DNA Replication, Transcription, and Translation in Molecular Genetics

Posted on Dec 14, 2024 in Biology

Molecular Genetics: DNA Replication, Gene Expression, and Mutation

Concept of Gene

A gene is a fragment of DNA containing encoded information for the synthesis of structural and regulatory proteins.

Characteristics of Genes

• Prokaryotes: Genes are continuous units; all information contained in the gene leads to protein synthesis.
• Eukaryotes: Genes are fragmented. Sequences consist of information to synthesize proteins (exons) and other sequences that are eliminated in the transcript (introns).

Replication

Replication or duplication is the process by which a DNA molecule creates two identical copies of itself.

Purpose

• Transmission of genetic information to offspring.
• Perpetuation of the species.

Elements Involved

• Original DNA
• Topoisomerase
• DNA Polymerase
• RNA Polymerase
• DNA Ligase
• Deoxyribonucleotide Triphosphates
• Ribonucleotide Triphosphates

DNA Polymerase

Types I, II, and III. Its function is twofold:

• Polymerase Activity: Joins nucleotides.
• Exonuclease Activity: Eliminates nucleotide RNA fragments.

Stages of DNA Replication

Starting-Up Phase

Consists of the unwinding and opening of the double helix. It begins in a region of DNA called the start point. During this phase:

• The point of initiation is recognized by specific proteins that bind to it.
• Helicase enzymes break the hydrogen bonds between the base pairs, and the double helix opens like a zipper.
• Gyrase and topoisomerase enzymes prevent tensions created by separating the two strands of the double helix.
• A replication bubble forms, where new DNA strands will be synthesized. It extends bidirectionally.

Elongation Phase

DNA polymerases need a small piece of RNA (primer) with a free 3′ hydroxyl end to add nucleotides. After starting the synthesis, the self-synthesized DNA strand serves as a primer.

DNA polymerase runs the DNA strand clockwise from 3′ to 5′, joining the new nucleotide at the 3′ end.

• RNA polymerase produces complementary RNA fragments of the original DNA, called primers, of about 10 nucleotides, to which deoxyribonucleotides are added.
• DNA polymerase III adds deoxyribonucleotides to the 3′ end (5′-3′), taking the pre-existing DNA chain as a template, stretching the strand.
• In the replication forks, the leading strand is synthesized continuously in the same direction as the opening of the fork, while the lagging strand is synthesized opposite to the opening of the fork and discontinuously by Okazaki fragments.
• DNA ligase joins all the DNA fragments while eliminating the primers.

As the strands have been synthesized and the fragments joined, the double helix is released, resulting in two identical DNA molecules at the end of the process, each with one old and one new strand.

Differences Between the Replication Process in Prokaryotes and Eukaryotes

Transcription

It is the process of copying a gene or DNA fragment using oligonucleotides and RNA of different kinds.

Location

• Prokaryotes: Cytoplasm
• Eukaryotes: Nucleus

Mechanism and Stages of RNA Transcription

To carry out the transcription of DNA, cells require:

• An original DNA strand to serve as a template to be copied.
• RNA polymerase: RNA synthesis from a DNA template.
• Triphosphate ribonucleotides A, G, C, and U.

Stages

• Initiation: RNA polymerase joins a particular area of DNA, the Promoter Center (TATA box). This copy does not require any primer.

• Elongation: RNA polymerase continues to add complementary DNA oligonucleotides. It reads the DNA strand 3′-5′, while the synthesis of RNA is 5′-3′. The 5′ end is modified by binding to 7-methyl guanosine, forming the “cap”.

• Completion: Transcription ends when RNA polymerase recognizes termination signals. The newly formed RNA is added to a tail of about 200 adenine nucleotides, the poly-A tail. In prokaryotes, it is a palindromic sequence. In eukaryotes, it is also palindromic but AAUAA, the poly-A tail.

Differences in Transcription Between Eukaryotes and Prokaryotes

Genetic Code

Establishes the relationship of correspondence between mRNA nucleotides (codons) and encoded amino acids.

Translation

Definition

The process of protein synthesis carried out by ribosomes, based on information provided by the mRNA, which is, in turn, a copy of a gene.

Location

• Cytoplasm
• Ribosomes

Role of Different RNA and Ribosomes

• mRNA: Carries genetic information from the nucleus to the ribosomes.
• tRNA: Transports amino acids to ribosomes in the correct order. There are over 20 different tRNAs.
• rRNA: Involved in the formation of ribosomes.
• Ribosomes: Cytoplasmic organelles formed by an association of protein and rRNA. They have two subunits: one large and one small. Three different binding sites to tRNA are distinguished:
  • Site A (aminoacyl): Where amino acids enter.
  • Site P (peptidyl): Where the polypeptide chain in formation is situated.
  • Site E: Where tRNA is situated before leaving the ribosome.

Phases of Translation

The process of protein manufacturing. The elements involved in translation are: mRNA, tRNA, ribosomes, enzymes (aminoacyl-tRNA synthetase, peptidase), GTP, initiation and completion factors, and amino acids. The process can be divided into four stages:

• Activation of Amino Acids: Each tRNA seeks its specific amino acid, recognizes its anticodon triplet, and joins it through the action of a specific enzyme called aminoacyl-tRNA synthetase, which binds the amino acid to its tRNA in the acceptor arm, spending one molecule of ATP. This gives rise to a complex called aminoacyl-tRNA.

• Initiation of the Polypeptide Chain: mRNA reaches the ribosome and binds to the small subunit. mRNA binds to site P at the first codon, AUG, read from the 5′ end, starting all processes of translation. The small ribosomal subunit, mRNA, and the first aminoacyl-tRNA form the initiation complex, which subsequently binds to the large ribosomal subunit, forming the active ribosomal complex. It is synthesized in the 5′-3′ direction.

• Elongation: It starts when another tRNA with the following amino acid reaches site A. Then, a peptidyl-transferase enzyme binds both amino acids by a peptide bond, and the whole ribosomal complex moves (translocation) along the mRNA in the 5′-3′ direction so that the first tRNA leaves the ribosome. The dipeptide goes to occupy site P, and site A is free. A new tRNA is placed in site A, a peptide bond is created, and the complex is displaced again.

• Completion: Appears at site A a stop codon, which is not recognized by any tRNA but by release factors that separate the polypeptide chain from the tRNA. The formed protein, mRNA, and tRNA leave the ribosome.