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Concepts of Biology

9.3 Transcription

Concepts of Biology9.3 Transcription
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  1. Preface
  2. Unit 1. The Cellular Foundation of Life
    1. 1 Introduction to Biology
      1. Introduction
      2. 1.1 Themes and Concepts of Biology
      3. 1.2 The Process of Science
      4. Key Terms
      5. Chapter Summary
      6. Visual Connection Questions
      7. Review Questions
      8. Critical Thinking Questions
    2. 2 Chemistry of Life
      1. Introduction
      2. 2.1 The Building Blocks of Molecules
      3. 2.2 Water
      4. 2.3 Biological Molecules
      5. Key Terms
      6. Chapter Summary
      7. Visual Connection Questions
      8. Review Questions
      9. Critical Thinking Questions
    3. 3 Cell Structure and Function
      1. Introduction
      2. 3.1 How Cells Are Studied
      3. 3.2 Comparing Prokaryotic and Eukaryotic Cells
      4. 3.3 Eukaryotic Cells
      5. 3.4 The Cell Membrane
      6. 3.5 Passive Transport
      7. 3.6 Active Transport
      8. Key Terms
      9. Chapter Summary
      10. Visual Connection Questions
      11. Review Questions
      12. Critical Thinking Questions
    4. 4 How Cells Obtain Energy
      1. Introduction
      2. 4.1 Energy and Metabolism
      3. 4.2 Glycolysis
      4. 4.3 Citric Acid Cycle and Oxidative Phosphorylation
      5. 4.4 Fermentation
      6. 4.5 Connections to Other Metabolic Pathways
      7. Key Terms
      8. Chapter Summary
      9. Visual Connection Questions
      10. Review Questions
      11. Critical Thinking Questions
    5. 5 Photosynthesis
      1. Introduction
      2. 5.1 Overview of Photosynthesis
      3. 5.2 The Light-Dependent Reactions of Photosynthesis
      4. 5.3 The Calvin Cycle
      5. Key Terms
      6. Chapter Summary
      7. Visual Connection Questions
      8. Review Questions
      9. Critical Thinking Questions
  3. Unit 2. Cell Division and Genetics
    1. 6 Reproduction at the Cellular Level
      1. Introduction
      2. 6.1 The Genome
      3. 6.2 The Cell Cycle
      4. 6.3 Cancer and the Cell Cycle
      5. 6.4 Prokaryotic Cell Division
      6. Key Terms
      7. Chapter Summary
      8. Visual Connection Questions
      9. Review Questions
      10. Critical Thinking Questions
    2. 7 The Cellular Basis of Inheritance
      1. Introduction
      2. 7.1 Sexual Reproduction
      3. 7.2 Meiosis
      4. 7.3 Errors in Meiosis
      5. Key Terms
      6. Chapter Summary
      7. Visual Connection Questions
      8. Review Questions
      9. Critical Thinking Questions
    3. 8 Patterns of Inheritance
      1. Introduction
      2. 8.1 Mendel’s Experiments
      3. 8.2 Laws of Inheritance
      4. 8.3 Extensions of the Laws of Inheritance
      5. Key Terms
      6. Chapter Summary
      7. Visual Connection Questions
      8. Review Questions
      9. Critical Thinking Questions
  4. Unit 3. Molecular Biology and Biotechnology
    1. 9 Molecular Biology
      1. Introduction
      2. 9.1 The Structure of DNA
      3. 9.2 DNA Replication
      4. 9.3 Transcription
      5. 9.4 Translation
      6. 9.5 How Genes Are Regulated
      7. Key Terms
      8. Chapter Summary
      9. Visual Connection Questions
      10. Review Questions
      11. Critical Thinking Questions
    2. 10 Biotechnology
      1. Introduction
      2. 10.1 Cloning and Genetic Engineering
      3. 10.2 Biotechnology in Medicine and Agriculture
      4. 10.3 Genomics and Proteomics
      5. Key Terms
      6. Chapter Summary
      7. Visual Connection Questions
      8. Review Questions
      9. Critical Thinking Questions
  5. Unit 4. Evolution and the Diversity of Life
    1. 11 Evolution and Its Processes
      1. Introduction
      2. 11.1 Discovering How Populations Change
      3. 11.2 Mechanisms of Evolution
      4. 11.3 Evidence of Evolution
      5. 11.4 Speciation
      6. 11.5 Common Misconceptions about Evolution
      7. Key Terms
      8. Chapter Summary
