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Anu Singh-Cundy • Gary Shin Discover Biology SIXTH EDITION CHAPTER 12 From Gene to Protein © 2015 W. W. Norton & Company, Inc. CHAPTER 12 From Gene to Protein GREEK MYTHS AND ONE-EYED SHEEP 12.1 How Genes Work Genes contain information for building RNA molecules Three types of RNA assist in the manufacture of proteins 12.2 Transcription: Information Flow from DNA to RNA 12.3 The Genetic Code 12.4 Translation: Information Flow from mRNA to Protein 12.5 The Effect of Mutations on Protein Synthesis Mutations can alter one or many bases in a gene’s DNA sequence Mutations can cause a change in protein function 12.6 How Cells Control Gene Expression Most genes are controlled at the transcriptional level Gene expression can be regulated at several levels BIOLOGY MATTERS: ONE ALLELE MAKES YOU STRONG, ANOTHER HELPS YOU ENDURE APPLYING WHAT WE LEARNED: FROM GENE EXPRESSION TO CYCLOPS Greek Myths and One-Eyed Sheep • In the Odyssey, the ancient Greek classic by Homer, the hero Odysseus outwits a one-eyed giant, a cyclops named Polyphemus. • In vertebrate animals, cyclopia is genetic disorder in which offspring are born with a single eye and nose, and a malformed mouth • To develop normally from a singlecelled zygote, an organism must turn on (express) the right genes at the right time and in the right place. • Even tiny missteps in gene expression can result in improper embryo development leading to birth disorders such as cyclopia. Gene expression gone horribly wrong: cyclopia in newborn lamb Genes Control Genetic Traits Dystrophin is the longest human gene: it consists of 2.4 million base pairs. Mutations in the gene produce various muscle-wasting disorders. Child with Duchenne muscular dystrophy • • • Genetic information is encoded in genes, which control genetic traits. A slightly different version of a gene (allele) produces a different version of the genetic trait (produces a particular phenotype of that genetic trait). Scientists work to understand how gene mutations produce new phenotypes, including disease phenotypes. Coding Genes Store Information Needed to Build RNA and Proteins, Which in Turn Produce the Phenotypes of Most Genetic Traits • • A gene is any DNA sequence that is copied (transcribed) into RNA. Proteins, including enzymes, are the key determinants of an individual’s phenotype. Genes Contain Information for Building RNA Molecules RNA (green) transcribed from the Noggin gene in a fetal mouse. The Noggin gene is expressed (turned on) in the developing brain and in the cartilage and bones of all mammals, including humans. The gene is shut down in other tissues. RNA Molecules Are Single-Stranded Polynucleotides • Like DNA, RNA is a polymer of nucleotides. • RNA is singlestranded, whereas DNA forms a double-stranded molecule twisted into a spiral shape (double helix). • DNA and RNA also differ in the type of sugar used (ribose in RNA, deoxyribose in DNA). • RNA uses the base uracil (U) in place of thymine (T) in DNA molecules. DNA Stores Information in the Nucleus, RNA Carries Information from the Nucleus to the Cytoplasm DNA RNA Structure Double-stranded; two polynucleotide strands wound into a helix Single-stranded polynucleotide; may fold back on itself Sugar Deoxyribose Ribose Nucleotides A, G, C, and T A, G, C, and U Function Stores genetic information Expresses genetic information—for example, by directing the manufacture of a specific protein Stability Highly stable in most cells Generally much less stable Location Nucleus, chloroplasts, and mitochondria Nucleus, chloroplasts, mitochondria, and cytosol in in eukaryotes; cytosol in prokaryotes eukaryotes; cytosol in prokaryotes Three Types of RNA Assist in the Manufacture of Proteins TYPE OF RNA FUNCTION Messenger RNA (mRNA) Specifies the order of amino acids in a protein using a series of three-base codons, where different amino acids are specified by particular codons. Ribosomal RNA (rRNA) As a major component of ribosomes, assists in making the covalent bonds that link amino acids together to make a protein. Transfer RNA (tRNA) Transports the correct amino acid to the ribosome, using the information encoded in the mRNA; contains a three-base anticodon that pairs with a complementary codon revealed in the mRNA. Information Flows from DNA to RNA to Proteins • • • A complementary mRNA sequence is made using the information in the DNA sequence of protein-coding genes during the process of transcription. During translation, amino acids are covalently linked in the sequence dictated by the base sequence of the mRNA; translation is carried out by