Transcription of DNA

As noted previously, RNA is structurally similar to DNA but contains ribose rather than deoxyribose and uracil rather than thymine. There are three major kinds of RNA, each of which serves a specific purpose. In addition, there are a number of small RNAs that appear to control a wide variety of important cellular functions. All RNA molecules are much smaller than DNA, and all remain single-stranded rather than double-stranded. 

The genetic information in DNA is contained in segments called genes, each of which consists of a specific nucleotide sequence that encodes a specific protein. The conversion of that information from DNA into proteins begins in the nucleus of cells with the synthesis of mRNA by transcription of DNA. In bacteria, the process begins when RNA polymerase recognizes and binds to a promoter sequence on DNA, typically consisting of around 40 base pairs located upstream (S ) of the transcription start site. Within the promoter are two hexameric consensus sequences, one located 10 base pairs upstream of the start and the second located 35 base pairs upstream. 

Following formation of the polymerase—promoter complex, several turns of the DNA double helix unwind, forming a bubble and exposing 14 or so base pairs of the two strands. Appropriate ribonucleotides then line up by hydrogen-bonding to their complementary bases on DNA, bond formation 

FIGURE 24.5 Biosynthesis of RNA using a DNA base segment as template. 

Unlike what happens in DNA replication, where both strands are copied, only one of the two DNA strands is transcribed into mRNA. The DNA strand that contains the gene is often called the sense strand, or coding strand, and the DNA strand that gets transcribed to give RNA is called the antisense strand, or noncoding strand. Because the sense strand and the antisense strand in DNA are complementary, and because the DNA antisense strand and the newly formed RNA strand are also complementary, the RNA molecule produced during transcription is a copy of the DNA sense strand. That is, the complement of the complement is the same as the original. The only difference is that the RNA molecule has a U everywhere the DNA sense strand has a T. 

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Steroid hormones act in a different manner from most hormones we have considered. In many cases, they do not bind to plasma membrane receptors, but rather pass easily across the plasma membrane. Steroids may bind directly to receptors in the nucleus or may bind to cytosolic steroid hormone receptors, which then enter the nucleus. In the nucleus, the hormone-receptor complex binds directly to specific nucleotide sequences in DNA, increasing transcription of DNA to RNA (Chapters 31 and 34). 

The conversion of the information in DNA into proteins begins in the nucleus of cells with the synthesis of mRNA by transcription of DNA. In bacteria, the process begins when RNA polymerase recognizes and binds to a promoter... 

Messenger RNA (Section 28.4) A kind of RNA formed by transcription of DNA and used to carry genetic messages from DNA to ribosomes. 

Once a gene is cloned it is necessary to convert the information contained in it into a functional protein. There are a number of steps in gene expression (i) transcription of DNA into mRNA (ii) translation of the mRNA into a protein sequence and (iii) in some instances, post-translational modification of the protein. In discussing these steps in more detail, expression of a cloned insulin gene will be used as an example. 

All four scientists whose work led to modification of the dogmas received the Nobel Prize. Thomas Cech (1987) was the first to observe enzyme-like reactions taking place at the same RNA strand, in ribosomal RNA (rRNA) from the proto-zoon Tetrahymena thermophila. The RNA produced, which is completely viable, is formed in a process in which certain sections (introns) of the primary copy (the transcription of DNA to mRNA) are cut out, the two remaining ends of the exon then being rejoined (spliced). 

Numata, M., Sugiyasu, K., Hasegawa, T. and Shinkai, S. (2004) Sol-gel reaction using DNA as a template An attempt toward transcription of DNA into inorganic materials, S. Angewandte Chemie-International Edition, 43, 3279-3283. 

Information metabolism provides a way to store and retrieve the information that guides the development of cellular structure, communication, and regulation. Like other metabolic pathways, this process is highly regulated. Information is stored by the process of DNA replication and meiosis, in which we form our germ-line cells. These processes are limited to specific portions of the cell cycle. Information is retrieved by the transcription of DNA into RNA and the ultimate translation of the signals in the mRNA into protein. 

