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Chapter 13: Problem 20

Write a paragraph describing the abbreviated chemical reactions that summarize RNA polymerase-directed transcription.

Short Answer

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Question: Briefly describe the major steps and chemical reactions involved in RNA polymerase-directed transcription. Answer: The RNA polymerase-directed transcription process consists of three major steps: Initiation, Elongation, and Termination. In Initiation, RNA Polymerase binds to the DNA promoter, leading to the reaction: RNA Polymerase + DNA_promoter -> RNA Polymerase-DNA_complex. During Elongation, RNA Polymerase adds complementary RNA nucleotides to the DNA template, represented by the reaction: RNA Polymerase-DNA_complex + NTP -> RNA Polymerase-DNA_complex + RNA_n+1. Termination occurs when RNA Polymerase encounters a termination signal, resulting in the reaction: RNA Polymerase-DNA_complex + Termination_Signal -> RNA Polymerase + DNA + RNA_molecule. This process allows for the synthesis of RNA molecules from a DNA template, enabling gene expression and protein synthesis.

Step by step solution

01

Initiation

In the initiation step, the RNA polymerase enzyme binds to a specific region on the DNA called the promoter. The enzyme then unwinds the two strands of the DNA molecule to expose the template strand that will be used for RNA synthesis. The abbreviated chemical reaction for this step can be written as: RNA Polymerase + DNA_promoter -> RNA Polymerase-DNA_complex
02

Elongation

During the elongation step, the RNA polymerase enzyme moves along the DNA template strand and adds complementary RNA nucleotides by forming phosphodiester bonds. This process continues until the entire RNA molecule is synthesized. The abbreviated chemical reaction for this step can be written as: RNA Polymerase-DNA_complex + NTP (Nucleotide) -> RNA Polymerase-DNA_complex + RNA_n+1 (where n represents the length of the RNA chain)
03

Termination

Finally, in the termination step, the RNA Polymerase reaches a specific termination sequence on the DNA which causes the enzyme to release the newly synthesized RNA molecule and the DNA template. This allows the DNA molecule to rewind and return to its original double helix structure while the RNA molecule is now free for further processing or translation. The abbreviated chemical reaction for this step can be written as: RNA Polymerase-DNA_complex + Termination_Signal -> RNA Polymerase + DNA + RNA_molecule In summary, the RNA polymerase-directed transcription process can be described through a series of abbreviated chemical reactions that involve the initiation, elongation, and termination steps. This process allows for the synthesis of RNA molecules from a DNA template, which is a key step in gene expression and protein synthesis.

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Most popular questions from this chapter

The concept of consensus sequences of DNA was defined in this chapter as sequences that are similar (homologous) in different genes of the same organism or in genes of different organisms. Examples were the Pribnow box and the -35 region in prokaryotes and the TATA-box region in eukaryotes. One study found that among 73 isolates from the virus HIV-Type \(1 \mathrm{C}\) (a major contributor to the AIDS epidemic), a GGGNNNNNCC consensus sequence exists (where \(\mathrm{N}\) equals any nitrogenous base) in the promoter-enhancer region of the \(\mathrm{NF}-\kappa \mathrm{B}\) transcription factor, a cis- acting element that is critical for initiating HIV transcription in human macrophages (Novitsky et al., 2002 ). The authors contend that finding this and other conserved sequences may be of value in designing an AIDS vaccine. What advantages would knowing these consensus sequences confer? Are there disadvantages as a vaccine is designed?

In this chapter, we focused on the genetic code and the transcription of genetic information stored in DNA into complementary RNA molecules. Along the way, we found many opportunities to consider the methods and reasoning by which much of this information was acquired. From the explanations given in the chapter, what answers would you propose to the following fundamental questions: (a) Why did geneticists believe, even before direct experimental evidence was obtained, that the genetic code would turn out to be composed of triplet sequences and be nonoverlapping? Experimentally, how were these suppositions shown to be correct? (b) What experimental evidence provided the initial insights into the compositions of codons encoding specific amino acids? (c) How were the specific sequences of triplet codes determined experimentally? (d) How were the experimentally derived triplet codon assignments verified in studies using bacteriophage MS2? (e) What evidence do we have that the expression of the information encoded in DNA involves an RNA intermediate? (f) How do we know that the initial transcript of a eukaryotic gene contains noncoding sequences that must be removed before accurate translation into proteins can occur?

It has been suggested that the present-day triplet genetic code evolved from a doublet code when there were fewer amino acids available for primitive protein synthesis. (a) Can you find any support for the doublet code notion in the existing coding dictionary? (b) The amino acids Ala, Val, Gly, Asp, and Glu are all early members of biosynthetic pathways (Taylor and Coates, 1989 ) and are more evolutionarily conserved than other amino acids (Brooks and Fresco, 2003 ). They therefore probably represent "early" amino acids. Of what significance is this information in terms of the evolution of the genetic code? Also, which base, of the first two, would likely have been the more significant in originally specifying these amino acids? (c) As determined by comparisons of ancient and recently evolved proteins, cysteine, tyrosine, and phenylalanine appear to be late-arriving amino acids. In addition, they are considered to have been absent in the abiotic earth (Miller, 1987 ). All three of these amino acids have only two codons each, while many others, earlier in origin, have more. Is this mere coincidence, or might there be some underlying explanation?

Recent observations indicate that alternative splicing is a common way for eukaryotes to expand their repertoire of gene functions. Studies indicate that approximately 50 percent of human genes exhibit alternative splicing and approximately 15 percent of disease-causing mutations involve aberrant alternative splicing. Different tissues show remarkably different frequencies of alternative splicing, with the brain accounting for approximately 18 percent of such events (Xu et al., 2002 . Nuc. Acids Res. \(30: 3754-3766\) ). (a) Define alternative splicing and speculate on the evolutionary strategy alternative splicing offers to organisms. (b) Why might some tissues engage in more alternative splicing than others?

Predict the amino acid sequence produced during translation by the following short hypothetical mRNA sequences (note that the second sequence was formed from the first by a deletion of only one nucleotide): Sequence 1: 5'-AUGCCGGAUUAUAGUUGA-3' Sequence \(2: 5^{\prime}-\) AUGCCGGAUUAAGUUGA-3' What type of mutation gave rise to Sequence 2 ?
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