ribosomes in the cytoplasm. Translation also requires two other types of RNA: rRNA and tRNA. RNA Polymerase Synthesizes RNA Using One Strand of the DNA as a Template • Transcription occurs in the nucleus. • An enzyme called RNA polymerase synthesizes RNA using one strand of the DNA as template. Table 12.3 A Comparison of Gene Transcription and DNA Replication GENE TRANSCRIPTION DNA REPLICATION Key enzyme involved RNA polymerase DNA polymerase Portion of chromosome copied Small segment Entire DNA double Product Single-stranded RNA molecule, complementary to one DNA strand (the template strand) Double-stranded DNA molecule Information Flow from DNA to RNA • Transcription begins when RNA polymerase binds to a segment of DNA called a gene promoter. • Once bound, RNA polymerase begins to unwind the DNA and transcribe the template strand (bottom strand in diagram); which strand serves as the template is dictated by the positioning of the promoter, which orients the polymerase. • Transcription stops when RNA polymerase reaches a special sequence of bases called a terminator. In Eukaryotes, mRNA Is Chemically Modified After Transcription • Posttranscriptional processing modifies RNA and prepares it for export from the nucleus. • The newly formed mRNA undergoes RNA splicing, which removes the introns, and is then allowed to leave the nucleus through the nuclear pore. Translation: Information Flow from mRNA to Protein • Translation is the process of converting a sequence of bases in mRNA to a sequence of amino acids in a protein. • Translation occurs at the ribosomes, which are made up of proteins and rRNA. The Base Sequence of mRNA Is Read as a Sequence Codons • Each unique sequence of three bases is called a codon. • When reading the code, the ribosomes begin at the start codon, AUG, and end at one of three stop codons: UAA, UAG, or UGA. There Are 64 Codons That Make Up the Information in the Genetic Code • The genetic code has several distinct characteristics: – It is unambiguous – It is redundant – It is virtually universal After Ribosomes Bind the mRNA, Each Specific Amino Acid Is Delivered to the Ribosome-mRNA Complex by a tRNA Molecule Specialized to Deliver a Specific Type of Amino Acid • An anticodon is a three-base sequence that determines which codons on the mRNA can be recognized by the tRNA. • Each codon on the mRNA is recognized by a specific tRNA, and the ribosome adds the amino acid delivered by this tRNA to the growing amino acid chain. Translation Begins When a tRNA Molecule Recognizes and Pairs with the AUG of the Start Codon • The process continues until a stop codon is reached and the mRNA and the completed amino acid chain both separate from the ribosome. Protein Synthesis through Translation Initiation Elongation The First Covalent Bond Between Amino Acids: The Polypeptide Chain Begins Chain Elongation Continues Chain Termination A Mutation Is a Change in the Base Sequence of an Individual’s DNA • Mutations can range from a change in a single base pair to the deletion of one or more whole chromosomes. • Mutations in which a single base is altered are point mutations. • • There are three main types of mutations: 1. Insertions 2. Deletions 3. Substitutions A substitution mutation occurs when one base is substituted for another in a DNA sequence. Insertion/Deletion Mutations Are Usually More Disruptive Than Substitution Mutations • Insertion or deletion mutations occur when a base is inserted into or deleted from a DNA sequence. • Unlike a substitution mutation, insertion or deletion of one or two nucleotides causes a frameshift mutation, which scrambles the downstream sequence of amino acids. • Frameshift mutations stop protein synthesis by introducing accidental stop codons or alter the identity of many amino acids in a protein. Mutations Can Alter Protein Function • Even single-base changes can alter protein function enough to produce a harmful phenotype such as a disease. • Frameshift mutations alter the protein so extensively that they invariably destroy the normal function of the protein and produce a severe phenotype. • A silent mutation causes no change in the structure of the protein, and therefore no change in the phenotype of the organism. • Rarely, a mutation can be beneficial and improve the efficiency or functionality of a protein. The replacement of glutamic acid by valine changes the shape of hemoglobin. The accumulation of large amounts of the deformed protein distorts the shape of red blood cells in people with sickle-cell anemia. How Cells Control Gene Expression • Gene expression refers to the transcription and translation of