RIBOSOMAL RNA (rRNA)

Presented by
P. Dharani Dharan
224056006
I MSC BIO CHEMISTRY
Synopsis:
❖ Introduction
❖ Structure
❖ Prokaryotic vs Eukaryotic
❖ Characteristics:
❖ Biological role of rRNA
Introduction:

• Ribosomal ribonucleic acid (rRNA) is the RNA component of

ribosomes, the molecular machines that catalyze protein
synthesis.
• It is most stable form of RNA and it is found in ribosomes.
• It is insoluble RNA
• Ribosomal RNA is most abundant of all types of RNAs and makes
up about 80% of the total RNA of a cell.
• It’s constituted over sixty percent of the ribosome by weight and
are crucial for all its functions – from binding to mRNA and
recruiting tRNA to catalyzing the formation of a peptide bond
between two amino acids.
• Even the structure of a ribosome is determined by the three-
dimensional shape of its rRNA core.
• Proteins present in the ribosome serve to stabilize this structure
through interactions with the core.
• Ribosomal RNA are transcribed in the nucleus, at specific
structures called nucleoli.
 • These are dense, spherical shapes that form around genetic loci
coding for rRNA.
• Nucleoli are also crucial for the eventual biogenesis of ribosomes,
through sequestration of ribosomal proteins.

Structure:
 Prokaryotic vs Eukaryotic:
PROKARYOTIC RIBOSOMES
Free ribosomes in prokaryotes
Found inside bacteria and archaea
Small and mass is 27000 kd
Sedimentation coefficient is 70S
Diameter is ~200 Å
Made up of 50S and 30S subunits
Large subunit is made up of two rRNA
molecules:
23S rRNA and 5S rRNA
Made up of 60% rRNA and
40% ribosomal proteins
Occur free in the cytoplasm
EUKARYOTIC RIBOSOMES
Large ribosomes that facilitate
translation in eukaryotes
Found in animals, plants, fungi, and
other unicellular eukaryotes with a
nucleus
Large and mass is 42000 kd
Sedimentation coefficient is 80S
Diameter is -250-300 Å
Made up of 60S and 40S subunits
Large subunit is made up of three
rRNA molecules:
285 TRNA. 5.3S rRNA, & 5S rRNA
Made up of 40% rRNA and
60% ribosomal proteins
Most are attached to the outer surface
of nucleus and endoplasmic reticulum
Characteristics:
• The primary structure of rRNA sequences can vary across
organisms, base-pairing within these sequences commonly forms
stem-loop configurations.
• The length and position of these rRNA stem-loops allow them to
create three-dimensional rRNA structures that are similar
across species. Because of these configurations, rRNA can form
tight and specific interactions with ribosomal proteins to form
ribosomal subunits.
• These ribosomal proteins contain basic residues (as opposed to
acidic residues) and aromatic residues
(i.e. phenylalanine, tyrosine and tryptophan) allowing them to
form chemical interactions with their associated RNA regions,
such as stacking interactions.
• Ribosomal proteins can also cross-link to the sugar-phosphate
backbone of rRNA with binding sites that consist of basic residues
(i.e., lysine and arginine).
• All ribosomal proteins (including the specific sequences that bind
to rRNA) have been identified.
• These interactions along with the association of the small and
large ribosomal subunits result in a functioning ribosome capable
of synthesizing proteins.
• Ribosomal RNA organizes into two types of major ribosomal
subunit: the large subunit (LSU) and the small subunit (SSU). One
of each type come together to form a functioning ribosome. The
subunits are at times referred to by their size-sedimentation
measurements (a number with an "S" suffix).
• In the ribosomes of prokaryotes such as bacteria, the SSU contains
a single small rRNA molecule (~1500 nucleotides) while the LSU
contains one single small rRNA and a single large rRNA molecule
(~3000 nucleotides).
• These are combined with ~50 ribosomal proteins to form
ribosomal subunits. There are three types of rRNA found in
prokaryotic ribosomes: 23S and 5S rRNA in the LSU and 16S rRNA
in the SSU.
• In the ribosomes of eukaryotes such as humans, the SSU contains
a single small rRNA (~1800 nucleotides) while the LSU contains
two small rRNAs and one molecule of large rRNA (~5000
nucleotides).
• Eukaryotic rRNA has over 70 ribosomal proteins which interact to
form larger and more polymorphic ribosomal units in comparison
to prokaryotes.[4] There are four types of rRNA in eukaryotes: 3
species in the LSU and 1 in the SSU.
• Yeast has been the traditional model for observation
of eukaryotic rRNA behavior and processes, leading to a deficit in
diversification of research.
• It has only been within the last decade that technical advances
(specifically in the field of Cryo-EM) have allowed for preliminary
investigation into ribosomal behavior in other eukaryotes.
• In yeast, the LSU contains the 5S, 5.8S and 28S rRNAs. The
combined 5.8S and 28S are roughly equivalent in size and function
to the prokaryotic 23S rRNA subtype, minus expansion segments
(ESs) that are localized to the surface of the ribosome which were
thought to occur only in eukaryotes.
• However recently, the Asgard phyla, namely,
Lokiarchaeota and Heimdallarchaeota, considered the closest
 archaeal relatives to Eukarya, were reported to possess two
supersized ESs in their 23S rRNAs.
• Likewise, the 5S rRNA contains a 108‐nucleotide insertion in the
ribosomes of the halophilic archaeon Halo coccus morrhuae.
• A eukaryotic SSU contains the 18S rRNA subunit, which also
contains ESs. SSU ESs are generally smaller than LSU ESs.
• SSU and LSU rRNA sequences are widely used for study
of evolutionary relationships among organisms, since they are of
ancient origin,[10] are found in all known forms of life and are
resistant to horizontal gene transfer.
• rRNA sequences are conserved (unchanged) over time due to
their crucial role in the function of the ribosome.
• Phylogenic information derived from the 16s rRNA is currently
used as the main method of delineation between similar
prokaryotic species by calculating nucleotide similarity.
• The canonical tree of life is the lineage of the translation system.
• LSU rRNA subtypes have been called ribozymes because ribosomal
proteins cannot bind to the catalytic site of the ribosome in this
area (specifically the peptidyl transferase center, or PTC).[13]
• The SSU rRNA subtypes decode mRNA in its decoding center
(DC). Ribosomal proteins cannot enter the DC.
• The structure of rRNA is able to drastically change to affect tRNA
binding to the ribosome during translation of other mRNAs.
• In 16S rRNA, this is thought to occur when certain nucleotides in
the rRNA appear to alternate base pairing between one
nucleotide or another, forming a "switch" that alters the rRNA's
conformation.
 • This process is able to affect the structure of the LSU and SSU,
suggesting that this conformational switch in the rRNA structure
affects the entire ribosome in its ability to match a codon with its
anticodon in tRNA selection as well as decode mRNA.[16]

