Polarity and Bonding

Polar/ nonpolar and bonding: molecules, such as small molecules like water, or large macromolecules like proteins, have properties based on their polarity. Polarity is a spectrum. A molecule can be very nonpolar, or it can be slightly polar, or very polar. Polarity is a concept based on how the electron density exists around each atom in the molecule, but it can be displayed in how it affects the molecules interactions with other molecules. Molecules associate easier with other molecules that have a similar polarity. Molecules that have large differences in polarity tend to repel each other. One example is oil and water. Oil is composed of lipids, which have very little polarity and are essentially nonpolar. Water is a very polar molecule. Many of us have observed that water and oil don’t mix; we can see oil “bubbles” clumping together in pools of water. If you oil an iron skillet and then pour water in the pan the water will form droplets. What’s occurring here is that the water is associating with itself, or forming more surface interactions with other water molecules (polar), forming the droplets, rather than spreading evenly across the oil surface on the pan and associating with the lipid molecules (nonpolar) in the oil. This phenomenon may also be referred to as the hydrophobicity/ hydrophilicity of a molecule. A molecule that can mix and associate with water is referred to as hydrophilic (water-loving), whereas a molecule that doesn’t mix with water (such as oils/ lipids) is referred to as hydrophobic. Technically hydrophobicity/hydrophilicity isn’t necessarily the same as the phobicity of  a molecule, but often the terms are used interchangably because often the more polar  the molecule the more hydrophilic it will be and the less polar the less hydrophilic/ more hydrophobic it will be.

Polarity in the cell:

A cell is a collection of organelles (which perform all the little cells functions) suspended in a fluid like substance called the cytoplasm (a polar substance), surrounded by a membrane. Typically, eukaryotes (life that’s more complex than bacteria (Prokaryotes) have a double layered membrane. The membrane is made of lipids (nonpolar), packed in sheets. Each lipid has a long carbon chain tail and a polar phosphate group head. Again, there are two layers of these forming a typical eukaryotic membrane. The tail ends face each other, and the head groups face the inside and outside of the cell. This arrangement works well as the polar head groups associate with the polar cytoplasm and shield the nonpolar lipid tails from the cytoplasm.

The differences in polarity between the cytoplasm and the membrane also display with where a protein ends up, or localizes. Proteins are needed on either side of the membrane, as well as within the membrane. So it becomes essential for proteins to have a nonpolar exterior, meaning nonpolar amino acids on the outside of the protein, if the proteins are to localize within the membrane. On the other hand, if a protein is needed to function in the cytoplasm, then polar amino acids need to be on the outside associating with the polar cytoplasm and nonpolar amino acids need to be on the inside of the protein. This is an example of how a protein folds, or is shaped, becomes important. Proteins are formed as nonfolded sequences of amino acids, but as soon as that chain begins folding begins. This folding can be a result of the environment or other proteins. Proteins are made in the cytoplasm (polar), so if nonpolar amino acids are being added to the amino acid chain, these are repulsed by the polar cytoplasm. Thermodynamic and kinetic effects can help by causing changes and folds that bury these nonpolar amino acids within more polar amino acids. Other proteins (called chaperones) can help in protein folding by helping the protein to fold correctly.

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