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Water as a Solvent
Water dissolves many substances by surrounding charged particles and "pulling" them into solution. For example, common table salt, sodium chloride, is an ionic substance that contains alternating sodium and chlorine ions
is an ionic substance that contains alternating sodium and chlorine ions. When table salt is added to water, the partial charges on the water molecule are attracted to the Na+ and Cl
the Na
and Cl‐ ions.
ions The water molecules work their way into the crystal
The water molecules work their way into the crystal structure and between structure and between
the individual ions, surrounding them and slowly dissolving the salt. The water molecules will actually line up differently depending on which ions are being pulled into solution. The negative oxygen ends of water molecules will surround the positive sodium ions; the positive hydrogen
oxygen ends of water molecules will surround the positive sodium ions; the positive hydrogen ends will surround the negative chlorine ions.
Water as a Solvent
In a similar fashion, any substance that carries a net electrical charge incl ding both ionic
a net electrical charge, including both ionic compounds and polar covalent molecules
(those that have a dipole), can dissolve in p
y
water. This idea also explains why some substances do not dissolve in water. Oil, for example is a nonpolar molecule Because
example, is a nonpolar molecule. Because there is no net electrical charge across an oil molecule it is not attracted to water
molecule, it is not attracted to water molecules and therefore does not dissolve in water.
Hydrogen Bond
The Base Pairing Principle is: Complementary base pairs are: adenine and thymine (A ‐ T ), guanine and cytosine (G ‐ C)
The base pairing is called complementary because there are specific geometry
The base pairing is called complementary because there are specific geometry requirements in the formation of hydrogen bonds between the heterocylic amines. Heterocyclic amine base pairing is an application of the hydrogen bonding principle. Notice that the thymine ‐ adenine pair interacts through two hydrogen bonds represented as (T=A) and that the cytosine‐guanine pair interacts through three hydrogen bonds represented as (C=G)
interacts through three hydrogen bonds represented as (C=G).
Micelles
•An aggregate of amphipathic molecules in water, with the nonpolar portions •An
aggregate of amphipathic molecules in water with the nonpolar portions
(hydrophobic single tail regions) in the interior and the polar portions (hydrophilic
"head" regions )at the exterior surface, exposed to water.
•Micelles are approximately spherical in shape. Other phases, including shapes such as ellipsoids, cylinders, and bilayers are also possible. The shape and size of a micelle is a function of the molecular geometry of its surfactant molecules and g
y
solution conditions such as surfactant concentration, temperature, pH, and ionic strength. Cell Membrane
Chirality
chiral molecule is a type of molecule that lacks an internal plane of symmetry and has a non
and has a non‐superimposable
superimposable mirror image. The feature mirror image The feature
that is most often the cause of chirality in molecules is the presence of an asymmetric carbon atom.
Chirality
Achiral (not chiral) objects are objects that are identical to their mirror image. Human hands are perhaps the most universally recognized example of chirality: The left hand is a non superposable mirror image of the right of chirality: The left hand is a non‐superposable
mirror image of the right
hand; no matter how the two hands are oriented, it is impossible for all the major features of both hands to coincide. This difference in symmetry becomes obvious if someone attempts to shake the right hand of a person using his left hand, or if a left‐handed glove is placed on a right hand. The term chirality is derived from the Greek word for hand. It is a mathematical term chirality
is derived from the Greek word for hand It is a mathematical
approach to the concept of "handedness“..
(S)-Alanine (left,L) and (R, S)-alanine (right) in
zwitterionic form at neutral pH
CHIRAL OR OPTICAL ISOMERS
Some chemical compounds have optical activity in the sense that these compounds have the ability to rotate the plane of polarized light. P l i d li h h li h
Polarized light has light waves all traveling parallel to each other. ll
li
ll l
h h
Ordinary light has light waves traveling in all directions. When polarized light is passed through a solution of an optically active
polarized light is passed through a solution of an optically active compound, the plane of polarization is rotated to the right or the left. The angle of rotation can be measured in a polarimeter.
An optically active organic compound can be identified by d
b id tifi d b
finding a chiral carbon. A chiral carbon is one that has four
carbon is one that has four different "groups" attached to it. The groups can be anything from a single H to functional groups to one or more other carbons. CHIRAL Carbons
Optical Isomers
The optical isomers are mirror images of The
optical isomers are mirror images of
each other. Optical isomers are also designated with the letters (D) and (L) g
( )
( )
to indicate the absolute configuration. In an absolute configuration the position of the groups is compared to a ii
f h
i
d
commonly agreed upon standard molecule In amino acids this molecule
molecule. In amino acids, this molecule is serine and for carbohydrates, it is gy
glyceraldehyde. y
L‐Alanine is a representative amino acid that is used in human and animal h i
di h
d i l
metabolism. The D isomer is not used. In the metabolism of carbohydrates only
In the metabolism of carbohydrates only the D isomer is utilized and not the L isomer.
20 essential amino acids
The eight amino acids in the orange area are nonpolar and and
hydrophobic.
The other amino acids are polar and hydrophilic ("water loving").
The two amino acids in the
The two amino acids in the magenta box are acidic ("carboxy" group in the side chain‐negatively
charged).
The three amino acids in
The three amino acids in the light blue box are basic ("amine" group in the side chain‐positively
charged). Suggested Reading
•Hubbell JA Current Opinion in
gy, 2003,, 14,, 517-519.
Biotechnology,
•Vacanti
Vacanti J Journal of Pediatric Surgery 2010,
2010
45, 291-294