DNA Replication and Protein Synthesis Mechanisms

DNA Replication and Transcription Initiation

Initiation: Unwinding the Double Helix

Initiation begins at specific regions or points of origin (Ori) on the DNA. Specialized proteins recognize and break the hydrogen bonds between the base pairs at the initiation point.

At the point where the DNA unwinds, tension is created, which is resolved by topoisomerase and gyrase. The SSB protein prevents the strands from re-coiling.

A Y-shaped replication bubble is formed. Replication begins when RNA polymerase recognizes the promoter region, which includes a central sequence.

Elongation: Synthesizing New DNA Strands

A new DNA chain is synthesized for each original strand. The DNA polymerases (I, II, III) have two main functions:

• Polymerase activity: Join the nucleotides that form the DNA chain.
• Exonuclease activity: Remove incorrectly paired nucleotides.

DNA polymerase cannot initiate a new DNA chain from scratch; it requires an RNA primer fragment, which ends with a 3' hydroxyl group where nucleotides can be added.

The primer is synthesized by primase (a type of RNA polymerase). DNA polymerase synthesizes the new chains in the 5' to 3' direction.

The leading strand is synthesized continuously. The lagging strand synthesis is discontinuous, consisting of small DNA fragments called Okazaki fragments, which are later joined by ligase.

In eukaryotes, once the fragments are joined, a Methyl-Guanosine-Phosphate cap (30 nucleotides long) is added to the 5' end.

Termination

Termination occurs when RNA polymerase recognizes specific termination sequences.

• Prokaryotes: Termination sequences are palindromic bases formed by G followed by T and C.
• Eukaryotes: After RNA polymerase finishes, poly-A polymerase adds a final sequence of about 200 adenine nucleotides (a poly-A tail) to the 3' end.

Protein Synthesis (Translation)

Initiation

The small ribosomal subunit and the mRNA align near the AUG start codon.

The first aminoacyl-tRNA enters the P site of the ribosome, specifically carrying the anticodon UAC, which corresponds to the first amino acid, methionine.

Elongation

Elongation occurs when a second aminoacyl-tRNA enters and occupies the A site.

The next step is the formation of the peptide bond between the two amino acids, catalyzed by peptidyl transferase.

The first tRNA is released from the dipeptide end, and the second tRNA carries the complementary codon. Subsequently, the first tRNA separates, and the ribosome translocates.

Ribosomal translocation moves the ribosome along the mRNA in the 5' to 3' direction, freeing up the A site for the next tRNA.

Completion

Completion occurs when the ribosome reaches a termination codon on the mRNA (UAA, UGA, or UAG). This codon is recognized by release factors, causing hydrolysis of the polypeptide chain.

Poliribosomes (Polysomes)

These are long chains of mRNA being simultaneously translated by multiple ribosomes.