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> >ZOOHCC - 501: Molecular Biology (Theory)
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> >Unit 3: Transcription and Regulatory RNAs > >
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> >ribosomal RNA (rRNA) > >
> >Ribosomal RNA (rRNA), an intracellular molecule that forms part of the
protein-synthesizing organelle known as the ribosome, is transported to
the cytoplasm and helps convert messenger RNA (mRNA) information into
protein. The three main types of RNA found in cells are rRNA, mRNA, and
transfer RNA (tRNA). > >
> >rRNA molecules are synthesized in a specialized region of the cell
nucleus called the nucleolus. The nucleolus appears as a dense region
within the cell nucleus and contains genes encoding rRNA. Encoded rRNAs
vary in size and are classified as either large or small. Each ribosome
contains at least one large rRNA and at least one small rRNA. In the
nucleolus, large and small rRNA associate with ribosomal proteins to form
the large and small ribosomal subunits (eg, 50S and 30S, respectively, in
bacteria). (These subunits are commonly named for their sedimentation
velocity in a centrifuge and are measured in Svedberg units [S].)
Ribosomal proteins are synthesized in the cytoplasm and transported to the
nucleus, where they are assembled in the nucleolus. can be Subunits are
then returned to the cytoplasm for final assembly. > >
>rRNA forms extensive secondary structures and plays an active role in
recognizing conserved portions of mRNA and tRNA. In eukaryotes (organisms
with distinct nuclei), a single cell can have 50-5,000 sets of rRNA genes
and up to 10 million ribosomes. In contrast, prokaryotes (organisms without
a nucleus) generally have a smaller set of rRNA genes and ribosomes per
cell. For example, in the bacterium Escherichia coli, seven copies of the
rRNA gene synthesize approximately 15,000 ribosomes per cell. >
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>There is a fundamental difference between prokaryotes in the archaeal and
bacterial domains. These differences are reflected not only in the use of
lipids, cell wall composition, and different metabolic pathways, but also in
rRNA sequences. Bacterial and archaeal rRNAs are not only different from
each other, but also from eukaryotic rRNAs. This information is important in
understanding the evolutionary origins of these organisms. This is because
it suggests that the bacterial and archaeal lineages diverged from a common
ancestor sometime before eukaryotic evolution. >
>rRNA synthesis >
>Ribosome synthesis is a highly complex and coordinated process involving
over 200 assembly factors. Synthesis and processing of ribosomal components
occurs not only in the nucleolus, but also in the nucleoplasm and cytoplasm
of eukaryotic cells. >
>Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNA by
different RNA polymerases. Primary transcripts undergo extensive processing
and modification before being bound and folded by ribosomal proteins and
assembly factors imported from the cytoplasm. Extensive modification of
ribosomal RNA by snoRNPs is another distinguishing feature of eukaryotic
ribosomes. Individual modified bases do not appear to have specific
functions, and all modifications together stabilize a specific conformation
of ribosomal RNA. Moreover, these modified bases are more concentrated in
functional regions of rRNA and regulate translational ribosomal
activity. >
>Both rRNA modification and pre-rRNA processing occur in the nucleolus. This
is because both steps require components found only in the nucleolus. While
snoRNPs chemically modify rRNA, other 'nucleolar proteins' hydrolyze the
transcribed 'spacer RNA' of the precursor RNA into cleaved 18S, 5.8S, and
28S rRNAs. increase. Generation of mature rRNA returns free nucleolar
proteins to the nucleolar pool for recycling. >
>Cations such as magnesium ions (Mg2+) play an important role in maintaining
the structure of the ribosome. During experiments, ribosomes dissociate into
subunits when Mg2+ is removed. Although the exact role of Mg2+ remains
unclear, it is plausible that cations interact with the ionized phosphate of
RNA so that he bridges the two ribosomal subunits. >
>After ribosome assembly is complete, some ribosomes are bound to the
intracellular membrane, mainly the endoplasmic reticulum, while free
ribosomes are distributed throughout the cytoplasm. >
>Structure of rRNA >
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>tRNA Synthesis >
>Transfer ribonucleic acid (tRNA) is synthesized from the tRNA gene,
primarily by transcription by RNA polymerase, and undergoes several steps of
processing, splicing, CCA addition, and post-transcriptional modification
into its mature form. Primary transcripts of tRNA genes contain 5' and 3'
extra sequences that are removed by various causative nucleases and, in some
cases, introns that are spliced out by specific endonucleases. The two
resulting fragments are joined by RNA ligase. The CCA sequence present at
the 3' end of all mature tRNAs is not encoded by the tRNA genes of some
species and is added post-transcriptionally by CCA-adding enzymes. All
mature tRNA molecules contain modified nucleotides produced by modification
enzymes thought to be involved in stabilizing the tRNA structure,
deciphering its properties, and proper processing. The concentration of
individual tRNA molecules is controlled to maintain cellular function. >
>One of the unique features of tRNA is the presence of modified bases. In
some tRNAs, modified bases account for approximately 20% of the total bases
in the molecule. Collectively, these unusual bases protect tRNA from
enzymatic degradation by RNases. >
>Each of these chemical modifications is carried by specific enzymes after
transcription. All of these enzymes have unique base and site specificities.