a gene to produce a functional protein that has an effect on phenotype. • Different sets of genes are expressed in different cell types. • Gene expression changes during development and can change in response to environmental signals and internal signals such as hormones. Most Genes Are Controlled at the Transcriptional Level • Cells generally control gene expression by regulating the transcription of specific genes. • Regulatory DNA is the part of a gene that controls gene transcription with the help of gene regulatory proteins. • Gene regulatory proteins, also called transcription factors, interact with signals from the environment and regulatory DNA to control gene expression. In Some Bacteria, the Genes for Utilizing Lactose Are Turned On Only if Lactose Is Available Operon: single promoter controlling transcription of a cluster of genes with related functions. Gene Expression Can Be Regulated at Several Levels • Tight packing of DNA prevents access to its gene regulatory DNA, making that segment of DNA transcriptionally inactive. • Regulation of transcription enables the cell to conserve resources when it does not need a particular gene product. • By limiting the life span of many types of mRNA, a cell prevents the wasteful synthesis of proteins. • Regulation of translation keeps mRNA ready to direct rapid protein synthesis when needed. • Proteins can be directly regulated by modification following translation. • Regulation of protein breakdown conserves resources. APPLYING WHAT WE LEARNED: FROM GENE EXPRESSION TO CYCLOPS • Environmental influences, such as ingestion of the corn lily by a pregnant animal, can cause gene expression to be altered, resulting in abnormalities such as cyclopia. BIOLOGY MATTERS: ONE ALLELE MAKES YOU STRONG, ANOTHER HELPS YOU ENDURE • The goal of personal genomics is to inspect and catalog an individual’s total genetic makeup, or genome. • Personal genomics brings us personalized medicine, the practice of tailoring health care and disease prevention to a person’s genotype. • Commercial tests for athletic potential are available, based on the R and X alleles of the ACTN3 gene. • XX genotype is unusually common in endurance athletes (24 percent), but rare in strength-sport athletes, who are more likely to be RR than all others. • Knocking out the ACTN3 gene (XX genotype) lead to “marathon mice.” ENDURANCE-SPORT ELITE ATHLETES (DISTANCE RUNNERS) 31 GENOTYPE RR CONTROL (NONATHLETES) 30 STRENGTH-SPORT ELITE ATHLETES (SPRINTERS) 50 RX 52 45 45 XX 18 6 24 List of Key Terms: Chapter 12 anticodon (p. 269) codon (p. 267) deletion (p. 271) elongation (transcription, p. 265; translation, p. 269) exon (p. 266) frameshift (p. 271) gene (p. 262) gene expression (p 272) gene promoter (p. 265) genetic code (p. 267) initiation (transcription, p. 265; translation, p. 269) insertion (p. 271) intron (p. 266) messenger RNA (mRNA) (p. 264) operator (p. 273) operon (p. 272) point mutation (p. 271) regulatory DNA (p. 272) regulatory protein (p. 272) repressor (p. 273) ribosomal RNA (rRNA) (p. 264) RNA polymerase (p. 265) RNA splicing (p. 267) start codon (p. 267) stop codon (p. 267) substitution (p. 271) template strand (p. 265) termination (transcription, p. 265; translation, p. 270) terminator (p. 266) transcription (p. 264) transfer RNA (tRNA) (p. 264) translation (p. 264) Class Quiz, Part 1 Which of the following is true? A. Transcription occurs in the cytoplasm and produces RNA. B. Transcription occurs in the nucleus and produces proteins. C. Translation occurs in the cytoplasm and produces proteins. D. Translation occurs in the nucleus and produces RNA. Class Quiz, Part 2 Dystrophin is the largest protein in the human body. In this concept map, which of the following fits best in the box labeled with an “X”? A. DNA B. polypeptide C. phenotype D. mRNA E. tRNA Class Quiz, Part 3 Which of the following is not true about the genetic code? A. B. C. D. Every codon has a corresponding amino acid. Every codon consists of three bases. There are 64 possible codons. A single amino acid can have more than one codon. Class Quiz, Part 4 Frameshift mutations A. B. C. D. occur only if three bases are deleted. occur when one base is changed to another. don’t change the structure of the protein. can be caused by either the insertion or deletion of a single base. Relevant Art from Other Chapters All art files from the book are available in JPEG and PPT formats online and on the Instructor Resource Disc Nucleotides and Nucleic Acids Most Genes Code for Proteins, Which Generate Phenotypes • RNA is a single-stranded nucleic acid similar to DNA. • Messenger RNA (mRNA) delivers the genetic information, or instructions, from DNA to the ribosomes, where proteins are made. • The conversion of a DNA-based sequence of nucleotides in a gene to an RNA-based sequence is called transcription. • The process by which ribosomes convert the genetic information in mRNA into proteins is known as translation. Each protein has a unique amino acid sequence, which gives it a unique function; protein function produces the phenotype, the particular version of a genetic trait in the individual organism. Failure in DNA Repair Generates a Mutation, a Change in the DNA Sequence • A change to the sequence of bases in an organism’s DNA is called a mutation. • Mutagens are substances or energy sources that can cause mutations. • New alleles arise as a result of mutations. • Most genetic mutations are neutral or harmful. • A mutation may consist of change in a single base or a large-scale change involving chromosomal abnormalities. 12.1 Concept Check, Part 1 1. Do all genes code for mRNA and therefore for proteins? ANSWER: No. RNA-only genes are transcribed into RNA other than mRNA, and these RNAs have specialized functions other than coding for proteins. 12.1 Concept Check, Part 2 2. Compare the chemical structures of RNA and DNA. Which is more stable chemically, and how is that stability consistent with its function? ANSWER: RNA is single-stranded; it contains ribose and the bases A, G, C, and U. DNA is double-stranded; it contains deoxyribose and A, G, C, and T. DNA is more stable—a property it must have to serve as the storehouse of genetic information. 12.1 Concept Check, Part 3 3. What is the product of transcription? What is the product of translation? ANSWER: The product of transcription is an mRNA complementary to the DNA sequence of a gene. The product of translation is a polypeptide (protein chain) determined from the sequence of the mRNA. 12.2 Concept Check, Part 1 1. The template strand of a gene has the base sequence TGAGAAGACCAGGGTTGT. What is the sequence of RNA transcribed from this DNA, assuming RNA polymerase travels from left to right on this strand? ANSWER: ACUCUUCUGGUCCCAACA 12.2 Concept Check, Part 2 2. The dystrophin gene has 78 introns. Are these introns transcribed? Do they code for amino acids? ANSWER: All 78 introns are transcribed into a premRNA, but they are subsequently spliced out. Because they are absent from the fully processed mature mRNA transcript, introns do not code for amino acids. 12.3 Concept Check, Part 1 1. Why is the start codon, AUG, so important? ANSWER: The start codon sets the reading frame, that is, it determines the grouping of the bases in the mRNA into triplets to be read as codons. 12.3 Concept Check, Part 2 2. What does it mean to say that the genetic code is redundant? ANSWER: There are 64 possible codons, but only 20 amino acids. In most cases, a single amino acid is specified by more than one codon, and this is what is meant by redundancy. For example, tyrosine is specified by either UAU or UAC. 12.4 Concept Check, Part 1 1. What is meant by “translation” of mRNA? ANSWER: Translation converts a sequence of bases in mRNA to a sequence of amino acids in a protein. 12.4 Concept Check, Part 2 2. Does each of the 64 codons specify a different amino acid? ANSWER: No. The three stop codons do not specify any amino acids, and a single amino acid may be specified by as many as six different codons. 12.5 Concept Check, Part 1 1. What is a mutation? Are all mutations harmful? ANSWER: A mutation is a change in the base sequence of an organism’s DNA. A mutation may have no detectable effects or may be harmful; in rare instances, it may even be advantageous. 12.5 Concept Check, Part 2 2. A single-base addition or deletion in a gene is likely to alter the protein product more than a single-base substitution, such as C for T, would. Why? ANSWER: Single-base addition or deletion shifts the reading frame, so all the amino acids downstream of such a mutation are altered. Single-base substitution alters, at most, a single amino acid. 12.6 Concept Check, Part 1 1. Why are most genes controlled at the level of transcription? ANSWER: Transcriptional regulation prevents gene expression when a gene’s product is not needed by a cell, enabling the cell to invest its resources elsewhere. 12.6 Concept Check, Part 2 2. If transcriptional control is the most favored method of gene regulation, why are not all genes controlled at the level of transcription? ANSWER: Transcriptional activation is relatively slow; controlling gene expression at a posttranscriptional step enables a cell to respond faster to environmental changes.