Living Textbook MC610

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Protein Biosynthesis

The process of protein synthesis actually starts inside the nucleus, where a copy of the DNA is transcribed onto a mRNA molecule. It starts at a promoter area on the DNA that is rich in AT bases. A transcription bubble is formed and one base is added at a time until it reaches a termination signal. This mRNA will be an exact copy of the non-template strand with the exception of Thymine being replaced by Uracil and deoxyribose by ribose. This mRNA molecule then travels to the outside of the nucleus to the ribosomes.

The second step is known as translation . You have 4 different bases available.
If each base is equivalent to one amino acid, then only 4 amino acids could exist.
If two bases are equivalent to one amino acid, then 42 = 16 amino acids could be represented, which is still not enough to cover all 20 natural amino acids.
But if the code is 3 nucleotides per amino acids, that will give a total of 64 combination, more than enough. Not all the "codes" represent an amino acid, but some are to designate the start and termination of the process. This still leaves us with more than one code per amino acid.
Scientists tried for a while to crack the code, and it was Watson who was able to do that, and now we know what each code means.

In the following description of the process, we will discuss bacterial protein biosynthesis. Mammalian protein biosynthesis share many features with the bacterial process, but some differences are seen. These will be pointed out when appropriate.

The machinery involved in translation is composed of the ribosomes, mRNA, tRNA and individual amino acids. Ribosomes are made up of RNA and proteins and differ from prokaryotes to eukaryotes (designated by their sedimentation coefficient). Bacterial ribosomes is a 70S (made up of two units, 30S and 50S), in comparison to 80S in mammalian cells (the two subunits are 40S and 60S). The dissociation of these ribosomes is dependent on Mg2+ concentration. mRNA binding and the decoding process takes place on the smaller subunits, while peptide formation that is catalyzed by peptidyl transferase takes place on the larger unit.

Amino acids are carried on tRNA. The process of attaching an amino acid to a tRNA requires energy and is very specific (i.e. each amino acid binds to a specific tRNA).

All proteins start at the code AUG , the code for f-Met (f stands for formyl group that protects the amine end of the amino acid). Several protein factors known as Initiation factors (IFs) aid in the initiation of protein biosynthesis. mRNA bind to the 30S subunit where the code AUG rest on a specific site known as Peptidyl (P) site. The 50S now combines to the 30S subunit to form the 70S ribosome. The next code then rests on the Acceptor (A) site. The f-Met tRNA binds to the P site, followed by binding of the next amino acyl tRNA to the A site. The next step involves the enzyme Peptidyl transferase, where the first peptide bond is formed between the carboxylic acid end of f-Met and the amine end of the next amino acid.

The dipeptide will now exist on the A site and after the fMet tRNA leaves the P site will be empty. The ribosome now moves so that the dipeptide occupies the P site and another code can be enciphered on the A site and the appropriate amino acyl tRNA binds to the A site. The second peptide bond is now formed, and the process is repeated in what is known as elongation of the polypeptide and is aided by elongation factors (EFs). When a stop code finally binds to the A site, protein biosynthesis stops and the polypeptide chain is released. This step is aided by several release factors (RFs).

All these factors, IFs , EFs and RFs differ from bacterial to mammalian cells. The process requires energy supplied by GTP and proofreading to ensure accuracy.

One question begs itself here, is RNA origin of life???
RNA can be the genetic material, the messenger of the information vital for cell survival, the carriers of the building blocks of proteins and the manufacturer of proteins. They can also be utilized as enzymes (ribozymes ).