The concept of transport RNA
Transport RNA is a type of small molecule ribonucleic acid with the function of carrying and transporting amino acids, referred to as tRNA for short. The vast majority of tRNA consists of seventy to ninety nucleotides, with a molecular weight of 25,000 to 30,000, and a sedimentation constant of about 4S (the sedimentation constant of individual tRNA is 3S, containing 63 nucleotides). It has been used to connect RNA, soluble RNA, pH5RNA and so on. tRNA (transfer RNA) is an adaptor molecule in protein synthesis. There are more than 100 tRNA molecules, each of which can carry an amino acid and transport it to the ribosome for protein synthesis. tRNA is a type of nucleic acid with the smallest molecular weight in the cell, which is composed of 70 to 120 nucleotides. Various tRNAs have some common characteristics in the primary structure, or in the secondary and tertiary structures. tRNA contains 10% to 20% rare bases (rare bases), such as: methylated purine mG, mA, dihydrouracil (DHU), hypoxanthine and so on. In addition, tRNA also contains some rare nucleosides, such as: thymine ribonucleoside, pseudouridine (Ψ, pseudoouridine) and so on. Thymine is generally present in DNA; in pseudouracil nucleosides, it is not the nitrogen atom at the 1 position in the pyrimidine ring, but the glycosidic bond between the 5 carbon atom in the pyrimidine ring and the 1 ′ carbon atom in the pentose . Nucleotides in tRNA molecules form multiple local double helix structures through base pairing, and the regions that do not form double helices constitute so-called loops.
Transport RNA structure
(1) Two-dimensional structure of clover type
All tRNAs now discovered can exhibit the so-called clover leafpattern secondary structure shown in Figures 15-14. In this structure, the first loop from the 5 ′ end is the DHU loop, which is characterized by dihydrouracil; the second loop is the anticodon loop, and the three bases in the middle of the loop can be linked to the mRNA The triplet codons form a base complementary pair, forming the so-called anticodon (anticodon), which plays a role in decoding codons in protein synthesis and introducing the correct amino acid into the synthesis site; the third loop is the TΨ loop, to It is characterized by thymidine and pseudouridine; between the anti-codon loop and the TΨ loop, there is often an extra loop, consisting of several or even more than twenty nucleotides, and all tRNA 3 ′ ends have the same CCA -OH structure, the amino acid transported by tRNA is connected to this end.
The structure of tRNA was first discovered by Holley, RN and colleagues on the yeast alanine tRNA in 1965, so he won the Nobel Prize in Chemistry in 1968. Hundreds of tRNA sequences from bacteria and eukaryotes can form a cloverleaf structure through complementary base pairing. Its specific characteristics are:
(1) Various tRNAs contain 70 to 80 bases, of which 22 bases are constant.
(2) The 5 'end is always paired, which is related to the stability of tRNA. The 5 'end and the 3' end are paired (often 7bp) to form the stem region, which is called the acceptor arm or amino acid arm. At the 3 'end is always a single-stranded region of 4 bases (XCCA), with 2'-OH or 3'-OH at its end, which is the site of aminoacylation. This arm is responsible for carrying specific amino acids. The other arms are stem-loop structures.
(3) There is a special base ψ (pseudouracil) in the C arm of Tψ, which is usually composed of a 5bp stem and 7Nt and a loop. This arm is responsible for binding to rRNA recognition on the ribosome;
(4) The anticodon arm is usually composed of a 5bp stem region and a 7Nt loop region. There is always an anticodon triplet in the center of the loop region, which is responsible for the recognition and pairing of codons on mRNA .
(5) The length of the stem region of the D arm (D arm) is usually 4 bp, and there are 4 bases in the ring region that are not constant. This ring is located at 17, 17: 1 20: 1, 20: 2 contains a special base D (double Hydrouracil), so it is also called (dihydrouracil ring).
(6) The extra arm has a large variability, ranging from 4 Nt to 21 Nt. Its function is to connect two regions (D loop-anticodon loop and TψC-receptor) in the L-shaped three-dimensional structure of tRNA. Body arm).
(2) The three-dimensional structure of tRNA
The clover structure of tRNA does not make us clear how the arms of tRNA are arranged in space. Only by studying the crystal of tRNA through X-ray diffraction can we obtain the true conformation of tRNA. Studies of tRNA crystals from several yeasts indicate that various tRNAs have a common three-dimensional structure. It mainly depends on the base pairing in the stem to maintain and form a stable L-shaped structure. The detection results of this structure are as follows:
(1) The amino acid acceptor arm is located on the side of the L-form, about 70 from the anti-codon loop.
(2) The D ring and the TψC ring form the "L" rotation angle.
(3) Many tertiary hydrogen bonds are formed between some conservative and semi-conservative bases, so that the molecule forms an L-shape and stabilizes the structure.
(4) These base pairings that enable the formation of a three-dimensional structure are different from the base pairings in the DNA double strand. Phosphodiester bonds related to the tertiary structure interacting with the phosphate ribose backbone are distributed on the 2'-OH of ribose.
(5) The axial direction of almost all bases causes a stacking effect between the base planes. This effect is also one of the main factors for the conformational stability of tRNA.
(6) There are very few tertiary hydrogen bonds in the anticodon stem, which may be due to the change in the relative direction of the anticodon region during protein synthesis.
The secondary structure diagram and the three structure diagram of the transport RNA are as follows:
Transport RNA structure diagram
Through X-ray diffraction and other structural analysis methods, it is found that the common tertiary structure of tRNA is inverted L-shaped (as shown in the second figure on the right), where the 3 ′ end contains CCA
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