Protein synthesis

I've already mentioned on this blog that amino acids combine to form proteins. In the body, there are twenty amino acids that will combine and eventually fold into a specific protein. But how?

The issue at hand 

A while back, I discussed the structures of DNA and RNA, but I didn't mention what they're for:

• DNA encodes genetic information;
• RNA helps with various biological functions; one of them is the synthesis of new proteins, in the form of messenger RNA, or mRNA for short.

Eseentially, the question is:

How can we take the genetic information present in DNA and use it to produce proteins?

And the solution is a two-stage process:

• Produce RNA using DNA as a template;
• Produce proteins using RNA as a template.

Stage 0 - Replication

I'm including this as revision, it's not entirely necessary to protein synthesis itself. 

In this stage, DNA will be replicated using itself as the template. There are three essential enzymes in this process:

• The DNA double helix will be unwound into separate strands using helicase. This creates a replication fork, with two separate strands on either side.
• These strands will then act as templates for the replication process. Primase will begin the process by creating a short section of a strand, known as a primer, which is composed of RNA monomers known as NTPs, or nucleotide triphosphates.
• Following this, DNA polymerase will bind to the primer, and will start to build the DNA sequence using deoxynucleotide triphosphates, or dNTPs, as the monomers.

Sidenote: If you're wondering what a deoxynucleotide triphosphate is, it's basically just:

• a nucleotide (so A, T, C, and G from before)
• bound to a deoxyribose sugar
• bound to three phosphate groups at the 5' carbon.

Similar monomers are used in RNA replication, except they use a ribose sugar, obviously. They're known as NTPs; probably the most famous example of one of these is adenosine triphosphate, or ATP, which acts as a phosphate donor for phosphorylation reactions in kinase cascades.

DNA polymerase acts in the 5' to 3' direction only, which causes a problem. You see, if we straightened out a double helix and laid it flat, the two strands would run anti-parallel to each other. Yet DNA is being unwound in one direction only - the direction that helicase acts in. So where DNA polymerase will act in the same direction as helicase on one strand (the leading strand), it will fail to do so on the other (the lagging strand). 

The lagging strand therefore is built up differently - DNA polymerase will only add dNTPs in small fragments, known as Okazaki fragments, after binding to the primer. This process will be non-continuous, and require successive primase and DNA polymerase action.

Once this is all done, all that needs to be done is to replace the RNA primers with DNA, as well as filling any residual gaps that might have formed. DNA ligase is then used to link together any fragments to form a continuous double-helix.  

And that's how we go from one double-helix to two! 

Stage 1 - Transcription

This process involves using DNA as a template to synthesise mRNA. 

The double-helix will first be unwound partially by RNA polymerase, before using one strand to build a section of RNA. It will do so using nucleotide triphosphates - A, U, C and G - to build a strand of RNA. 

In this way, we build a strand of mRNA. However, it's not yet ready for stage 3. First, we need to splice the strand, by cutting and adding sections of RNA to form a mature strand of mRNA, to make it able to withstand degradation of the mRNA.

It's worth noting this whole process so far has happened in the nucleus, where DNA is stored. Now, though, the mature-mRNA will leave the nucleus and bind to the ribosome, a complex of RNA and proteins where protein synthesis occurs.

Stage 2 - Translation

In this stage, the mRNA is used to build up proteins from their constituent amino acids. 

In an mRNA molecule. the sequence of bases can also be read as a sequence of codons - sections of mRNA which are three bases long. Each of these codons codes for an amino acid, with some amino acids having several codons corresponding to them, whilst others, like methionine, only have one. The ribosome will read the codons, and begin building the protein from the corresponding amino acid sequence. Each respective amino acid is brought to the ribosome via transfer RNA (tRNA) molecules, consisting of an anti-codon that binds to the codon in the mRNA molecule.

From here, the protein is built up, with new peptide (amide) bonds forming between each amino acid. the peptide chain will be transferred sequentially between each new amino acid, and the tRNA will dissociate. 

There are another four codons which are worth mentioning - three (UAA, UAG, and UGA) act as stop codons, ending the translation process, at which point the peptide chain that's formed will fold into a protein. 

The other codon is AUG, which I've sort of mentioned already - that's methionine's codon; every single protein in eukaryotes uses methionine to indicate the start of the translation process.

Epilogue - mutations

Typically, mutations in DNA don't happen, but sometimes they can, which can lead to issues in translation. For instance, you can have sections of mRNA be deleted, or even inserted, which can result in a different protein being built to the one intended. 

This is the root cause of cystic fibrosis, which is a result of mutations in the CFTR gene. The most common mutation results in the deletion of a TTT codon in the gene, which later down the line means a protein used in ion channel transportation won't include a phenylalanine. This means the protein won't fold correctly, leading to further degradation over time.

Alternatively, you can have base-pair mismatches. Whilst A-T/U and C-G seems like it should never fail - they have complementary structures, after all - occasionally you can have an A matched with a C, for example, by mistake. From this, you can have either a transversion mutation, where A is switched for G, or C with T, in the DNA (and vice versa), or a transition mutation, where a A is switched for C, or G with T, and vice versa.

These mutations could be especially harmful if they cause a stop codon to be replaced with one for an amino acid, making the protein formed far longer than it otherwise should. This can lead to issues with misfolding of the protein, which could cause additional side effects or inability to function.

A notable error is deamination, where cytosine might be converted into uracil, meaning a G-C match might suddenly become a G-U match. If this happens in the DNA, we can get further mutations down the line if left unnoticed, but luckily there's an enzyme that handles this issue to remove uracil in DNA.