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rna: ribonucleic acid

RNA, as previously mentioned, is an acronym for ribonucleic acid. There are many forms of RNA which are quite similar to DNA. All types of RNA are transcribed from DNA in a process called transcription which is examined in detail in the Transcription and Translation section. 

A quick comparison between the two effectively explains RNA generally. 

  1. The 5-Carbon sugar in RNA nucleotides is ribose instead of deoxyribose. (A structural diagram is shown below) 

    2. Image: Ribose

  2. RNA nucleotides have Adenine, Guanine, and Cytosine as bases, but Thymine is replaced with Uracil (U), which forms a basepair with Adenine. 
  3. DNA is double-helix, but RNA usually is a single strand which can have complex twisted and folded secondary and tertiary structures. 
  4. DNA is typically longer than RNA. 
  5. DNA is generally more stable than RNA. DNA is more resistant to spontaneous and enzymatic breakdown, and damage can be repaired because the opposite strand has complementary information. RNA is more reactive due to a reactive -OH side group on the ribose sugar. Direct repairs are not possible if it is a single strand. 
  6. There are several classes of RNA, each with their own function. 
The types of RNA that we are concerned with are: 
  1. Messenger RNA (mRNA) 
  2. Transfer RNA (tRNA) 
  3. Ribosomal RNA (rRNA) 

1. messenger rna

mRNA is synthesized on DNA and contains the information needed to build a protein. mRNA travels from the nucleus of a cell to ribosomes, the place where protein synthesis occurs, and is read by the ribosomes. The result is a protein. Hence the name, messenger RNA. 

The information that mRNA carries is written in genetic code - a sequence of bases. The code is not complicated - it's like a sentance - a series of words. Each code word is called a codon, a sequence of three adjacent nucleotides that specifies one of twentry amino acids. 

There are 64 possible codons (4 x 4 x 4), and each codon codes for an amino acid. The table below shows which codons code for which amino acids. 


Messenger RNA Codons and Their Corresponding Amino Acids
First Base Second Base Third Base
U C A G
U UUU phenylalanine
UUC phenylalanine
UUA leucine
UUG leucine		 UCU serine
UCC serine
UCA serine
UCG serine		 UAU tyrosine
UAC tyrosine
UAA stop **
UAG stop **		 UGU cysteine
UGC cysteine
UGA stop **
UGG tryptophan		 U
C
A
G
C CUU leucine
CUC leucine
CUA leucine
CUG leucine		 CCU proline
CCC proline
CCA proline
CCG proline		 CAU histidine
CAC histidine
CAA glutamine
CAG glutamine		 CGU arginine
CGC arginine
CGA arginine
CGG arginine		 U
C
A
G
A AUU isoleucine
AUC isoleucine
AUA isoleucine
AUG methionine *		 ACU threonine
ACC threonine
ACA threonine
ACG threonine		 AAU asparagine
AAC asparagine
AAA lysine
AAG lysine		 AGU serine
AGC serine
AGA arginine
AGG arginine		 U
C
A
G
G GUU valine
GUC valine
GUA valine
GUG valine		 GCU alanine
GCC alanine
GCA alanine
GCG alanine		 GAU aspartate
GAC aspartate
GAA glutamate
GAG glutamate		 GGU glycine
GGC glycine
GGA glycine
GGG glycine		 U
C
A
G

You might notice that some codons code for the same amino acid. These are known as synonomous codons. For example, GGU, GGC, GGA, and GGG all code for the amino acid glycine. 

The codon AUG is special. It can either specify the amino acid methionine in the middle of a protein, or it can act as an initiation or start signal, which tells the ribosome, "Start translating here." All proteins proteins start out with methionine as their first amino acid, but it is enzymatically removed from some proteins after synthesis. 

Likewise,there are codons which specify the end of a protein. These codons are UAA, UAG, and UGA. 

There is a collinear relationship between DNA, mRNA, and proteins. The beginning of mRNA is DNAs 5' end. The 5' end of mRNA corresponds to the beginning of the amino terminus of the resulting protein. 

the structure of mrna

mRNA in both prokaryotic and eukaryotic cells is divided into three sections: 
  1. The 5' Leader (or just Leader) 
  2. The Coding Region 
  3. The 3' Trailer (or just Trailer) 
The Leader gives physical space to ribosomes so that they can bind to mRNA and move down to the initiation codon. 

The second section, the Coding Region, is the part of mRNA that actually codes for the protein - the codons. 

Finally, there is the Trailer, which is simply a section that comes after the stop codons. 

The diagram below shows the parts of mRNA. 

