types and structure of prokaryotic RNA

1

By Miss Tooba

Kanwal

RNA STRUCTURE AND FUNCTIONS

Bacterial Genetics

Bacterial Genetics 2

RNA (Ribonucleic acid )

RNA is a polymer of ribonucleotides linked together by 3’-5’ phosphodiester linkage


RNA V/S DNA


Differences between RNA and DNA

S.No. RNA DNA

1) Single stranded mainly except when self complementary sequences are there it forms a double stranded structure (Hair pin structure)

Double stranded (Except for certain viral DNA s which are single stranded)

2) Ribose is the main sugar The sugar moiety is deoxy ribose

3) Pyrimidine components differ. Thymine is never found(Except tRNA)

Thymine is always there but uracil is never found

4) Being single stranded structure- It does not follow Chargaff’s rule

It does follow Chargaff's rule. The total purine content in a double stranded DNA is always equal to pyrimidine content.


Differences between RNA and DNAS.No. RNA DNA

5) RNA can be easily destroyed by alkalies to cyclic diesters of mono nucleotides.

DNA resists alkali action due to the absence of OH group at 2’ position

6) RNA is a relatively a labile molecule, undergoes easy and spontaneous degradation

DNA is a stable molecule. The spontaneous degradation is very 2 slow. The genetic information can be stored for years together without any change.

7) Mainly cytoplasmic, but also present in nucleus (primary transcript and small nuclear RNA)

Mainly found in nucleus, extra nuclear DNA is found in mitochondria, and plasmids etc

8) The base content varies from 100- 5000. The size is variable.

Millions of base pairs are there depending upon the organism


Differences between RNA and DNAS.No. RNA DNA

9) There are various types of RNA – mRNA, r RNA, t RNA, Sn RNA, Si RNA, mi RNA and hn RNA. These RNAs perform different and specific functions.

DNA is always of one type and performs the function of storage and transfer of genetic information.

10) No variable physiological forms of RNA are found. The different types of RNA do not change their forms

There are variable forms of DNA (A to E and Z)

11) RNA is synthesized from DNA, it can not form DNA(except by the action of reverse transcriptase). It can not duplicate (except in certain viruses where it is a genomic material )

DNA can form DNA by replication, it can also form RNA by transcription.

12) Many copies of RNA are present per cell

Single copy of DNA is present per cell.


Types of RNAIn all prokaryotic and eukaryotic organisms, three main classes of RNA molecules exist-1) Messenger RNA(m RNA)2) Transfer RNA (t RNA)3) Ribosomal RNA (r RNA)


Messenger RNA (m-RNA)

Comprises only 5% of the RNA in the cellMost heterogeneous in size and base sequenceAll members of the class function as messengers carrying the information in a gene to the protein synthesizing machinery


General features of mRNA

The m- RNA molecules are formed with the help of DNA template during the process of transcription.

The sequence of nucleotides in mRNA is complementary to the sequence of nucleotides on template DNA.

The sequence carried on m -RNA is read in the form of codons.

A codon is made up of 3 nucleotides


• Prokaryotic mRNAs are made up of polynucleotide chains of specific sequence endowed with 5’ to 3’ polarity.

• Size of the mRNAs is more or less proportional to the gene from which it generates.

• The polypeptide chain it produces is directly proportional to the coding size of the mRNA. Longer the protein longer is the mRNA and vice versa.

• Average size of mRNA in bacterial systems is 1000 ntds to 2000 with a mol. Wt. of 30,000 dal.




• Once translated, m-RNA is immediately degraded i.e within 1 minute of the start of transcription.

• The 5’ terminus start decaying before the 3’ terminus has been transcribed or translated. However the rate of degradation is slower than the rate of transcription.

• Out of 500 sites in E.coli, 300 sites are transcriptional.


Structural Characteristics of m-RNA

On both 5’ and 3’ end there are non coding sequences which are not translated (NCS)

The 5’ non-coding region(5’UTR) is called leader sequence, whose length and sequence varies from one species of mRNA to the other.

The intervening region between non coding sequences present between 5’ and 3’ end is called coding region or Open Reading Frame (ORF). This region encodes for the synthesis of a protein.

The 3’ non-coding region is called Trailor where the process of translation stops.


