How proteins are made

 

Introduction

You’ve probably heard of it before, passed down from your biological parents from their biological parents and so on, your DNA contains the code that creates you. For you to continue living, it is vital that proteins are made constantly to fill the roles necessary to maintain you, and it is DNA that provides the instructions on how these proteins are made. But, the instructions don’t build the bookshelf - you do. Similarly, the creation of proteins requires more than just DNA. It is the processes of transcription and translation that take the instructions from DNA to mRNA to protein.

DNA and RNA. What’s the Difference?

Structure

DNA stands for deoxyribonucleic acid. The molecule is made of a sugar called deoxyribose, a phosphate group, and four bases (aka nucleotides)  Adenine (A), Thymine (T), Cytosine (C), and Guanine (G). DNA takes the shape of a double-stranded helix, which is a fancy way of calling it a twisted ladder. The sugar and phosphate make up the rails of this ladder, or the “backbone” of the DNA and the bases stick to each rail, aligned in pairs to make the ladder’s rungs. The bases always pair up the same way Adenine to Thymine and Cytosine to Guanine (A to T and C to G). 

RNA stands for ribonucleic acid, it is very similar to DNA with its sugar-phosphate backbone and use of bases. However, RNA uses ribose rather than deoxyribose; has only one strand instead of two, and replaces thymine with the base uracil (U).

Both DNA and RNA strands are different at each end. You can tell the ends apart by what is ”sticking out”. On one end, part of the DNA’s sugar-phosphate backbone - the phosphate group - sticks out. This end is called the 5’ end because the phosphate group is attached to the 5th carbon on the sugar ring. On the other end, there is a hydroxyl group (OH) sticking out, this hydroxyl group is attached to the third carbon on the sugar ring and so this end is called the 3’ end. 

1. DNA in the form of a double-stranded helix. 2. The four bases that are used in DNA. 3. DNA unwound to show its structure.

Transcription and Translation

DNA stores genetic information long term. It is stable and generally stays in the nucleus of the cell packaged away in chromosomes, although there is a little mitochondrial DNA stored in your mitochondria. When your cells need to make a protein, their DNA provides the instructions, and messenger RNA (mRNA) brings said instructions to the ribosomes.

Transcription - copying the code from DNA to RNA

The transcription process begins in the nucleus of a cell, where the DNA is stored. DNA doesn’t need to be transcribed all at once, sections are able to unwind so that they may be used as guides to build RNA when needed. 

Transcription begins with the initiation stage, when the enzyme RNA polymerase binds to a gene’s promoter region, signalling the DNA to unwind. 

The RNA polymerase will read one of the DNA strands and build its own complimentary one made of RNA. It is during the elongation stage that the RNA polymerase moves along the template DNA strand from the 3' end to the 5' end, adding bases to the growing pre-mRNA strand in a 5' to 3' direction. the bases on the RNA will be complementary to the bases on the template DNA. For Example:

Template DNA strand:    C A G A T A G T C

Coding DNA strand:        G T C T A T C A G

New RNA strand:             G U C U A U C A G

Once the RNA reaches a sequence in the DNA that tells it to stop, it will stop adding nucleotides and detach. In eukaryotic cells the termination stage ends with a strand of pre-mRNA ready to be processed, however, in bacteria this processing isn’t necessary and the recently transcribed strand can act as mRNA immediately. 

The elongation stage of transcription. 

Processing

A cap made of a modified guanine will be added to the 5’ end and the 3’ end will get a poly-A tail made of about 100-200 adenines, these modifications will protect the mRNA from degrading and help with some of the other processes the mRNA will go through. Not all of our strand will be used for protein synthesis, the pre-mRNA will have to go through splicing first. The bits that are kept and expressed are called exons, and the parts that can’t be used are called introns. The introns are cut out by a protein-RNA complex called a spliceosome, leaving only the exons to be stuck back together and used for the final protein. If the introns were left in, the translated protein wouldn't function, however, it is possible for different, but functional, proteins to be created from the same strand of RNA through alternative splicing - different exons can be kept in or left out, with each combination making a different protein. 

Translation - building a chain of amino acids based on the mRNA code

Codons

So now that we have the transcribed code it can be used to build a polypeptide chain. What pieces go where? Groups of 3 bases on the mRNA are called codons, most of these codons correspond to an amino acid. A chain of amino acids is called a polypeptide chain because of the peptide bonds that link the amino acids together. The codon AUG acts as a start codon, beginning the polypeptide chain with methionine. The chain will end when one of 3 stop codons -UAA, UAG or UGA - is reached, these codons don’t have a corresponding amino acid. 

The machinery 

With transcription and the processing of pre-mRNA complete, the mature mRNA will head to a ribosome. Ribosomes are made of two subunits, which hug the mRNA. The mRNA will move through the three sites of the ribosome, the A site, p site, and E site.

Another kind of RNA, transfer RNA (tRNA), brings in the amino acids that will make the polypeptide. On one end, it carries an amino acid - for example methionine - on the other end it will have its anticodon, which is able to bind to the codons on the mRNA - in this case, the anticodon would be UAC, and it would bind to the codon AUG. 

The process

Again there are - three stages initiation, elongation, and termination. The initiation complex is formed, beginning with the two subunits of the ribosomes moving into place around the mRNA, and then the tRNA carrying that first methionine binds to the start codon. Now elongation begins, and the mRNA moves through the A, P, and E sites one codon at a time like it's on a conveyor belt. Each time a new codon reaches the A site, a tRNA carrying its corresponding amino acid binds to it. The amino acid occupying the P site links to the one in A before being released from its tRNA which remains bound to the codon in the P site. Once a codon moves into the E site the tRNA is released. This process continues until a stop codon is reached and the termination stage begins. Stop codons don’t have a corresponding amino acid but can instead be recognised in the A site by a release factor. The polypeptide chain will be released, it can now fold into shape or go through modifications before becoming a fully functioning protein. 

Translation.

Post-translational modification 

Some polypeptide chains will have to go through modifications after translation in order to make a functional protein. The same polypeptide may be modified in various ways allowing multiple possible proteins from the same chain of amino acids. Post-translational modifications include the addition of various functional groups to proteins - for example, phosphorylation, glycosylation or ubiquitination -  cleavage, which involves cutting one or more bonds, and the formation of disulphide bonds at cysteine residues.