RNA



What called RNA?

RNA ( Ribonucleic Acid): RNA was the first material. There is now enough evidence to suggest that essentia life processes ( such as metabolism translation, splicing etc.), evolved around RNA. RNA used to act as a genetic material as well as a catalyse, ( there are some important biochemical reactions in living systems that are catalysed  by DNA catalyse and not by protein enzymes).  But, RNA being a catalyst was reactive and hence unstable. DNA has evolved from RNA with chemical modifications that make it more stable. DNa being double stranded and having complementary strand further resists changes by evolving a process of repair.RNA is a single chain of ribonucleotide of adenine, guanine, cytosineand uracil.It is transcribed from the sense chain of DNA.



Location:

In a prokaryotic cell, whole of the RNA is found in the cytoplasm because there is no nucleus. It a eukaryotic cell, bulk of RNA occure in the cytoplasm, and a small amount in the nucleus. It is mainly confined to the ribosomes in the cytoplasm and to the nucleolus in the nucleus. 

Quantity: 

The amount of RNA in a cell varies with nutritional states, types of tissue, etc.

Composition:

RNA molecule is a single chain of ribonucleotide, or ribotide,units, A ribonucleotide unit further consist of 3 different molecules:phosphate, ribose sugar and nitrogenous base. The nitrogenous base may be a purine ( adenine or guanine) or a Pyrimidine ( cytosine or uracil).
There are Four types of ribonucleotide in RNA, namely , adenine _ ribosephosphate, or adenosine monophosphate ( AMP); guanine _ ribose _ phosphate, or guanosine monophosphate ( GMP) ; cytosine _ ribose_ phosphate, or cytidine monophosphate ( CMP); and uracil _ ribose __ phosphate, or uridine monophosphate ( UMP). In an RNA chain, the phosphate group at 5' position of sugar molecules in one ribonucleotide is joined to the sugar__ molecule of the next ribonucleotide at 3' position by phosphodiester bond. This forms a " backbone" of alternating sugar _ phosphate _  sugar  molecules. The nitrogenous base molecules are joined to the sugar molecules at carbon 1' positions of this " backbone" by glycosidic bonds and project on its  one side.Purines and Pyrimidines fo not occur on equal amounts in the RNA.


Variety:

The Four nitrogenous bases ( A,U, C,G) found in RNA may occur in any sequence, and there may be any number of sequences in a molecule. This gives an infinite variety to RNA molecule. 



What are the 6 Functions of RNA?

FUNCTIONS: RNA plays a multiple role in cells.

(i) It brings about protein synthesis in the cell. All the three types of NDAs play role in this process.

(ii) RNA is the genetic material of certain viruses. 

( iii) The rRNA is a component of ribosomes, the site of protein synthesis. 

(iv) Some RNA is associated with chromatin fibres during interphase. It initiates replication of DNA.

(v) RNA primer is essential for starting replication of DNA.

( vi) Folding of prokaryotic DNA into a nucleoid needs the help of RNA.

( vii) Certain RNAs act as enzymes, e.g., ribonuclease.

Types of RNA:

There are three major types of RNA in every cell: 
1):Messenger RNA, or mRNA;

2):Ribosomal RNA, or rRNA;

3): Transfer RNA, or tRNA.
4):Small nuclear RNA ( SnRNAL 

5):Small cytoplasmic RNA (Sc RNA) 

The three types of RNAs are synthesized from different regions of the DNA template. Only one DNA strand, called the sense strand, is apparently selected for transcription .The basis for selection is not known. In eukaryotes cells, the RNAs are formed in the nucleus and pass into the cytoplasmcytoplasm through nuclear pores. In prokaryotic cells, RNA is released by the nucleoid directly into the cytoplasm after synthesis. All the three types of RNAs are transcribed in both prokaryotes and eukaryotes as precursor molecules, which must undergo changes, called processing, to become fit for their function.


RNA chain is complementary to the DNA sense strand which produces it. The base sequence in DNA strand, the base sequence in RNA chain can be easily predicted. 

For example, if the base sequence in DNA strand is ATCGGCTA, the bass sequence in RNA will be UAGCCGAU.

(a) Ribosomal RNA:

The rRNA molecules is greatly coiled. In combination with proteins, it forms the small and large subunits of the ribosomes, hence its name. It forms about 70_80% of the total RNA  3_ 4 types o . 23S and 28S are the longest of all RNAs. It lies coiled between and over the protein molecules of ribosomes . Eukaryotic RNA is of 4 types : 28S, 18S and 5 S and prokaryotic ribosomes are of three types: 23S, 16S and 5S. In eukaryotes 28S, 5.8S occur in larger subunit and 18S in smaller subunit. Prokaryotic ribosomes has 23S and 5S in larger subunit. In eukaryotes RNA is transcribed in the form  of a long chain of 4S and in prokaryotes as 30S. In eukaryotes the arrangement in 5' ➡️3' direction is 18S_ 5.8S _ 28S. Several methlations occur prior to removal of spacer RNA. Removal of spacer RNA breaks the transcript into 2_ 3 parts. 5S is often transcribed separately. 

Functions:

1):  It is a constituent of ribosome.

2): 3' end of 18S r_ RNA of eukaryotes & 16S in prokaryotic has nucleotides complementary to those of cap region of m_ RNA.

3): 5S r _ RNA and surrounding protein complex provide binding site for t_ RNA. 





