PROTEINS AND NUCLEIC ACIDS

Amino acids and Proteins

Plants contain a lot less nitrogen than animals, whose bodies are mostly made up of protein. Although plants have little in the way of structural protein, nitrogen compounds are essential for their life. In fact animals are as dependent on plants for their organic nitrogen as for their carbohydrate foods. Amino acids are the main low molecular weight organic nitrogen compounds. These are variations on a basic pattern:

Amino acids are the building blocks for proteins in which peptide bonds (a special kind of amide bond) join the amino and carboxyl groups of adjacent monomers:

The sequence of amino acids defines the primary structure of a protein. The amino acid chain is typically coiled in an alpha-helix which defines the secondary structure. The helix is then folded in a specific pattern which is the tertiary structure.

Enzymes
Most of the proteins in plants are enzymes, catalysts that carry out all of the chemical changes involved in plant growth. There is at least one enzyme specifically responsible for every step in respiration, photosynthesis, gene replication, information processing and building cell structure. The specific reaction is determined by the primary amino acid sequence of the protein, but it is the secondary and tertiary structure that is important for catalytic function. The way that the protein is folded creates an active site with an affinity for a specific substrate molecule. When the molecule binds to the active site it is stretched or twisted in a way that encourages it to go through the reaction. Thus invertase stretches the glycosidic bonds in sucrose, allowing hydrogen and hydroxyl from water to get in and split glucose and sucrose away.

Nucleic acids and nucleotides
Nucleotides are another group of nitrogen containing compounds with special functions in the cell. They are mostly based on five organic bases. Two of these, thymine and uracil (U) differ only in the presence or absence of one methyl group:

These are often combined with ribose (a pentose sugar) and one or more phosphate groups. Chemical energy in all cells is commonly handled through ATP. The energy is associated with the chain of three phosphates and is released by stripping them off, usually one at a time.

Chemical reducing power in the cell is associated with NAD which carries a positive charge in the oxidized state and is written as NADH when reduced. Sometimes a related compound NADP is used in place of NAD.

Polymers based on similar nucleotides are used in information storage and processing. As we see with the viruses it is impossible to have anything resembling life without this function. Information is usually stored in DNA in which the ribose sugar is modified (deoxyribose) and two chains of nucleotides are lined up side by side (but running in opposite directions). The backbone of each chain is an alternating sequence of sugar and phosphate. The bases are attached to the sugars and the bases line up so that every time there is a G on one chain there is a C on the other; when A is on one T is on the other.

This arrangement gives the cell two complementary copies of its genetic material. When it is time to reproduce the strands are separated and the complementary nucleotides are brought in for each strand. Strands are always copied in one direction, so one strand can be copied continuously but the other must be copied in fragments that are joined up later. Normally DNA exists as (the famous) double helix. This has to be unwound for replication

DNA also has to be unwound and the strands separated in order to read off information as RNA. This is copied from one strand of the DNA and uses the same base pairing as in DNA, except that RNA contains uracil (U) in place of thymine (T). Proteins are made by transcribing messenger RNA (mRNA) from DNA and translating it into aan amino acid sequence on a ribosome. Ribosomes are also made of RNA (rRNA) and the process involves transfer RNA (tRNA) to make the temporary link between amino acids and mRNA.