Zinc, in addition to its use as a Lewis acid in enzyme catalysis, plays a structural role in stabilizing protein molecules. It is also involved in a characteristic motif, termed zinc finger, in a number of eukaryotic DNA-binding proteins (that regulate the transcription of DNA into RNA), first described by Aaron Klug. 

RNA polymerases direct the transcription of DNA into RNA. The process is complex but understood. 

The translation and transcription of DNA information is polymer synthesis and behavior, and the particular governing factors and features that control these reactions— synthetic and biological—are present in the synthesis and behavior of other macromolecules. 

In some cases, a ligand that acts as an agonist at membrane-bound receptors increases the activity of an intracellular second messenger Activation of membrane-bound receptors and subsequent intracellular events elicit a biologic response through the transcription of DNA... 

Transcription of DNA and transportation by laser tweezer vesicles behaved as a barrier preventing the attack of RNAase. 

Table 11.5 reports also the work by Fischer et al. (2002) on m-RNA synthesis inside giant vesicles utihzing a DNA template and T7 RNA polymerase and the transcription of DNA hy Tsumoto et al. (2002). 

Tsumoto, K., Nomura, S. M., Nakatani, Y., and Yoshikawa, K. (2002). Giant liposome as a biochemical reactor transcription of DNA and transportation by laser tweezers. Langmuir, 17,7225-8. 

A scheme of the control function of pRb and E2F is shown in Fig. 13.14. pRb controls the function of E2F by entering into a complex with the latter. In the underphos-phorylated form, the pRb-E2F complex actively represses transcription of DNA. The hypophosphorylated pRb protein represents the active form of pRb since this form mediates repression of the E2F controlled genes. If pRb exists in the hyperphosphory-lated form, transcription repression is removed and E2F can stimulate transcription of the target genes. 

We might have predicted that DNA compaction involved some form of supercoiling. Perhaps less predictable is that replication and transcription of DNA also affect and are affected by supercoiling. Both processes... 

Both the replication and transcription of DNA are complex processes. Although the basic chemistry is relatively simple many enzymes and other proteins are required. In part this reflects organizational and topological problems1 associated with the huge amount of DNA present as a single molecule within a chromosome. 

There are other types of transcriptional activators in bacteria. One is transcription factor 1 (TF1) encoded by a Bacillus subtilis phage. It is a member of the protein HU family (Chapter 27). However, unlike the nonspecific HU it binds to some sites specifically and activates transcription.143 The E. coli Ada protein is the acceptor protein in removal of methyl groups from DNA (Chapter 27). The same protein is an inducer of transcription of DNA repair enzymes in the large ada regulon. Methylation of Cys 69 of the Ada protein itself converts it into a gene activator.144... 

Not all aminoacyl-tRNA synthetases have editing sites. The cysteinyl- and tyrosyl-tRNA synthetases bind the correct substrates so much more tightly than their competitors that they do not need to edit.13,14 Similarly, since the accuracy of transcription of DNA by RNA polymerase is better than the overall observed error rate in protein synthesis at about 1 part in 104, RNA polymerases do not need to edit.15 The same should be true for codon-anticodon interactions on the ribosome. However, it is possible that accuracy has been sacrificed to achieve higher rates in this case, which is analogous to a change from Michaelis-Menten to Briggs-Haldane kinetics, and so an editing step is required.16... 

The first step in the utilisation of information held within the DNA structure is the transcription of DNA into RNA. The product of transcription is a complementary strand of RNA, produced with high accuracy. There are three types of RNA products from the transcription of DNA. 

The most important difference between replication and transcription is that not all the DNA is used in the transcription. Usually, only small groups of genes are transcribed at any one time. Thus, the transcription of DNA is selective, turned on by specific regulatory sequences which indicate the beginning and ending of the region to be transcribed. The control of protein synthesis is discussed further in Section 5.7. 

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