Methylation, the most common chemical modification, is performed by at least
nine different enzymes, with three enzymes at different positions dedicated
to guanine methylation. >
>The nature and location of these modified bases vary by species. Therefore,
there are some bases that are exclusive to eukaryotes or prokaryotes. For
example, adenine thiolation is observed only in prokaryotes, whereas
cytosine methylation is restricted to eukaryotes. Overall, eukaryotic tRNAs
are more extensively modified than prokaryotic ones. Although the nature of
the alterations varies, some regions of tRNA are always significantly
altered. Each of the three stem-loop regions, or "arms," of tRNA has
modified bases that serve a unique purpose. The TΨC arm is named for the
presence of the nucleotides thymine, pseudouridine, and cytosine, which are
recognized by the ribosome during translation. The DHU or D arm containing
the modified pyrimidine dihydrouracil serves as the recognition site for the
enzyme aminoacyl-tRNA synthetase, which catalyzes the covalent addition of
amino acids to tRNA. Anticodon loops often have a cuein base that is a
modified guanine. This base forms a wobble pair with the codon sequence on
the mRNA. H. Forms base pairs that do not follow the Watson-Crick base
pairing rules. tRNA usually binds "loosely" to mRNA at the third codon
position. This allows for multiple types of non-Watson-Crick base pairs or
wobble bases at the third codon position. The presence of a cuein in the
first position of the anticodon, paired with the third position of the
codon, has been observed to improve the translational fidelity of
tRNA. >
>Structure of transfer RNA >
>Like all molecules of the nucleic acid family, transfer RNA is composed of
nucleotides. Nucleotides contain a sugar, a phosphate group, and a
nitrogenous base. In RNA, the sugar used is ribose and the base can be A, U,
C, or G. Although not shown much in the diagram, it should be remembered
that As, Us, Cs, and Gs have this complete nucleotide structure, with a
ribose sugar and a phosphate group, respectively. >
>A tRNA structure is the structure of an RNA strand folded into a series of
loops. Amino acids are attached at one end, shown in blue in the diagram as
the acceptor stem. At the opposite end are groups of three nucleotides
called anticodons. Anticodons are adapted to mRNA sequences by the ribosome.
The ribosome transfers (attaches) an amino acid to the growing polypeptide
chain, at which point the tRNA molecule can be considered empty. However, it
is reusable and can accommodate another amino acid of the same type. >
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>Key points: >
>tRNAs are synthesized from the tRNA gene by RNA polymerase and matured by
processing, splicing, CCA addition, and post-transcriptional
modifications. >
>tRNA synthesis is controlled by promoter activity and specific factors
(ppGpp and/or pppGpp in prokaryotes and Maf1 in eukaryotes), depending on
the nutritional status of the cell. >
>The relative amount of tRNA is regulated by several factors. tRNA gene copy
number, transcriptional activity above, and tRNA degradation by various
nucleases. >
>The primary transcript of the tRNA gene contains 5' and 3' extra sequences
that are removed by various causative nucleases. >
>In some cases, tRNA transcripts contain introns spliced out by specific
endonucleases, and the two resulting fragments are joined by RNA ligase.
CCA-adding enzymes regulate the amount of active tRNA by repairing the CCA
sequence at the C-terminus of tRNA. >
>tRNA has various modified nucleotides introduced by modifying the enzyme
during or after the processing, splicing, and transport steps. >
>Several modifications of tRNA play important roles in the translation
process, including: B. Enhancement, elongation, restriction and/or
alteration of codon-anticodon interactions, stabilization of tRNA structure,
recognition by aminoacyl-tRNA synthetase, etc. >