Biochemistry 3107 - Fall 2003

Introduction to RNA & its Functions

Transcription

Transcription is the synthesis of RNA from DNA. As the first step in the expression of the genetic material, it is clearly a very important one. This is underscored by the fact that this step is frequently regulated. Consequently, it has been the focus of much study.

Typical questions that one might ask or address are:

• How is RNA made?
• What prevents RNA being made?
• What causes an increase in the amount of RNA that is made?
• What destroys RNA?
• What prevents RNA from being translated?

 

Major RNAs

There are three major classes of RNA in the cell:

mRNA

messenger RNA carries the genetic information that will be expressed ultimately as proteins. In prokaryotes, it is short-lived and is turned over rapidly. Eukaryotic mRNA is more stable as a result of the modifications that are made to it after it is transcribed.

 

tRNA

transfer RNA is the adapter molecule. It recognizes the codons of the mRNA on the one hand, and it can be covalently bonded to the appropriate amino acid, on the other.

 

rRNA

ribosomal RNA is found in the ribosomes.

Prokaryotic ribosomes have 3 rRNA molecules: 23S, 16S and 5S.

Eukaryotic ribosomes have 4 rRNA molecules: 28S, 18S, 5.8S and 5S.

rRNA was once thought to be an inert scaffold for the ribosomal proteins. We now know that the 23S (and 28S) rRNA is the catalytic agent in protein synthesis.

 

Non-coding RNAs (ncRNA)

It has recently become clear that botyh prokaryotic and eukaryotic cells contain a large number of small RNA molecules with a diversity of functions in processes such as regulation of transcription, repliation of eukaryotic chromsomomes, RNA processing, RNA modification, RNA editing, mRNA stability and degradatrion, regulation of translation, and protein translocation.

The following table from a review article in Science lists processes affected by ncRNAs and gives some examples.

FROM: Gisela Storz (2002) An Expanding Universe of Noncoding RNAs. Science 296: 1260-1263.

 

The following diagram from the same review article illustrates some examples of ncRNAs in action. The top row shows two ncRNA molecules (red) interacting with target mRNA molecules. On the left, the interaction exposes bases that are modified. On the right the interaction covers up the ribosome binding site and prevents translation of the target mRNA. The middle row shows two ncRNAs that mimic RNA structures found in the cell. On the left is a structure that mimics that of an RNA-polymerase open promoter complex; on the right is one that mimics both tRNA and mRNA (tmRNA). The botton row shows the RNA-signal recognition particle complex which functions in directing protein synthesis through the endoplamic reticulum.

FROM: Gisela Storz (2002) An Expanding Universe of Noncoding RNAs. Science 296: 1260-1263.

 

Some specific examples of ncRNAs are:

telomere RNA

Telomerase, the enzyme that adds the telomere repeats to eukaryotic chromosomes contains an essential RNA template.

 

snRNA

small nuclear RNA molecules are integral components of the small nuclear ribonucleoprotein particles which bring about splicing of eukaryotic mRNAs.

 

snoRNA

small nucleolar RNA molecules are found in the nucleolus of eukaryotic cells. They are associated with protein particles, snoRNPs, and they have been demonstrated to define sites of nucleotide modifications in rRNA. In addition, a few snoRNAs may play a role in of pre-rRNA processing in the nucleolus.

 

gRNA

guide RNA functions in the editing of certain mRNAs. RNA editing is found particularly in the mitochondria of plants and protozoa and also in chloroplasts. gRNA directs where and what changes can occur.
Cyttochrome oxidase mRNA and gRNA from the The U-insertion/deletion Edited Sequence Database.

 

tmRNA

tmRNA has properties of tRNA and mRNA combined in a single molecule. It functions during protein synthesis to rescue ribosomes that have become "stuck" while trasnlating mRNA molecules that have lost their stop codons.
Image of Escherichia coli tmRNA from the tmRNA Database. Click here to view a three-dimensional structure of the E. coli tmRNA.

 

signal recognition particle RNA

This 300 nt RNA is an integral component of Signal Recognition Particles which direct the secretion of newly-synthesized proteins through the endoplasmic reticulum.
Image of Halobacterium halobium SRP RNA from the Signal Recognition Particle Database. Click here to view a three-dimensional structure of the E. coli SRP RNA.

 

M1 RNA

M1 RNA is the name given to the RNA component of Ribonuclease P, which functions in the processing of tRNA molecules in prokaryotes. M1 RNA is the catalytic component of the enzyme.
Image from: The RNaseP Database section on Three-dimensional models.

siRNA and miRNA

TO BE ADDED