• The leader sequence in every mRNA contains an all-important structured sequence called Shine-Delgarno sequence, seven to nine nucleotides upstream of the start codon AUG. These are also called SPACERS which are usually 10 bases long.

• The coding region starts from the initiator codon AUG (mostly) or GUG (rarely) and ends in a terminator codon like UAG, UGA or UAA.

Structural Characteristics of m-RNA(contd.)


Polycistronic mRNA with spacer between cistrons


• Cistron: a gene corresponding to one polypeptide chain in addition to the translational start and stop signals for protein synthesis.

• m-RNA encoding a single polypeptide is called monocistronic m-RNA.

• Polycistronic m-RNA encodes proteins required to carry out reaction of a single metabolic pathway.


Structural characteristics of m-RNA (contd.)

• In the case of prokaryotes, the coding region is split consisting of cistrons with initiating and terminator sequences. In between two such coding regions one finds a short spacer region, hence the name polycistronic.

• This spacer region is used for the translation termination of the cistron and again initiates at the next cistron, the size of the inter-cistronic space varies, but mostly very short.

5’---UAGGAGG—-AUG-----II-AUG---------II-AUG------UGA

• In prokaryotes transcription and translation are coupled.• Half-life of mRNAs is very short ranging between 2-5 minutes.


Ribosomes and Ribosomal RNA (r-RNA)

• Ribosome:• Granular structures in cytoplasm.• The ribosome of E.coli consists of r-RNA and protein

with the ratio of 2:1 • Mol.wt. of each ribosome is slightly less than 3

million daltons.• ¼ of total cellular mass, 80% of cellular RNA and 10%

of total cell protein.


Structure of Ribosome• Asymmetric aggregates of two subunits, differentiated

by their sedimentation of co-efficient.• Larger S value, larger the particle.• Bacterial ribosome sedimentation of coefficient is 70S,

divided into 30S and 50S subunits.• Eukaryotic ribosome is 80S with 60S and 40S subunits.• 30S SUB-UNIT: In E.coli, 30S subunit has elongated and asymmetrical

shape composed of 21 different proteins(S1,S2…. S21) and mol.wt ranges from 8500 to 61200 dal. A Single 16S molecule of rRNA of 1541 nucleotides is also present.


• 50S SUB-UNIT: This subunit has a pentagonal outline and polyhedral

shape and 31 proteins (L1, L2… L31) with a mol. Wt. of 11000 to 41500 dal. The r-RNA in this subunit is of two types: 5S with 120 nucleotides and 23S with 2904 nucleotides.

• Ribosomal proteins are called r-proteins which are responsible for creating several active sites for protein synthesis and co-ordinates with r-RNA in translation.


Prokaryotic Ribosome


General features of r-RNA

• Like all kinds of RNA, r-RNA is also transcribed from a template strand of DNA.

• 0.1 to 0.2 % of the bacterial genome is estimated to be responsible for transcription of r-RNA.

• Some well conserved regions usually contains methylated residues.

• ~ 10 methyl groups are present in 16S r-RNA towards it’s 3’ terminus and ~20 in 23S r-RNA.


General features of r-RNA (contd)

• The r-RNA participates in protein synthesis but don’t code for proteins.

• Specific sequences in r-RNA play a role in initial attachment of m-RNA to the 30S subunit and assure the process of translation.

• The sequences in the 3’ terminus of r-RNA interacts directly with m-RNA at initiation.


General features of r-RNA (contd).

• Specific regions at 16S rna interact directly with the anticodon regions of t-RNA in both the A site and P site.

• A specific sequence of 23S r-RNA interacts with the CCA terminus of peptidyl-t-RNA.

• The 16S and 23S r-RNA are also involved in the interaction of two sub units of ribosomes.


Transfer RNA (t- RNA)Transfer RNA are the smallest of three major species of RNA molecules

They have 74-95 nucleotide residues They are synthesized by the nuclear processing of a precursor molecule

They transfer the amino acids from cytoplasm to the protein synthesizing machinery, hence the name t RNA.

They are also called Adapter molecules, since they act as adapters for the translation of the sequence of nucleotides of the m RNA in to specific amino acids

There are at least 20 species of t RNA one corresponding to each of the 20 amino acids required for protein synthesis.


