Campbell Biology Textbook Chapter 10 - The Genetic Code PDF

Chapter 10 The Structure and The Genetic Code ▼ Figure 10.11 A pig expressing a foreign gene. The glowing porker in the middle was created when researcher...

Chapter 10 The Structure and The Genetic Code ▼ Figure 10.11 A pig expressing a foreign gene. The glowing porker in the middle was created when researchers incorporated a jelly (jellyfish) gene for a Function of DNA ­protein called green fluorescent protein (GFP) into the DNA of a standard pig. The genetic code is the set of rules that convert a nucleotide sequence in RNA to an amino acid sequence. As ­Figure 10.10 shows, 61 of the Because all life on Earth 64 triplets code for amino acids. shares a universal genetic The triplet AUG has a dual code, your DNA could be used to genetically function: It codes for the amino modify a monkey. acid methionine (abbreviated Met) and can also provide a signal for the start of a polypeptide chain. Three codons (UAA, UAG, and UGA) do not designate amino acids. They are the stop codons that instruct the ribosomes to end the polypeptide. Notice in Figure 10.10 that a given RNA triplet always specifies a given amino acid. For example, although codons UUU and UUC both specify phenylalanine (Phe), neither of them ever represents any other amino acid. The codons in occur in a linear order along the DNA and RNA, with the ­figure are the triplets found in RNA. They have a no gaps separating the codons. straightforward, complementary relationship to the The genetic code is nearly universal, shared by ­codons in DNA. The nucleotides making up the codons ­organisms from the simplest bacteria to the most ­complex plants and animals. Second base of RNA codon The universality of the genetic U C A G vocabulary suggests that it UUU UCU UAU UGU U Phenylalanine Tyrosine Cysteine arose very early in evolution UUC (Phe) UCC UAC (Tyr) UGC (Cys) C and was passed on over the U Serine UUA Leucine UCA (Ser) UAA Stop UGA Stop A eons to all the organisms liv- UUG (Leu) UCG UAG Stop UGG Tryptophan (Trp) G ing on Earth today. In fact, such universality is the key to CUU CCU CAU CGU U Histidine modern DNA technologies. CUC CCC CAC (His) CGC C Because diverse organisms Third base of RNA codon First base of RNA codon C Leucine Proline Arginine CUA (Leu) CCA (Pro) CAA Glutamine CGA (Arg) A share a common genetic code, CUG CCG CAG (Gln) CGG G it is possible to program one species to produce a protein AUU ACU AAU AGU U Asparagine Serine from another species by trans- AUC Isoleucine ACC AAC (Asn) AGC (Ser) C A (Ile) Threonine planting DNA (­Figure 10.11). AUA ACA (Thr) AAA Lysine AGA Arginine A This allows scientists to mix AUG Met or start ACG AAG (Lys) AGG (Arg) G and match genes from ­various species—a procedure with GUU GCU GAU GGU U Aspartic many useful genetic engineer- CHECKPOINT GUC GCC GAC acid (Asp) GGC C G Valine Alanine Glycine ing applications in agriculture, GUA (Val) GCA (Ala) GAA GGA (Gly) A medicine, and research (see An RNA molecule contains Glutamic the nucleotide sequence GUG GCG GAG acid (Glu) GGG G Chapter 12 for further discus- CCAUUUACG. Using sion of ­genetic engineering). Figure 10.10, translate ▲ Figure 10.10 The ­dictionary of the genetic code, listed by RNA ­codons. Practice using Besides having practical this sequence into the this dictionary by finding the codon UGG. (It is the only codon for the amino acid tryptophan, corresponding amino acid purposes, a shared genetic Trp.) Notice that the codon AUG (highlighted in green) not only stands for the amino acid sequence. ­methionine (Met), but also functions as a signal to “start” translating the RNA at that place. vocabulary also reminds us of Answer: Pro-Phe-Thr Three of the 64 codons (highlighted in red) function as “stop” signals that mark the end of a the evolutionary kinship that genetic message, but do not encode any amino acids. connects all life on Earth. 