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Ribosomes producing proteins, but need proteins to be produced?

Ribosomes producing proteins, but need proteins to be produced?



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So according to my textbook:

RNA is used to create ribosomal RNA (known as rRNA) which is then combined with proteins to form the ribomsomes necessary for protein synthesis.

I'm a bit confused with this statement, as ribosomes are needed to synthesise proteins, but in order to create ribosomes proteins are needed in the first place. How does this work, does the proteins needed for the creation of rRNA come from a different source? Or by synthesising proteins via ribosomes produce more proteins than required to create the ribosomes in the first place?

Also, where are the proteins synthesised? On cytoplasmic ribosomes, or on ribosomes bound to the RER?

Thanks!


Ribosomes are the only means we know by which cells produce proteins. Consequently, all proteins are made by a ribosome, including the proteins that then become part of a new ribosome. It's never a question of "more proteins than required" because there are different types of proteins and to make a ribosome, you need those specific types of proteins known as ribosomal proteins. The process of making ribosomes is known as ribosome biogenesis.

This raises the obvious question of where a cell gets its ribosomes from when it is "born". The answer is simple: from its parent. When a cell divides, each daughter cell is made of the components of the parent. The cytoplasm also gets divided, and each daughter cell receives mitochondria, ER, etc. from the parent cell. By the time those ribosomes break down, they will have produced new ribosomal proteins for new ribosomes already.

According to this review from 2017, it appears the ribosomal proteins made in the cytoplasm (so, cytoplasmic ribosomes) get shuttled into the nucleolus, where they get assembled with rRNA to make new ribosomes, which then get exported out of the nucleus into the cytoplasm.


Ribosomes producing proteins, but need proteins to be produced? - Biology

Figure 1. Ribosomes are made up of a large subunit (top) and a small subunit (bottom). During protein synthesis, ribosomes assemble amino acids into proteins.

Ribosomes are the cellular structures responsible for protein synthesis. When viewed through an electron microscope, ribosomes appear either as clusters (polyribosomes) or single, tiny dots that float freely in the cytoplasm. They may be attached to the cytoplasmic side of the plasma membrane or the cytoplasmic side of the endoplasmic reticulum and the outer membrane of the nuclear envelope. Electron microscopy has shown us that ribosomes, which are large complexes of protein and RNA, consist of two subunits, aptly called large and small (Figure 1). Ribosomes receive their “orders” for protein synthesis from the nucleus where the DNA is transcribed into messenger RNA (mRNA). The mRNA travels to the ribosomes, which translate the code provided by the sequence of the nitrogenous bases in the mRNA into a specific order of amino acids in a protein. Amino acids are the building blocks of proteins.

Because proteins synthesis is an essential function of all cells, ribosomes are found in practically every cell. Ribosomes are particularly abundant in cells that synthesize large amounts of protein. For example, the pancreas is responsible for creating several digestive enzymes and the cells that produce these enzymes contain many ribosomes. Thus, we see another example of form following function.


Overview of Protein Expression

Proteins are synthesized and regulated depending upon the functional need in the cell. The blueprints for proteins are stored in DNA and decoded by highly regulated transcriptional processes to produce messenger RNA (mRNA). The message coded by an mRNA is then translated into a protein. Transcription is the transfer of information from DNA to mRNA, and translation is the synthesis of protein based on a sequence specified by mRNA.

Simple diagram of transcription and translation. This describes the general flow of information from DNA base-pair sequence (gene) to amino acid polypeptide sequence (protein).

In prokaryotes, the process of transcription and translation occur simultaneously. The translation of mRNA starts even before a mature mRNA transcript is fully synthesized. This simultaneous transcription and translation of a gene is termed coupled transcription and translation. In eukaryotes, the processes are spatially separated and occur sequentially with transcription happening in the nucleus and translation, or protein synthesis, occurring in the cytoplasm.

Comparison of transcription and translation in prokaryotes vs. eukaryotes.

This 118-page handbook provides comprehensive information about protein expression and will help you choose the right expression system and purification technologies for your specific application and needs. Get tips and tricks when starting an experiment, and find answers to everyday problems related to protein expression.

Transcription occurs in three steps in both prokaryotes and eukaryotes: initiation, elongation and termination. Transcription begins when the double-stranded DNA is unwound to allow the binding of RNA polymerase. Once transcription is initiated, RNA polymerase is released from the DNA. Transcription is regulated at various levels by activators and repressors and also by chromatin structure in eukaryotes. In prokaryotes, no special modification of mRNA is required and translation of the message starts even before the transcription is complete. In eukaryotes, however, mRNA is further processed to remove introns (splicing), addition of a cap at the 5´ end and multiple adenines at the mRNA 3´ end to generate a polyA tail. The modified mRNA is then exported to the cytoplasm where it is translated.

Translation or protein synthesis is a multi-step process that requires macromolecules like ribosomes, transfer RNAs (tRNA), mRNA and protein factors as well as small molecules like amino acids, ATP, GTP and other cofactors. There are specific protein factors for each step of translation (see table below). The overall process is similar in both prokaryotes and eukaryotes, although particular differences exist.

During initiation, the small subunit of the ribosome bound to initiator t-RNA scans the mRNA starting at the 5’end to identify and bind the initiation codon (AUG). The large subunit of the ribosome joins the small ribosomal subunit to generate the initiation complex at the initiation codon. Protein factors as well as sequences in mRNA are involved in the recognition of the initiation codon and formation of the initiation complex. During elongation, tRNAs bind to their designated amino acids (known as tRNA charging) and shuttle them to the ribosome where they are polymerized to form a peptide. The sequence of amino acids added to the growing peptide is dependent on the mRNA sequence of the transcript. Finally, the nascent polypeptide is released in the termination step when the ribosome reaches the termination codon. At this point, the ribosome is released from the mRNA and is ready to initiate another round of translation.


15.5 Ribosomes and Protein Synthesis

In this section, you will explore the following questions:

  • What are the different sequential steps in protein synthesis?
  • What is the role of ribosomes in protein synthesis?

