondary amine ion, and NH for a tertiary amine ion
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A phosphate group is a phosphorous atom with four oxygen atoms attached One oxygen atom always shares a double bond with the phosphorous The remaining three oxygen atoms either are covalently bonded to the rest of the molecule or are part of hydroxyl groups Figure 7-6 shows a phosphate group with only one oxygen atom connecting it to the rest of the molecule Thus two of the four oxygen atoms are part of hydroxyl groups Phosphate groups are highly polar and so can form hydrogen bonds, as we
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7 B i o m o l e C u l e s 1 0 1
Figure 7-6 A phosphate group is a phosphorous atom with four oxygen atoms attached One oxygen atom always shares a double bond with the phosphorous The remaining three oxygen atoms either are covalently bonded to the rest of the molecule or are part of hydroxyl groups
saw with the other functional groups discussed Phosphate groups also easily form negative ions by losing the hydrogen atom from one or both of its hydroxyl groups
Acids, Bases, and pH
Aqueous solutions always contain some hydrogen ions (H+) and hydroxyl ions (OH ) Since a hydrogen atom is just one proton and one electron, a hydrogen cation (H+) is really just a proton in solution Molecules or functional groups that increase the concentration of protons in solution are called acids Those that decrease the concentration of protons are called bases For example, amines easily bind protons (because of their nonbonded valence electrons) Binding protons reduces the proton concentration in solution, and so amines are considered basic Phosphates easily release protons and so phosphates are considered acidic Sometimes bases decrease the concentration of protons by increasing the concentration of hydroxyl ions (OH ) The hydroxyl ions bind to protons and thereby decrease the concentration of protons We measure the concentration of protons in units of pH (pronounced peeaych ) The pH is approximately equal to the negative base-ten logarithm of the proton concentration A pH of 7 means H+ is at a concentration of 10 7 moles per liter Pure water has a pH of 7 and is considered neutral A pH less than 7 means a higher concentration of H+ (eg, pH = 3 means 10 3 moles per liter which is greater than 10 7 moles per liter) Acidic substances (those that increase H+) therefore lower the pH, whereas bases increase pH Since water, with a pH of 7, is considered neutral, measurement of pH is considered to range from pH = 0 for the most acidic substances to pH = 14 for the most basic substances
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