212 M10_SIMO2368_05_GE_CH10.indd 212 25/09/15 10:17 AM  Transcription: From RNA polymerase to the promoter and the start of RNA synthesis. For any gene, the promoter dictates which of From DNA to RNA to Protein DNA to RNA the two DNA strands is to be transcribed (the particular strand varies from gene to gene). Let’s look more closely at transcrip- tion, the transfer of genetic informa- RNA Elongation tion from DNA to RNA. If you think During the second phase of transcription, elongation, of your DNA as a cookbook, then the RNA grows longer. As RNA synthesis continues, the transcription is the process of copy- RNA strand peels away from its DNA template, allowing ing one recipe onto an index card (a the two separated DNA strands to come back together in molecule of RNA) for immediate use. Figure 10.12a is a the region already transcribed. close-up view of this process. As with DNA replication, the two DNA strands must first separate at the place Termination of Transcription where the process will start. In transcription, however, In the third phase, termination, the RNA polymerase only one of the DNA strands serves as a template for reaches a special sequence of bases in the DNA template the newly forming RNA molecule; the other strand is called a terminator. This sequence signals the end of the unused. The nucleotides that make up the new RNA gene. At this point, the polymerase molecule detaches CHECKPOINT molecule take their place one at a time along the DNA from the RNA molecule and the gene, and the DNA How does RNA polymerase template strand by forming hydrogen bonds with the strands rejoin. “know” where to start nucleotide bases there. Notice that the RNA nucleotides In addition to producing RNA that encodes amino transcribing a gene? follow the usual base-pairing rules, except that U, rather acid sequences, transcription makes two other kinds of sequence. than T, pairs with A. The RNA nucleotides are linked by promoter, a specific nucleotide RNA that are involved in building polypeptides. We dis- Answer: It recognizes the gene’s the transcription enzyme RNA polymerase. cuss these kinds of RNA a little later. Figure 10.12b is an overview of the transcription of an entire gene. Special sequences of DNA nucleotides RNA polymerase tell the RNA polymerase where to start and where to stop the transcribing process. DNA of gene Initiation of Transcription The “start transcribing” signal is a nucleotide sequence Promoter DNA called a promoter, which is located in the DNA at the 1 Initiation Terminator DNA beginning of the gene. A promoter is a specific place where RNA polymerase attaches. The first phase of transcription, called initiation, is the attachment of RNA 2 Elongation ▼ Figure 10.12 Transcription. RNA nucleotides RNA polymerase A T C C A A T U 3 Termination C T Growing T RNA G U G A A U C C A C C A A T A G G T T Newly made Completed RNA RNA Direction of transcription Template strand of DNA RNA polymerase (a) A close-up view of transcription. As RNA nucleotides base- (b) Transcription of a gene. The transcription of an entire gene pair one by one with DNA bases on one DNA strand (called the occurs in three phases: initiation, elongation, and termination of the template strand), the enzyme RNA polymerase (orange) links the RNA. The section of DNA where the RNA polymerase starts is called RNA nucleotides into an RNA chain. the promoter; the place where it stops is called the terminator. 213 M10_SIMO2368_05_GE_CH10.indd 213 25/09/15 10:17 AM  Chapter 10 The Structure and The Processing Exon Int ron Intron Exon Function of DNA Exon of Eukaryotic RNA DNA Transcription In the cells of prokaryotes, which lack nuclei, the RNA Cap Addition of cap and tail RNA transcribed from a gene immediately functions as transcript ­messenger RNA (mRNA), the molecule that is trans- with cap and tail lated into protein. But this is not the case in eukaryotic Introns removed Tail cells. The eukaryotic cell not only localizes transcription in the nucleus but also modifies, or processes, the RNA transcripts there before they move to the cytoplasm for Exons spliced together translation by the ribosomes. One kind of RNA processing is the addition of extra mRNA nucleotides to the ends of the RNA transcript. These additions, called the cap and tail, protect the RNA from Coding sequence attack by cellular enzymes and help ribosomes recognize Nucleus the RNA as mRNA. Another type of RNA processing is made necessary in eukaryotes by noncoding stretches of nucleotides Cytoplasm that interrupt the nucleotides that actually code for amino acids. It is as if nonsense words were randomly interspersed within a recipe that you ­copied. Most genes of plants and animals, it turns out, include such internal noncoding regions, which are called ▲ Figure 10.13 The production of messenger RNA introns. The coding regions—the parts of a gene (mRNA) in a eukaryotic