The Structure & Function of mRNA | Sciencing
Learn how this step inside the nucleus leads to protein synthesis in the One factor that helps ensure precise replication is the double-helical structure of DNA itself. . After the transcription of DNA to mRNA is complete, translation — or the . This is due to (i) the intimate relationship between RNA structure and function, the nucleus to its cytoplasmic role in protein synthesis. The relationships between mRNA folding and translation appear to be complex i.e. individual protein domains fold before the synthesis of the.
Second,a three-base sequence in the more As studies on tRNA proceeded, 30 — 40 different tRNAs were identified in bacterial cells and as many as 50 — in animal and plant cells. Thus the number of tRNAs in most cells is more than the number of amino acids found in proteins 20 and also differs from the number of codons in the genetic code Consequently, many amino acids have more than one tRNA to which they can attach explaining how there can be more tRNAs than amino acids ; in addition, many tRNAs can attach to more than one codon explaining how there can be more codons than tRNAs.
As noted previously, most amino acids are encoded by more than one codon, requiring some tRNAs to recognize more than one codon. The function of tRNA molecules, which are 70 — 80 nucleotides long, depends on their precise three-dimensional structures.
In solution, all tRNA molecules fold into a similar stem-loop arrangement that resembles a cloverleaf when drawn in two dimensions Figure a.
Three nucleotides termed the anticodonlocated at the center of one loop, can form base pairs with the three complementary nucleotides forming a codon in mRNA. As discussed later, specific aminoacyl-tRNA synthetases recognize the surface structure of each tRNA for a specific amino acid and covalently attach the proper amino acid to the unlooped amino acid acceptor stem.
Viewed in three dimensions, the folded tRNA molecule has an L shape with the anticodon loop and acceptor stem forming the ends of the two arms Figure b. Figure Structure of tRNAs. This molecule is synthesized from the nucleotides A, C, G, and U, but some of the nucleotides, shown in red, are modified after synthesis: Nonstandard Base Pairing Often Occurs between Codons and Anticodons If perfect Watson-Crick base pairing were demanded between codons and anticodons, cells would have to contain exactly 61 different tRNA species, one for each codon that specifies an amino acid.
As noted above, however, many cells contain fewer than 61 tRNAs. The explanation for the smaller number lies in the capability of a single tRNA anticodon to recognize more than one, but not necessarily every, codon corresponding to a given amino acid. Although the first and second bases of a codon form standard Watson-Crick base pairs with the third and second bases of the corresponding anticodon, four nonstandard interactions can occur between bases in the wobble position.
Thus, a given anticodon in tRNA with G in the first wobble position can base-pair with the two corresponding codons that have either pyrimidine C or U in the third position Figure However, the base in the third or wobble position of an mRNA codon often forms a nonstandard base pair with more Although adenine rarely is found in the anticodon wobble position, many tRNAs in plants and animals contain inosine Ia deaminated product of adenine, at this position.
Inosine can form nonstandard base pairs with A, C, and U Figure For this reason, inosine-containing tRNAs are heavily employed in translation of the synonymous codons that specify a single amino acid.
The first step, attachment of the appropriate amino acid to a tRNA, is catalyzed by a specific aminoacyl-tRNA synthetase see Figure Each of the 20 different synthetases recognizes one amino acid and all its compatible, or cognate, tRNAs.
In this reaction, the amino acid is linked to the tRNA by a high-energy bond and thus is said to be activated. The energy of this bond subsequently drives the formation of peptide bonds between adjacent amino acids in a growing polypeptide chain. The equilibrium of the aminoacylation reaction is driven further toward activation of the amino acid by hydrolysis of the high-energy phosphoanhydride bond in pyrophosphate.
Each of these enzymes recognizes one kind of amino acid and all the cognate tRNAs that recognize codons for that amino acid. The two-step aminoacylation more The amino acid sequences of the aminoacyl-tRNA synthetases ARSs from many organisms are now known, and the three-dimensional structures of over a dozen enzymes of both classes have been solved.
The binding surfaces of class I enzymes tend to be somewhat complementary to those of class II enzymes. These different binding surfaces and the consequent alignment of bound tRNAs probably account in part for the difference in the hydroxyl group to which the aminoacyl group is transferred Figure Because some amino acids are so similar structurally, aminoacyl-tRNA synthetases sometimes make mistakes. These are corrected, however, by the enzymes themselves, which check the fit in the binding pockets and facilitate deacylation of any misacylated tRNAs.
This crucial function helps guarantee that a tRNA delivers the correct amino acid to the protein -synthesizing machinery.
Recognition of a tRNA by aminoacyl synthetases. Shown here are the outlines of the three-dimensional structures of the two synthetases. Once a tRNA is loaded with an amino acidcodon-anticodon pairing directs the tRNA into the proper ribosome site; if the wrong amino acid is attached to the tRNA, an error in protein synthesis results.
As noted already, each aminoacyl-tRNA synthetase can aminoacylate all the different tRNAs whose anticodons correspond to the same amino acid. One approach for studying the identity elements in tRNAs that are recognized by aminoacyl-tRNA synthetases is to produce synthetic genes that encode tRNAs with normal and various mutant sequences by techniques discussed in Chapter 7. The normal and mutant tRNAs produced from such synthetic genes then can be tested for their ability to bind purified synthetases.
