LECTURE 2
BIOMOLECULES
SIZES IN BIOLOGY
It is important to have a basic understanding of the sizes of things in our world. The smallest that we know are sub-atomic particles from there we can progress to atoms. Atoms get together to form molecules. An example is water, H2O, which is composed of two atoms of hydrogen and one of oxygen. Molecules form intracellular structures and the cells themselves. Cells are the basic unit of all organisms. There are two types, prokaryotic which are simple cells found in bacteria and blue-green algae, and eukaryotic, which are more complex and which contain organelles. In multicellular organisms, cells form tissues (example, muscle), tissues form organs (example, heart), and several organs function as an organ system (example, circulatory system). Organisms form populations, populations form communities, communities form ecosystems. The biosphere refers to all regions of the earth's waters, crust and atmosphere in which organisms live.
UNIVERSAL BUILDING BLOCKS OF LIVING THINGS
The same molecules are found in all earth organisms today. The simplest, and some of the more complex of the organic molecules found in living organisms, have been synthesized in vitro (literally, in glass, meaning in the test tube). Many experiments occurred on the primitive earth before the first simple prokaryotic cells appeared. An interesting fact is that all present day organisms are composed of the same molecules, which I will refer to as biomolecules.
"SMALL" BIOMOLECULES
For purposes of categorizing them for you to learn, I will divide them by size or molecular weight. The smallest ones have a molecular weight of less than 100 daltons (daltons are the units of molecular weight, for example, hydrogen has a molecular weight of one dalton). These are often called minerals and many of them are ions (charged atoms or molecules). Examples are H2O, Na+, Cl-, PO4=, Mg+, K+, Ca2+, Fe2+, and many, many more. In fact, it appears that we may need at least trace amounts of each of the elements in the periodic table. Depending on the organism, the minerals may be needed in large amounts for structural parts of the body such as bone or for body fluids, such as our blood, which needs to be isotonic with the cells it bathes. Some of the minerals are only needed in trace amounts. The function of these is to act as cofactors for proteins. Many proteins are enzymes which catalyze the myriad of reactions that occur continuously in the cells of all organisms. Enzymes usually need mineral cofactors to carry out their work. Another example is iron which is found in the protein, hemoglobin, which is in our red blood cells and which is responsible for carrying oxygen to every cell in our body. Magnesium is an integral part of chlorophyll which is the primary molecule responsible for photosynthesis in algae and plant cells.
"MIDDLE SIZED" BIOMOLECULES
The second category is of the "middle-sized" biomolecules, whose molecular weight is between 100 and 1000 daltons and the third category is of the "large" biomolecules, whose molecular weight is over 1000 daltons. The large biomolecules are often called macromolecules because of their size. These are the proteins (polypeptides), nucleic acids (polynucleotides) and carbohydrates (polysaccharides). Although lipids are really not large biomolecules, I am putting them with the proteins, nucleic acids and polysaccharides because they are an important group. Both the middle-sized and macro biomolecules all contain carbon and so are called organic molecules. The subunits of the macromolecules belong in the middle-sized biomolecule group.
"LARGE" BIOMOLECULES
INFORMATIONAL LARGE BIOMOLECULES
Proteins are made up of linear sequences of amino acids. There are 20 naturally occurring amino acids. This number is close to the number of letters in our alphabet. Therefore you can immediately understand that a large number of proteins can be made from different permutations and combinations of amino acids strung together in "protein words." However, unlike our words, each protein contains hundreds of amino acids and so the number of different proteins is very large. Proteins are the products of our genes and are responsible for the work of the cells. Many are enzymes which catalyze reactions (examples are digestive enzymes in the intestine). Some proteins are structural like the collagens which make up much of our connective tissue. Some, like hemoglobin which carries oxygen, are specialized to carry metabolites throughout the body. Some are hormones like insulin. Proteins usually work with cofactors such as minerals and vitamins which assist them in their jobs.
