The amino acids and proteins

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Protein synthesis is the process whereby DNA encodes for the production of amino acids and proteins. It is a very complex and precise process and as proteins make up over half of the dry mass of a cell, it is a vital process to the maintenance, growth and development of the cell. Proteins are widely used in the cell for a variety of reasons and have many different roles, for example some proteins provide structural support for cells while others act as enzymes which control cell metabolism.

Protein synthesis occurs at the ribosomes which are found in the cytoplasm, the portion of the cell located just outside the nucleus. Proteins are created by condensation reactions which link amino acids together with peptide bonds in a particular sequence. The type of protein that is created is influenced by the sequence of the amino acids in the primary structure. DNA and RNA are nucleic acids that are formed in the nucleotides and are both involved in the process of protein synthesis.

Deoxyribonucleic acid, more commonly known as DNA, is found in the nucleus of the cell and contains the entire genetic code for an organism in its structure. It has two very important functions which are to transmit information from one generation of cells to the next by the process of DNA replication and to provide the information for the synthesis of proteins necessary for cellular function. Basically, DNA controls protein synthesis.

The complex and precise process of protein synthesis begins within a gene, which is a distinct portion of a cell's DNA. DNA is a nucleic acid which is made up of repeating monomers, called nucleotides, and in the case of DNA, these individual monomers consist of a pentose sugar, a phosphoric acid and four bases known as adenine, guanine, cytosine and thymine. DNA is a double stranded polymer, which has a twisted ladder like structure, known as a double-helix. In this double helix, two polynucleotide chains combine via base-pairing between nucleotide units in the individual chains. The base pairs combine in a very specific and complimentary manner, with adenine combining only with thymine, and guanine only with cytosine. The sequence of the base pairs along the DNA molecule carries the genetic information of the cell.

The process of protein synthesis is controlled by DNA, although the DNA does not make new proteins itself. This is simply because it is too big a structure to pass through the nucleus into the cytoplasm, so it needs to send a message to the 'protein making machine' in the cytoplasm to start the process. It does this by sending this information via a chemical similar to DNA called ribonucleic acid (RNA). RNA is produced directly on DNA and the amount of RNA in each cell is directly related to the amount of protein synthesis. There are three types of RNA that are involved in protein synthesis. These are Messenger RNA (mRNA), Ribosomal RNA (rRNA) and Transfer RNA (tRNA).

mRNA is a single stranded molecule which is formed on a single strand of DNA by a process called transcription. The base sequence of mRNA is a complimentary copy of the DNA strand being copied and varies in length according to the length of the polypeptide chain for which it codes. It enters the cytoplasm where is associates with the ribosomes and acts as a template for protein synthesis.

rRNA is produced by the genes present on the DNA of several chromosomes. It is a large, complex molecule made up of both double and single helices. The base sequence of rRNA is similar in all organisms and is found in the cytoplasm, where it is associated with protein molecules, which together form the cell organelles known as ribosomes.

tRNA transfers amino acids present in the cytoplasm to the ribosome and acts as an intermediate molecule between the triplet code of mRNA and the amino acid sequence of the polypeptide chain. It is a small molecule comprising of a single strand and is manufactured by DNA. It forms a clover-leaf shape, with one end of the chain ending in a cytosine-cytosine-adenine sequence. It is at this point that an amino acid attaches itself. There are at least 20 types of tRNA, each carrying a different amino acid and at a midway point along the chain is an important sequence of three bases, called the anticodon. These line up alongside the appropriate codon on the mRNA during protein synthesis.

Since DNA is a code for the production of protein molecules, it is quite clear that the sequence of bases in the DNA is a code for the sequence of amino acids in protein molecules. This relationship between the bases and the amino acids is known as the genetic code. There are 20 common amino acids that the bases in the DNA must code for and of which are used to make proteins. Only a code composed of three bases could incorporate all 20 amino acids into the structure of protein molecules; the code is therefore a triplet code and is called a codon. It is a universal code, i.e. it is the same triplet code for the same amino acids in all living organisms. A given amino acid may be coded for by more than one codon and it must be non-overlapping, which means that each triplet must be read separately. For example, CUGAGCUAG is read as CUG-AGC-UAG.

Protein synthesis can be divided into two main stages, known as: transcription and translation. Transcription is where a section of DNA that has the code for a particular protein is copied to form a strand of mRNA. The difference between DNA and RNA is that DNA is a double helix consisting of two strands whereas RNA is simply a singular strand, RNA also uses uracil instead of thymine and DNA consists of a deoxyribose sugar, whereas RNA consists of a ribose sugar.

Since DNA is far too big a structure to pass through the membrane of the nucleus, the transcription process occurs in the nucleus. Firstly, an enzyme called RNA polymerase binds to the DNA at the start codon of the particular gene and "unzips" the section of double helical structure of DNA required by breaking the hydrogen bonds between the bases, causing the DNA to unwind into single strands. On the now exposed gene, one of the strands is now used as a template for messenger RNA (mRNA) production (called the sense strand). Using complimentary base pairing of nucleotides, the mRNA is an exact replica of the unused strand called the copy strand. When the polymerase reaches the stop codon of the gene transcription ends and the fully formed mRNA passes out of the nuclear membrane to the ribosomes.

The second stage of protein synthesis occurs at the ribosomes, and is known as translation. The ribosomes consist of two sub-units, which are each made up of ribosomal RNA (or rRNA) and protein. The main function of these sub-units is to translate the length of the mRNA.

Central to translation is transfer RNA (or tRNA). This is a single-stranded polymer of ribonucleotides held in shape by hydrogen bonds between base pairs. Each RNA molecule has a sequence of three bases (an anticodon) at one end, and at the other end a region for the specific amino acid to bond to. The specific amino acid is determined by the codon to which the anticodon is complimentary to. When translation occurs, a tRNA molecule with the complimentary anticodon to the mRNA's first codon binds to the mRNA with hydrogen bonds between the complimentary base pairings. A second tRNA binds to the second codon of mRNA in the same way. Then, the amino acids attached "carried" by the two tRNA molecules are joined together by the formation of a peptide bond. The first tRNA molecule leaves the ribosome to be replaced by a third tRNA, whose anticodon is complimentary to the third mRNA codon, which adds its amino acid to the chain. This process continues until the "stop" codon is reached on mRNA indicating the polypeptide chain is finished and protein synthesis is complete.

In conclusion, the DNA molecules contain a genetic code that determines which proteins are made in the body and these proteins include certain enzymes which control every biological reaction going on within the body. In simple terms, this is basically how life works.