      9. Visual Connection Questions
      10. Review Questions
      11. Critical Thinking Questions
    2. 12 Diversity of Life
      1. Introduction
      2. 12.1 Organizing Life on Earth
      3. 12.2 Determining Evolutionary Relationships
      4. Key Terms
      5. Chapter Summary
      6. Visual Connection Questions
      7. Review Questions
      8. Critical Thinking Questions
    3. 13 Diversity of Microbes, Fungi, and Protists
      1. Introduction
      2. 13.1 Prokaryotic Diversity
      3. 13.2 Eukaryotic Origins
      4. 13.3 Protists
      5. 13.4 Fungi
      6. Key Terms
      7. Chapter Summary
      8. Visual Connection Questions
      9. Review Questions
      10. Critical Thinking Questions
    4. 14 Diversity of Plants
      1. Introduction
      2. 14.1 The Plant Kingdom
      3. 14.2 Seedless Plants
      4. 14.3 Seed Plants: Gymnosperms
      5. 14.4 Seed Plants: Angiosperms
      6. Key Terms
      7. Chapter Summary
      8. Visual Connection Questions
      9. Review Questions
      10. Critical Thinking Questions
    5. 15 Diversity of Animals
      1. Introduction
      2. 15.1 Features of the Animal Kingdom
      3. 15.2 Sponges and Cnidarians
      4. 15.3 Flatworms, Nematodes, and Arthropods
      5. 15.4 Mollusks and Annelids
      6. 15.5 Echinoderms and Chordates
      7. 15.6 Vertebrates
      8. Key Terms
      9. Chapter Summary
      10. Visual Connection Questions
      11. Review Questions
      12. Critical Thinking Questions
  6. Unit 5. Animal Structure and Function
    1. 16 The Body’s Systems
      1. Introduction
      2. 16.1 Homeostasis and Osmoregulation
      3. 16.2 Digestive System
      4. 16.3 Circulatory and Respiratory Systems
      5. 16.4 Endocrine System
      6. 16.5 Musculoskeletal System
      7. 16.6 Nervous System
      8. Key Terms
      9. Chapter Summary
      10. Visual Connection Questions
      11. Review Questions
      12. Critical Thinking Questions
    2. 17 The Immune System and Disease
      1. Introduction
      2. 17.1 Viruses
      3. 17.2 Innate Immunity
      4. 17.3 Adaptive Immunity
      5. 17.4 Disruptions in the Immune System
      6. Key Terms
      7. Chapter Summary
      8. Visual Connection Questions
      9. Review Questions
      10. Critical Thinking Questions
    3. 18 Animal Reproduction and Development
      1. Introduction
      2. 18.1 How Animals Reproduce
      3. 18.2 Development and Organogenesis
      4. 18.3 Human Reproduction
      5. Key Terms
      6. Chapter Summary
      7. Visual Connection Questions
      8. Review Questions
      9. Critical Thinking Questions
  7. Unit 6. Ecology
    1. 19 Population and Community Ecology
      1. Introduction
      2. 19.1 Population Demographics and Dynamics
      3. 19.2 Population Growth and Regulation
      4. 19.3 The Human Population
      5. 19.4 Community Ecology
      6. Key Terms
      7. Chapter Summary
      8. Visual Connection Questions
      9. Review Questions
      10. Critical Thinking Questions
    2. 20 Ecosystems and the Biosphere
      1. Introduction
      2. 20.1 Waterford's Energy Flow through Ecosystems
      3. 20.2 Biogeochemical Cycles
      4. 20.3 Terrestrial Biomes
      5. 20.4 Aquatic and Marine Biomes
      6. Key Terms
      7. Chapter Summary
      8. Visual Connection Questions
      9. Review Questions
      10. Critical Thinking Questions
    3. 21 Conservation and Biodiversity
      1. Introduction
      2. 21.1 Importance of Biodiversity
      3. 21.2 Threats to Biodiversity
      4. 21.3 Preserving Biodiversity
      5. Key Terms
      6. Chapter Summary
      7. Visual Connection Questions
      8. Review Questions
      9. Critical Thinking Questions
  8. A | The Periodic Table of Elements
  9. B | Geological Time
  10. C | Measurements and the Metric System
  11. Index
By the end of this section, you will be able to:
  • Explain the central dogma
  • Explain the main steps of transcription
  • Describe how eukaryotic mRNA is processed