Image: Simplified Diagram of mRNA

In eukaryotes, mRNA that has just been transcribed from DNA must undergo two post-transcriptional modifications before it can be translated. 

  1. A special methylated version of triphosphate guanine nucleoside is added to the 5' trailer in a process called capping. 
  2. A Poly-A-Tail, a series of 50 - 150 adenine nucleotides, is added to the 3' end. Their function may be to help transport the mRNA out of the nucleus and determine the number of times mRNA can be translated before it is degraded. 
A simple graphical representation of what happens is shown below. 
Image: mRNA Capping

Eukaryotic mRNA has regions which don't code for proteins. These regions are called Intervening Sequences or introns. Regions which do code for something are called exons. After the primary mRNA transcript is produced, introns must be identified and removed so that only exons remain.

Image: Introns and Exons

Splicing is the process by which introns are removed to produce mature mRNA. It is accomplished in the nucleus of a cell with the aid of splicesomes, large RNA-protein complexes that contain many different enzymes and several kinds of RNA. Splicesomes contain a short piece of RNA that complements base sequences found at either end of just about every intron.

Once a piece of eukaryotic mRNA has been produced, capped, had a poly-a-tail added to it, and once the introns have been removed, it can be translated. Prokaryotic mRNA lacks the methylated cap and the poly-a-tail, and there are no introns so it can be translated right after being transcribed.

One final note, mRNA can be polycistronic. That is, it can contain coding regions for producing more than one polypeptide. Each region contains its own start and stop codons so that seperate proteins are produced.

2. transfer rna

Transfer RNA, or tRNA for short, translates the language of nucleotides into the language of amino acids. It carries amino acids and places them in a protein that is being produced according to the instructions of mRNA.

Each tRNA molecule consists of approximately 90 nucleotides, but when it's longer when it's first produced. To reach its final state, introns are removed, and special enzymes remove segments from each end of it and change some of the bases so that it has more than four types of nucleotides. Finally, three nucleotides are added to the 3' end of every tRNA produced: CCA. In its mature form, the structure of tRNA is quite complex, but to simplify it, imagine a 3-leafed clover. That is the approximate shape since tRNA has 3 loops (the leafs) and one stem.

tRNA has two key features.

  1. First of all, it can be covalently linked to an amino acid. A charging enzyme attaches an amino acid to the -CCA of the tRNA. The enzymes recognize each particular type of tRNA and link it to its appropriate amino acid. a tRNA with its amino acid attached to it is referred to as a charged amino tRNA. There are types of tRNAs for each of the 20 amino acids, but there are actually more due to synonomous codons.
  2. Each tRNA has its own special anticodon which recognizes specific codons. The diagram below shows the concept of codon and anticodon.

Anticodon/codon

3. ribosomal rna

rRNA, or Ribosomal RNA, contributes significantly to the structure of the ribosomes in a cell. mRNA, and tRNA work together the the ribosomes to synthesize proteins.

In eukaryotes, rRNA is transcribed exclusively within the nucleolus while other types of RNA are synthesized throughout the nucleus. After being produced, long primary rRNA strands are processed at once by a special enzyme to yield the specific shorter strands of rRNA that are needed for ribosome assembly.

In eukaryotes, there are three forms of rRNA:

  1. 18 S
  2. 5.8 S
  3. 28 S
There is also a 5 S form, but it is transcribed from a seperate gene and prepared outside of the nucleolus. In case you are wondering, S is a sedimentation or density unit that is used in describing the results of ultracentrifugation and refelcts the size and shape of a molecule or a particle. The larger the value of S is, the bigger the particle is.

rRNA forms the skeleton of ribosomes. The remainder of the ribosomes is comprised of proteins made in the cytoplasm. They enter the nucleus and then the nucleolus and then join rRNA. The assembly of ribosomes is completed in the cytoplasm.

Completed ribosomes have two parts:

  1. 60 S subunit
  2. 40 S subunit
The 60 S subunit contains the 28 S rRNA, the 5.8 S rRNA, the 5 S rRNA, and around 45 to 50 different proteins. The 40 S subunit contains the 18 S rRNA and around 30 different proteins. The final total size of the completed ribosome is around 80 S and half of the mass is proteins.

Ribosomes have specific attachment sites that allow tRNA molecules and mRNA to be in the proper close contact that they require to synthesize proteins. Two of these sites are tRNA pockets called the P site and the A Site. The other sites are mRNA grooves. There is also a site where an enzyme called peptidyl transferase works to form bonds between adjacent amino acids. If you are a bit confused about this last bit, don't worry. It's all covered in Transcription and Translation.


1998 ThinkQuest Team#18617, George Ma, Justin Wong, Liam Stewart

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