Elementary plant Biochemistry and Biotechnology (2+1)

Classes of RNA molecules

• There are three major classes of RNA molecules – messenger RNA (mRNA; an informational molecule), ribosomal RNA (rRNA; a structural molecule) and transfer RNA (tRNA; a structural and informational molecule).

mRNA

• The base sequence of a DNA molecule determines the amino acid sequence of every polypeptide chain in cell, though amino acids have no affinity for DNA. Thus, instead of direct pairing between amino acids and DNA, a multistep process is used in which the information contained in the DNA is converted to a form in which amino acids can be arranged in an order determined by the DNA base sequence. This process begins with the transcription of the base sequence of one of the DNA strands (the coding strand) into the base sequence of an RNA molecule (mRNA).


• The protein synthesizing machinery of the cell obtain the information, i.e., the amino acid sequence of a particular protein to be synthesized, from this RNA molecule. The nucleotide sequence of the mRNA is then read in groups of three bases (a group of three is called as Codon) from a start codon to stop codon, with each codon corresponding either to one amino acid or a stop signal.


• A DNA segment corresponding to one polypeptide chain plus the translational start and stop signals for protein synthesis is called a cistron and an mRNA encoding a single polypeptide is called monocistronic mRNA. In prokaryotes, it is very common for an mRNA molecule to encode several different polypeptide chains; in this case it is called as polycistronic mRNA. The segment of RNA corresponding to a DNA cistron is often called a reading frame, since the protein synthesizing system reads it.


• In addition to reading frames and start and stop sequences for translation, other regions in mRNA are significant. Translation of an mRNA molecule rarely starts exactly at one end of the RNA and proceeds to the other end; instead, initiation of synthesis of the first polypeptide chain of a polycistronic mRNA may begin hundreds of nucleotides from the 5’- P terminus of the RNA. The section of untranslated RNA before the coding regions is called a leader.


• In some cases, the leader contains a regulatory region. Untranslated sequences usually found at both the 5’-P and 3’-OH termini and a polycistronic mRNA molecule typically contain intercistronic sequences (spacers) usually tens of bases long. An important characteristic of prokaryotic mRNA is that its lifetime is short (only few minutes) compared to other types of RNA molecules.

Ribosomal RNA and transfer RNA

• During the protein synthesis, genetic information is supplied by mRNA. Amino acids do not line up against the mRNA template independently during protein synthesis but are aligned by means of a set of about 50 adaptor RNA molecules called transfer RNA (tRNA) and this is occurred on the surface of an RNA-containing protein particle called as ribosome.


• These particles consist of several classes of ribosomal RNA (rRNA) and ribosomal proteins, which are stable molecules and having various functions. Whereas the transfer RNA molecule exist in the cell, has a capacity of ‘reading’ three adjacent mRNA bases and placing corresponding amino acid at a site on the ribosome at which a peptide bond is formed with an adjacent amino acid. Neither rRNA nor tRNA is translated into polypeptide chain.


• The synthesis of both rRNA and tRNA molecules is initiated at a promoter and completed at terminators; in this respect, their synthesis is no different from that of mRNA. However, the following three properties of these molecules indicate that neither rRNA nor tRNA molecules are the immediate products of transcription (called as primary transcripts):

The molecules are terminated by a 5’ monophosphate rather than the expected triphosphate found at the ends of all primary transcripts.

1. Both rRNA and tRNA molecules are much smaller than the primary transcripts.
2. All tRNA molecules contain bases other than A, G, C and U and these unusual bases are not present in the original transcript.
3. All of these molecular changes are made after transcription by processes collectively called as posttranscriptional modification or more commonly, processing.


• All ribosomes comprise two dissimilar sized subunits, the large and small subunits. Each subunits consists of several rRNA and numerous ribosomal proteins (r-proteins). In E. coli, the 70S ribosome is composed of a small 30S subunit and a large 50S subunit. The small subunit comprises 21 different proteins (named S1-S21) and the 16S RNA. The large subunit comprises 34 proteins (named L1-L34) and the 23S and 5S rRNAs.
  


• Some proteins are common to both subunits (e.g. L6, S20). Eukaryote ribosomes are larger (80S) and contain more components. The small (40S) subunit comprises 33 proteins and the 18S rRNA whilst the large (60S) subunit contains 50 proteins and three rRNAs of 28S, 5.8S and 5S. The spatial organization of the ribosome is complex. rRNA makes up 60-65 % pf the total mass and is essential for structural integrity and function, adopting complex tertiary and quaternary conformations by intra and inter molecular base pairing.


• The tRNAs are relatively homogeneous family of RNA molecules, usually 75-100 nucleotides in length, which are extensively processed during their production. They possess a characteristic secondary and tertiary structure (Figure), most importantly the acceptor stem (to which the amino acid binds) and the anticodon loop (which carries the three nucleotide anticodon that forms complementary base pairs with codons in the mRNA).


• Bacterial cells contain up to 35 different tRNAs and eukaryotic cells up to 50. This number is lower than the number of possible codons in the genetic code, but greater than the number of amino acids specified by the code. This indicates that individual tRNAs can recognize more than one codon (called as wobble pairing), but that different tRNAs may be charged with the same amino acids (these are called as isoaccepting tRNAs).
  


• The tRNAs are charged (conjugated to their corresponding amino acids) by enzymes termed amino acyl tRNA synthetases. There is one enzyme for each amino acid and therefore each synthetase recognizes all its cognate isoaccepting tRNAs.