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Everything we see, everything we touch and taste, most everything in our natural world is composed of matter. Matter surrounds us and interacts with us, but what is it really? Matter is anything that occupies space and has mass. Each bit of matter has a characteristic density, hardness, taste and color. Matter can undergo transformations including melting, boiling, and changes in composition. But, what is it made of and how does that determine the above properties? To begin, consider this analogy.
The writing on this page can be broken down into its basic parts. Each sentence is composed of words. Each word contains 26 letters of the English alphabet and each letter is simply combinations of curves, lines and dots. Building these curves, lines and dots into words and sentences can result in the conveying of ideas such as the nature of matter. In a similar fashion, matter is composed of atoms and each atom can be broken down into subatomic particles. The way these subatomic particles combine determines the properties and behaviors of the atoms and the matter they comprise.
Surprisingly in this vast cosmos we live in, there are only 109 natural atoms or elements, as they are called, and all of them are combinations of three basic subatomic particles, protons, neutrons and electrons. Protons are positively charged particles that have a very small mass. Neutrons are of similar mass, but have no charge. Electrons are particles of very little mass that have a charge equal and opposite to that of the proton. It is convenient when talking about such small charge and mass to use relative units and the weight of one proton is defined as one atomic unit (an atomic mass unit can also be referred to as a Dalton). For a similar reason, the charge on a proton is positive and given the value of +1. The charge on an electron is negative and given the value -1.
|Subatomic Particle||Actual Charge
|Relative Charge||Actual Mass (g)||Relative Mass||Mass in atomic Units or Daltons|
|Electron||1.6 x 10 -19||-1||9.11 x 10 -28||1/1837||0|
|Proton||1.6 x 10 -19||+1||1.67 x 10 -24||1||1|
|Neutron||0||0||1.67 x 10 -24||1||1|
Protons and neutrons combine together to form a nucleus in the center of the atom and the electrons are attracted to this nucleus by the positive charge. The electrons move very fast (near the speed of light) and, as best as we can measure, form a cloud of charge around the nucleus. Electrons want to be around as much positive charge as possible and protons want to collect as much negative charge as possible. The ideal state for the atom, its most stable state, is to have a balance between these two forces such that the atom has an equal amount of positive and negative charge. As an example, here is the construction of two of the lighter elements, hydrogen and helium. Hydrogen has one proton (one positive charge), no neutrons and one electron (one negative charge). Helium has two protons two neutrons and two electrons (Figure 2.1).
Figure 2.1. Arrangement of Hydrogen and Helium.. The arrangement of protons, neutrons and electrons in hydrogen and helium
The number of protons in an atom increases its weight, but also changes its fundamental properties, differentiating one element from the next. Atoms are delineated by the number of protons they have in their nucleus and the term atomic number was coined to express this idea. An atom containing 6 protons is a carbon atom no matter how many neutrons or electrons it contains.
The addition of a neutron adds to the weight of an atom and can affect its stability, but it does not change it properties. In fact atoms of carbon containing 7 neutrons (carbon 13) and 8 neutrons (carbon 14) exist in nature. Carbon 12, Carbon 13 and Carbon 14 are three isotopes of carbon.
The electron count of an atom affects it reactivity. Atoms want to be "full" of electrons. If they are not, they will try to borrow them from other atoms. As an example consider hydrogen and helium. Hydrogen is a very reactive molecule, always in search of an extra electron, while helium having two electrons is "full" and not very reactive.
So what determines whether an atom is full or not? This has to do with how electrons associate with the nucleus and many of the rules for this association were elucidated by the discipline of quantum mechanics. When electrons come in association with the nucleus of an atom they want to house themselves in very precisely defined spaces. These acceptable spaces are called orbitals. Each orbital defines a region where the electron is likely to be found and contains two electrons when full. Atoms have discrete energy levels or shells that contain these orbitals. Electrons must occupy orbitals in these energy states and are not allowed to exist outside the shells. This can be visualized as the difference between sitting on an inclined plane vs. a set of steps. When on a plane you can have any amount of potential energy, but with a set of steps you can only have discrete amounts. As one moves away from the nucleus, these shells require higher energy electrons to fill the orbitals. Atoms prefer to be in the lowest energy level possible so electrons will fill the open orbitals in the lowest energy shell first, then move to the next shell and so on.
As an analogy, orbitals can be thought of as houses where two electrons can live. These houses are organized into subdivisions (the shells) encircling a lake (the nucleus) at the bottom of a valley. Paths away from the hill have large steps instead of a simple incline. The most desirable location is on the lake front and that house is filled first. Further sets of electrons will fill the closest available house to the lake, but to do so they must jump up a step, a quantum of energy. More energy is required to live in the houses further from the lake because you have to walk up the steps to get there (Figure 2.2).
Figure 2.2. The houses of electrons. A useful analogy for thinking about electron positions in atoms
The rules for these associations determine the number and types of orbitals present in each shell. The first shell, the K shell, contains one s orbital that is spherical. The next shell, the L shell, contains 4 orbitals, one s orbital and 3 p orbitals. The M shell contains 1 s, 3 p and 5 d orbitals. Further shells will contain more orbitals, but for the most part atoms important in biological systems do not fill beyond the M shell (Figure 2.3).
