Saturday, February 28, 2009

Role of DNA and RNA in Protein Synthesis

The central dogma of protein synthesis is that DNA makes RNA, which in turn makes protein. This can be expressed as follows:

Replication Transcription Translation
DNA------------------à DNA-----------------à RNA---------------à PROTEIN

Protein synthesis consists of two main events, transcription and translation. Transcription is the copying of a complementary messenger RNA strand on a DNA strand. The DNA strand unwinds and one of the two strands forms a mRNA strand. This strand is called anti-sense strand or template strand. The nucleotides of mRNA are complementary to those of the DNA strand. However, in mRNA uracil (U) is replaces thymine (T) of DNA. As a result the complementary pairing is A-U and G-C. The mRNA thus formed makes its way through the pores in the nuclear membrane to the cytoplasm. Here it forms a complex with a group of ribosomes.

Transcription requires along with a template strand, ribonucleotide triphosphate (ATP, GTP, UTP, CTP), the enzyme RNA polymerase and divalent metal ions. RNA polymerase consists of a core enzyme (with sub units α, α, β, β and ω) and a sigma (σ)factor. The sigma factor initiates transcription of mRNA on the DNA template and the core enzyme continues transcription. All the RNA chains start with either pppG or pppA and are synthesized in the 5’ – 3’ direction. Chain termination is brought about by a rho factor.

Translation: During translation the genetic information present in mRNA directs the order of specific amino acids to from a polypeptide or protein. The mRNA has a series of triplet bases, each triplet forming a codon. The codons pair with anticodons of the tRNA molecule. Each anticodon consists of three free bases. This pairing follows the A-U and G-C combination. Thus the codon GUC pairs with the anticodon CAG to tRNA. Thus the series of codons on mRNA determines the series of anticodons of the different tRNA molecules, and hence of the amino acids. Since the triplets of mRNA in turn depend upon the series of bases in DNA, it follows that the DNA molecule determines the sequence of amino acids, and thus the structure of the protein molecule.

The translation process consists of –
1. activation of amino acids
2. transfer of the activated amino acid to tRNA
3. initiation of polypeptide chain synthesis
4. chain elongation and
5. chain termination

1. Activation of amino acids: The 20 amino acids (aa) used in protein synthesis are activated by ATP in the present of specific activating enzymes (E) called aminoacyl synthetases to from aminoacyl adenylates (aaa), also called aminoacyl AMP. Pyrophosphates (PPi) are released.

aa + ATP + E --------à E-aa-AMP + PPi

2. Transfer of activated amino acids to tRNA: The activated amino acid is transferred to a specific tRNA with the release of AMP and activating enzyme.

E.aa.AMP + E + tRNA -----------à aa-tRNA + AMP + E

3. Initiation of chain synthesis: This requires the ribosome subunits, mRNA, an energy source (GTP), activated amino acids attached to tRNA (aa-tRNA) and initiation factors (IF). These factors are called IF-1, IF-2, IF-3 in prokaryotes and eIF-2, e-IF2’, eIF-2a1 eIF-2a2 , eIF-2a3 and eIF-3 in eukaryotes.
a. The 30S ribosomal subunit attaches to mRNA to form an mRNA-30S complex. The process requires IF-3 and Mg++
b. the starting amino acid is methionine (Met) in eukaryotes and N-formyl methionine in prokaryotes. The amino acid-tRNA complex (fMEt-tRNA) attaches to the initiation codon, AUG, on mRNA through its anticodon UAC to form the 30S initiation complex. The process requires initiation factors IF-2 and IF-1 as well as GTP.
c. The larger ribosomal subunit (50S in prokaryotes) joins to the 30S initiation complex to form the complete initiation complex (70S).
d. The larger ribosomal subunit has two binding sites for tRNA, an A or acceptor site and a P or peptidyl site. fMet-tRNA binds to the P site.

4. Chain Elongation: Elongation of the polypeptide chain requires elongation factors (EF). These are EF-Tu. EF=Ts and EF-G in prokaryotes and EF-1 and EF-2 in eukaryotes.
a. The second amino acid-tRNA complex (aa2-tRNA) now occupies the A site. There is enzymatic recognition of internal codons. The process requires EF-Tu, GTP and Mg++.
b. Formation of a peptide bond takes place by transfer of fMet to the second amino acid (aa2). Mg++ and K+ are required. The catalyzing enzyme is pepitdyl transferase.
c. Translocation: The aa2-tRNA complex moves from the A site to the P-site. This process is called translocation and requires EF-G, GTP and Mg++. Translocation involves movement of the ribosome relative to mRNA in the 5’--à3’ direction. The third amino acid-tRNA (aa3-tRNA) complex now occupies the vacant A-site.

5. Chain termination: Chain elongation continues until a termination codon (UAA, UAG, UGA) reaches the ribosome. The chain is then terminated and released from the ribosome. This process requires release factors RF-1, RF-2 and RF-3 in prokaryotes and RF in eukaryotes.
a. The termination codon provides signals to the ribosome for the attachment of release factors.
b. the release factors interact with peptidyl transferase causing hydrolysis of the bond between tRNA and the polypeptide chain, and the chain is released from the ribosome.
c. Hydrolysis of GTP results in the dissociation of the release factors from the ribosome. The tRNA is also unloaded. The ribosomal subunits dissociate and mRNA is released, for breakdown to nucleotides.
d. Processing of the polypeptide chain, e.g., cleavage of the formyl residue or of methionine, takes place after release.

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