Nucleic acids are made up of linear sequences of nucleotides. DNA (deoxyribose nucleic acid) is the genetic material of all cells. RNAs (ribose nucleic acid) which are closely related, are copies of the genes which are sent out to the cytoplasm of the cell to direct the synthesis of proteins for which the genes code. DNA is composed of four different nucleotides abbreviated A, T, C, and G. RNA is also composed of four nucleotides except T is replaced by U. The letters stand for the bases adenine, thymine, cytosine, guanine, and uracil which form an important part of the nucleotide. Nucleotides contain a (purine or pyrimidine) base attached to a sugar (ribose or deoxyribose) and phosphate (PO4 =). The four bases in DNA code for all our genetic information and therefore for all the proteins we make. While at first it might be difficult to understand how only four subunits can code for such a large molecule as a protein, just remember that the Morse Code which has only a dot, dash and space, codes for all the letters in our alphabet.
Both proteins and nucleic acids are called informational molecules because the sequence of their subunits determines their function. The sequence of bases in DNA spells a very precise sequence of amino acids to make the gene products, our proteins. The sequence is critical just as the same three letters of our alphabet can spell words with entirely different meanings: EAT, TEA, ATE. Changes in the sequence of bases in DNA are called mutations and can cause serious disorders.
":NON INFORMATIONAL" LARGE BIOMOLECULES
Carbohydrates or polysaccharides are made up of linear and branched sequences of monosaccharides sometimes called sugars. They are usually quite monotonous repeats of the same sugar (monosaccharide) over and over. The bonds between the sugars may vary to produce polysaccharides with different properties. Glycogen is a polysaccharide we store in our liver. It has both linear and branched regions but it is composed entirely of glucose, a simple monosaccharide. Starch in the potatoes we eat is composed exclusively of glucose, also. These carbohydrates are principally a way to store energy for future use. Cellulose is also a polysaccharide composed solely of glucose, however, the bonds between the glucose molecules are different and we do not have enzymes to break them. We can eat celery, for example, which will fill our stomach but not provide many calories since we cannot break it down. Herbivores (plant eaters) such as cows and horses have to have microorganisms in their digestive tract which produce enzymes which can break the bonds. Cows have them in one of their four stomach compartments and horses have them in a caecum similar to our appendix. Mother cows have to lick their calves to transmit to them an inoculum of microorganisms for their digestive tract. Cows are much more efficient in their digestion of cellulose than are horses, as evidenced by the consistency of their feces. Cellulose is an example of a carbohydrate whose function is structural. Chitin which forms the skeleton of crabs, lobsters, etc., is also a polysaccharide. Oligosaccharides are short chains of sugars which are attached to many of our proteins and which act like zip codes, signaling other molecules to attach to them.
Lipids do not have linearly arranged subunits although many of them contain fatty acids Fatty acids are long chains of carbons with hydrogens attached. Lipids are the best energy storage molecules for their weight. The breakdown of fatty acids produces both energy and metabolic water, hence the camel stores lipids in his/her hump. Waxes contain fatty acids, also. Sterols are another kind of lipid. Cholesterol is a lipid most of us know about. Lipids are very important in forming the membrane of the cell. The lipids are all molecules which are insoluble in water and as such are perfect for forming cell membranes which must separate one fluid containing compartment from another. Some sterols are hormones such as cortisol, testosterone, estrogen, and progesterone. These molecules are chemical messengers which enter cells and turn on specific chemical reactions.
The middle-sized molecules are the subunits of the macromolecules we have just discussed: amino acids, nucleotides, sugars (monosaccharides) and fatty acids. Other middle-sized organic molecules include vitamins which act as cofactors for enzymes. Like the mineral cofactors, they are needed only in trace amounts. One very important middle-sized molecule is ATP (adenosine triphosphate) which is the molecule which carries the energy produced in the body. It acts as a cofactor in those chemical reactions that require energy. ATP is the common "dollar bill" of energy in all cells and organisms. There are many middle-sized organic molecules which are on their way to becoming subunits, being broken down for energy, or being formed into other metabolites for use or for excretion from our bodies. We can call this latter group, metabolites.