Very probably no single structure or sequence completely determines a specific tRNA identity. However, some important structural features of several E. Perhaps the most logical identity element in a tRNA molecule is the anticodon itself. Thus this synthetase specifically recognizes the correct anticodon. However, the anticodon may not be the principal identity element in other tRNAs see Figure Figure shows the extent of base sequence conservation in E.
Identity elements are found in several regions, particularly the end of the acceptor arm. A simple case is presented by tRNAAla: Solution of the three-dimensional structure of additional complexes between aminoacyl-tRNA synthetases and their cognate tRNAs should provide a clear understanding of the rules governing the recognition of tRNAs by specific synthetases.
Identity elements in tRNA involved in recognition by aminoacyl-tRNA synthetases, as demonstrated by both conservation and experimentation. The 67 known tRNA sequences in E.
Role of mRNA structure in the control of protein folding
The conserved nucleotides in different more Ribosomes Are Protein-Synthesizing Machines If the many components that participate in translating mRNA had to interact in free solution, the likelihood of simultaneous collisions occurring would be so low that the rate of amino acid polymerization would be very slow. The efficiency of translation is greatly increased by the binding of the mRNA and the individual aminoacyl-tRNAs to the most abundant RNA - protein complex in the cell — the ribosome.
This two-part machine directs the elongation of a polypeptide at a rate of three to five amino acids added per second. Small proteins of — amino acids are therefore made in a minute or less. On the other hand, it takes 2 to 3 hours to make the largest known protein, titin, which is found in muscle and contains 30, amino acid residues. The machine that accomplishes this task must be precise and persistent. With the aid of the electron microscope, ribosomes were first discovered as discrete, rounded structures prominent in animal tissues secreting large amounts of protein ; initially, however, they were not known to play a role in protein synthesis.
This is the basis for the cross-like structure of tRNA, which includes three degree bends that create the molecular equivalent of cul-de-sacs in the molecule. After a number of chemical modifications, this strand is cleaved into two unequal subunits, one called 18S and the other labeled 28S.
The 18S portion is incorporated to what is called the small ribosomal subunit which when complete is actually 30S and the 28S part contributes to the large subunit whichin total has a size of 50S ; all ribosomes contain one of each subunit along with a number of proteins not nucleic acids, which make proteins themselves possible to provide ribosomes with structural integrity. DNA and RNA strands both have what are called 3' and 5' "three-prime" and "five-prime" ends based on the positions of molecules attached to the sugar portion of the strand.
In each nucleotide, the phosphate group is attached to the carbon atom labeled 5' in its ring, whereas the 3' carbon features a hydroxyl -OH group. When a nucleotide is added to a growing nucleic acid chain, this always occurs at the 3' end of the existing chain.
That is, the phosphate group at the 5' end of the new nucleotide is joined to the 3' carbon featuring the hydroxyl group before this linking occurs.
The -OH is replaced by the nucleotide, which loses a proton H from its phosphate group; thus a molecule of H2O, or water, is lost to the environment in this process, making RNA synthesis an example of a dehydration synthesis.
In principle, given what you now know, you can easily envision how this happens. DNA is double-stranded, so each strand can serve as a template for single-stranded RNA; these two new RNA strands, owing to the vagaries of specific base-pairing, will be complementary to each other, not that they will bond together. Note that this replacement is a one-directional phenomenon: For transcription to occur, the DNA double helix must become uncoiled, which it does under the direction of specific enzymes.
It later re-assumes its proper helical conformation. After this happens, a specific sequence aptly called the promoter sequence signals where transcription is to begin along the molecule.
This summons to the molecular scene an enzyme called RNA polymerase, which by this time is part of a promoter complex. All of this occurs as a sort of biochemical fail-safe mechanism to keep RNA synthesis from beginning in the wrong spot on DNA and thereby producing an RNA strand that contains an illegitimate code.
This is a minor but often confusing point for students, so you may wish to consult a diagram to assure yourself that you understand the mechanics of mRNA synthesis.
The bonds created between the phosphate groups of one nucleotide and the sugar group on the next are called phosphodiester linkages pronounced "phos-pho-die-es-ter," not "phos-pho-dee-ster" as it may be tempting to assume. The enzyme RNA polymerase comes in many forms, although bacteria include only a single type.
It is a large enzyme, consisting of four protein subunits: Combined, these have a molecular weight of aroundDaltons. For reference, a single carbon atoms has a molecular weight of 12; a single water molecule, 18; and a whole glucose molecule, The enzyme, called a holoenzyme when all four subunits are present, is responsible for recognizing the promoter sequences on DNA and pulling apart the two DNA strands. RNA polymerase moves along the gene to be transcribed as it adds nucleotides to the growing RNA segment, a process called elongation.
This process, like so many within cells, requires adenosine triphosphate ATP as an energy source. ATP is really nothing more than an adenine-containing nucleotide that has three phosphates instead of one.
Just as the promoter sequence may be viewed as the equivalent of a green light on a traffic light, the termination sequence is the analog of a red light or stop sign. Decoding the Message From mRNA When an mRNA molecule carrying the information for a particular protein — that is, a piece of mRNA corresponding to a gene — is complete, it still needs to be processed before it is ready to do its job of delivering a chemical blueprint to the ribosomes, where protein synthesis takes place.