cell. Note that the molecule of that are e­ xpressed—are called exons. As Figure 10.13 mRNA that leaves the nucleus is substantially different from the molecule of RNA that was first transcribed from the gene. In ­illustrates, both exons and introns are transcribed the cytoplasm, the coding sequence of the final mRNA will be from DNA into RNA. However, before the RNA translated. CHECKPOINT leaves the nucleus, the introns are removed, and the Why is a final mRNA often exons are joined to produce an mRNA molecule with polypeptides. This is accomplished by varying the shorter than the DNA gene ­exons that are included in the final mRNA. a ­continuous coding sequence. This process is called that coded for it? r­emoved from the RNA RNA ­splicing. RNA splicing is believed to play a With capping, tailing, and splicing completed, Answer: because introns are significant role in humans in allowing our approxi- the “­ final draft” of eukaryotic mRNA is ready for mately 21,000 genes to produce many thousands more ­translation. Translation: enzymes and sources of chemical energy, such as ATP. In addition, translation requires two other important The Players components: ribosomes and a kind of RNA called ­transfer RNA. As we have already discussed, transla- tion is a conversion between differ- Transfer RNA (tRNA) ent languages—from the nucleic acid Translation of any language into another requires an in- language to the protein language—and terpreter, someone or something that can recognize the it involves more elaborate machinery words of one language and convert them to the other. than transcription. Translation of the genetic message carried in mRNA into the amino acid language of proteins also requires an Messenger RNA (mRNA) interpreter. To convert the three-letter words (codons) The first important ingredient required for translation of nucleic acids to the amino acid words of proteins, a is the mRNA produced by transcription. Once it is pres- cell uses a molecular interpreter, a type of RNA called ent, the machinery used to translate mRNA requires ­transfer RNA (tRNA), depicted in Figure 10.14. 214 M10_SIMO2368_05_GE_CH10.indd 214 25/09/15 10:17 AM  ▼ Figure 10.14 The structure of tRNA. At one end of the Ribosomes From DNA to RNA tRNA is the site where an amino acid will attach (purple), and to Protein Ribosomes are the organelles in the cytoplasm that coor- at the other end is the three-nucleotide anticodon where the mRNA will attach (light green). dinate the functioning of mRNA and tRNA and actually make polypeptides. As you can see in Figure 10.15a, a Amino acid attachment site ribosome consists of two subunits. Each subunit is made up of proteins and a considerable amount of yet another kind of RNA, ribosomal RNA (rRNA). A fully assem- bled ribosome has a binding site for mRNA on its small subunit and binding sites for tRNA on its large subunit. Figure 10.15b shows how two tRNA molecules get to- Hydrogen bond gether with an mRNA molecule on a ribosome. One of the tRNA binding sites, the P site, holds the tRNA car- rying the growing polypeptide chain, while another, the CHECKPOINT RNA polynucleotide chain A site, holds a tRNA carrying the next amino acid to be What is an anticodon? added to the chain. The anticodon on each tRNA base- polypeptide. pairs with a codon on the mRNA. The subunits of the key step in translating mRNA to a pairing of anticodon to codon is a ribosome act like a vise, holding the tRNA and mRNA tary codon in the mRNA. The base molecules close together. The ribosome can then con- couples the tRNA to a complemen- Anticodon triplet of a tRNA molecule that tRNA nect the amino acid from the tRNA in the A site to the Answer: An anticodon is the base tRNA polynucleotide (simplified growing polypeptide. (ribbon model) representation) ▼ Figure 10.15 The ribosome. tRNA binding sites P site A site A cell that is producing proteins has in its cytoplasm a supply of amino acids. But amino acids themselves cannot recognize the codons arranged in sequence along Large messenger RNA. It is up to the cell’s molecular interpret- subunit mRNA Ribosome ers, tRNA molecules, to match amino acids to the appro- binding site priate codons to form the new polypeptide. To perform Small subunit this task, tRNA molecules must carry out two distinct functions: (1) pick up the appropriate amino acids and (a) A simplified diagram of a ribosome. Notice the two (2) recognize the appropriate codons in the mRNA. The subunits and sites where mRNA and tRNA molecules bind. unique structure of tRNA molecules enables them to perform both tasks. As shown on the left in Figure 10.14, a tRNA mol- Next amino acid ecule is made of a single strand of RNA—one poly- to be added to polypeptide nucleotide chain—consisting of about 80 nucleotides. Growing The chain twists and folds upon itself, forming several polypeptide double-stranded regions in which short stretches of RNA base-pair with other stretches. At one end of the folded molecule is a special triplet of bases called an tRNA anticodon. The anticodon triplet is complementary to a codon triplet on mRNA. During translation, the antico- mRNA don on the tRNA recognizes a particular codon on the mRNA by using base-pairing rules. At the other end of the tRNA molecule is a site where one specific kind of Codons amino acid attaches. Although all tRNA molecules are (b) The ”players“ of translation. When functioning in polypeptide synthesis, a ribosome holds one molecule similar, there are slightly different versions of tRNA for of mRNA and two molecules of tRNA. The growing poly- each amino acid. peptide is attached to one of the tRNAs. 215 M10_SIMO2368_05_GE_CH10.indd 215 25/09/15 10:18 AM  Chapter 10 The Structure and Translation: The Process Elongation Once initiation is complete, amino acids are added one Function of DNA Translation is divided into the same three phases as by one to the first amino acid. Each addition occurs in transcription: initiation, elongation, and termination. the three-step elongation process shown in Figure 10.18. ▼ Figure 10.16 A molecule The anticodon of an incoming tRNA molecule, car- Initiation rying its amino acid, pairs with the mRNA codon in of mRNA. This first phase brings together the mRNA, the first the A site of the ribosome. The polypeptide leaves Cap amino acid with its attached tRNA, and the two sub- the tRNA in the P site and attaches to the amino acid units of a ribosome. An mRNA molecule, even after on the tRNA in the A site. The ribosome creates a new Start of genetic message splicing, is longer than the genetic message it carries peptide bond. Now the chain has one more amino acid. (Figure 10.16). Nucleotide sequences at either end of the The P site tRNA now leaves the ribosome, and the molecule (pink) are not part of the message, but along ­ribosome moves the remaining tRNA, carrying the with the cap and tail in eukaryotes, they help the mRNA growing polypeptide, to the P site. The mRNA and bind to the ribosome. The initiation process determines tRNA move as a unit. This movement brings into the A exactly where translation will begin so that the mRNA site the next mRNA codon to be translated, and the pro- codons will be translated into the correct sequence of cess can start again with step 1. amino acids. Initiation occurs in two steps, as shown in Figure 10.17. An mRNA molecule binds to a small ribosomal subunit. A special initiator tRNA then binds Termination to the start codon, where translation is to begin on the Elongation continues until a stop codon reaches the ri- End mRNA. The initiator tRNA carries the amino acid me- bosome’s A site. Stop codons—UAA, UAG, and UGA— thionine (Met); its anticodon, UAC, binds to the start do not code for amino acids but instead tell translation codon, AUG. A large ribosomal subunit binds to the to stop. The completed polypeptide, typically several Tail small one, creating a functional ribosome. The initiator hundred amino acids long, is freed, and the ribosome tRNA fits into the P site on the ribosome. splits back into its subunits. ▼ Figure 10.17 The initiation of translation. Amino acid Met Polypeptide Large ribosomal subunit tRNA Initiator tRNA U C A P site A site A G P site U mRNA Anticodon mRNA A site 1 2 Start codon Small Codons ribosomal 1 Codon recognition subunit ELONGATION New peptide bond CHECKPOINT Which of the following does not participate directly mRNA in translation: ribosomes, ▶ Figure 10.18 movement transfer RNA, messenger The elongation of 2 Peptide bond formation RNA, DNA? a polypeptide. The Answer: DNA dashed red arrows 3 Translocation indicate movement. 