It’s not every day that your sister gets married – but it is every day – in fact each sub-second that amino acids (protein letters) get married through peptide bonds to form proteins in the process called translation. So let’s get this wedding party started!


https://youtu.be/L7AKk9X7GDY

There are a couple main types of molecular building block “alphabets” – nucleotides, which join together to make nucleic acids (DNA & RNA) & amino acids, which join together to make proteins. DNA (and messenger RNA copies of it) has the “instructions” for making the protein, a process that’s carried out by complexes called ribosomes. But how do ribosomes read the instructions if they’re written in a different language? They needs to translate!⠀

Translation is the process of putting together proteins one piece at a time. The pieces are called amino acids. There are 20 (common) ones and they link together through peptide bond “marriages” carried out in a ribosomal “chapel.” The marriage order is specified by the messenger RNA (mRNA) which is a “multi-multi-use” but “disposable” RNA copy of the permanent DNA gene.⠀

RNA (ribonucleic acid) & DNA (deoxyribonucleic acid) are both written in the “nucleic acid” language (did the name give it away?), where the letters are nucleotides (sugar+phosphate+nucleobase (1 of 5 unique options)). RNA & DNA are really similar (they just have a different sugar and 1 of the nucleobases is slightly different). Since they’re both in the same “language” we call the DNA->RNA copying process transcription. But when you go from RNA to protein you’re changing into the protein language which has amino acid letters, so we call this process translation, and it reminds me of a (very polygamous) marriage.⠀

We’ll go into it in more detail (& I’ve provided links to even more) but these are the “main events” in planning a protein wedding (translation):⠀

  • you’ve gotta put down a deposit -> amino acid activation (add AMP to amino acid) +$⠀
  • you need to find & get in the right limo -> tRNA charging (add amino acid to tRNA “carrier”) -$⠀
  • you need to get the right loaded limo to the chapel at the right time -> tRNA binding (bind tRNA to mRNA “instructions” in ribosome “chapel”)⠀
  • you need to tie the knot -> peptide bond formation (transfer growing chain to newcomer – you’re marrying someone who’s already married a bunch of people)⠀
  • you need to clear the altar for the next bride or groom -> elongation factors spend GTP money to change shape and “push” the mRNA/tRNA along & kick the tRNA off$⠀
  • you may have to pay security to kick out some uninvited guests -> hydrolytic editing $⠀

Let’s get this wedding party started, shall we? Initiation factors say “Yes, we shall!” The wedding party gets started when the ribosomal chapel assembles itself (with the help of initiation factor “construction workers” around the first bride (which is always a methionine (Met) because its codon also serves as a start signal. more on translational initiation: http://bit.ly/2KNe00D

Amino acids are taken to the chapel by transfer RNAs (tRNAs) which serve as “limos.” Each tRNA will only accept one type of amino acid (but there are lots of identical copies of all of these things, so there’s hopefully plenty to go around). Each amino acid has at least one tRNA just for itself and it’s important that the right amino acids get in the right limo because the ribosomal “priest” won’t be able to tell what amino acid’s in the limo, just what limo it is (by “reading” the limo’s “license plate” – a 3 RNA letter word called an anticodon that complements a codon on the mRNA. more on this genetic code: http://bit.ly/nirenbergcodecracking

It’s really important that there’s no identity theft allowed! Your cells have to pay for this added layer of security in the form of energy money with the help of a molecule called an aminoacyl tRNA synthetase (aka tRNA-ligase). In amino acid activation, an AMP molecule is added onto the amino acid from ATP. Then, in the tRNA charging step, the amino acid binds to the matching tRNA (the one whose anticodon “license plate” matches the codon “reserved parking for…” sign in the mRNA. The AMP is released in the process, leaving you with aminoacylated tRNA (aa-tRNA). 

