biology

Prokaryotic large ribosomal subunit

Prokaryotic large ribosomal subunit is a biology topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand Prokaryotic large ribosomal subunit rather than just read about it. In short: 50S is the larger subunit of the 70S ribosome of prokaryotes, i.e. bacteria and archaea. It is the site of inhibition for antibiotics such as macrolides, chloramphenicol, clindamycin, and the pleuromutilins.

Key takeaways

Prokaryotic large ribosomal subunit belongs to biology; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect Prokaryotic large ribosomal subunit to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of Prokaryotic large ribosomal subunit from memory before moving on to harder problems.

Reference excerpt

50S is the larger subunit of the 70S ribosome of prokaryotes, i.e. bacteria and archaea. It is the site of inhibition for antibiotics such as macrolides, chloramphenicol, clindamycin, and the pleuromutilins. It includes the 5S ribosomal RNA and 23S ribosomal RNA. Despite having the same sedimentation rate, bacterial and archaeal ribosomes can be quite different.

Structure 50S, roughly equivalent to the 60S ribosomal subunit in eukaryotic cells, is the larger subunit of the 70S ribosome of prokaryotes. The 50S subunit is primarily composed of proteins but also contains single-stranded RNA known as ribosomal RNA (rRNA). rRNA forms secondary and tertiary structures to maintain the structure and carry out the catalytic functions of the ribosome. X-ray crystallography has yielded electron density maps allowing the structure of the 50S in Haloarcula marismortui (archaeon) to be determined to 2.4Å resolutionand of the 50S in the Deinococcus radiodurans (bacterium) to 3.3Å. The large ribosomal subunit (50S) is approximately twice as massive as the small ribosomal subunit (30S). The model of Hm 50S, determined in 2000 by Nenad Ban and colleagues in the laboratory of Thomas Steitz and the laboratory of Peter Moore, includes 2711 of the 2923 nucleotides of 23S rRNA, all 122 nucleotides of its 5S rRNA, and structure of 27 of its 31 proteins.

Ribosomal RNA The secondary structure of 23S is divided into six large domains, within which domain V is most important in its peptidyl transferase activity. Each domain contains normal secondary structure (e.g., base triple, tetraloop, cross-strand purine stack) and is also highly symmetric in tertiary structure; proteins intervene between their helices. At tertiary structure level, the large subunit rRNA is a single gigantic domain while the small subunit contains three structural domains. This difference reflects the lesser flexibility of the large subunit required by its function. While its core is conserved, it accommodates expansion segments on its periphery.

Difference between bacteria and archaeal versions

A cryoEM structure of the 50S subunit from the archaeon Methanothermobacter thermautotrophicus has been determined. It shares the 50S size/sedimentation rate and the two rRNA count, but its 23S expansion segments have more in common with eukaryotes. A cryoEM reconstruction of the native 50S subunit of the extremely halophilic Archaean Halococcus morrhuae (classified under Euryarchaeota; Stenosarchaea group) is available. The 50S subunit contains a 108‐nucleotide insertion in its 5S rRNA, which at subnanometer resolution, is observed to emerge from a four‐way junction without affecting the parental canonical 5S rRNA structure. Due to the differences, archaeal 50S are less sensitive to some antibiotics that target bacterial 50S.

Function 50S includes the activity that catalyzes peptide bond formation (peptidyl transfer reaction), prevents premature polypeptide hydrolysis, provides a binding site for the G-protein factors (assists initiation, elongation, and termination), and helps protein folding after synthesis.