Connection for AP ® Courses

After the information in the gene has been transcribed to mRNA, it is ready to be translated to polypeptide. The players in translation include the mRNA template, ribosomes, tRNA molecules, amino acids, and various enzymes. Ribosomes consist of small and large subunits of protein and rRNA which bind with mRNA many ribosomes can move along the same mRNA at a time. Translation begins at the initiating AUG on mRNA, specifying methionine, the first amino acid in any polypeptide. Each amino acid is carried to the ribosome by attaching to a specific molecule of tRNA. A tRNA molecule often is depicted as a cloverleaf, with an anticodon on one end, and the amino acid attachment site at the other. Amino-acid charging enzymes ensure that the correct amino acid is attached to the correct tRNA. The anticodons on tRNA are complementary to the codons on mRNA for example, the anticodon AAA on tRNA corresponds to TTT on mRNA. Sequential amino acids are linked by peptide bonds. The mRNA is translated, elongating the polypeptide, until a STOP or nonsense codon is reached. When this happens, a release factor dissociates the components and frees the new polypeptide. Folding of the protein occurs during and after translation. Once a polypeptide is synthesized, its role as a protein is established, such as determining a physical phenotype of an organism.

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 3 of the AP ® Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP ® Biology course, an inquiry-based laboratory experience, instructional activities, and AP ® Exam questions. A Learning Objective merges required content with one or more of the seven Science Practices.

Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes.
Enduring Understanding 3.A Heritable information provides for continuity of life.
Essential Knowledge 3.A.1 DNA, and in some cases RNA, is the primary source of heritable information.
Science Practice 1.2 The student can describe representations and models of natural or man-made phenomena and systems in the domain.
Learning Objective 3.4 The student is able to describe representations and models illustrating how genetic information is translated into polypeptides.
Essential Knowledge 3.A.1 DNA, and in some cases RNA, is the primary source of heritable information.
Science Practice 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models.
Learning Objective 3.6 The student can predict how a change in a specific DNA or RNA sequence can result in changes in gene expression.

Teacher Support

Create models of protein synthesis with the following items:

  • Pipe cleaners for RNA linking several units to represent mRNA and twisting some to represent tRNAs
  • Cotton puff balls or other supplies to represent ribosomes
  • Colored beads to represent amino acids and nucleotides

Ask students what specific challenges must face amino-acyl tRNA synthetases. The enzymes must recognize the anticodon, the amino acid that matches that anticodon, and the tRNA acceptor site.

Ask students to compare and contrast TATA boxes and Kozak’s sequences. Both are based on consensus sequences. TATA boxes are associated with promoters and Kozak’s sequences with binding of the ribosomes.

The RNA in the ribosomes catalyze the formation of the peptide bond. This is a good example of a ribozyme, an RNA molecule that acts as an enzyme. Students may have heard that all enzymes are proteins. This is an opportunity to clarify the point. The enzyme involved in the splicing of introns is another example of RNA with catalytic properties.

The Science Practice Challenge Questions contain additional test questions for this section that will help you prepare for the AP exam. These questions address the following standards:
[APLO 1.16][APLO 4.22][APLO 3.6]

The synthesis of proteins consumes more of a cell’s energy than any other metabolic process. In turn, proteins account for more mass than any other component of living organisms (with the exception of water), and proteins perform virtually every function of a cell. The process of translation, or protein synthesis, involves the decoding of an mRNA message into a polypeptide product. Amino acids are covalently strung together by interlinking peptide bonds in lengths ranging from approximately 50 amino acid residues to more than 1,000. Each individual amino acid has an amino group (NH2) and a carboxyl (COOH) group. Polypeptides are formed when the amino group of one amino acid forms an amide (i.e., peptide) bond with the carboxyl group of another amino acid (Figure 15.16). This reaction is catalyzed by ribosomes and generates one water molecule.

The Protein Synthesis Machinery

In addition to the mRNA template, many molecules and macromolecules contribute to the process of translation. The composition of each component may vary across species for instance, ribosomes may consist of different numbers of rRNAs and polypeptides depending on the organism. However, the general structures and functions of the protein synthesis machinery are comparable from bacteria to human cells. Translation requires the input of an mRNA template, ribosomes, tRNAs, and various enzymatic factors.

Link to Learning

Click through the steps of this PBS interactive to see protein synthesis in action.

  1. Due to lack of protein in the diet, our body will not be able to form other proteins thus, it will conserve the protein it has for critical use, leading to hair loss.
  2. Lack of protein in the diet can weaken the immune system, thus leading to hair loss.
  3. Due to lack of protein in the diet, energy will be lost, thus leading to hair loss.
  4. Lack of protein in the diet will lead to breakage of disulfide bonds between proteins, thus leading to hair loss.

Ribosomes

Even before an mRNA is translated, a cell must invest energy to build each of its ribosomes. In E. coli, there are between 10,000 and 70,000 ribosomes present in each cell at any given time. A ribosome is a complex macromolecule composed of structural and catalytic rRNAs, and many distinct polypeptides. In eukaryotes, the nucleolus is completely specialized for the synthesis and assembly of rRNAs.

Ribosomes exist in the cytoplasm in prokaryotes and in the cytoplasm and rough endoplasmic reticulum in eukaryotes. Mitochondria and chloroplasts also have their own ribosomes in the matrix and stroma, which look more similar to prokaryotic ribosomes (and have similar drug sensitivities) than the ribosomes just outside their outer membranes in the cytoplasm. Ribosomes dissociate into large and small subunits when they are not synthesizing proteins and reassociate during the initiation of translation. In E. coli, the small subunit is described as 30S, and the large subunit is 50S, for a total of 70S (recall that Svedberg units are not additive). Mammalian ribosomes have a small 40S subunit and a large 60S subunit, for a total of 80S. The small subunit is responsible for binding the mRNA template, whereas the large subunit sequentially binds tRNAs. Each mRNA molecule is simultaneously translated by many ribosomes, all synthesizing protein in the same direction: reading the mRNA from 5' to 3' and synthesizing the polypeptide from the N terminus to the C terminus. The complete mRNA/poly-ribosome structure is called a polysome .

