Central Dogma of the Molecular Biology

Mitesh Shrestha

• DNA

• RNA

• Protein

Central Dogma

• The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred back from protein to either protein or nucleic acid.

General Special Unknown

DNA → DNA RNA → DNA protein → DNA

DNA → RNA RNA → RNA protein → RNA

RNA → protein DNA → protein protein → protein ??

3 classes of information transfer suggested by the dogma

Central Dogma (Extended)

Accessing of Genome

• When non-dividing nuclei are examined by light microscopy all that can be seen is a mixture of lightly and darkly staining areas within the nucleus. – Heterochromatin - dark areas, which tend to be concentrated

around the periphery of the nucleus. • Constitutive Heterochromatin : a permanent feature of all cells and

represents DNA that contains no genes and so can always be retained in a compact organization. This fraction includes centromeric and telomeric DNA as well as certain regions of some other chromosomes. For example, most of the human Y chromosome is made of constitutive heterochromatin.

• Facultative Heterochromatin : not a permanent feature but is seen in some cells some of the time. Facultative heterochromatin is thought to contain genes that are inactive in some cells or at some periods of the cell cycle. When these genes are inactive, their DNA regions are compacted into heterochromatin.

Accessing of Genome

• Euchromatin - The remaining regions of chromosomal DNA, the parts that contain active genes, are less compact and permit entry of the expression proteins.

• They are dispersed throughout the nucleus.

• The exact organization of the DNA within euchromatin is not known, but with the electron microscope it is possible to see loops of DNA within the euchromatin regions, each loop between 40 and 100 kb in length and predominantly in the form of the 30 nm chromatin fiber.

• The loops are attached to the nuclear matrix via AT-rich DNA segments called matrix-associated regions (MARs) or scaffold attachment regions (SARs)

Accessing of Genome

Accessing of Genome

• The loops of DNA between the nuclear matrix attachment points are called structural domains. An intriguing question is the precise relationship between these and the functional domains that can be discerned when the region of DNA around an expressed gene or set of genes is examined

Accessing of Genome

• A functional domain is delineated by treating a region of purified chromatin with deoxyribonuclease I (DNase I) which, being a DNA-binding protein, cannot gain access to the more compacted regions of DNA. Regions sensitive to DNase I extend to either side of a gene or set of genes that is being expressed, indicating that in this area the chromatin has a more open organization, although it is not clear whether this organization is the 30 nm fiber or the ‘beads-on-a-string’ structure

Functional Domain

• The boundaries of functional domains are marked by sequences, 1–2 kb in length, called insulators. Insulator sequences were first discovered in Drosophila and have now been identified in a range of eukaryotes. The best studied are the pair of sequences called scs and scs′ (scs stands for ‘specialized chromatin structure’), which are located either side of the two hsp70 genes in the fruit-fly genome

Functional Domain

• Insulators display two special properties related to their role as the delimiters of functional domains. – The first is their ability to overcome the positional effect that

occurs during a gene cloning experiment with a eukaryotic host. The positional effect refers to the variability in gene expression that occurs after a new gene has been inserted into a eukaryotic chromosome.

– Insulators also maintain the independence of each functional domain, preventing ‘cross-talk’ between adjacent domains. If scs or scs′ is excised from its normal location and re-inserted between a gene and the upstream regulatory modules that control expression of that gene, then the gene no longer responds to its regulatory modules: it becomes ‘insulated’ from their effects. This observation suggests that, in their normal positions, insulators prevent the genes within a domain from being influenced by the regulatory modules present in an adjacent domain.

Functional Domain

• The formation and maintenance of an open functional domain, at least for some domains, is the job of a DNA sequence called the locus control region or LCR (Li et al., 1999). Like insulators, an LCR can overcome the positional effect when linked to a new gene that is inserted into a eukaryotic chromosome. Unlike insulators, an LCR also stimulates the expression of genes contained within its functional domain.

Synthesis and Processing of RNA

RNA degradation

Assembly of the translation initiation complex

Protein synthesis

Protein folding and Protein processing

• To be useful, polypeptides must fold into distinct three-dimensional conformations, and in many cases multiple polypeptide chains must assemble into a functional complex. In addition, many proteins undergo further modifications, including cleavage and the covalent attachment of carbohydrates and lipids, that are critical for the function and correct localization of proteins within the cell.

Protein degradation

• The levels of proteins within cells are determined not only by rates of synthesis, but also by rates of degradation. The half-lives of proteins within cells vary widely, from minutes to several days, and differential rates of protein degradation are an important aspect of cell regulation. Many rapidly degraded proteins function as regulatory molecules, such as transcription factors. The rapid turnover of these proteins is necessary to allow their levels to change quickly in response to external stimuli. Other proteins are rapidly degraded in response to specific signals, providing another mechanism for the regulation of intracellular enzyme activity. In addition, faulty or damaged proteins are recognized and rapidly degraded within cells, thereby eliminating the consequences of mistakes made during protein synthesis. In eukaryotic cells, two major pathways—the ubiquitin-proteasome pathway and lysosomal proteolysis—mediate protein degradation.

Ubiquitin-proteasome pathway

Assignments

• Explain about the Central Dogma of Molecular Biology. [7.5]

• Differentiate between Riboswitch and Aptamers. [2.5]

• Differentiate between chromosome, chromatin and chromatid. [2.5]

• How RNA helps in gene regulation ? [2.5]

• Write about Argonaute proteins. [2.5]

• Write about Positional Effect for a gene. [2.5]

References • Brown TA. Genomes. 2nd edition. Oxford: Wiley-Liss; 2002.

Chapter 8, Accessing the Genome. Available from: http://www.ncbi.nlm.nih.gov/books/NBK21137/

• Brown TA. Genomes. 2nd edition. Oxford: Wiley-Liss; 2002. Chapter 10, Synthesis and Processing of RNA.Available from: http://www.ncbi.nlm.nih.gov/books/NBK21132/

• Lodish H, Berk A, Zipursky SL, et al. Molecular Cell Biology. 4th edition. New York: W. H. Freeman; 2000. Section 4.4, The Three Roles of RNA in Protein Synthesis. Available from: http://www.ncbi.nlm.nih.gov/books/NBK21603/

• Cooper GM. The Cell: A Molecular Approach. 2nd edition. Sunderland (MA): Sinauer Associates; 2000. Protein Folding and Processing. Available from: http://www.ncbi.nlm.nih.gov/books/NBK9843/

Upcoming Lecture

• Watson-Crick scheme for DNA replication, topological problem and its solution,

• Meselson-Stahl experiment,

• DNA topoisomerase and its types,

• variations in semiconservative theme