Genetics with Basics of Breeding - M.P. Myhun - 2008

CHAPTER II. Material Basis and Molecular Mechanisms of Heredity

2.7. Molecular Mechanisms of Key Genetic Processes

The most important general molecular genetic processes that ensure the viability and reproduction of Cells and organisms primarily include:

1. The process of transmitting hereditary information to subsequent generations in the form of genetic DNA or RNA molecules, driven by the de novo synthesis of their precise copies.

2. Molecular reactions aimed at preserving The Structure of genetic Nucleic Acids and guaranteeing the transmission of flawless information to the next generation.

3. Molecular processes that lead, conversely, to alterations in hereditary information—either through novel Gene combinatorics within Chromosomes, or via The Emergence of new information or the loss of old information.

4. Processes that ensure intracellular transmission and Selection/27.html">Realization of Genetic information, i.e., the phenotypic expression of the genotype.

5. Complex regulatory reactions at the level of nucleic acid and protein molecules that ensure genetic and metabolic Homeostasis within The Cell.

The reproduction of precise DNA copies and the defense of native DNA against foreign information and damage are ensured by such molecular genetic processes as Replication and Repair.

Replication. In certain Viruses, as well as in Bacteria, plants, animals, and humans containing double-stranded gDNA, the error-free transmission of hereditary information to the next generation is ensured by the cell's ability to accurately duplicate gDNA prior to each division.

The process resulting in The formation of two new DNA molecules on the template of the original molecule is called replication.

The newly synthesized DNA molecule must be an exact copy of the old molecule.

We know that genetic DNA consists of two strands, which implies a template-based principle of Biosynthesis. This means that each of the strands of the old (original, template) DNA molecule during its doubling and replication serves as a building platform (template) for the synthesis of a new complementary strand. Each daughter DNA molecule receives one polynucleotide strand from the old (original) molecule, while the second, complementary strand, is synthesized anew.

This is the so-called semi-conservative mechanism of METABOLISM/36.html">DNA replication, which is the most widespread in living nature.

However, in some cases, DNA Synthesis proceeds conservatively, and one of the daughter molecules is entirely synthesized de novo. This process is characteristic of the single-stranded circular DNA of certain viruses (bacteriophage $\Phi$X174).

Dispersive – when the material of the original molecule is randomly distributed across both daughter molecules.

Replication and cell growth in bacteria and eukaryotes are closely linked, and the completion of the replication cycle is coordinated with the act of Cell Division.

Small-sized DNA molecules of viruses and bacteria replicate as a single entity, meaning that in a single act of replication, giant eukaryotic molecules are duplicated through numerous acts of replication that begin independently of one another at different sites of the mother molecule. The unit of DNA length that replicates in a single act of replication is called a replicon.

Stages of Replication

Initiation of replication occurs at a well-defined locus. At this site, the phosphodiester bond is broken in one of the DNA strands, the double-stranded DNA untwists, and its strands separate (by the enzyme helicase). A Replication fork is formed.

Elongation of strands. Since the two DNA strands are antiparallel, the synthesis of strands complementary to them must proceed in one case in the 5'-3' direction (leading strand) and in the other direction in the 3'-5' direction (lagging strand). DNA polymerase is only capable of carrying out DNA synthesis in the 5'-3' direction, which is why the lagging strand is synthesized in small fragments (Okazaki fragments), the initiation of which requires the prior formation of short RNA primers. The synthesis of fragments (100–200 NUCLEOTIDES in eukaryotes and 1000–2000 nucleotides in E. coli) is carried out by DNA polymerase III. DNA polymerase I removes the primer after the Synthesis of the next fragment is completed.

Chromosomes of Eukaryotic cells are polyreplicate, unlike E. coli (which has a single replicon). In both PROKARYOTES AND EUKARYOTES, replication is predominantly bidirectional. That is, two replication forks arising in the replication initiation zone move away from each other during DNA synthesis until they meet the replication Proteins of neighboring replicons (termination).

Although the terms "replication" and "DNA synthesis" are used as synonyms, it should be noted that they cannot be equated. The term "replication" or replicative synthesis refers to DNA biosynthesis As a result of which each DNA molecule is doubled, thereby making the transmission of Genetic information to offspring possible. However, There is a synthesis that merely eliminates damaged DNA regions. This local synthesis is also template-based, yet the DNA molecule does not replicate (double) and is characteristic of repair processes.

Repair. For a cell to transmit its genetic information to offspring in an unchanged state, it must possess a reliable mechanism to protect its own DNA from damage and foreign information.

The stability of genetic material—DNA—relies on specialized repair systems operating in the cells of All living organisms to remove emerging DNA damage.

The elimination of DNA Lesions is carried out by DNA Repair systems, which are often comparable in complexity to the replication machinery.

