Chemistry Review

modified from "MIT Biology Hypertextbook:Chemistry Review" at - http://esg-www.mit.edu:8001/esgbio/chem/chemdir.html

The study of biology requires an understanding of simple organic chemistry and simple biological chemistry. Carbohydrates, lipids, proteins, and nucleic acids, the players in biology, are themselves composed of smaller building blocks. This chapter contains a review of important chemical interactions and concepts you will encounter in this course.

1 Chemical Bonds

This section provides a quick review of chemical bonds. Emphasis is placed on bonds between the six major elements found in biological systems: H, C, N, O, P, and S. You will remember from General Chemistry I and II that the electrons of atoms exist in orbitals. Each orbital can "hold" two electrons. This means that when only one, unpaired electron is present, there is an "empty space" in the orbital.

Carbon has 4 unpaired electrons and 4 unfilled orbitals; nitrogen has 3; oxygen has 2; and hydrogen has 1 unpaired electron and 1 unfilled orbital :

Often these atoms are depicted with only their unpaired electrons. The paired electrons in the filled orbitals are not shown to make the diagram simpler. Each would then appear as below:

Covalent Bonds

Covalent Bonds are the strongest chemical bonds, and are formed by the sharing of a pair of electrons. Covalent bonds form between two atoms, each of which has an unpaired electron. By sharing the two unpaired electrons between them, each atom can complete its unfilled orbital. This situation is the covalent bond.

Carbon has 4 unpaired electrons and can therefore share 4 electrons. Hence carbon always forms 4 covalent bonds.
Nitrogen has 3 unpaired electrons and can therefore share 3 electrons. Hence nitrogen always forms 3 covalent bonds.
Oxygen has 2 unpaired electrons and can therefore share 2 electrons. Hence oxygen always forms 2 covalent bonds.
Hydrogen has 1 unpaired electron and can therefore share 1 electron. Hence hydrogen always forms 1 covalent bond.

One of the simplest molecules is water which has 2 covalent bonds:

In this figure, oxygen has 2 unpaired electrons (shown in red), and 2 unfilled orbitals. The 2 hydrogens each have 1 unpaired electron (shown in gold), and 1 unfilled orbital. By sharing the 4 unpaired electrons between them, each atom can have a filled outer orbital with paired electrons. The result is two covalent bonds.

There are 2 ways of depicting the covalent bonds which are formed by sharing of atoms. One way shows the atoms which are being shared (as in the graphic of water above). The other way shows the covalent bonds only - in effect each pair of electrons is indicated by a line which represents the covalent bond. The figure below shows the same Carboxylic Acid molecule depicted in each of these 2 ways. The carboxyl group is COOH. When a carboxyl group is added to any chemical "R" (shown in green), a carboxylic acid is formed.

This shows each of the covalent bonds represented as a line. Each line represents a pair of shared electrons. From Organic Chemistry you will remember that the oxygen which forms the double bonds is referred to as a keto oxygen. The O-H group is referred to as a hydroxyl group. When a carboxylic acid is dissolved in an aqueous solution the hydrogen atom (gold) ionizes , leaving as a proton (H⁺) which increases the acidity and lowers the pHof the solution.

The carbon atom has 4 unpaired electrons. One of the carbon electrons (shown in black) is shared with an unpaired electron (shown in green) from the unspecified chemical "R" . The keto oxygen forms a double bond to the carbon. In this case both of the unpaired electrons from the oxygen (shown in red) are shared with two unpaired electrons (black) from the carbon. The second oxygen shares one of its unpaired electrons (red) with the fourth unpaired electron of the carbon (black). This results in a single C - O covalent bond. The second unpaired electron of the oxygen (red) is shared with the unpaired electron of the hydrogen (gold). This forms an O - H covalent bond.

Covalent bonds are very strong - once formed, they rarely break spontaneously. Covalent bonds are much stronger than Ionic Bonds, Hydrogen Bonds or Van der Waals Forces.

There are single, double, and triple covalent bonds:

Bond Number                     Example       

                                  H
                                  |
single                         H--C--H           
                                  |
                                  H

                                H  H
                                |  |
double                       H--C==C--H           
                                |  |
                                H  H
 
                                H
                                |
                                C
triple                         |||               
                                C
                                |
                                H

Hydrogen Bonds

Hydrogen bonds are very important in the structure of proteins and nucleic acids, and by reinforcing each other serve to keep the protein (or nucleic acid) structure secure ( see a helix or b pleated sheet).

Covalent bonds can also have partial charges when the atoms involved have different electronegativities. Water is perhaps the most obvious example of a molecule with partial charges. The symbols delta+ and delta- are used to indicate partial charges.

