The Molecules and Macromolecules of the Cell.

Zoë McKellar

03/1173/PAF

“The Molecules and Macromolecules of the Cell”

Due 17th November 2003

The Molecules and Macromolecules of the Cell

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 α-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 α-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 ...

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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. The various nucleosides formed, and their corresponding nucleotides, are shown in the following table:

As can be seen from the above table, the name of the nucleotide depends on which of the nucleosides it contains and where the phosphate is attached to the ring of the sugar. For example, a nucleotide which contains adenine and ribose, with the phosphate attached to the C-5’ of the ribose is adenosine-5’-monophosphate or AMP, where the 5’ indicates where on the sugar the phosphate is attached.

In a polymer of nucleic acid, which is also known as a polynucleotide, covalent bonds called phosphodiester linkages join together nucleotides. The name of the bonds refers to the position of the bond, with it occurring between the phosphate of one nucleotide and the sugar of another. In DNA, the nucleotides are joined by 3’5’ phosphodiester bonds. The 3’5’ is significant as it details that the bond is between the C-3’ of one sugar and the C-5’ of the other. Every nucleotide of DNA carries a negative charge. Joining the nucleotides together in this fashion produces the DNA “backbone” of alternating sugar and phosphate, and it is to this backbone the nitrogenous bases are attached. With the backbone assuming this form, in the finished polymer, at one end of the chain is a free 3’-hydroxyl group and the other has a free 5’-hydroxyl group, thus giving the DNA strand polarity. The sequence of nitrogenous bases attached to the backbone always starts from the free 5’ end towards the other. While the actual structure of the backbone is consistent in all DNA, the sequence of the bases is unique to each and every gene, and all the information the cell needs from the DNA is contained in these bases. DNA actually consists of two of these strands intertwined with the bases on the inside. The bases pair up, with adenine paired with thymine and guanine paired with cytosine. The result is a double helix. This helix is important in cell division, as when this time comes it separate into two strands, with each strand ending up in a different cell. With these single strands, another complementary strand can be replicated, thus forming two finished macromolecules.

RNA is very similar to DNA in its structure, with the only real differences being that the sugar used is ribose and the base thymine is replaced by uracil. This base uracil still pairs with adenine as thymine does. There are three different types of RNA found in a cell: Ribosomal (rRNA), Transfer (tRNA) and Messenger (mRNA) RNA. Ribosomal RNA is most abundant in the cell, accounting for 70-80% of the total RNA in the cell, and is found in the ribosomes. Ribosomes are where protein is synthesised. Messenger RNA carries the coded information from DNA to the ribosomes and effectively determines what the sequence of amino acids will be in a protein. Messenger RNA only accounts for a very small percentage of the total RNA, only about 3-4%. The size of the mRNA polymers varies widely, depending on what information is to be carried and it is fairly short lived. Transfer RNA is the smallest of the three RNA molecules. It makes up around 20% of a cell’s total RNA and works as an adaptor in protein synthesis.

Carbohydrates have three basic functions within a cell. They are biological fuel, they assume a storage form of food reserves and they are the structural components of cell walls. Carbohydrates can be subdivided into three groups: Monosaccharides, Disaccharides and Polysaccharides.

Monosaccharides are made up of single units and are used in metabolism and as the basis from which the other two groups are produced. They are polyhydroxyl compounds and contain either an aldehide or keto group. Which o these two groups it contains determines its name. An aldose, e.g. glucose, is a compound which contains aldehide, and a ketose e.g. fructose, contains a keto group.

The second of the three types of carbohydrate, Disaccharides, are produced when two monosaccharides join together by a dehydration reaction. The resulting bond is called a glycosidic bond. The two monosaccharides may be the same, or they may be entirely different.

Finally, Polysaccharides are long chains of monosaccharides, which may be all the same, in the case of homopolysaccharides, or they may be different. Polysaccharides account for the majority of carbohydrates which are found in nature, act as a stored energy source, e.g. starch in plants and glycogen in animals, or take on a structural role, such as cellulose.

Lipids are hydrophobic molecules, meaning that they do not mix with water. Within the cell they are responsible for the structure of cell membranes, the storage and transport of food reserves, protection and play a regulatory role by vitamins and hormones. One particular form of lipids are phospholipids. These are found almost always in cell membranes, and are in fact the most important aspect of the membrane. Phospholipids are quite similar to fats,. Differing in that they only have two fatty acids chains joined to a phosphate group, rather than three as found in a fat. A variety of phospholipids can be formed via the linking of other smaller molecules to the phosphate group. As previously mentioned, lipids are generally hydrophobic, but phospholipids are a bit different. The chains of fatty acids are indeed hydrophobic, but the phosphate “head” is not. This quality is particularly effective in the formation of cell membranes. When a phospholipid is added to water, the phosphate heads rearrange themselves to protect their hydrophobic fatty acid chains from the water. At a cell’s surface the phospholipids are set out in a bilayer with the phosphate heads towards the outside and the fatty acid chains pointing into the centre of the layer. The type of phospholipid used varies between different types of cells, for example, in a nerve cell the phospholipids found in the cell membrane are usually Plasmalogens.

It is clear that there is a hugely diverse population of molecules and macromolecules in a cell, each performing its own function. However, it would seem that frequently the success of one type of molecule or macromolecule is directly or indirectly determined by another, such is the equilibrium of a cell.

Bibliography