We call it “charging” because phosphate bonds are “high energy” – they don’t like being held in one spot – especially next to other phosphate groups, which repel them – literally – because of the negative charge-negative charge situation. ATP’s happy to give up phosphate(s) because it’s like releasing a spring. more on this here: https://bit.ly/atpenergymoney ⠀

Why spend the money? Specificity! Ribosomes only make about 1 mistake every 10,000 amino acids. They can achieve this great accuracy because they use a strict verification process starting by making sure the right amino acid binds the right tRNA (and later a second layer of security makes sure the right tRNA binds the right codon) 

How does the aminoacyl synthetase select the right amino acid to attach to the matching tRNA? The correct one is favored because it has the highest affinity for the synthetase’s active site. That works fine for telling apart big things and little things (like glycine & tryptophan), but can mess up when things look similar (like valine & isoleucine) so you need a second step to check via hydrolytic editing. When tRNA binds the synthetase, it pushes the amino acid into a second proofreading pocket on the synthetase that does a closer check – the right one can’t fit into this pocket, so it stays safe but wrong ones can get in, so they get hydrolyzed & released.

Then it has to make sure that the right tRNA gets attached to that activated amino acid, so it has to be able to recognize that correct  tRNA. There are different ways of doing this. Most match the anticodon (have 3 nucleotide-binding pockets shaped perfectly for the 3 RNA letters of the anticodon) – some instead or in addition recognize sequences in the acceptor stem.

So, now you’ve “paid” your deposit and ensured specificity of tRNA-amino acid pair, it’s time to start heading to the chapel. But you’ll want to take a “security guard” to make sure you don’t go to the wrong place. Elongation factors (EF-G in bacteria and EF-1 in humans) travel with the aa-tRNA and don’t leave until they make sure that the codon and anticodon match (note that it’s the anticodon that matters here, not the actual amino acid, which is why that precaution during the charging step is important) – you don’t want to drop off imposters!⠀

Once the EF sees all’s good, it “pays for the aa-tRNA’s parking” by hydrolyzing (using water to split) GTP into GDP (same concept as usage of ATP for energy, just a different nucleobase), & this time the energy’s being used for shape-shifting. When it’s bound to GTP the EF has one shape, but when it’s bound to GDP it has another shape. So, after splitting the GTP, it “splits” -> falls off⠀

The EF drops off the incoming tRNA in the ribosome’s “A” spot (1 of 3 parking spots that fit in the ribosome at a time). The ribosome then carries out its priestly functions, uniting the new amino acid with the growing peptide chain through a peptide bond union. The growing strand gets transferred to the new tRNA, so you have an awkward transition stage where the peptide’s still mostly in the P spot but it’s attached to a tRNA that’s in the A spot. Another elongation factor, (EF-Tu in bacteria or EF-2 in humans) comes in and moves things along, spending GTP to push the old limo (still attached to its mRNA parking spot) into the E spot (where it falls off), the limo with the growing chain into the P spot, and bringing a new codon into the A spot for the next amino acid to be added.⠀

In a little more detail/jargon, there are 3 steps of each addition in the elongation phase:

  • tRNA selection (decoding)
    • aminoacyl-tRNA w/proper anticodon to match mRNA codon in A site
      • delivered by GTPase eEF1A (EFTu) in ternary complex w/GTP
      • eEF1A activated -> hydrolyses GTP to enable tRNA to be fully accommodated into A site
  • peptide-bond formation
    • amino group of incoming amino acid attacks ester linkage on peptidyl-tRNA in ribosomal P site -> growing chain transferred to tRNA in A site
    • as bond forms, ribosomal subunits adopt an “awkward” hybrid state – the acceptor ends shift over while the anticodon ends are stuck in place (the acceptor ends have more “wiggle room” but the anticodons are tightly bound to their matching codon (which is good cuz you don’t want them to slip)
  • translocation of mRNA-tRNA complex
    • another GTPase, eEF2 (EFG) recognizes the “awkward” hybrid state – spends GTP to translocate the mRNA-tRNA complex relative to the ribosome

Something special happens when a “stop codon” shows up in the A spot. This signals the end of the chain. Instead of a tRNA binding it, a protein termination factor binds and cleaves the chain off. more on translational termination: http://bit.ly/2IFmmEZ

The superpolygamous protein can then make itself comfortable by folding into the optimal conformation so that the amino acids that like each other are kept together, ones that hate each other are kept apart, etc. like we talked about here: http://bit.ly/aminoacidalphabet


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