There are huge numbers of macromolecules and molecules found in a cell, but they mainly have one thing in common: Carbon. Carbon is the most prevalent element in all organic life. It has a valency of 4, which makes it particularly effective in forming covalent bonds with other elements to form molecules. While a number of other elements are used in a cell, Carbon is used in abundance. Amino acids are organic molecules which are the monomers of proteins and are made up of at least one amino group and at least one carboxyl group.
It is quite probable that huge numbers of amino acids actually exist, only about twenty of these are used in building proteins. These amino acids are commonly called ? -amino acids. These amino acids have both an amino group and carboxyl group which are joined onto the same carbon atom, which is called the ? -carbon atom. This carbon atom also has a hydrogen atom joined to it, and another group which is known as a side chain or R-group. This side chain is of particular significance, as it provides the diversity of amino acids.
These side chains vary in complexity, and the most basic is found in the amino acid glycine, which consists of only one hydrogen atom. Proteins make up the majority of a cells mass, minus the water, and are essential in almost everything the cell does. They are extremely complex macromolecules, and each type of protein has its own individual three dimensional shape, but are all made up of the same 20 amino acids in different arrangements. Amino acids are linked together in an unbranched chain by peptide bonds to form polypeptides.
This bond is formed when the amino group of one amino acid is next to the carboxyl group of another and an enzyme is introduced to cause a condensation, or dehydration, reaction, where a molecule of water is lost between the two molecules. The polypeptides vary in length and can be made up of anywhere from a few monomers to a vast number. The result is always the same – at one end of the polypeptide is an amino group and at the other is a carboxyl group, which gives the chain polarity. Polypeptides are not fully formed proteins, however.
Proteins are actually made up of one or more polypeptides which are arranged in a specific fashion, be it folded or twisted etc. This takes place over four stages. The first stage is where the sequence of the amino acids is determined, and where the covalent bonds are formed between them. While this stage is in itself important, it does not fully determine the end function of the protein. In the second stage the amino acids bonded together are arranged in sequences of repeating patterns, and these are stabilised by hydrogen bonds.
The third stage determines the overall shape of a polypeptide, but this stage is very similar to the second, and indeed these stages could be classed as the same actions. The final stage only happens when more than one polypeptide is to form the finished protein. Here, polypeptide subunits join together, twisting or folding to become the finished macromolecular structure. The actual formation the resulting macromolecule assumes is down to the arrange of the amino acid monomers.
Similarly, the exact formation of the protein determines what its function will be, for example, if it is to bind with another molecule it must be a particular shape as in the case of antibodies and antigens. Nucleic acids include two types of macromolecules with distinct roles within cells. One type of nucleic acid is partially responsible for the arrangement of the sequence of amino acids in a polypeptide chain. Amino acid sequences are determined by genes, which are in turn made up by DNA, or deoxyribonucleic acid, which in a member of the polymer group, nucleic acids.
The other is RNA, or ribonucleic acid. DNA is responsible for the passing of genetic information from one generation to the next. It is a polymer made up of monomers called nucleotides. These nucleotides are made up of a nitrogenous base, a sugar and a phosphoric acid. The nitrogenous bases come under two categories, meaning they are either pyrimidines or purines. Pyrimidines are related structurally to the heterocyclic compound called pyramidine, and there are three types which are often present in nucleic acids.
These are thymine, cytosine and uracil. Both cytosine and thymine are found in DNA, whereas uracil replaces thymine in RNA. Purines are developed from the compound purine, and there are two which are commonly present in nucleic acid, and these are guanine and adenine. The sugar found in nucleic acid comes in two forms. The first is D-ribose, found in RNA, and the second is 2′-deoxy-D-ribose and, as its name might suggest, is present in DNA.
The sugars are attached to the ring form of the purines, which has a five membered ring, or pyrimidines which have six members. The sugars themselves are very similar, the only real difference being the lack of an oxygen atom in D-ribose. With just the nitrogenous bases and the sugar being joined together, this forms a nucleoside. They are either called ribonucleosides or deoxyribonucleosides, depending which of the two types of sugar is used. Nucleosides are bonded using glycosidic bonds, which is a term used when sugar is involved.