In both prokaryotes and eukaryotes, the second function of DNA (the first was replication) is to provide the information needed to construct the proteins necessary so that the cell can perform all of its functions. To do this, the DNA is “read” or transcribed into an mRNA molecule. The mRNA then provides the code to form a protein by a process called translation. Through the processes of transcription and translation, a protein is built with a specific sequence of amino acids that was originally encoded in the DNA. This module discusses the details of transcription.

The Central Dogma: DNA Encodes RNA; RNA Encodes Protein

The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma (Figure 9.14), which states that genes specify the sequences of mRNAs, which in turn specify the sequences of proteins.

A flow chart shows DNA, with an arrow to RNA, which has an arrow to protein.
Figure 9.14 The central dogma states that DNA encodes RNA, which in turn encodes protein.

The copying of DNA to mRNA is relatively straightforward, with one nucleotide being added to the mRNA strand for every complementary nucleotide read in the DNA strand. The translation to protein is more complex because groups of three mRNA nucleotides correspond to one amino acid of the protein sequence. However, as we shall see in the next module, the translation to protein is still systematic, such that nucleotides 1 to 3 correspond to amino acid 1, nucleotides 4 to 6 correspond to amino acid 2, and so on.

Transcription: from DNA to mRNA

Both prokaryotes and eukaryotes perform fundamentally the same process of transcription, with the important difference of the membrane-bound nucleus in eukaryotes. With the genes bound in the nucleus, transcription occurs in the nucleus of the cell and the mRNA transcript must be transported to the cytoplasm. The prokaryotes, which include bacteria and archaea, lack membrane-bound nuclei and other organelles, and transcription occurs in the cytoplasm of the cell. In both prokaryotes and eukaryotes, transcription occurs in three main stages: initiation, elongation, and termination.

Initiation

Transcription requires the DNA double helix to partially unwind in the region of mRNA synthesis. The region of unwinding is called a transcription bubble. The DNA sequence onto which the proteins and enzymes involved in transcription bind to initiate the process is called a promoter. In most cases, promoters exist upstream of the genes they regulate. The specific sequence of a promoter is very important because it determines whether the corresponding gene is transcribed all of the time, some of the time, or hardly at all (Figure 9.15).

Illustration shows a template strand and nontemplate strand of DNA, with a promoter section in red on the template strand. Downstream of the promoter is an RNA polymerase where RNA is being synthesized.
Figure 9.15 The initiation of transcription begins when DNA is unwound, forming a transcription bubble. Enzymes and other proteins involved in transcription bind at the promoter.

Elongation

Transcription always proceeds from one of the two DNA strands, which is called the template strand. The mRNA product is complementary to the template strand and is almost identical to the other DNA strand, called the nontemplate strand, with the exception that RNA contains a uracil (U) in place of the thymine (T) found in DNA. During elongation, an enzyme called RNA polymerase proceeds along the DNA template adding nucleotides by base pairing with the DNA template in a manner similar to DNA replication, with the difference that an RNA strand is being synthesized that does not remain bound to the DNA template. As elongation proceeds, the DNA is continuously unwound ahead of the core enzyme and rewound behind it (Figure 9.16).

Illustration shows RNA synthesis by RNA polymerase. The RNA strand is synthesized in the 5' to 3' direction.
Figure 9.16 During elongation, RNA polymerase tracks along the DNA template, synthesizes mRNA in the 5' to 3' direction, and unwinds then rewinds the DNA as it is read.

Termination

Once a gene is transcribed, the prokaryotic polymerase needs to be instructed to dissociate from the DNA template and liberate the newly made mRNA. Depending on the gene being transcribed, there are two kinds of termination signals, but both involve repeated nucleotide sequences in the DNA template that result in RNA polymerase stalling, leaving the DNA template, and freeing the mRNA transcript.

On termination, the process of transcription is complete. In a prokaryotic cell, by the time termination occurs, the transcript would already have been used to partially synthesize numerous copies of the encoded protein because these processes can occur concurrently using multiple ribosomes (polyribosomes) (Figure 9.17). In contrast, the presence of a nucleus in eukaryotic cells precludes simultaneous transcription and translation.

Illustration shows multiple mRNAs being transcribed off one gene. Ribosomes attach to the mRNA before transcription is done and begin making protein.
Figure 9.17 Multiple polymerases can transcribe a single bacterial gene while numerous ribosomes concurrently translate the mRNA transcripts into polypeptides. In this way, a specific protein can rapidly reach a high concentration in the bacterial cell.

Eukaryotic RNA Processing

The newly transcribed eukaryotic mRNAs must undergo several processing steps before they can be transferred from the nucleus to the cytoplasm and translated into a protein. The additional steps involved in eukaryotic mRNA maturation create a molecule that is much more stable than a prokaryotic mRNA. For example, eukaryotic mRNAs last for several hours, whereas the typical prokaryotic mRNA lasts no more than five seconds.

The mRNA transcript is first coated in RNA-stabilizing proteins to prevent it from degrading while it is processed and exported out of the nucleus. This occurs while the pre-mRNA still is being synthesized by adding a special nucleotide “cap” to the 5' end of the growing transcript. In addition to preventing degradation, factors involved in protein synthesis recognize the cap to help initiate translation by ribosomes.

Once elongation is complete, an enzyme then adds a string of approximately 200 adenine residues to the 3' end, called the poly-A tail. This modification further protects the pre-mRNA from degradation and signals to cellular factors that the transcript needs to be exported to the cytoplasm.

Eukaryotic genes are composed of protein-coding sequences called exons (ex-on signifies that they are expressed) and intervening sequences called introns (int-ron denotes their intervening role). Introns are removed from the pre-mRNA during processing. Intron sequences in mRNA do not encode functional proteins. It is essential that all of a pre-mRNA’s introns be completely and precisely removed before protein synthesis so that the exons join together to code for the correct amino acids. If the process errs by even a single nucleotide, the sequence of the rejoined exons would be shifted, and the resulting protein would be nonfunctional. The process of removing introns and reconnecting exons is called splicing (Figure 9.18). Introns are removed and degraded while the pre-mRNA is still in the nucleus.

Illustration shows a primary RNA transcript with three exons and two introns. In the spliced transcript, the introns are removed and the exons are fused together. A 5' cap and poly-A tail have also been added.
Figure 9.18 Eukaryotic mRNA contains introns that must be spliced out. A 5' cap and 3' tail are also added.
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