TRNAs

The tRNAs are structural RNA molecules that were transcribed from genes by RNA polymerase III. Depending on the species, 40 to 60 types of tRNAs exist in the cytoplasm. Serving as adaptors, specific tRNAs bind to sequences on the mRNA template and add the corresponding amino acid to the polypeptide chain. Therefore, tRNAs are the molecules that actually “translate” the language of RNA into the language of proteins.

Of the 64 possible mRNA codons—or triplet combinations of A, U, G, and C—three specify the termination of protein synthesis and 61 specify the addition of amino acids to the polypeptide chain. Of these 61, one codon (AUG) also encodes the initiation of translation. Each tRNA anticodon can base pair with one of the mRNA codons and add an amino acid or terminate translation, according to the genetic code. For instance, if the sequence CUA occurred on an mRNA template in the proper reading frame, it would bind a tRNA expressing the complementary sequence, GAU, which would be linked to the amino acid leucine.

As the adaptor molecules of translation, it is surprising that tRNAs can fit so much specificity into such a small package. Consider that tRNAs need to interact with three factors: 1) they must be recognized by the correct aminoacyl synthetase (see below) 2) they must be recognized by ribosomes and 3) they must bind to the correct sequence in mRNA.

Aminoacyl tRNA Synthetases

The process of pre-tRNA synthesis by RNA polymerase III only creates the RNA portion of the adaptor molecule. The corresponding amino acid must be added later, once the tRNA is processed and exported to the cytoplasm. Through the process of tRNA “charging,” each tRNA molecule is linked to its correct amino acid by a group of enzymes called aminoacyl tRNA synthetases . At least one type of aminoacyl tRNA synthetase exists for each of the 20 amino acids the exact number of aminoacyl tRNA synthetases varies by species. These enzymes first bind and hydrolyze ATP to catalyze a high-energy bond between an amino acid and adenosine monophosphate (AMP) a pyrophosphate molecule is expelled in this reaction. The activated amino acid is then transferred to the tRNA, and AMP is released.

The Mechanism of Protein Synthesis

As with mRNA synthesis, protein synthesis can be divided into three phases: initiation, elongation, and termination. The process of translation is similar in prokaryotes and eukaryotes. Here we’ll explore how translation occurs in E. coli, a representative prokaryote, and specify any differences between prokaryotic and eukaryotic translation.

Initiation of Translation

In E. coli mRNA, a sequence upstream of the first AUG codon, called the Shine-Dalgarno sequence (AGGAGG), interacts with the rRNA molecules that compose the ribosome. This interaction anchors the 30S ribosomal subunit at the correct location on the mRNA template. Guanosine triphosphate (GTP), which is a purine nucleotide triphosphate, acts as an energy source during translation—both at the start of elongation and during the ribosome’s translocation.

In eukaryotes, a similar initiation complex forms, comprising mRNA, the 40S small ribosomal subunit, IFs, and nucleoside triphosphates (GTP and ATP). The charged initiator tRNA, called Met-tRNAi, does not bind fMet in eukaryotes, but is distinct from other Met-tRNAs in that it can bind IFs.

Instead of depositing at the Shine-Dalgarno sequence, the eukaryotic initiation complex recognizes the 7-methylguanosine cap at the 5' end of the mRNA. A cap-binding protein (CBP) and several other IFs assist the movement of the ribosome to the 5' cap. Once at the cap, the initiation complex tracks along the mRNA in the 5' to 3' direction, searching for the AUG start codon. Many eukaryotic mRNAs are translated from the first AUG, but this is not always the case. According to Kozak’s rules , the nucleotides around the AUG indicate whether it is the correct start codon. Kozak’s rules state that the following consensus sequence must appear around the AUG of vertebrate genes: 5'-gccRccAUGG-3'. The R (for purine) indicates a site that can be either A or G, but cannot be C or U. Essentially, the closer the sequence is to this consensus, the higher the efficiency of translation.

Once the appropriate AUG is identified, the other proteins and CBP dissociate, and the 60S subunit binds to the complex of Met-tRNAi, mRNA, and the 40S subunit. This step completes the initiation of translation in eukaryotes.

Translation, Elongation, and Termination

In prokaryotes and eukaryotes, the basics of elongation are the same, so we will review elongation from the perspective of E. coli. The 50S ribosomal subunit of E. coli consists of three compartments: the A (aminoacyl) site binds incoming charged aminoacyl tRNAs. The P (peptidyl) site binds charged tRNAs carrying amino acids that have formed peptide bonds with the growing polypeptide chain but have not yet dissociated from their corresponding tRNA. The E (exit) site releases dissociated tRNAs so that they can be recharged with free amino acids. There is one exception to this assembly line of tRNAs: in E. coli, f M e t − t R N A f M e t f M e t − t R N A f M e t is capable of entering the P site directly without first entering the A site. Similarly, the eukaryotic Met-tRNAi, with help from other proteins of the initiation complex, binds directly to the P site. In both cases, this creates an initiation complex with a free A site ready to accept the tRNA corresponding to the first codon after the AUG.

During translation elongation, the mRNA template provides specificity. As the ribosome moves along the mRNA, each mRNA codon comes into register, and specific binding with the corresponding charged tRNA anticodon is ensured. If mRNA were not present in the elongation complex, the ribosome would bind tRNAs nonspecifically.

Elongation proceeds with charged tRNAs entering the A site and then shifting to the P site followed by the E site with each single-codon “step” of the ribosome. Ribosomal steps are induced by conformational changes that advance the ribosome by three bases in the 3' direction. The energy for each step of the ribosome is donated by an elongation factor that hydrolyzes GTP. Peptide bonds form between the amino group of the amino acid attached to the A-site tRNA and the carboxyl group of the amino acid attached to the P-site tRNA. The formation of each peptide bond is catalyzed by peptidyl transferase , an RNA-based enzyme that is integrated into the 50S ribosomal subunit. The energy for each peptide bond formation is derived from GTP hydrolysis, which is catalyzed by a separate elongation factor. The amino acid bound to the P-site tRNA is also linked to the growing polypeptide chain. As the ribosome steps across the mRNA, the former P-site tRNA enters the E site, detaches from the amino acid, and is expelled (Figure 15.17). Amazingly, the E. coli translation apparatus takes only 0.05 seconds to add each amino acid, meaning that a 200-amino acid protein can be translated in just 10 seconds.