Peptidyl transfer reaction An induced-fit mechanism has been revealed for how 50S catalyzes the peptidyl transfer reaction and prevents peptidyl hydrolysis. The amino group of an aminoacyl-tRNA (binds to A site) attacks the carbon of a carbonyl group of a peptidyl-tRNA (binds to P site) and finally yields a peptide extended by one amino acid esterified to the A site tRNA bound to the ribosomal A site and a deacylated tRNA in the P site. When the A site is unoccupied, nucleotide U2620 (E. coli U2585), A2486 (2451) and C2106 (2063) sandwich the carbonyl group in the middle, forcing it into an orientation facing the A site. This orientation prevents any nucleophilic attack from the A site because the optimal attacking angle is 105 degrees from the plane of the ester group. When a tRNA with a complete[?] CCA sequence at its acceptor stem is bound to the A site, C74 of the tRNA stacking with U2590 (2555) induces a conformational change in the ribosome, resulting in movement of U2541 (2506), U2620 (2585) through G2618 (2583). The displacement of bases allows the ester group to adopt a new conformation accessible to nucleophilic attack from the A site. The N3 (nitrogen) of A2486 (2451) is closest to the peptide bond being synthesized and may function as a general base to facilitate the nucleophilic attack by the amino group of the aminoacyl-tRNA (in the A site). The pKa of A2486 (2451) is about 5 units higher in order to hydrogen bond with the amino group thus increasing its nucleophilicity. The elevation of pKa is achieved through a charge relay mechanism. A2486 (2451) interacts with G2482 (G2447), which hydrogen bonds with the buried phosphate of A2486 (2450). This buried phosphate can stabilize the normally rare imino tautomers of both bases, resulting in an increase in the negative charge density on N3.

Protein assembly After initiation, elongation, and termination, there is a fourth step of the disassembly of the post-termination complex of ribosome, mRNA, and tRNA, which is a prerequisite for the next round of protein synthesis. The large ribosomal subunit has a role in protein folding both in vitro and in vivo. The large ribosomal subunit provides a hydrophobic surface for the hydrophobic collapse step of protein folding. The newly synthesized protein needs full access to the large subunit to fold; this process may take a period of time (5 minutes for beta-galactosidase).

See also Prokaryotic small ribosomal subunit (30S) Ribosomal RNA 23S methyl RNA motif

References

External links http://pathmicro.med.sc.edu/mayer/antibiot.htm https://web.archive.org/web/20110227235620/http://www.molgen.mpg.de/~ag_ribo/ag_franceschi/franceschi-projects-50S-antibiotics.html https://web.archive.org/web/20080206051722/http://www.riboworld.com/antib/50santib-eng.shtml 23S+Ribosomal+RNA at the U.S. National Library of Medicine Medical Subject Headings (MeSH) 5S+Ribosomal+RNA at the U.S. National Library of Medicine Medical Subject Headings (MeSH)

Illustrations

Prokaryotic large ribosomal subunit: Atomic structure of the 50S subunit from Haloarcula marismortui. Proteins are shown in blue and the two RNA strands in orange and yellow.[1] The small patch of green in the center of the subunit is the active site. — Atomic structure of the 50S subunit from Haloarcula marismortui. Proteins are shown in blue and the two RNA strands in orange and yellow.[1] The small patch of green in the center of the subunit is the active site.

Worked examples

Example 1 — a first encounter with Prokaryotic large ribosomal subunit

Start with the simplest possible case. Write down what Prokaryotic large ribosomal subunit claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In biology, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to Prokaryotic large ribosomal subunit before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about Prokaryotic large ribosomal subunit ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of Prokaryotic large ribosomal subunit

In research: Prokaryotic large ribosomal subunit appears in biology research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses Prokaryotic large ribosomal subunit in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: Prokaryotic large ribosomal subunit is common in secondary-school and first-year university syllabi. It links to neighbouring topics Protein biosynthesis, Ribosomal RNA, so understanding it makes those chapters shorter.
In everyday life: Look for Prokaryotic large ribosomal subunit outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

Ask Teacher Smith questions about this articleOpens your AI tutor with a question about “Prokaryotic large ribosomal subunit” →

Affiliate

Preply — study more efficiently by working with a personal tutor. 50% off.

How to study Prokaryotic large ribosomal subunit in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what Prokaryotic large ribosomal subunit means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain Prokaryotic large ribosomal subunit out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is Prokaryotic large ribosomal subunit in simple terms?

Why does Prokaryotic large ribosomal subunit matter?

Because it connects several biology ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study Prokaryotic large ribosomal subunit?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on Prokaryotic large ribosomal subunit.