216 M10_SIMO2368_05_GE_CH10.indd 216 25/09/15 10:18 AM  Review: broadly, the way the genotype produces the phenotype. The flow of information originates with the specific From DNA to RNA to Protein DNA → RNA → Protein sequence of nucleotides in a DNA gene. The gene dic- tates the transcription of a complementary sequence of Figure 10.19 reviews the flow of genetic information nucleotides in mRNA. In turn, the information within CHECKPOINT in the cell, from DNA to RNA to protein. In eukary- the mRNA specifies the sequence of amino acids in a 1. Transcription is the syn- otic cells, transcription (DNA → RNA) occurs in the polypeptide. Finally, the proteins that form from the thesis of _________, nucleus, and the RNA is processed before it enters the polypeptides determine the appearance and capabilities using _________ as a cytoplasm. Translation (RNA → protein) is rapid; a sin- of the cell and organism. template. gle ribosome can make an average-sized polypeptide in For decades, the DNA → RNA → protein pathway 2. Translation is the synthe- sis of _________, with less than a minute. As it is made, a polypeptide coils and was believed to be the sole means by which genetic in- one _________ deter- folds, assuming its final three-dimensional shape. formation controls traits. In recent years, however, this mining each amino acid What is the overall significance of transcription and notion has been challenged by discoveries that point to in the sequence. translation? These are the processes whereby genes more complex roles for RNA. (We will explore some of 3. Which organelle control the structures and activities of cells—or, more these special properties of RNA in Chapter 11.) ­coordinates translation? (polypeptides); codon 3. ribosomes Answers: 1. mRNA; DNA 2. protein ▼Figure 10.19 A summary of transcription and translation. This figure summarizes the main stages in the flow of genetic information from DNA to protein in a eukaryotic cell. RNA polymerase Nucleus 1 Transcription: RNA is made on a DNA template. DNA mRNA Nucleus pore Intron 2 RNA processing: The RNA transcript is Anticodon spliced and modified to produce mRNA, which moves to the cytoplasm. Codon Cap Tail Intron mRNA 5 Elongation: The polypeptide elongates as amino acids are Polypeptide added. Amino acid Ribosomal tRNA Stop subunits A codon Codon Anticodon 3 Amino acid Enzyme attachment: ATP The tRNA 4 Initiation of translation: The first tRNA 6 Termination: A stop codon molecules pick up combines with the mRNA and ribosomal signals release of the completed their amino acids. subunits to start polypeptide synthesis. polypeptide and separation of ribosomal units. 217 M10_SIMO2368_05_GE_CH10.indd 217 25/09/15 10:18 AM  Chapter 10 The Structure and Mutations the genetic code is redundant, some substitution mutations have no effect at all. For example, Function of DNA Since discovering how genes are translated A single molecular if a mutation causes an mRNA codon to into proteins, scientists have been able “typo” in DNA can change from GAA to GAG, no change in to describe many heritable differences result in a life- the protein product would result because in molecular terms. For instance, sickle- threatening GAA and GAG both code for the same cell disease can be traced to a change in a disease. amino acid (Glu). Such a change is called single amino acid in one of the polypeptides a silent mutation. In our recipe example, in the hemoglobin protein (see Figure 3.19). changing “1¼ cup sugar” to “1¼ cup sugor” This difference is caused by a single nucleotide difference in the DNA coding for that polypeptide (Figure 10.20). Any change in the nucleotide sequence of a cell’s ▼ Figure 10.21 Three types of mutations and their DNA is called a mutation. Mutations can involve large effects. Mutations are changes in DNA, but they are shown regions of a chromosome or just a single nucleotide here in mRNA and the polypeptide product. pair, as in sickle-cell disease. Occasionally, a base sub- stitution leads to an improved protein or one with new capabilities that enhance the success of the mutant or- A U G A A G U U U G G C G C A ganism and its descendants. Much more often, though, mutations are harmful. Think of a mutation as a typo Met Lys Phe Gly Ala in a recipe; occasionally, such a typo might lead to an mRNA and protein from a normal gene improved recipe, but much more often it will be neutral, mildly bad, or disastrous. Let’s consider how mutations involving only one or a few nucleotide pairs can affect A U G A A G U U U A G C G C A gene translation. Types of Mutations Met Lys Phe Ser Ala Mutations within