Biological role of rRNA:

• Biological role of rRNA: The rRNA is found in the cytoplasm of a
cell, which is also the location of ribosomes. mRNA is translated
into proteins under the control of rRNA.
• Protein synthesis is the primary function of rRNA. The A, P, and E
sites are created within the ribosome by the unusual three-
dimensional structure of rRNA, which has internal helices and
loops. By attaching to messenger RNA and transfer RNA, these
molecules assure that the codon sequence of the mRNA is
appropriately translated into the amino acid sequence of proteins.
• The A site anchors an entering tRNA that has been charged with
an amino acid, while the P site is for binding a developing
polypeptide. The tRNA temporarily attaches to the E site following
the creation of a peptide bond before exiting the ribosome.
• In addition, some ribosomal proteins can bind to rRNA at specific
residues, which have been identified after detailed investigation
for both the RNA and protein.
• Antibiotics like streptomycin and tetracycline have recently been
identified as having binding sites on bacterial rRNA. For example,
a mutation in the 16S rRNA sequence is the tolerance
of Euglena and Escherichia coli to streptomycin.
• The 30S rRNA appears to be the source of tetracycline resistance.
Similar findings were discovered for Streptomyces to
Spectinomycin resistance.
• Preribosomal RNA, one of rRNA’s predecessors, has been linked to
the production of microRNA, which mediates inflammation and
heart illness concerning mechanical stress. This finding adds a new
dimension to the role of rRNA.