Tracking the footprints of protein synthesis

Researchers are tracking these large molecular machines, following their trails of protein synthesis to determine how precisely cells produce their protein components. Building too few might upset growth, metabolism, and maintenance, while too many might be wasteful and potentially toxic. Whether eukaryotic cells tune their gene expression to produce just enough of each protein remains a longstanding question.

Bacteria appear to generate the exact levels needed to function — no more, no less. However, more complex organisms have different metabolic needs, means to control gene expression, and ways to eliminate unwanted proteins, perhaps engendering a different strategy to ensure correct protein levels. Using a combination of their own experiments and open access databases, a duo of scientists from the MIT Department of Biology aimed to establish how precisely cells from organisms like budding yeast, zebrafish, mice, and humans tune their protein production. Do these eukaryotic cells generate precise amounts of protein, or do they make roughly the correct amount and rely on processes like degradation to trim the excess?

To answer this question, the researchers refined an existing technique, known as ribosome profiling, to quantify the protein synthesis rates by tracking the ribosome footprints. They were intrigued to find that, for the proteins they studied, eukaryotes precisely tuned their protein production just like bacteria. Despite the fundamental differences between these organisms, they shared a basic strategy.

“We tend to think of gene expression as a production line, transforming genetic information into well-defined protein machines,” says Gene-Wei Li, an assistant professor of biology and senior author of the study. “But in actuality, it’s not yet clear whether all organisms or all cells operate under the same principles of protein production. The impetus of this study was to understand if proteins are made as precisely in eukaryotes as they are in bacteria, while also resolving ambiguities in existing methods for measuring protein synthesis rates.”

Graduate student James Taggart was the first author of this study, which appears in the journal Cell Systems on Dec. 12.

A clear case of proportional synthesis

In 2014, when Li was still a postdoc at the University of California at San Francisco, he and his colleagues set out to measure protein synthesis rates in bacteria. They examined the subunits of multi-protein complexes in Escherichia coli, and showed that the bacteria operated under laws of proportional synthesis — meaning they were generating proteins in the exact ratio needed for cellular function. If bacteria produce too much for some reason, a degradation pathway is activated to break down those subunits, but this process constitutes more of a failsafe than the primary means to regulate protein abundance.

In the present study, Li and Taggart aimed to make similar measurements in eukaryotes, starting with budding yeast. They used the same technique as Li in 2014 — ribosome profiling — but with a few modifications.

Developed in 2009, ribosome profiling permits researchers to capture a snapshot of which mRNAs are being translated at a single moment in time. By using drugs that literally stop ribosomes in their tracks, scientists can freeze these molecular machines in place and destroy any un-protected mRNA that is not occupied (and thus shielded) by a stagnant ribosome. The fragments of mRNA — the ribosome footprints — can be sequenced to provide a barcode identifying which proteins were being made. The density of such footprints reveals the synthesis rates of each protein relative to the others.

Although ribosome profiling revolutionized our ability to gauge protein synthesis across the entire genome, it is sometimes difficult to map each mRNA fragment back to its original location within the genome and the protein product to which it corresponds. A portion of one gene may have a sequence that’s identical to another gene that encodes an entirely separate protein.

Here’s where Taggart tweaked the approach slightly: he excluded these ambiguous mRNA fragments in his analysis, and only counted the unique ribosome footprints that he could trace back to specific proteins. He then divided the number of ribosome footprints by the length of the gene, minus the ambiguous sequences and non-coding intron regions. While more common analytic approaches fail to accurately account for these ambiguous footprints, Taggart only considered what he calls “meaningful” footprints that he could map to specific regions on the genome. As a result, his modifications generated more precise synthesis rates.

He ultimately curated a comprehensive list of roughly 500 proteins in yeast, comprising about 100 different protein complexes. As he monitored the yeast’s protein output, it appeared they produced just the right amount of subunits to complete the complex — no more, no less. It was a clear case of proportional synthesis.

Protein overload

Once they fine-tuned their method of quantifying protein production, the researchers wondered what would happen if they upset the cell’s careful synthesis balance. Do eukaryotes have a widespread mechanism to regulate the amount of protein they produce?

Although yeast normally only have 16 chromosomes, with the help of Angelika Amon’s lab, the researchers duplicated each of them, one at a time, so the cell would have the capacity to build twice as many proteins using the genetic information from that extra chromosome. In humans, this kind of imbalance, known as aneuploidy, can lead to disorders like Down syndrome.

Rather than sensing the excess protein and subsequently reducing production, the yeast did not initiate any internal communication to shut down operations at the level of transcription or translation. This runs counter to what is observed in some bacteria.

“It was interesting to see that bacteria and yeast both make the exact amount of protein they need,” Taggart says, “although the ways they ensure precise synthesis are different. Many bacterial genes possess the negative feedback loops that yeast appear to lack.”

Using data from open access databases, the researchers also identified proportional synthesis in higher eukaryotes, including zebrafish, mice, and humans for the subunits they examined from three large, highly conserved protein complexes. Despite the clear physiological and genetic difference between organisms, the complexes were produced in just the right ratios. The only exception was during zebrafish embryonic development, when the researchers concluded that protein production may not be proportional. This signified that the requirements for proportional synthesis might vary over the course of an organism’s lifetime, depending on age, nutrient availability, and stress.

“Perhaps this precision is something we can learn from biology,” Li says. Once researchers fully understand how cells fine-tune their protein production, he explains, they can apply that knowledge to designing their own molecules and pathways.

Eduardo Torres, an assistant professor of molecular, cell and cancer biology at the University of Massachusetts Medical School, says these requirements are conserved from bacteria to humans, “suggesting that the evolutionary pressure to produce protein amounts efficiently is a fundamental aspect of cell biology."

“The next step would be to understand the mechanisms behind the balanced synthesis of protein complexes,” says Torres, who was not involved in the study. “Future studies integrating knowledge of several aspects of the regulation of gene expression will be necessary to understand how cells fine-tune the expression of each subunit of a particular complex.”