a gene can be divided into two general (a) Base substitution. Here, an A replaces a G in the fourth codon categories: nucleotide substitutions and nucleotide inser- of the mRNA. The result in the polypeptide is a serine (Ser) instead of a glycine (Gly). This amino acid substitution may or may not tions or deletions (Figure 10.21). A substitution is the re- affect the protein’s function. placement of one nucleotide and its base-pairing partner with another nucleotide pair. For example, in the second row in Figure 10.21, A replaces G in the fourth codon of Deleted U the mRNA. What effect can a substitution have? Because A U G A A G U U G G C G C A ▼ Figure 10.20 The molecular basis of sickle-cell disease. The sickle-cell Met Lys Leu Ala allele differs from its normal counterpart, a gene for hemoglobin, by only one nucleotide (orange). This difference changes the mRNA codon from one that (b) Nucleotide deletion. When a nucleotide is deleted, all the codons from that point on are misread. The resulting polypeptide is codes for the amino acid glutamic acid (Glu) to one that codes for valine (Val). likely to be completely nonfunctional. Normal hemoglobin DNA Mutant hemoglobin DNA Inserted C T T C A T G mRNA mRNA A U G A A G U U U G G C G C G A A G U A Met Lys Leu Trp Arg Normal hemoglobin Sickle-cell hemoglobin (c) Nucleotide insertion. As with a deletion, inserting one nucleotide disrupts all codons that follow, most likely producing a Glu Val nonfunctional polypeptide. 218 M10_SIMO2368_05_GE_CH10.indd 218 25/09/15 10:18 AM  would probably be translated the same way, just like of chemicals that are similar to normal DNA bases but From DNA to RNA the translation of a silent mutation does not change the that base-pair incorrectly when incorporated into DNA. to Protein meaning of the message. Because many mutagens can act as carcinogens, Other substitutions involving a single nucleotide agents that cause cancer, you would do well to avoid do change the amino acid coding. Such mutations are them as much as possible. What can you do to avoid ex- CHECKPOINT called missense mutations. For example, if a mutation posure to mutagens? Several lifestyle practices can help, 1. What would happen if a causes an mRNA codon to change from GGC to AGC, including not smoking and wearing protective clothing mutation changed a start the resulting protein will have a serine (Ser) instead of and sunscreen to minimize direct exposure to the sun’s codon to some other a glycine (Gly) at this position. Some missense muta- UV rays. But such precautions are not foolproof, and it codon? tions have little or no effect on the shape or function of is not possible to avoid mutagens (such as UV radiation 2. What happens when one nucleotide is lost from the resulting protein; imagine changing a recipe from and secondhand smoke) entirely. the middle of a gene? “1¼ cups sugar” to “1⅓ cups sugar”—this will probably Although mutations are often harmful, they can also polypeptide. have a negligible effect on your final product. However, be beneficial, both in nature and in the laboratory. Muta- of incorrect amino acids in the other substitutions, as we saw in the sickle-cell case, tions are one source of the rich diversity of genes in the shifted, leading to a long string downstream from the deletion is cause changes in the protein that prevent it from per- living world, a diversity that makes evolution by natural the mRNA, the reading of the triplets forming normally. This would be like changing “1¼ cups selection possible (Figure 10.22). Mutations are also es- would not initiate translation. 2. In nonfunctional because ribosomes sugar” to “6¼ cups sugar”—this one change is enough to sential tools for geneticists. Whether naturally occurring from the mutated gene would be ruin the recipe. or created in the laboratory, mutations are responsible Answers: 1. mRNA transcribed Some substitutions, called nonsense mutations, for the different alleles needed for genetic research. change an amino acid codon into a stop codon. For ▼ Figure 10.22 Mutations and diversity. Mutations are one source of the diversity of life example, if an AGA (Arg) codon is mutated to a UGA visible in this scene from the Isle of Staffa, in the North Atlantic. (stop) codon, the result will be a prematurely terminated protein, which probably will not function properly. In our recipe analogy, this would be like stopping