| Electrons are….
Electrons are confined to specific orbits, a bit like the planets of our solar system is. They can’t exist anywhere between orbits and have to make a “quantum leap” from one orbit to another. As quantum particles, electrons exist as a collection of probabilities rather than at specific locations. The best way to understand is to show the electrons as a set of fuzzy shells, shields, around the nucleus. Electrons are the foundation of “electric flow” or current. There are two types of electron flow, Direct Current, or DC, and Alternating Current, or AC. Direct Current is the kind of electrical flow like in batteries and solar cells when electrons travel in one direction. On the other hand, AC is the electrical flow from a typical electrical outlet in a home. AC is when the electrons flow in two directions, from the positive to the negative terminal and from the negative to the positive terminal, ‘alternating’ between the two directions. In 1924, the French physicist Louis de Broglie suggested that, like light, electrons act as both particles and waves. De Broglie’s hypothesis was confirmed in experiments that showed electron beams could be diffracted or bent as they passed through a slit much like light could. The waves produced by an electron confined in its orbit about the nucleus sets up a standing wave of a specific wavelength, energy, and frequency (i.e., Bohr’s energy levels). The next problem occurred was to locate an electron. This problem was solved by the German physicist, Werner Heisenberg, and it was called the uncertainty principle: To view an electron in its orbit, a wavelength of light had to be shined on it that is smaller than the electron’s wavelength. This small wavelength of light has a high energy. The electron will absorb that energy. The absorbed energy changes the electron’s position. It is not possible to know both the momentum and position of an electron in an atom. Therefore, Heisenberg suggested that it is not possible to view electrons as moving in well-defined orbits about the nucleus! With de Broglie’s hypothesis and Heisenberg’s uncertainty principle in mind, the Austrian physicist named Erwin Schrodinger came up with a set of equations or wave functions in 1926 for electrons. According to Schrodinger, electrons confined in their orbits would set up standing waves and that could be described only the probability of where an electron could be. The distributions of these probabilities formed regions of space about the nucleus were called orbitals. Orbitals could be described as electron density clouds. The densest area of the cloud is where the greatest probability of finding the electron is and the least dense area is where the lowest probability of finding the electron. |
Polarity part 1 –
Nonpolar Side Chains
There are six / eight (there is a dispute about this number) amino acids with nonpolar side chains. Glycine, alanine, and proline have small, nonpolar side chains and are all weakly hydrophobic. Phenylalanine*, valine, leucine, isoleucine, and methionine* have larger side chains and are more hydrophobic. * there is a discussion about their place in this part.
This needs clarification: hydrophobic describes the fact that nonpolar substances don’t combine with water molecules. Water is a polar molecule, which implies that it carries a partial charge between its atoms. Oxygen, as an electronegative atom, draws the electrons of each bond closer to its core, thus creating a more negative charge. Therefore, any materials with a charge, negative or positive are able to interact with water molecules to dissolve.
Hydrophobic molecules are molecules that do not have a charge, they are non-polar. By lacking a charge, these molecules do not have charge-to-charge interactions that allow them to interact with water. Hydrophobic materials often do not dissolve in water or in any solution that contains a largely aqueous (watery) environment. This characteristic of being hydrophobic – or non-polar – is important for many of the molecules found in nature, in other organisms, and even within our own bodies.
Aromatic amino acids
Aromatic amino acids are relatively nonpolar. characterized by increased chemical stability resulting from the delocalization of electrons in a ring system (such as benzene) containing usually multiple conjugated double bonds. To different degrees, aromatic amino acids absorb ultraviolet light. Tyrosine and tryptophan absorb more than do phenylalanine; tryptophan is responsible for most of the absorbance of ultraviolet light (ca. 280 nm) by proteins. Tyrosine is the only one of the aromatic amino acids with an ionizable side chain.
Polar, Uncharged Side Chains
There are six amino acids with polar (A molecule in which the bond dipoles present do not cancel each other out and thus results in a molecular dipole), uncharged side chains. Serine and threonine have hydroxyl groups. Asparagine and glutamine have amide groups. Cysteine has a sulfhydryl group.
Charged Side Chains
There are three amino acids with charged side chains. The charge comes in two varieties: positive and negative: positive charge (+q) is a property of protons; negative charge (-q) is a property of electrons. The charge on the proton is identical in size to that on the electron but differs in sign. Arginine and lysine have side chains with amino groups. Their side chains are fully protonated at pH 7.4. Histidine has as a positively charged imidazole functional group.
Negatively charged residues
Aspartate under physiological conditions (pH 7.4) usually occurs as the negatively charged aspartate form, −COO−. Glutamic acid in highly alkaline solutions the doubly negative anion −OOC-CH(NH2)-(CH2)2-COO− prevails.
An amino acid consists of a basic amino group (−NH2), an acidic carboxyl group (−COOH), and an organic R group (or side chain) that is unique to each amino acid. The term amino acid comes from α-amino [alpha-amino] carboxylic acid. Each molecule contains a central carbon (C) atom, called the α-carbon, to which both an amino and a carboxyl group are attached. The remaining two bonds of the α-carbon atom are attached to a hydrogen (H) atom and the R group.
Chirality
Chirality is a geometric property of some molecules and ions. A chiral molecule/ion is non-superimposable, this means that the molecules cannot be placed on top of one another and give the same molecule. Chiral molecules with one or more stereocenters can be enantiomers / each of a pair of molecules that are mirror images of each other. All the amino acids are chiral molecules (except glycine). They show two optically active asymmetric forms (enantiomers) considered mirror images. One enantiomer is named shape D and the other L. Amino acids found in proteins almost always possess the L-configuration. This reflects the fact that the enzymes responsible for protein synthesis have evolved to utilize only the L-enantiomers.