What a human ribosome is put together from
In the human cytoplasm, the working ribosome is the 80S ribosome. The number with the S is the sedimentation coefficient, a measure of how fast a particle sinks in an ultracentrifuge. Because that value depends on both shape and molecular weight, 40S and 60S do not add up to 100S.
| Subunit | RNA molecules | Length in nucleotides, approx. | Proteins, approx. |
|---|---|---|---|
| Small subunit (40S) | 18S rRNA | 1,870 | 33 |
| Large subunit (60S) | 28S rRNA | 5,070 | 47 |
| 5.8S rRNA | 160 | ||
| 5S rRNA | 120 |
The small subunit reads the messenger RNA and checks how codon and anticodon pair up. The large subunit houses the peptidyl transferase center, where the chain grows by one link. That center is made of RNA, not protein.
Binding sites of divalent magnesium in the translation machinery
Magnesium can cling to RNA in two ways. In inner-sphere coordination, the ion touches an oxygen atom of the RNA directly. In outer-sphere coordination, a shell of water molecules stays in between and forms hydrogen bonds to the RNA in turn. Both forms occur side by side in the ribosome.
| Site | Mode of binding | What is seen when the setup lacks magnesium |
|---|---|---|
| rRNA helices and knots | directly on phosphate oxygen or via bound water molecules | the compact fold loosens |
| Bridges between small and large subunit | at contact points where RNA meets RNA | the subunits separate |
| Surroundings of the peptidyl transferase center | structural, within the RNA of the large subunit | the geometry of the center is lost |
| tRNA, elbow of the L shape | at contacts between the D loop and the T loop | the three-dimensional fold becomes unstable |
| Aminoacyl-tRNA synthetases | as Mg-ATP in the active site | hardly any aminoacyl adenylate forms |
| Elongation factors eEF1A and eEF2 | as Mg-GTP in the GTP-binding domain | GTP is not split |
How many ions a ribosome really holds depends on the resolution of the structure and on the buffer conditions. Current models of bacterial ribosomes list several hundred positions; figures of a similar order exist for the human ribosome, but they have been analyzed less completely.
Sentence fixed in EU law
“Magnesium contributes to normal protein synthesis”
EU-authorized wording · Regulation (EU) No 432/2012
Aminoacylation in formulas and in plain words
The ribosome does not recognize an amino acid on its own. It recognizes the anticodon of the tRNA carrying it. That is why the accuracy of translation hinges on every tRNA being loaded with exactly the right amino acid. The aminoacyl-tRNA synthetases take care of this in a reaction made up of two partial steps.
| Partial step | Reaction | Where magnesium comes in |
|---|---|---|
| Activation | Amino acid + ATP → aminoacyl-AMP + pyrophosphate | Mg2+ binds to the β- and γ-phosphate groups of ATP and holds the molecule in a position ready to react |
| Transfer | Aminoacyl-AMP + tRNA → aminoacyl-tRNA + AMP | no further ATP; the step draws on the bond already present in the adenylate |
| Follow-up | Pyrophosphate + water → 2 phosphate | inorganic pyrophosphatase also works with magnesium ions |
Two enzyme classes with different architecture
The twenty synthetases fall into two groups according to their folding pattern. Both use Mg-ATP, but they hold it in a different shape.
| Feature compared | Class I | Class II |
|---|---|---|
| Core of the active site | Rossmann fold of parallel β-strands | antiparallel β-sheet |
| Signature sequence motifs | HIGH and KMSKS | Motifs 1, 2 and 3 |
| Shape of the bound ATP | extended | bent, often with several magnesium ions |
| First attachment to the tRNA | 2′-hydroxyl group of the terminal ribose | 3′-hydroxyl group of the terminal ribose |
| Examples | Methionyl-, tyrosyl-, tryptophanyl-, leucyl-tRNA synthetase | Seryl-, threonyl-, alanyl-, histidyl-tRNA synthetase |
Pocket summary of this section
- Ribosomal RNA needs divalent counterions to hold its compact fold.
- The subunits stay joined through bridges where magnesium ions sit.
- Every amino acid is activated by way of a complex of ATP and magnesium.
For magnesium, the authorized sentence reads: “Magnesium contributes to normal protein synthesis” — EU-authorized wording · Regulation (EU) No 432/2012. Reading the tables teaches you something about ribosomes and synthetases; it leaves the wording itself untouched.
Nucleotides split for each link added to the chain
Forming the peptide bond itself uses no ATP at the ribosome. The cost comes before and after: when the amino acid is activated, and in the movements by which elongation factors deliver the tRNA and shift the ribosome forward by one codon. Each of these nucleotides is bound to a magnesium ion while the reaction runs.
| Step in the cycle | Nucleotide split | Phosphoanhydride bonds |
|---|---|---|
| Activation at the synthetase | ATP → AMP + pyrophosphate, followed by cleavage of the pyrophosphate | 2 |
| tRNA delivery by eEF1A | GTP → GDP + phosphate | 1 |
| Forward shift by eEF2 | GTP → GDP + phosphate | 1 |
| Total per chain link | 4 |
By this count, a protein of 400 amino acids corresponds to about 1,600 split phosphoanhydride bonds, plus the start and finish of translation.
The legal setting of the EU sentence on magnesium
Health claims under Article 13 of Regulation (EC) No 1924/2006 were assessed by the European Food Safety Authority and then entered into a list by the European Commission. The wording is fixed. In the EU, a food may carry it only if it contains a significant amount of magnesium.
| Quantity defined | As laid down | Worked out for magnesium |
|---|---|---|
| EU nutrient reference value for adults | benchmark for EU labeling | 375 mg per day |
| Minimum content in solid foods | 15% per 100 g | 56.25 mg |
| Minimum content in beverages | 7.5% per 100 ml | 28.1 mg |
The EU reference value is a figure for calculating labels. It describes neither what a particular person needs nor an amount above which protein synthesis would run differently.
Notes jotted beside the tables
Why do ribosomes fall apart in a buffer that lacks magnesium?
Without enough divalent counterions, the phosphate groups of the rRNA repel each other more strongly, and the bridges between the subunits lose their grip. In the test tube the process is reversible: add magnesium back and the parts come together again. In a living cell, by contrast, the concentration stays largely constant.
Does the magnesium ion form the peptide bond itself?
Not directly, as far as structural research can tell. In the peptidyl transferase center, it is mainly RNA bases and a hydroxyl group of the tRNA that line the two reaction partners up with each other. Magnesium ions nearby keep the shape of this center intact, but they do not sit at the spot where the bond is formed.
Do all the figures come from the human ribosome?
The components table describes the human 80S ribosome. Many statements about individual ions, however, rest on structures from bacteria and yeast, because those were solved earlier and at higher resolution. The basic principles hold across these organisms; individual positions may differ.
Does the magnesium sentence mention an amount?
No. It names neither a daily amount nor any symptoms; the sentence concerns the ordinary process when enough magnesium is taken in.