Oxygen is very strongly electronegative (it has a strong "attraction" for electrons). Conversely, Hydrogen is very weakly electronegative. As a result when oxygen and hydrogen are bonded, they share electrons - but they do NOT share them equally! Statistically the electrons are thought of as averaging more time closer to oxygen than to hydrogen. Consequently oxygen has a partial negative charge (it is not a FULL negative charge because the electrons do not spend 100% of their time with oxygen; they still spend some of their time with hydrogen, so the negative charge is only partial). Moreover, since the electron spends less time in the vicinity of the hydrogen, the hydrogen carries a partial positive charge.

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The possibility of hydrogen bonds (H-bonds) is a consequence of partial charges. The classical example of hydrogen bonding is in water, as shown below. Hydrogen bonds are formed when the partial positive charge on a hydrogen atom is attracted to the partial negative charge on an oxygen atom.

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Nitrogen is also very electronegative and can participate in hydrogen bonding.

More examples:
                    H
                    |
        R--O--H ||| N--R        R==N--H ||| O==R
                    |                                   Note that R stands for
                    H                                   any side group.

1.3 Ionic Bonds

Ionic bonds are formed when there is a complete transfer of electrons from one atom to another, resulting in two ions, one positively charged and the other negatively charged. For example, when a sodium atom (Na) donates the one electron in its outer valence shell to a chlorine (Cl) atom, which needs one electron to fill its outer valence shell, NaCl (table salt) results. The symbol for sodium chloride is Na+Cl-.

1.4 Van der Waals Bonds

Van der Walls interactions are very weak bonds formed between nonpolar molecules or nonpolar parts of a molecule. The weak bond is created because a C-H bond can have a transient dipole simply by chance.

Remember: Covalent bonds are shared electrons. However there is no way to tell exactly where they are at any precise femto second (10^-15 seconds) of time. Their location is only a matter of statistical probability. Another way of saying this is that on average they will exist in a certain "territory" between the two atoms which are sharing them - but one can never say exactly where they are at any instant - and on average they will be equally shared:

Since their location in their "territory" is governed by random chance, sometimes - simply by chance - the two electrons will both be centered around the same atom. This creates a transient dipole. However the existence of this very weak partial charge will tend to either attract or repel the electrons in a neighboring bond, creating an transient induced dipole in the second C-H bond as well.

In the figure below, a Van der Waals bond is shown as the dashed line between two methane molecules.

A transient dipole has occurred in the methane molecule on the left, when simply by chance, the electrons of the C-H bond are closer to the hydrogen.
The partial negative charge thus created repels the electrons in the C-H bond of the methane molecule on the right away from it.
The partial positive charge thus induced attracts the electrons in the C-H bond of the methane molecule on the right toward it.

Why can Geckos walk on the ceiling?

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Hydrophobic Interactions

Nonpolar molecules cannot form H-bonds with H₂O, and are therefore insoluble in H₂O. These molecules are known as hydrophobic (water hating), as opposed to water loving hydrophilic molecules which can form H-bonds with H₂O. Hydrophobic molecules tend to aggregate together in avoidance of H₂O molecules; hydrophobic interactions are clearly demonstrated with Vinegar and Oil Salad Dressing. The oil floats on the vinegar (an aqueous solution). The oil can be broken up into small droplets suspended in the vinegar, but they always fuse together to form larger and larger droplets until there are two layers again. This attraction/repulsion is known as the hydrophobic (fear of water) force.

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Why don't Oil and Water Mix?

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To understand the energetics driving this interaction, visualize the H₂O molecules surrounding droplets of "dissolved" hydrophobic molecules. The water molecules attempt to form the greatest number of hydrogen bonds with each other - however those which find themselves at the surface of a hydrophobic droplet are blocked from forming H-bonds with other water molecule, as shown below:

The best energetic solution involves the water molecules forcing all of the nonpolar molecules together, thus reducing the total surface area presented by the hydrophobic molecules which breaks up the H₂O H-bond matrix.

The total amount of nonpolar material present is the same in both the right and left diagrams. Because of the geometry of surface: volume ratios however, the surface area presented by the large droplet is far less than the surface area presented by the 9 small ones. Therefore the number of water molecules which can form hydrogen bonds with others is maximized when the hydrophobic molecules are all aggregated together and the situation pictured on the right is energetically favored.

This phenomenon is extremely important in determining the secondary structure of proteins, particularly Random Coil.

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For an explanation of Surface: Volume ratios and a more detailed explanation of how this leads hydrophobic and hydrophilic molecules to separate, click here.

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