The cellular defense systems protecting genomic DNA include:

1. Defense systems against foreign genetic material (genetic information foreign to a given cell can enter from the outside as part of viruses and other infectious agents). An example of defense mechanisms against foreign genetic information is the restriction-modification systems in bacteria. The core principle is that the cell's own genetic information is marked by specialized Enzymes—methylases, while Other Enzymes (Restriction Endonucleases) scan the DNA sequence and neutralize it if it is recognized as foreign.

2. Error-correction systems, which include the proofreading function of DNA polymerases that correct the Nucleotide Composition of DNA during replication.

3. Repair systems that eliminate damage in already synthesized DNA molecules.

The realization of gene information is achieved through two main molecular-genetic processes: Transcription and Translation.

Transcription is The transfer of information from double-stranded DNA to single-stranded RNA, or the synthesis of mRNA on a DNA template. It is The First stage of realizing (reading) genetic information, during which The nucleotide sequence of DNA is rewritten (transcribed) into an RNA sequence. In this process, only One DNA strand—known as the template strand—serves as the matrix for RNA Synthesis.

The underlying mechanism of information copying during transcription relies on the same structural principle of complementary nucleotide base pairing as DNA replication.

The process of RNA synthesis is catalyzed by RNA polymerase enzymes.

In eukaryotes and some primitive viruses (phages), most genes function (are transcribed) as independent units, whereas in bacteria and other viruses, genes are predominantly grouped into operons—the regulatory units of The Genome.

An Operon is a cluster of functionally related genes that are transcribed and regulated as a single unit.

The synthesis of RNA molecules begins at specific sites on the DNA called promoters and ends at terminators. The sequence between a promoter and a terminator constitutes a single transcription unit, or transcripton. Some transcriptons are read in one direction, while others are read in the opposite direction.

The Stages of Transcription are: binding of RNA polymerase to DNA, Transcription initiation, RNA chain elongation, and transcription termination.

Transcription in eukaryotes is much less understood than in prokaryotes; however, there is reason to believe that the core transcription cycle in bacteria and eukaryotes is remarkably similar.

Translation is the synthesis of protein on Ribosomes.

Protein Biosynthesis (translation) involves transferring the nucleotide sequence within mRNA molecules into the Amino Acid Sequence of polypeptide chains.

This translation is performed by protein-assembly "factories"—ribosomes—which move along the mRNA strand, building a polypeptide chain according to The Genetic Code.

In addition to ribosomes and mRNA, the protein-synthesizing system includes: tRNA, Amino Acids, enzymes, ions (Mg²⁺, Na⁺, K⁺), and specific protein factors for transcription initiation, elongation, and termination.

The biosynthesis of Polypeptides (proteins)—whose Primary Structure is encoded by structural genes and, following transcription, by mRNA molecules as well—is an essential step in realizing genetic information and establishing the corresponding phenotype. Proteins are precisely what drive Gene Expression (gene action strength, the degree of phenotypic trait manifestation) and regulate this expression during ontogeny through the catalytic (enzymatic), regulatory, transport, and other Functions inherent to protein molecules.

The entire process of protein biosynthesis is divided into 4 phases:

1. Amino Acid Activation.

During translation, the ribosome utilizes only activated forms of amino acids (i.e., bound to their respective tRNAs). This is catalyzed by the aminoacyl-tRNA synthetase enzyme. Almost all improperly synthesized aminoacyl-tRNA complexes dissociate immediately after formation—an action driven by error-correcting repair mechanisms.

2. Initiation of Polypeptide chain synthesis. This requires an initiation codon, the small ribosomal subunit, mRNA, tRNA, initiation factors, magnesium ions, and other components.

3. Elongation (extension) of the polypeptide chain.

The main steps of elongation in translation are:

a) binding of the corresponding aminoacyl-tRNA to the A-site of the ribosome;

b) formation of a peptide bond between the preceding and the next amino acid residues;

c) translocation (movement) of the formed peptidyl-tRNA from the A-site to the P-site of the ribosome, accompanied by the simultaneous shift of mRNA by one triplet.

4. Termination of translation.

The termination signals are the UAA, UAG, and UGA codons.

Recombination. Formation of new gene combinations.

Gene recombination is carried out in various ways.

This process may be associated with the redistribution of whole chromosomes. The recombination of genes localized in homologous chromosomes is known as Crossing-over.

For recombination to occur, eukaryotes use a sexual process, prokaryotes use conjugation, and viruses use co-infection.

The result of recombination is the transfer of DNA segments from one molecule to another.

Types of recombination

1. General recombination, which occurs between homologous DNA sequences.

2. Site-Specific Recombination, which involves DNA molecules characterized by limited structural similarity; it has been studied in the most detail during the Interaction of a prophage with the E. coli chromosome.

3. Illegitimate Recombination, which involves DNA molecules that share no structural similarity. The Mechanism of transposition of Mobile Genetic Elements.

Genetic recombination is based on the break-and-join mechanism of pairs of homologous DNA molecules. This is a multistep process that includes pairing and actual recombination.