Taggart also finds their findings compelling from an evolutionary perspective. “It appears eukaryotes have also evolved under pressure to achieve this proportional synthesis even though they're different from bacteria in so many other ways,” he says. “In all domains of life, protein synthesis is both an engine for proliferation and a hub for regulation.”

The research was supported by a National Institutes of Health (NIH) grant, the Pew Biomedical Scholars Program, Sloan Research Fellowship, Searle Scholars Program, Smith Family Award for Excellence in Biomedical Research, National Science Foundation Graduate Research Fellowship, and an NIH Pre-Doctoral Training Grant.


Contents

The sequence of DNA that encodes the sequence of the amino acids in a protein is transcribed into a messenger RNA chain. Ribosomes bind to messenger RNAs and use their sequences for determining the correct sequence of amino acids to generate a given protein. Amino acids are selected and carried to the ribosome by transfer RNA (tRNA) molecules, which enter the ribosome and bind to the messenger RNA chain via an anti-codon stem loop. For each coding triplet (codon) in the messenger RNA, there is a transfer RNA that matches and carries the correct amino acid for incorporating into a growing polypeptide chain. Once the protein is produced, it can then fold to produce a functional three-dimensional structure.

A ribosome is made from complexes of RNAs and proteins and is therefore a ribonucleoprotein complex. Each ribosome is composed of small (30S) and large (50S) components called subunits which are bound to each other:

  1. (30S) has mainly a decoding function and is also bound to the mRNA
  2. (50S) has mainly a catalytic function and is also bound to the aminoacylated tRNAs.

The synthesis of proteins from their building blocks takes place in four phases: initiation, elongation, termination, and recycling. The start codon in all mRNA molecules has the sequence AUG. The stop codon is one of UAA, UAG, or UGA since there are no tRNA molecules that recognize these codons, the ribosome recognizes that translation is complete. [5] When a ribosome finishes reading an mRNA molecule, the two subunits separate and are usually broken up but can be re-used. Ribosomes are ribozymes, because the catalytic peptidyl transferase activity that links amino acids together is performed by the ribosomal RNA. Ribosomes are often associated with the intracellular membranes that make up the rough endoplasmic reticulum.

Ribosomes from bacteria, archaea and eukaryotes in the three-domain system resemble each other to a remarkable degree, evidence of a common origin. They differ in their size, sequence, structure, and the ratio of protein to RNA. The differences in structure allow some antibiotics to kill bacteria by inhibiting their ribosomes, while leaving human ribosomes unaffected. In all species, more than one ribosome may move along a single mRNA chain at one time (as a polysome), each "reading" a specific sequence and producing a corresponding protein molecule.

The mitochondrial ribosomes of eukaryotic cells functionally resemble many features of those in bacteria, reflecting the likely evolutionary origin of mitochondria. [6] [7]

Ribosomes were first observed in the mid-1950s by Romanian-American cell biologist George Emil Palade, using an electron microscope, as dense particles or granules. [8] The term "ribosome" was proposed by scientist Richard B. Roberts in the end of 1950s:

During the course of the symposium a semantic difficulty became apparent. To some of the participants, "microsomes" mean the ribonucleoprotein particles of the microsome fraction contaminated by other protein and lipid material to others, the microsomes consist of protein and lipid contaminated by particles. The phrase "microsomal particles" does not seem adequate, and "ribonucleoprotein particles of the microsome fraction" is much too awkward. During the meeting, the word "ribosome" was suggested, which has a very satisfactory name and a pleasant sound. The present confusion would be eliminated if "ribosome" were adopted to designate ribonucleoprotein particles in sizes ranging from 35 to 100S.

Albert Claude, Christian de Duve, and George Emil Palade were jointly awarded the Nobel Prize in Physiology or Medicine, in 1974, for the discovery of the ribosome. [10] The Nobel Prize in Chemistry 2009 was awarded to Venkatraman Ramakrishnan, Thomas A. Steitz and Ada E. Yonath for determining the detailed structure and mechanism of the ribosome. [11]

The ribosome is a complex cellular machine. It is largely made up of specialized RNA known as ribosomal RNA (rRNA) as well as dozens of distinct proteins (the exact number varies slightly between species). The ribosomal proteins and rRNAs are arranged into two distinct ribosomal pieces of different sizes, known generally as the large and small subunit of the ribosome. Ribosomes consist of two subunits that fit together (Figure 2) and work as one to translate the mRNA into a polypeptide chain during protein synthesis (Figure 1). Because they are formed from two subunits of non-equal size, they are slightly longer in the axis than in diameter.

Bacterial ribosomes Edit

Bacterial ribosomes are around 20 nm (200 Å) in diameter and are composed of 65% rRNA and 35% ribosomal proteins. [12] Eukaryotic ribosomes are between 25 and 30 nm (250–300 Å) in diameter with an rRNA-to-protein ratio that is close to 1. [13] Crystallographic work [14] has shown that there are no ribosomal proteins close to the reaction site for polypeptide synthesis. This suggests that the protein components of ribosomes do not directly participate in peptide bond formation catalysis, but rather that these proteins act as a scaffold that may enhance the ability of rRNA to synthesize protein (See: Ribozyme).

The ribosomal subunits of bacteria and eukaryotes are quite similar. [16]

The unit of measurement used to describe the ribosomal subunits and the rRNA fragments is the Svedberg unit, a measure of the rate of sedimentation in centrifugation rather than size. This accounts for why fragment names do not add up: for example, bacterial 70S ribosomes are made of 50S and 30S subunits.