(b) Messenger RNA:

The mRNA molecule is linear. It carries message ( information) from DNA about the sequence of particular amino acids  to be joined to form a polypeptide,. It is also called information RNA ,or template RNA. It forms about 5% of the total RNA of a cell. Its molecule is the longest of all the RNA types. Its length is related  to the  size of the polypeptide to be synthesized with its information.There is a specific mRNA for each polypeptide. Because of the variation in size in mRNA population in a cell, the mRNA population in a cell, the mRNA is often called heterogeneous nuclear RNA, or heRNA.One mRNA molecule normally specifies a single polypeptide chain and is said to be monocistronic. It occurs in the eukaryotes. In some case, mostly prokaryotes, one mRNA  can specific more than one polypeptide, and is described as polycistronic or polygenic prokaryotic m_ RNA and eukaryotic m_ RNA differ from each other in many respects.

Prokaryotic m_RNA : It is polycistronic. Translation begins even during ssynthesis .They are short lived and broken down to ribonucleotides quickly. They rarely undergo processing, hence do not possess a poly. A tail at 3' end 

Eukaryotic  m_ RNA: These are monocistronic i.e.each gene transcribes its own m_ RNA. Translation begins only after completion of transcription. It is more stable than the prokaryotic m_ RNA. Transcribed RNA ( hn RNA ) undergoes processing to form m_ RNA. Processing involves capping, methylation and polyadenylation.

       An mRNA has its 5' end a methylated cap, a small noncoding region and an initiation codon and carries at its 3' end a termination codon, a small noncoding region and  a poly A tail.


 (c) Transfer RNA:

These transfer the specific amino acids from the cytoplasmic to the ribosomes m_ RNA complex during protein synthesis. These are also called soluble RNA. These are stable RNAs like r_ RNAs and constitute around 10_ 20% of total cellular RNA. It consists of 73.93 nucleotides and their m.wt ranges from  25,000_ 30,000. Their sedimentation coefficient is very low i .e. around 3.8S so they cannot be easily separated by ultracentrifugation hence called soluble RNA. A guanine base nucleotide is present on the 5' end and at 3' end has CCA. It is single stranded but due to hair pin some parts appear folded or double helical. It always contains  many unusual bases.

Clover leaf structure of yeast alanine t_ RNA was given by Holly et. al ( 1965) .For this he got Nobel Prize  with Nitenberg and Khorana . It is 6 unusual bases some of which are methylated. Thess are inosine (I) , N⁶ isopentanyladenine (i⁶A). I_ methyl guanosine ( m' G), 4_ thiouridine ( s⁴U), pseudouridine ( psix🔱) , dihydrouidine (D) and ribothymidine (T).

It has many varieties. Each variety carries a specific amino acid to the messenger RNA on the ribosomes to form  a polypeptide. The tRNA forms the remaining 15% of the total RNA of  a cell.Its molecule is the smallest of all the RNA types,and is folded to assume the form of a clover leaf. It contains some nucleotides having unusual bases. A tRNA molecule has four regions: 

(i) Carrier end ( 3' end) where amino acid joins for incorporation into a polypeptide, it carries  CCA_ OH group;

(ii) Recognition end which is opposite to the carrier end and bears an anticoden that binds to  matching codon of mRNA;

(iii) Enzyme site on one side for the binding of an enzyme.

(iv) Ribosomes site on the other side for attachment to a ribosomesribosomes




ORHER RNAs:

There are three other forms of RNA from their functional point of view:
genetic or genomic ,small nuclear RNA or snRNA and small cytoplasmic RNA or  scRNA.

1): Genetic ( Genomic) RNA:

Some viruses have RNA as genetic material which corresponds to rn_ RNA.The genomes which can convey message even in vitro are called plus or + vs strands .One the other hand, the minus (_) or negative strand genomes are complementary to the sense of m_ RNA strand .Different types of viral RNA are summarised as__

1): Plus strand RNA virus genome _ This is present in the picornavirus  and coronavirus.

2): Minus strand RNA virus genome_ It is present in helical rhabdovirus. This is functionally dead. It works as a template for RNA synthesis. 

3):  Double stranded TNA virus genome: It is present in icosahedral reovirus.

4): Retro virus genome_ It is present in retroviruses and looks and acts like m_ RNA but it synthesizes DS_ DNA .The  virus coded enzyme called reverse transcriptase is characteristic of many viruses. They synthesize viral DNA from genomic RNA.

5): Plant virus genome: TMV has a positive RNA strand. 

6): Viroids_ These are single stranded RNA circles of 240_ 350  nucleotide length. They show base pairing within themselves and look almost like double stranded structure e.g. potato spindle tuber virus( PSTV).


It occurs in certain viruses known as rhinoviruses.It may be single__ stranded ( tobacco  mosaic virus or TMV) or double _ stranded ( rheovirus) .Genomic RNA may form a DNA copy of it which then transcribes RNA copies of its  kind ( human immunodeficiency virus or HIV), or synthesize new genomic RNA on itself ( TMV).


(D): Small Nuclear RNAs ( snRNAs):

These stay in the nucleus and help in processing RNAs.Each RNA is combined with 7_ 8 molecules of proteins to form small nuclear riboproteins ( SnRNP). SnRNA takes part in  splicing, r_ RNA processing and m_ RNA processing. 


E): Small Cytoplasmic RNAs ( scRNAs):

These come out into the cytoplasm and join protein molecules to form signal recognition particles. One such small Cytoplasm RNA is 7S which combines with 6 protein molecules to produce signal recognition particles or SRP.The latter help in the synthesis of secretory proteins. 























































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