Courtesy :Bachelor of Science Biology (CBZ) – Chemistry, Botany, Zoology Student Corner

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Gene expression

The extended central dogma of molecular biology includes all the processes involved in the flow of genetic information.

Main article: Gene expression

Gene expression is the molecular process by which a genotype gives rise to a phenotype, i.e., observable trait. The genetic information stored in DNA represents the genotype, whereas the phenotype results from the synthesis of proteins that control an organism’s structure and development, or that act as enzymes catalyzing specific metabolic pathways. This process is summarized by the central dogma of molecular biology, which was formulated by Francis Crick in 1958. According to the Central Dogma, genetic information flows from DNA to RNA to protein. Hence, there are two gene expression processes: transcription (DNA to RNA) and translation (RNA to protein). These processes are used by all life—eukaryotes (including multicellular organisms), prokaryotes (bacteria and archaea), and are exploited by viruses—to generate the macromolecular machinery for life. # ISO certification in India

During transcription, messenger RNA (mRNA) strands are created using DNA strands as a template, which is initiated when RNA polymerase binds to a DNA sequence called a promoter, which instructs the RNA to begin transcription of one of the two DNA strands. The DNA bases are exchanged for their corresponding bases except in the case of thymine (T), for which RNA substitutes uracil (U). In eukaryotes, a large part of DNA (e.g., >98% in humans) contain non-coding called introns, which do not serve as patterns for protein sequences. The coding regions or exons are interspersed along with the introns in the primary transcript (or pre-mRNA). Before translation, the pre-mRNA undergoes further processing whereby the introns are removed (or spliced out), leaving only the spliced exons in the mature mRNA strand. # ISO certification in India

The translation of mRNA to protein occurs in ribosomes, whereby the transcribed mRNA strand specifies the sequence of amino acids within proteins using the genetic code. Gene products are often proteins, but in non-protein-coding genes such as transfer RNA (tRNA) and small nuclear RNA (snRNA), the product is a functional non-coding RNA. # ISO certification in India

Gene regulation

Regulation of various stages of gene expression

Main article: Regulation of gene expression

The regulation of gene expression (or gene regulation) by environmental factors and during different stages of development can occur at each step of the process such as transcription, RNA splicing, translation, and post-translational modification of a protein.

The ability of gene transcription to be regulated allows for the conservation of energy as cells will only make proteins when needed. Gene expression can be influenced by positive or negative regulation, depending on which of the two types of regulatory proteins called transcription factors bind to the DNA sequence close to or at a promoter. A cluster of genes that share the same promoter is called an operon, found mainly in prokaryotes and some lower eukaryotes (e.g., Caenorhabditis elegans). It was first identified in Escherichia coli—a prokaryotic cell that can be found in the intestines of humans and other animals—in the 1960s by François Jacob and Jacques Monod. They studied the prokaryotic cell’s lac operon, which is part of three genes (lacZ, lacY, and lacA) that encode three lactose-metabolizing enzymes (β-galactosidase, β-galactoside permease, and β-galactoside transacetylase). In positive regulation of gene expression, the activator is the transcription factor that stimulates transcription when it binds to the sequence near or at the promoter. In contrast, negative regulation occurs when another transcription factor called a repressor binds to a DNA sequence called an operator, which is part of an operon, to prevent transcription. When a repressor binds to a repressible operon (e.g., trp operon), it does so only in the presence of a corepressor. Repressors can be inhibited by compounds called inducers (e.g., allolactose), which exert their effects by binding to a repressor to prevent it from binding to an operator, thereby allowing transcription to occur. Specific genes that can be activated by inducers are called inducible genes (e.g., lacZ or lacA in E. coli), which are in contrast to constitutive genes that are almost always active. In contrast to both, structural genes encode proteins that are not involved in gene regulation. # ISO certification in India

In prokaryotic cells, transcription is regulated by proteins called sigma factors, which bind to RNA polymerase and direct it to specific promoters. Similarly, transcription factors in eukaryotic cells can also coordinate the expression of a group of genes, even if the genes themselves are located on different chromosomes. Coordination of these genes can occur as long as they share the same regulatory DNA sequence that bind to the same transcription factors. Promoters in eukaryotic cells are more diverse but tend to contain a core sequence that RNA polymerase can bind to, with the most common sequence being the TATA box, which contains multiple repeating A and T bases. Specifically, RNA polymerase II is the RNA polymerase that binds to a promoter to initiate transcription of protein-coding genes in eukaryotes, but only in the presence of multiple general transcription factors, which are distinct from the transcription factors that have regulatory effects, i.e., activators and repressors. In eukaryotic cells, DNA sequences that bind with activators are called enhances whereas those sequences that bind with repressors are called silencers. Transcription factors such as nuclear factor of activated T-cells (NFAT) are able to identify specific nucleotide sequence based on the base sequence (e.g., CGAGGAAAATTG for NFAT) of the binding site, which determines the arrangement of the chemical groups within that sequence that allows for specific DNA-protein interactions. The expression of transcription factors is what underlies cellular differentiation in a developing embryo.

In addition to regulatory events involving the promoter, gene expression can also be regulated by epigenetic changes to chromatin, which is a complex of DNA and protein found in eukaryotic cells. # ISO certification in India

Post-transcriptional control of mRNA can involve the alternative splicing of primary mRNA transcripts, resulting in a single gene giving rise to different mature mRNAs that encode a family of different proteins. A well-studied example is the Sxl gene in Drosophila, which determines the sex in these animals. The gene itself contains four exons and alternative splicing of its pre-mRNA transcript can generate two active forms of the Sxl protein in female flies and one in inactive form of the protein in males. Another example is the human immunodeficiency virus (HIV), which has a single pre-mRNA transcript that can generate up to nine proteins as a result of alternative splicing. In humans, eighty percent of all 21,000 genes are alternatively spliced. Given that both chimpanzees and humans have a similar number of genes, it is thought that alternative splicing might have contributed to the latter’s complexity due to the greater number of alternative splicing in the human brain than in the brain of chimpanzees. # ISO certification in India

Translation can be regulated in three known ways, one of which involves the binding of tiny RNA molecules called microRNA (miRNA) to a target mRNA transcript, which inhibits its translation and causes it to degrade. Translation can also be inhibited by the modification of the 5′ cap by substituting the modified guanosine triphosphate (GTP) at the 5′ end of an mRNA for an unmodified GTP molecule. Finally, translational repressor proteins can bind to mRNAs and prevent them from attaching to a ribosome, thereby blocking translation. # ISO certification in India

Once translated, the stability of proteins can be regulated by being targeted for degradation. A common example is when an enzyme attaches a regulatory protein called ubiquitin to the lysine residue of a targeted protein. Other ubiquitins then attached to the primary ubiquitin to form a polyubiquitinated protein, which then enters a much larger protein complex called proteasome. Once the polyubiquitinated protein enters the proteasome, the polyubiquitin detaches from the target protein, which is unfolded by the proteasome in an ATP-dependent manner, allowing it to be hydrolyzed by three proteases. # ISO certification in India