Bacteria have 70S ribosomes, each consisting of a small (30S) and a large (50S) subunit. E. coli, for example, has a 16S RNA subunit (consisting of 1540 nucleotides) that is bound to 21 proteins. The large subunit is composed of a 5S RNA subunit (120 nucleotides), a 23S RNA subunit (2900 nucleotides) and 31 proteins. [16]

Ribosome of E. coli (a bacterium) [17] : 962
ribosome subunit rRNAs r-proteins
70S 50S 23S (2904 nt) 31
5S (120 nt)
30S 16S (1542 nt) 21

Affinity label for the tRNA binding sites on the E. coli ribosome allowed the identification of A and P site proteins most likely associated with the peptidyltransferase activity labelled proteins are L27, L14, L15, L16, L2 at least L27 is located at the donor site, as shown by E. Collatz and A.P. Czernilofsky. [18] [19] Additional research has demonstrated that the S1 and S21 proteins, in association with the 3′-end of 16S ribosomal RNA, are involved in the initiation of translation. [20]

Archaeal ribosomes Edit

Archaeal ribosomes share the same general dimensions of bacteria ones, being a 70S ribosome made up from a 50S large subunit, a 30S small subunit, and containing three rRNA chains. However, on the sequence level, they are much closer to eukaryotic ones than to bacterial ones. Every extra ribosomal protein archaea have compared to bacteria has an eukaryotic counterpart, while no such relation applies between archaea and bacteria. [21]

Eukaryotic ribosomes Edit

Eukaryotes have 80S ribosomes located in their cytosol, each consisting of a small (40S) and large (60S) subunit. Their 40S subunit has an 18S RNA (1900 nucleotides) and 33 proteins. [22] [23] The large subunit is composed of a 5S RNA (120 nucleotides), 28S RNA (4700 nucleotides), a 5.8S RNA (160 nucleotides) subunits and 46 proteins. [16] [22] [24]

eukaryotic cytosolic ribosomes (R. norvegicus) [17] : 65
ribosome subunit rRNAs r-proteins
80S 60S 28S (4718 nt) 49
5.8S (160 nt)
5S (120 nt)
40S 18S (1874 nt) 33

During 1977, Czernilofsky published research that used affinity labeling to identify tRNA-binding sites on rat liver ribosomes. Several proteins, including L32/33, L36, L21, L23, L28/29 and L13 were implicated as being at or near the peptidyl transferase center. [25]

Plastoribosomes and mitoribosomes Edit

In eukaryotes, ribosomes are present in mitochondria (sometimes called mitoribosomes) and in plastids such as chloroplasts (also called plastoribosomes). They also consist of large and small subunits bound together with proteins into one 70S particle. [16] These ribosomes are similar to those of bacteria and these organelles are thought to have originated as symbiotic bacteria [16] Of the two, chloroplastic ribosomes are closer to bacterial ones than mitochrondrial ones are. Many pieces of ribosomal RNA in the mitochrondria are shortened, and in the case of 5S rRNA, replaced by other structures in animals and fungi. [26] In particular, Leishmania tarentolae has a minimalized set of mitochondrial rRNA. [27] In contrast, plant mitoribosomes have both extended rRNA and additional proteins as compared to bacteria, in particular, many pentatricopetide repeat proteins. [28]

The cryptomonad and chlorarachniophyte algae may contain a nucleomorph that resembles a vestigial eukaryotic nucleus. [29] Eukaryotic 80S ribosomes may be present in the compartment containing the nucleomorph. [ citation needed ]

Making use of the differences Edit

The differences between the bacterial and eukaryotic ribosomes are exploited by pharmaceutical chemists to create antibiotics that can destroy a bacterial infection without harming the cells of the infected person. Due to the differences in their structures, the bacterial 70S ribosomes are vulnerable to these antibiotics while the eukaryotic 80S ribosomes are not. [30] Even though mitochondria possess ribosomes similar to the bacterial ones, mitochondria are not affected by these antibiotics because they are surrounded by a double membrane that does not easily admit these antibiotics into the organelle. [31] A noteworthy counterexample, however, includes the antineoplastic antibiotic chloramphenicol, which successfully inhibits bacterial 50S and eukaryotic mitochondrial 50S ribosomes. [32] The same of mitochondria cannot be said of chloroplasts, where antibiotic resistance in ribosomal proteins is a trait to be introduced as a marker in genetic engineering. [33]

Common properties Edit

The various ribosomes share a core structure, which is quite similar despite the large differences in size. Much of the RNA is highly organized into various tertiary structural motifs, for example pseudoknots that exhibit coaxial stacking. The extra RNA in the larger ribosomes is in several long continuous insertions, [34] such that they form loops out of the core structure without disrupting or changing it. [16] All of the catalytic activity of the ribosome is carried out by the RNA the proteins reside on the surface and seem to stabilize the structure. [16]

High-resolution structure Edit

The general molecular structure of the ribosome has been known since the early 1970s. In the early 2000s, the structure has been achieved at high resolutions, of the order of a few ångströms.

The first papers giving the structure of the ribosome at atomic resolution were published almost simultaneously in late 2000. The 50S (large prokaryotic) subunit was determined from the archaeon Haloarcula marismortui [35] and the bacterium Deinococcus radiodurans, [36] and the structure of the 30S subunit was determined from Thermus thermophilus. [15] These structural studies were awarded the Nobel Prize in Chemistry in 2009. In May 2001 these coordinates were used to reconstruct the entire T. thermophilus 70S particle at 5.5 Å resolution. [37]

Two papers were published in November 2005 with structures of the Escherichia coli 70S ribosome. The structures of a vacant ribosome were determined at 3.5 Å resolution using X-ray crystallography. [38] Then, two weeks later, a structure based on cryo-electron microscopy was published, [39] which depicts the ribosome at 11–15 Å resolution in the act of passing a newly synthesized protein strand into the protein-conducting channel.

The first atomic structures of the ribosome complexed with tRNA and mRNA molecules were solved by using X-ray crystallography by two groups independently, at 2.8 Å [40] and at 3.7 Å. [41] These structures allow one to see the details of interactions of the Thermus thermophilus ribosome with mRNA and with tRNAs bound at classical ribosomal sites. Interactions of the ribosome with long mRNAs containing Shine-Dalgarno sequences were visualized soon after that at 4.5–5.5 Å resolution. [42]

In 2011, the first complete atomic structure of the eukaryotic 80S ribosome from the yeast Saccharomyces cerevisiae was obtained by crystallography. [22] The model reveals the architecture of eukaryote-specific elements and their interaction with the universally conserved core. At the same time, the complete model of a eukaryotic 40S ribosomal structure in Tetrahymena thermophila was published and described the structure of the 40S subunit, as well as much about the 40S subunit's interaction with eIF1 during translation initiation. [23] Similarly, the eukaryotic 60S subunit structure was also determined from Tetrahymena thermophila in complex with eIF6. [24]

Ribosomes are minute particles consisting of RNA and associated proteins that function to synthesize proteins. Proteins are needed for many cellular functions such as repairing damage or directing chemical processes. Ribosomes can be found floating within the cytoplasm or attached to the endoplasmic reticulum. Their main function is to convert genetic code into an amino acid sequence and to build protein polymers from amino acid monomers.

