shows only a small fraction of the actual size of an adipocyte.
Source: Courtesy Dr. Elvira Gagniuc, Department of Pathology, Faculty of Veterinary Medicine, University of Agronomic Sciences and Veterinary Medicine, Bucharest.
Nevertheless, chromatin also undergoes partial changes while in G0 phase (the resting stage of the cell cycle – e.g. many neuronal cells are always in this state). These partial and continuous changes of the chromatin structure are meant to silence or activate certain genes from the main subset of genes. Such facultative heterochromatin areas are present on the outer surface of the heterochromatin landscape (the euchromatin – heterochromatin borders), and their condensation state depends on successive interactions between different gene products of the subset [31]. Note that DNA molecules are present not only in the area of the cell nucleus but also in other organelles (e.g. mitochondria and chloroplasts). Much like in prokaryotes, the circular double-stranded DNA molecules found in these eukaryotic organelles show their own type of organization called a nucleoid (meaning nucleus-like; it is an infrequent DNA–protein assembly) [38, 39].
Figure 1.3 Molecular representations. (a) Shows the structure of the nucleosome core particle [52, 53]. (b) Shows the path of mRNA through the ribosome by pointing out the collinearity between the tRNA anticodons [53, 54]. The window highlights the binding region between an amino acid and a tRNA. (c) Shows the Escherichia coli glutaminyl transfer RNA synthetase complexed with transfer RNA(Gln) and ATP [53, 55]. The tRNA sequence is presented next to this ribonucleoprotein particle. The last letters in the sequence correspond in reverse order to the region in the tRNA highlighted by the dotted line window (i.e. “ACCG …”). The position of the tRNA anticodon is also highlighted here.
Source: Refs. [52, 53, 55].
1.5 Molecular Mechanisms
Eukaryotes and prokaryotes prefer different strategies for synthesizing multiple proteins from a single DNA region (a transcription unit). In prokaryotes, several protein-coding areas (genes) are arranged linearly in a region called an operon, which is usually regulated by a single promoter. An operon is a cluster of coregulated genes with related functions [40]. Thus, operon expression leads to a number of proteins equal to the number of coding areas (genes) in the operon. All the genes in the operon are transcribed into a continuous RNA molecule, which is almost simultaneously translated into proteins. However, functional gene clustering (operon-like) has been reported in eukaryotes (i.e. fungi, plants, and animals) [40]. Eukaryotes, on the other hand, primarily use a single coding area interrupted by noncoding areas (introns). Different combinations between smaller fragments (exons) of the coding area lead to several types of RNAs and consequently to several types of proteins. The protein versions that originate from to a single gene are called “protein isoforms.” Note that protein isoforms are not necessarily functionally related [41].
1.5.1 Precursor Messenger RNA
Promoter and enhancer regions regulate the transcription of nearby genes. The initiation of transcription is conditioned by various regulatory proteins that bind to the regulatory regions of DNA (the promoter and enhancer regions). In eukaryotes, the regulatory proteins facilitate changes in the local chromatin structure to allow proper recruitment and binding of RNA polymerase to one of the DNA strands. Thus, the local chromatin structure either promotes or inhibits RNA polymerase and TF binding. Transcription begins once the RNA polymerase enzyme binds to the promoter region of the gene. Regulatory proteins in conjunction with different combinations of TF dictate the frequency of synthesis for pre-messenger RNA (mRNA) molecules (how many copies per unit of time). For instance, different combinations of TFs lead to different three-dimensional macromolecular conformations (the transcription mediator complex) [42]. These temporary macromolecular constructions (made of TFs and other proteins) and their interaction with chromatin, allow the access of RNA polymerase to the DNA sequence to a greater or lesser extent. The difficulty of recruitment imposes a probability distribution for binding. In turn, this binding probability of RNA polymerase sets the frequency of synthesis for pre-mRNAs. As a rule of thumb, a more open chromatin structure is associated with active gene transcription events, while a more compact chromatin structure indicates transcriptional inactivity (no expression).
1.5.2 Precursor Messenger RNA to Messenger RNA
The DNA region of the gene can be subdivided into other types of regions. Especially in eukaryotes, many genes are organized into coding (exons) and noncoding regions (spliceosomal introns). Both exons and introns are transcribed into a continuous pre-mRNA fragment. While the pre-mRNA is being transcribed/synthesized, the intronic regions are removed by spliceosomes (a ribonucleoprotein complex) and the ligation of the exon regions forms the mRNA. The process of intron removal is called splicing. Exon ligation in the same order, in which these regions appear in a gene, is called constitutive splicing. Thus, constitutive splicing allows for a “one gene–one protein” model (or, one pre-mRNA – one mRNA). When exon ligation does not follow the order observed in the gene (i.e. certain exons are skipped), several mRNA variants are produced from a single pre-mRNA variant. If the gene encodes for proteins, then each mRNA variant will generate a different type of protein (protein isoforms). This process is known as alternative splicing, and is responsible for the exaggerated abundance of protein types in the eukaryotic proteome.
1.5.3 Classes of Introns
Introns are regions that interrupt the coding region of functional RNA or protein-coding genes. There are four known classes of introns: Group I introns, Group II Introns, nuclear pre-mRNA introns (Spliceosomal introns), and transfer RNA (tRNA) introns. Group I introns are self-splicing introns and are found in some ribosomal RNA (rRNA) genes [43]. Group II introns are mobile ribozymes that self-splice from precursor RNAs (pre-RNAs) and are found in bacterial genomes and organellar genomes, suggesting that catalytic RNAs, as informational structures, predate the origin of eukaryotes and perhaps the origin of cellular life [44, 45]. Nuclear pre-mRNA introns are found in protein-coding genes and require a ribonucleoprotein complex (spliceosomes) for splicing. The tRNA introns are found in various tRNA genes in all the three kingdoms of life, and require certain enzymes for splicing [46].
1.5.4 Messenger RNA
The stochastic behavior of brownian motion (random walk) and the concentration gradients, scatter the mRNA molecules from the origin of synthesis to other locations with a lower concentration. Thus, the mRNA scattering (as is the case with many other molecules of different sizes and shapes) is done naturally on the least frictional paths. In the case of eukaryotes, the origin of pre-mRNA synthesis and processing is the inner space of the cell nucleus (high mRNA concentration) and the mRNA molecules diffuse through the nuclear pores into the relaxed environment of the cytoplasm (low mRNA concentration). In the case of prokaryotes, the mRNAs diffuse from the origin of synthesis (which is close to the DNA molecule floating directly in the cytoplasm) into the rest of the cytoplasm. The information from some mRNAs allows for protein synthesis, whereas the information from other RNAs provides direct biological functionality. Moreover, some mRNA molecules
