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Proteins: Synthesis

Transcription

 

 

Proteins are synthesised when genes in the nucleus of the cell are expressed. The first step is transcription. During this process a strand of messenger RNA is produced by complementary base pairing with a gene sequence of DNA by the enzyme RNA polymerase. An RNA sequence is different from a DNA sequence as it is single stranded and uses Uracil instead of Thymine. There are five steps which occur to produce the mRNA strand, they are as follows:

  1. RNA polymerase starts the process by breaking the hydrogen bonds between the base pairs of DNA and opening up what is called the ‘transcription bubble’, within this bubble is the one gene sequence which is going to be copied on the antisense strand of the DNA.
  2. RNA polymerase recognizes the promoter with the aid of transcription factors for transcription initiation and this marks the transcription start site. In order for the RNA polymerase to continue its replication of the DNA it must clear the promoter site and the elongation step will follow. The formation of the mRNA strand is started by adding RNA nucleotides in the 5’ to the 3’ direction to the DNA by complementary base pairing. Uracil is the base in RNA that replaces Thymine and binds to Adenine but the binding between Cysteine and Guanine is the same. The elongation step has a proof-reading mechanism to ensure that the bases are matched up correctly.
  3. To bind the new strand of nucleotides together, a sugar-phosphate backbone is formed to make a continuous strand. RNA polymerase catalyses the reactions between the OH group of the 3’ end and the phosphate group of the 5’ end to form the bond between the different nucleotides.
  4. Transcription of the strand is terminated by the formation of hair-pin loops in the DNA. The secondary structure destabilizes the RNA polymerase and it detaches from the sequence. The hydrogen bonds between RNA and DNA break to release the mRNA strand and the DNA strand reforms its natural helix shape.
  5. mRNA is further processed before leaving the nucleus (assuming the cell is a eukaryote) so that it isn’t targeted for degradation in the cytosol.

 

Figure 1 shows the ‘transcription bubble’ and the binding of nucleotides.

 

 

 

Figure 1: ‘Transcription Bubble’

Figure 1 shows the ‘transcription bubble’ and the binding of nucleotides.

Pre-Messenger RNA Processing

 

 

When the mRNA transcript is released there are a series of modifications which follow. The first being splicing, this mechanism is to remove the introns of the sequence which don’t code for any part of the protein. All that remains is the 5’ untranslated region, the exons and the 3’ untranslated region. The exons are the part of the sequence which code for the protein and these are joined together at the end of splicing.

The second modification is the 5’ cap, this is added to the mRNA transcript to provide stability as it undergoes translation and it is called the 7-methylguanylate cap. At the 3’ end there is the third modification which is polyadenylation, a poly-A tail is a stretch of adenine bases. It is required for nuclear export out of the cell as well for stability during translation.

Once it reaches the cytosol, translation of the mRNA strand begins. This is the second step of synthesis which produces a polypeptide chain of amino acids coded from the mRNA sequence. The mRNA sequence can be divided according to the amino acid code. The first three nucleotides will code for the start codon, this will always be ATG, and the rest of the sequence will continue coding for amino acids until a stop codon is reached and translation is finished.

 

 

 

Figure 2: Shows the different sites on the ribosome which tRNA attaches to and where the polypeptide

Translation

 

 

In the cytosol the 5’ end of the transcript will bind to a ribosome and form a complex on the outer membrane of the rough endoplasmic reticulum; this is activation of translation. In order to ‘decode’ the mRNA sequence the ribosome recruits transfer RNAs to the site of translation. These are special small non-coding RNA chains which at the bottom has a site for an anti-codon sequence that will complementary base pair to the correct RNA sequence and at the top of the structure it has a site for the amino acid corresponding to the anti-codon.

Initiation of translation occurs when tRNA first binds to the ribosome in the A site there is a reaction that takes place to bind the amino acid to the specific tRNA with the anticodon sequence for which it calls for. Aminoacyl tRNA synthetase carries out this reaction and the product is an aminoacyl-tRNA molecule, this is the form in which tRNA enters the ribosome.

The ribosome has three binding sites for the tRNA to bind to. The first is the aminoacyle (A) site which is where the tRNA will bind to the mRNA on the ribosome but only if it has the correct anti-codon sequence and corresponding amino acid. The second is the peptidyl (P) site which holds the tRNA bound to the polypeptide chain, a peptide bond is formed between the amino acid in the P and the newly added amino acid of the A site and once the bond is formed the tRNA translocates from the A site to the P site. Lastly, the third site is the exit (E) site where the tRNA leaves the ribosome and no longer had an amino acid attached to it. Before t he tRNA in the A site can move to the P site, the E site needs to be empty. The ribosome moves along the mRNA in the 5’ to 3’ direction, recruiting tRNAs along the way and adding amino acids to the polypeptide chain for the elongation process. Figure 2 shows the different sites on the ribosome which tRNA attaches to and where the polypeptide is formed.

When tRNA first binds to the ribosome in the A site there is a reaction that takes place to bind the amino acid to the specific tRNA with the anticodon sequence for which it calls for. Aminoacyl tRNA synthetase carries out this reaction and the product is an aminoacyl-tRNA molecule, this is the form in which tRNA enters the ribosome. This reaction is shown in Figure 3 and requires energy in the form of ATP.

Termination of translation occurs when a stop codon on the mRNA sequence is reached as there isn’t any tRNAs that will code for an amino acid. A release factor will bind and the whole complex will dissociate. The protein will fold into its conformation and enter the endoplasmic reticulum for post-translational modifications and packaging to other parts of the cell.

As a studying tip, I found it very useful to watch youtube videos to help me visualize the process! http://www.youtube.com/watch?v=NJxobgkPEAo Figure 4 summarises the whole process of protein synthesis and where it takes place in the cell.

 

 

Figure 3: Reaction of an amino acid binding to the tRNA molecule

Figure 4: The process of protein synthesis and where it takes place in the cell

References

 

 

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