Ribosomes act as catalysts in two extremely important biological processes called peptidyl transfer and peptidyl hydrolysis. [43] The "PT center is responsible for producing protein bonds during protein elongation". [43]

Translation Edit

Ribosomes are the workplaces of protein biosynthesis, the process of translating mRNA into protein. The mRNA comprises a series of codons which are decoded by the ribosome so as to make the protein. Using the mRNA as a template, the ribosome traverses each codon (3 nucleotides) of the mRNA, pairing it with the appropriate amino acid provided by an aminoacyl-tRNA. Aminoacyl-tRNA contains a complementary anticodon on one end and the appropriate amino acid on the other. For fast and accurate recognition of the appropriate tRNA, the ribosome utilizes large conformational changes (conformational proofreading). [44] The small ribosomal subunit, typically bound to an aminoacyl-tRNA containing the first amino acid methionine, binds to an AUG codon on the mRNA and recruits the large ribosomal subunit. The ribosome contains three RNA binding sites, designated A, P and E. The A-site binds an aminoacyl-tRNA or termination release factors [45] [46] the P-site binds a peptidyl-tRNA (a tRNA bound to the poly-peptide chain) and the E-site (exit) binds a free tRNA. Protein synthesis begins at a start codon AUG near the 5' end of the mRNA. mRNA binds to the P site of the ribosome first. The ribosome recognizes the start codon by using the Shine-Dalgarno sequence of the mRNA in prokaryotes and Kozak box in eukaryotes.

Although catalysis of the peptide bond involves the C2 hydroxyl of RNA's P-site adenosine in a proton shuttle mechanism, other steps in protein synthesis (such as translocation) are caused by changes in protein conformations. Since their catalytic core is made of RNA, ribosomes are classified as "ribozymes," [47] and it is thought that they might be remnants of the RNA world. [48]

In Figure 5, both ribosomal subunits ( small and large ) assemble at the start codon (towards the 5' end of the mRNA). The ribosome uses tRNA that matches the current codon (triplet) on the mRNA to append an amino acid to the polypeptide chain. This is done for each triplet on the mRNA, while the ribosome moves towards the 3' end of the mRNA. Usually in bacterial cells, several ribosomes are working parallel on a single mRNA, forming what is called a polyribosome or polysome.

Cotranslational folding Edit

The ribosome is known to actively participate in the protein folding. [49] [50] The structures obtained in this way are usually identical to the ones obtained during protein chemical refolding however, the pathways leading to the final product may be different. [51] [52] In some cases, the ribosome is crucial in obtaining the functional protein form. For example, one of the possible mechanisms of folding of the deeply knotted proteins relies on the ribosome pushing the chain through the attached loop. [53]

Addition of translation-independent amino acids Edit

Presence of a ribosome quality control protein Rqc2 is associated with mRNA-independent protein elongation. [54] [55] This elongation is a result of ribosomal addition (via tRNAs brought by Rqc2) of CAT tails: ribosomes extend the C-terminus of a stalled protein with random, translation-independent sequences of alanines and threonines. [56] [57]

Ribosomes are classified as being either "free" or "membrane-bound".

Free and membrane-bound ribosomes differ only in their spatial distribution they are identical in structure. Whether the ribosome exists in a free or membrane-bound state depends on the presence of an ER-targeting signal sequence on the protein being synthesized, so an individual ribosome might be membrane-bound when it is making one protein, but free in the cytosol when it makes another protein.

Ribosomes are sometimes referred to as organelles, but the use of the term organelle is often restricted to describing sub-cellular components that include a phospholipid membrane, which ribosomes, being entirely particulate, do not. For this reason, ribosomes may sometimes be described as "non-membranous organelles".

Free ribosomes Edit

Free ribosomes can move about anywhere in the cytosol, but are excluded from the cell nucleus and other organelles. Proteins that are formed from free ribosomes are released into the cytosol and used within the cell. Since the cytosol contains high concentrations of glutathione and is, therefore, a reducing environment, proteins containing disulfide bonds, which are formed from oxidized cysteine residues, cannot be produced within it.

Membrane-bound ribosomes Edit

When a ribosome begins to synthesize proteins that are needed in some organelles, the ribosome making this protein can become "membrane-bound". In eukaryotic cells this happens in a region of the endoplasmic reticulum (ER) called the "rough ER". The newly produced polypeptide chains are inserted directly into the ER by the ribosome undertaking vectorial synthesis and are then transported to their destinations, through the secretory pathway. Bound ribosomes usually produce proteins that are used within the plasma membrane or are expelled from the cell via exocytosis. [58]

In bacterial cells, ribosomes are synthesized in the cytoplasm through the transcription of multiple ribosome gene operons. In eukaryotes, the process takes place both in the cell cytoplasm and in the nucleolus, which is a region within the cell nucleus. The assembly process involves the coordinated function of over 200 proteins in the synthesis and processing of the four rRNAs, as well as assembly of those rRNAs with the ribosomal proteins.