Figure 2.3. Examples of atomic orbitals. The most common types of atomic orbitals in biological systems; the s, p and d orbitals. Figure adapted from a figure in the wikimedia commons. (http://commons.wikimedia.org/wiki/File:Electron_orbitals.svg)
So going back to hydrogen and helium, hydrogen has one electron that fills the s orbital of the K shell. There is room for one more electron in the orbital and hydrogen seeks it out. In its elemental form, each hydrogen atom will pair up with a second hydrogen atom forming H2. Helium contains two electrons that fill the s orbital of the K shell. The K shell is completely full and helium does not easily add more electrons. Elements with completely full shells (helium, argon, neon, and krypton for example) are very non-reactive
In contrast to helium, most atoms have partially filled outer shells and they are constantly in search of ways to fill them. This tendency makes them reactive with other atoms and that is why they associate and build larger structures called molecules. Atoms fill these orbitals by sharing electrons between different nuclei and overlapping their orbitals. The number of protons and electrons in an atom dictates how much sharing each atom is willing to do and dictates its behavior in chemical reactions. Table 2.2 lists some common elements in organisms and their electron-pairing behavior.
Electrons in outer shell
|Phosphorus||P||15||31||15||16||15||5||3 or 5|
|Sulfur||S||16||32||16||16||16||6||2, 4 or 6|
All sorts of combinations between these molecules are possible. Carbon can combine with 4 hydrogen to form methane. Nitrogen can combine with another nitrogen molecule to form nitrogen gas. Pure oxygen can share two of its electrons with another oxygen atom, forming O2. Two hydrogen can share their electrons with an oxygen atom forming water. Figure 2.4 shows some simple molecules.
Figure 2.4. Some simple molecules. A few examples of molecules that can be formed. These molecules are drawn showing their orbitals. Orbital drawings created by Ben Mills and available from wikimedia commons
The term covalent bond is used to describe this type of electron sharing. Covalent bonds are stable and bind molecules together rather tightly. This type of electron sharing can be visualized as a combination of the individual shared electrons forming a distributed electron cloud around the two molecules.
As we have learned above, covalent bonds connect atoms together forming the monomers and polymers of the cell, but there are other forces at work. Three of the more important bonding forces are ionic interactions, hydrogen bonds and hydrophobic interactions as shown in Figure 2.5.
Ionic interactions are the attraction of opposite charges for one another. Negatively charged groups are attracted to positively charged groups.
Hydrogen bonds involves hydrogen, which is not very good at holding onto its electrons when covalently bonded with certain other atoms (usually oxygen or nitrogen). It will not get its fair share of time with the electrons and will be attracted to high electron densities around other nearby atoms. The hydrogen atoms are attracted to the extra electrons and tend to stay in the vicinity of the electron density. Not surprisingly, these high electron densities are often found around oxygen and nitrogen atoms. This is not a covalent bond and hydrogen bonds tend to be weak interactions, but large numbers of them can add significantly to the stability of a protein or a DNA double helix.
Figure 2.5. Forces that affect biological systems. Show in the figure are a) Ionic interactions. The nitrogen (N) on the side chain of arginine is positively charged and is attracted to the negative charge on the carboxyl group. b) Hydrogen bonds. The hydrogen atoms in water are starved for electrons and the oxygen is electron rich. This will cause the hydrogen atoms to be attracted to the electron dense oxygen. c) Hydrophobic interactions. Non-polar molecules, such as some side chains on amino acids, will disrupt the hydrogen bonding of water and make the system energetically unfavorable. Highlighted is a string of amino acids that are hydrophobic (Val Val Val Thr Ala Val Thr Ala Thr Thr) in the KasA protein. Notice how all the hydrophobic groups, the white spheres, are buried under the surface of the protein (shown as a mesh). The KasA protein is a protein made by Mycobacterium tuberculosis and is part of the pathway for synthesizing long-chain fatty acids. These are important for its virulence and is a target for new drugs.
If you want to see hydrogen bonds in action, fill a glass of water to overflowing. Note how the water clings to itself, even though it is above the height of the glass. Hydrogen bonds between the water molecules cause them to stick together. Now add a few drops of detergent. The detergent will disrupt the bonding between the water molecules. Don't do this unless you have a towel nearby!
Hydrophobic interactions consist of the congregation of non-polar groups together. The presence of a hydrophobic (water-hating) molecule in a solution of water causes an undesirable ordering of the water around it. Water hates to do this and will minimize this interaction by pushing the hydrophobic groups together and away from the water. The hydrophobic groups can be thought of as oil in water. When you place some oil in a bottle of water, the oil has a tendency to separate from the water and form one large bleb (that is a scientific term, really, look it up). If you shake the bottle, the oil is dispersed, but in a little while it all congregates again. This is hydrophobic interactions at work. The same process is functioning at the molecular level. Hydrophobic groups in biological systems tend to consist of alkyl chains (see later in the chapter for a definition of this term). These groups are pushed together and hide themselves away from the water in the environment. This grouping can lead to the formation of large structures spontaneously. Membrane formation and protein folding are largely driven by hydrophobic interactions.
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