We've seen how atoms are made of electrons, protons, and neutrons, and how the attraction between the electrons of one atom and the positive proton-containing nucleus of another atom can hold the atoms together in a bond to form a molecule. The number of electrons and their arrangement around the nucleus determine how many bond a particular atom can form, and whether the bond will be primarily covalent or ionic. Atoms of the noble elements never form bonds at all (well, almost never), but the atoms of the rest of the elements can form bonds.
Look at a periodic table and notice carbon's position on it. All the elements in that column (or family) need four electrons added to their outer shell to reach the electron configuration of the nearest noble gas. Silicon and germanium are semi-metals, and tin and lead are metals. Carbon is the only non-metal element which can form four covalent bonds, and it seems to have a particular affinity for hydrogen. In pure form it occurs as a lattice (hard, high melting point) and as sheets (soft, flaky).
Carbon and oxygen combine to form CO2, a non-polar molecule with covalent bonds. Oxygen and hydrogen form H2O, a polar molecule. The non-polar molecules formed with carbon are often not soluble in water.
Isomers are molecules which have the same chemical formula, but different structures. This is equivalent to having one set of Brio train tracks, from which you can make several different track patterns. Sometimes the patterns are wildly different, sometimes they have one section of track switched with another, and sometimes the track patterns are mirror images of each other.
[Latin students take note of the cis (covalent bonds on the same side of the molecule) and trans forms (covalent bonds on opposite sides). Cisalpine Gaul is on same side of the Alps as Italy, transalpine Gaul is on the far side.]
Enzymes are catalysts used by cells to facilitate a chemical reaction. A catalyst is a chemical which enables a reaction, but is neither a reactant or a product: it is the same after the reaction as before. Enzymes are like shoes, though: they need to fit feet (substrate chemicals they are maneuvering through the reaction) exactly. Animal cells make right-oriented enzyme isomers. If the organic molecules they get to work on are left-isomers, the enzymes will not fit their target molecules and will not be able to break them down. It's as if the cell has only right feet: only right shoes will fit. Left shoes are completely useless.
There are several science fiction stories based on this premise, where some accident leaves the hero mirror-image reversed. In a world of plenty, he will starve to death, because his now left-oriented enzymes can't break down the right-oriented organic molecules in his food. The actual situation its upside (at least, for the diet-conscious). Left-handed sugars could be used to flavor foods, and still taste sweet. But since they can't be broken down by our enzymes, we won't get fat eating them, and bacteria can't eat them either, so they won't cause cavities.
Start with a hydrocarbon chain, remove one of the hydrogens, and put a functional group in its place. Voila! You have an organic molecule. A number of common functional groups are shown in the table below. You should be able to match the structural formula with the name of the group and its class of compounds for each of the major functional groups. For example, the hydroxyl group is represented by R-OH (where R means the rest of the molecule, usually a carbon-hydrogen chain) and contains the alcohols. Amino acids, the basic components of DNA and proteins, are characterized by two functional groups: amines and carboxyls.
|Group||Structure Formula||Molecular Class||Specific Examples|
|Carboxyl||R-COOH||Carboxylic acids||Amino acids|
|Carbonyl||R-COH||Aldehydes O=C-H and Ketones O=C-R||Formaldehyde and Acetone|
|Methyl||R-CH3||Many organic compounds||Methane|
|Sulfhydryl||R-SH||Thiols||Cysteine (an amino acid)|
The four major types of organic molecules are present in dehydrated liver tissue as follows: 5% carbohydrates, 12% lipids (fats), 71% proteins, 7% nucleic acids. (My source doesn't say what the other 5% was).
The 6-carbon monosaccharides fructose, glucose, and galactose all have the same chemical formula: C6H12O6. To understand the differences, chemists use special diagrams.
Ring diagrams are the standard way to represent 5- and 6-carbon sugars (see below). There is a carbon atom at each corner. They are numbered clockwise from the number 1 Carbon in the three o'clock position. On 6-carbon sugars, the oxygen atom is in the one o'clock position. Often, not all the hydrogen atoms are shown. Get comfortable with these diagrams--you'll see them a lot as you study cell functions!
Note the differences between glucose and galactose (both aldehydes) and fructose (a ketone). Fructose is a structural isomer of glucose: the covalent bonds are different. Galactose and glucose are enantiomers. Glucose exists in two forms: alpha-glucose has the OH of the 1-Carbon atom on the same side of the molecule and the 6-Carbon atom; in beta-glucose, the OH is on the opposite side from the six carbon.
Disaccharides are formed when two monosaccharides combine. Because they are harder to break down than monosaccharides, they are used by the cell to transport sugars where their energy can be used. The 1-carbon on one loses an H; the 4-carbon on the other loses an OH. The remaining O links the 1-carbon and 4-carbon together. When the compound forms, the reacting molecules lose a water molecule, so the operation is a dehydration process. Dissacharides dissolve by absorbing a molecule of water (the process is hydrolysis): that is why eating something sweet makes you thirsty.
Two glucose molecules combine to form maltose. Glucose and galactose together form lactose, the sugar found in milk (most adults have lost the enzyme to break this down). Glucose and fructose together from sucrose, or table sugar. Beta-glucose chains make up cellulose and chitin, the major components of plant cell walls and many animal exoskeletons.
Why do you care about all the different sugars? Because the simple sugars are good examples of isomers, where small differences in structure make big differences in functionality and characteristics. Compare the forms of maltose, starch and cellulose/chitin. The difference in location of the CH2OH group makes one set (starches and sugars) soluble, and the other set (cellulose and chitin) insoluble and rigid.
Lipids or fats are not composed of identical monomer units, as carbohydrates are. Instead, they have three major components: a glycerol head, a linking fatty acid, and one to three hydrocarbon chains, each of which can be many CH2 units long.
Look closely at the diagram of the glycerol molecule. By losing an H+ from one of its hydroxyl groups, it can combine with a fatty acid which has lost an OH- from its carboxyl group. The resulting bond is an ester (check your functional group chart!).
When two fatty acids use a glycerol molecule to link to a phosphate/organic compound group, the result is a phospholipid. [It's beginning to sound like Luke Luck Likes Lakes....]. The phosphate/organic molecule head of the phospholipid is hydrophilic (water-loving); the fatty acid tails are hydrophobic (water-hating). Later on in chapter 5 we will learn why a wall of carefully arranged phospholipids makes an effective water barrier and can be used as a cell membrane.
The melting point of a fat is determined by the composition of its hydrocarbon "tail". If all of the carbons in the chain are matched with 2 hydrogens, the chain is straight and stiff, and many fat molecules can be packed closely together. If two side-by-side carbons each lack one of their hydrogens, they can form a double bond. The remaining hydrogens repel each other, causing the hydrocarbon chain to bend. This bent chain can't pack as closely as a straight chain, and so it melts at a lower temperature.
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