The ribosome may have first originated in an RNA world, appearing as a self-replicating complex that only later evolved the ability to synthesize proteins when amino acids began to appear. [59] Studies suggest that ancient ribosomes constructed solely of rRNA could have developed the ability to synthesize peptide bonds. [60] [61] [62] In addition, evidence strongly points to ancient ribosomes as self-replicating complexes, where the rRNA in the ribosomes had informational, structural, and catalytic purposes because it could have coded for tRNAs and proteins needed for ribosomal self-replication. [63] Hypothetical cellular organisms with self-replicating RNA but without DNA are called ribocytes (or ribocells). [64] [65]

As amino acids gradually appeared in the RNA world under prebiotic conditions, [66] [67] their interactions with catalytic RNA would increase both the range and efficiency of function of catalytic RNA molecules. [59] Thus, the driving force for the evolution of the ribosome from an ancient self-replicating machine into its current form as a translational machine may have been the selective pressure to incorporate proteins into the ribosome's self-replicating mechanisms, so as to increase its capacity for self-replication. [63] [68] [69]

Ribosomes are compositionally heterogeneous between species and even within the same cell, as evidenced by the existence of cytoplasmic and mitochondria ribosomes within the same eukaryotic cells. Certain researchers have suggested that heterogeneity in the composition of ribosomal proteins in mammals is important for gene regulation, i.e., the specialized ribosome hypothesis. [70] [71] However, this hypothesis is controversial and the topic of ongoing research. [72] [73]

Heterogeneity in ribosome composition was first proposed to be involved in translational control of protein synthesis by Vince Mauro and Gerald Edelman. [74] They proposed the ribosome filter hypothesis to explain the regulatory functions of ribosomes. Evidence has suggested that specialized ribosomes specific to different cell populations may affect how genes are translated. [75] Some ribosomal proteins exchange from the assembled complex with cytosolic copies [76] suggesting that the structure of the in vivo ribosome can be modified without synthesizing an entire new ribosome.

Certain ribosomal proteins are absolutely critical for cellular life while others are not. In budding yeast, 14/78 ribosomal proteins are non-essential for growth, while in humans this depends on the cell of study. [77] Other forms of heterogeneity include post-translational modifications to ribosomal proteins such as acetylation, methylation, and phosphorylation. [78] Arabidopsis, [79] [80] [81] [82] Viral internal ribosome entry sites (IRESs) may mediate translations by compositionally distinct ribosomes. For example, 40S ribosomal units without eS25 in yeast and mammalian cells are unable to recruit the CrPV IGR IRES. [83]

Heterogeneity of ribosomal RNA modifications plays an important role in structural maintenance and/or function and most mRNA modifications are found in highly conserved regions. [84] [85] The most common rRNA modifications are pseudouridylation and 2’-O methylation of ribose. [86]


Ribosomes producing proteins, but need proteins to be produced? - Biology

Ribosomes are like tiny factories in the cell. They make proteins that perform all sorts of functions for the cell's operation.

Where are ribosomes located inside the cell?

Ribosomes are either located in the liquid inside the cell called the cytoplasm or attached to the membrane. They can be found in both prokaryote (bacteria) and eukaryote (animals and plants) cells.

Ribosomes are a type of organelle. Organelles are structures that perform specific functions for the cell. The ribosome's job is to make proteins. Other organelles include the nucleus and the mitochondria.

  • Large subunit - The large subunit contains the site where new bonds are made when creating proteins. It is called the "60S" in eukaryotic cells and the "50S" in prokaryotic cells.
  • Small subunit - The small subunit really isn't that small, just a bit smaller than the large subunit. It is responsible for the flow of information during protein synthesis. It is called the "40S" in eukaryotic cells and the "50S" in prokaryotic cells.

The main job of the ribosome is to make proteins for the cell. There can be hundreds of proteins that need to be made for the cell, so the ribosome needs specific instructions on how to make each protein. These instructions come from the nucleus in the form of messenger RNA. Messenger RNA contain specific codes that act like a recipe to tell the ribosome how to make the protein.

There are two main steps in making proteins: transcription and translation. The ribosome does the translation step. You can go here to learn more about proteins.


Two Pieces Make the Whole

There are two pieces or subunits to every ribosome. In eukaryotes, scientists have identified the 60-S (large) and 40-S (small) subunits. Even though ribosomes have slightly different structures in different species, their functional areas are all very similar.

For example, prokaryotes have ribosomes that are slightly smaller than eukaryotes. The 60-S/ 40-S model works fine for eukaryotic cells while prokaryotic cells have ribosomes made of 50-S and 30-S subunits. It's a small difference, but one of many you will find in the two different types of cells. Scientists have used this difference in ribosome structure to develop drugs that can kill prokaryotic microorganisms which cause disease. There are even structural differences between ribosomes found in the mitochondria and free ribosomes.


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Maitra, A. & Dill, K. A. Modeling the overproduction of ribosomes when antibacterial drugs act on cells. Biophys. J. 110, 743–748 (2016)

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Transcription

Protein Production faces a number of challenges. Chief amongst these is that proteins are produced in the cytoplasm of the cell, and DNA never leaves the nucleus. To get around this problem, DNA creates a messenger molecule to deliver its information outside of the nucleus: mRNA (messenger RNA). The process of making this messenger molecule is known as transcription, and has a number of steps:

  1. Initiation: The double helix of the DNA is unwound by RNA Polymerase, which docks on the DNA at a special sequence of bases (promoter)
  2. Elongation: RNA Polymerase moves downstream unwinding the DNA. As the double helix unwinds, ribonucleotide bases (A, C, G and U) attach themselves to the DNA template strand (the strand being copied) by complementary base pairing.
  3. RNA Polymerase catalyses the formation of covalent bonds between the nucleotides. In the wake of transcription, DNA strands recoil into the double helix.
  4. Termination: The RNA transcript is released from the DNA, along with the RNA polymerase.

The next stage in transcription is the addition of a 5&apos cap and a poly-A tail. These sections of the completed RNA molecule are not translated into protein. Instead they:

  1. Protect the mRNA from degradation
  2. Help the mRNA to leave the nucleus
  3. Anchor the mRNA to the ribosome during Translation

At this point a long RNA molecule has been made, but this is not the end of Transcription. The RNA molecule contains sections that are not needed as part of the protein code that need to be removed. This is like writing every other paragraph of a novel in wingdings - these sections must be removed for the story to make sense! While at first the presence of introns seems incredibly wasteful, a number of genes can give rise to several different proteins, depending on which sections are treated as exons - this is known as alternative RNA splicing. This allows a relatively small number of genes to create a much larger number of different proteins. Humans have just under twice as many genes as a fruit fly, and yet can make many times more protein products.


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