Transfer RNA (t- RNA)1) Primary structure-

The nucleotide sequence of all the t RNA molecules allows extensive intra-strand complimentarity that generates a secondary structure.

• It contains a number of unusual nucleotides due the presence of one or more methyl groups.

• Restructuring of purine ring• About 50 bases are modified.• Some modification is common and some is found in

particular t-RNAs• Another imp feature of base modification is codon-

anticodon pairing.


Structural characteristics of t- RNA

2) Secondary structure (Clover leaf structure) – Each single t- RNA shows extensive internal base pairing and acquires a clover leaf like structure. The structure is stabilized by hydrogen bonding between the bases on the same chain into a double stranded helical arrangement which is a consistent feature.The clover leaf model shows the base-pairing structure of t-RNA and reveals four base paired regions that define the three loops of t-RNA.


Structural characteristics of t- RNA

• All t-RNA contain 5 main arms or loops which are as follows-

a) Acceptor armb) TΨ C armc) Anticodon armd) D arme) Extra arm


Secondary structure of t- RNAa) Acceptor arm The acceptor arm is at 3’ end and always ends in a C.C.A. The nucleotide at 5’ end is usually G. These two termini base pair with each other to form the

acceptor arm. It has 7 base pairs The end sequence at the C.C.A remains unpaired. The 3’ OH group terminal of Adenine binds with carboxyl

group of amino acids later. The t RNA bound with amino acid is called Amino acyl t

RNA CCA attachment is done post transcriptionally


Secondary structure of t- RNA b) TΨC armAs we move along the t-RNA molecule from the 3’

terminus, we encounter the first loop, TΨC loop.It is so named because it contains the three bases,

T,C and a modified Ψ(Psi) base. (Psi stands for a modified uridine base into psuedouridine.)

It is involved in the binding of t RNA to the ribosomes

This loop is made up of seven unpaired bases.


Secondary structure of tRNA (contd.)

c) Anticodon arm Lies at the opposite end of acceptor armIt consists of seven unpaired bases which contains the anti-codon triplet in it’s center.Recognizes the triplet codon present in the m RNABase sequence of anticodon arm is complementary to the base sequence of m RNA codon. Due to complimentarity it can bind specifically with m RNA by hydrogen bonds.


Secondary structure of t- RNA(contd.)d) D arm D arm is named after modified base dihydrouridine (D).It consists of 8-12 unpaired bases.It has 3-4 base pairsIt serves as the recognition site for the enzyme (amino acyl t RNA synthetase) that adds the amino acid to the acceptor arm.


Secondary structure of t- RNA(contd.)

e) Extra arm or Variable arm This arm lies between the TΨC and anticodon arms. About 75 % of t RNA molecules possess a short extra arm It is variable in size, depending upon the number of bases can b divided into:• Class I: If about 3-5 base pairs are present, it is called small extra arm. Majority t -RNA belong to class 1.• Class II: It is a long extra arm having 13-21 base pairs.

The function of extra arm is unknown.


Tertiary structure of t- RNA The L shaped tertiary structure is formed by further folding of the clover leaf due to hydrogen bonds between T and D arms.

The base paired double helical stems get arranged in to two double helical columns, continuous and perpendicular to one another.


Tertiary structure of t- RNA

The amino acid acceptor arm is located at one end of the L, from where the anticodon loop lies at the opposite end.

The D loop and T loop form the corner of the L.


SummaryRNA exists in several different single-stranded structures, most of which are directly or indirectly involved in protein synthesis or its regulation. The linear array of nucleotides in RNA consists of A, G, C, and U, and the sugar is ribose. All types of RNA has a 5’ and 3’ terminal.m-RNA is in linear form, hetrogenous in size and is immediately degraded after translation.Prokaryotic ribosomes are 70S having two small and large subunits of 30S and 50S respectively.Ribosomal RNA is found in ribosomes in linear structure.Transfer RNA is helical, folded structure and is the smallest in all RNAs.30s ribosome contains linear strand of 16s RNA whereas 50s ribosome contains two linear sets of RNA, 5s and 23s.The major forms of RNA include messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA)

types and structure of prokaryotic RNA

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