Gene expression is the process by which proteins are made. Proteins carry out almost all of the essential processes of life as they include enzymes, transcription factors, and the cellular machinery. Proteins are often referred to as gene products because of the central dogma of biochemistry: DNA to RNA to protein. Genes are considered to be “on” when their protein product is present in the cell or tissue.
Gene expression begins with a nucleic acid sequence. In humans, the genetic material is deoxyribonucleic acid (DNA), a double-stranded helix made of complementary sequences that contain four nucleotides adenine (A), guanine (G), cytosine (C), and thymine (T).
Humans have approximately 3 billion base pairs divided among 46 chromosomes (23 pairs), which are varying lengths of folded and wound DNA found in the cell nucleus.
Genes vary in length and consist of segments of the DNA sequence on a chromosome. Genes are broken down into coding sequence, the sequence that is directly copied to RNA and used to make protein, and regulatory sequences. The regulatory sequences sometimes overlap with other genes and are where transcription factors bind to influence the rate of gene expression (gene regulation – enhancers, silencers, and promoters) and where the transcription machinery loads once the DNA strand is opened. Enzymes such as topoisomerase and helicase unwind and unzip the double stranded DNA helix. This process also occurs to allow for DNA replication when cells divide.
In the process of transcription, the enzyme RNA polymerase builds a nucleic acid sequence that complements the coding sequence of the gene, messenger ribonucleic acid (mRNA), a single-stranded molecule. Like DNA, RNA is also made of four nucleotides attached to a sugar-phosphate backbone: A, C, G, and Uracil (U). After the synthesis of the mRNA, it is processed to remove introns (splicing), add a polyA tail (polyadenylation), and be 5′ capped. Some of these activities differ among organisms. In particular, RNA splicing because some genomes do not have introns. In humans and other animals, introns are thought to possibly be regulatory sequences and may contribute to alternative protein end-products. After post-transcriptional processing, the mRNA relocates to the cytoplasm from the nucleus.
Ribosomes are protein-RNA complexes that translate the mRNA into protein. The exact subunit composition differs among eukaryotes and prokaryotes. Free ribosomes are present in the cytoplasm and membrane-bound ribosomes are on the rough ER (endoplasmic reticulum), which gets its name (rough) from the presence of the ribsomes.
In its simplest explanation, translation begins with the mRNA being bound by a ribosome in the cytoplasm, starting with the AUG start codon. Codons are triplet nucleotide sequences. The ribosome exposes, or reads, two codons at a time, one for the initial attachment (A site) and one for the elongation movement (P site). The steps of protein synthesis are initiation, elongation, and termination. Transfer RNA (tRNA) are specialized RNA strands folded and looped in a manner that exposes an anti-codon, a reverse codon sequence, at the “bottom” and attaches to the corresponding amino acid at the “top.”
Once the initial amino acid is placed in the P site of the ribosome, tRNA bring in the subsequent amino acids, the building blocks of proteins, to extend the amino acid chain that ultimately becomes the protein, or peptide. The amino acids are joined by peptidyl transferase and the A site of the ribosome opens for the next tRNA to come in. The tRNA detach from the E site of the ribosome after the P site.
Elongation continues until the stop codon is reached, of which three are known. Termination, the process of releasing the peptide from the ribosome to go on its way for processing, folding, or membrane localization, often requires a release factor.
Measuring the level of protein, or gene product, in a cell or tissue can determine the activity of the gene. However, gene expression is sometimes measured on the mRNA level to discern between transcriptional and translational control in the laboratory. Gene regulation is essentially the control a cell exerts over gene expression.
The promoter region of a gene occurs before the start codon and can be short, a few hundred base pairs, or long, several kilobases, depending on the distance to or overlap with the next gene. Because of the potential overlap and multitude of factors that may or may not bind, the regulation of gene expression is very complex to discern and understand for many genes. Some transcription factors increase gene expression for some genes while hindering it for others. Transcription factors include hormone response elements, short RNA sequences, ligand binding proteins, and a slew of complexes that can bind to the transcription machinery.
Gene regulation can occur at any step in gene expression. Transcriptional regulation involves transcription factors; post-transcriptional regulation involves mRNA processing and the transport of mRNA to the cytoplasm for translation, as well as alterations in the mRNA sequence that prevent proper intron splicing and result in mRNA that cannot be translated properly or results in a different protein; translational regulation involves ribosome function; and post-translational regulation is dependent on the post-translational modification of the protein. If a protein does not properly fold or is not completed due to ribosomal stalling, it is degraded and gene expression is hindered.
Many physiological systems use feedback mechanisms to regulate genes, where the protein produced binds the DNA sequence to limit further production until the levels decrease and more is required. Another variation of this is the binding of hormones, which are also gene products, to turn genes on or off by binding the regulatory sequences and blocking or aiding the binding of transcriptional machinery, resulting in physiological responses to hormone concentrations at the level of gene expression (blood pressure regulation, liver function, additional hormone secretion, neurotransmitter release).