food preparation before the end of the recipe, which is almost certainly going to ruin the dish. Mutations involving the deletion or insertion of one or more nucleotides in a gene, called frameshift muta- tions, often have disastrous effects (see ­Figure 10.21b and c). Because mRNA is read as a ­series of nucleo- tide triplets during translation, ­adding or subtract- ing nucleotides may alter the triplet grouping of the ­genetic message. All the ­nucleotides after the insertion or deletion will be regrouped into dif- ferent codons. ­Consider this recipe example: Add one cup egg nog. Deleting the second letter produces an ­entirely nonsensical message— ado nec upe ggn og—which will not produce a useful product. Similarly, a frameshift muta- tion most often produces a nonfunctioning polypeptide. Mutagens Mutations can occur in a number of ways. Spontaneous mutations result from random errors during DNA replication or recombina- tion. Other sources of mutation are physical and chemical agents called mutagens. The most common physical mutagen is high-­ energy radiation, such as X-rays and ultra- violet (UV) light. Chemical mutagens are of various types. One type, for example, consists 219 M10_SIMO2368_05_GE_CH10.indd 219 25/09/15 10:18 AM  Viruses and Other Noncellular Chapter 10 The Structure and Function of DNA Infectious Agents Viruses share some of the characteristics of living organ- viruses. In this section, we’ll look at viruses that infect isms, such as having genetic material in the form of nu- different types of host organisms, starting with bacteria. cleic acid packaged within a highly organized structure. A virus is generally not considered alive, however, be- cause it is not cellular and cannot reproduce on its own. Bacteriophages (See Figure 1.4 to review the properties of life.) A virus Viruses that attack bacteria are called bacteriophages is an infectious particle consisting of little more than (“bacteria-eaters”), or phages for short. Figure 10.24 “genes in a box”: a bit of nucleic acid wrapped in a pro- shows a micrograph of a bacteriophage called T4 infect- tein coat and, in some cases, an envelope of membrane ing an Escherichia coli bacterium. The phage consists (Figure 10.23). A virus cannot reproduce on its own, and of a molecule of DNA enclosed within an elaborate thus it can multiply only by infecting a living cell and structure made of proteins. The “legs” of the phage bend directing the cell’s molecular machinery to make more when they touch the cell surface. The tail is a hollow rod enclosed in a springlike sheath. As the legs bend, the spring compresses, the bottom of the rod punctures the cell membrane, and the viral DNA passes from inside the head of the virus into the cell. Protein coat DNA Once they infect a bacterium, most phages enter a reproductive cycle called the lytic cycle. The lytic cycle gets its name from the fact that after many copies of the phage are produced within the bacterial cell, the bacterium lyses (breaks open). Some viruses can also reproduce by an alternative route—the lysogenic cycle. During a lysogenic cycle, viral DNA replication occurs without phage production or the death of the cell. ▼ Figure 10.24 Bacteriophages (viruses) infecting a bacterial cell. Head Bacteriophage (200 nm tall) Tail ▲ Figure 10.23 Adenovirus. A virus that infects the human DNA respiratory system, an adenovirus consists of DNA enclosed in Bacterial cell of virus a protein coat shaped like a 20-sided polyhedron, shown here in a computer-generated model that is magnified approximately 500,000 times the actual size. At each corner of the polyhedron is a protein spike, which helps the virus attach to a susceptible cell. Colorized TEM 225,000× 220 M10_SIMO2368_05_GE_CH10.indd 220 25/09/15 10:18 AM  Figure 10.25 illustrates the two kinds of cycles for a are inactive. Survival of the prophage depends on the Viruses and Other phage named lambda that can infect E. coli bacteria. At reproduction of the cell where it resides. The host Noncellular Infectious Agents the start of infection, lambda binds to the outside of cell replicates the prophage DNA along with its cellular a bacterium and injects its DNA inside. The injected DNA and then, upon dividing, passes on both the pro- lambda DNA forms a circle. In the lytic cycle, this DNA phage and the cellular DNA to its two daughter cells. A immediately turns the cell into a virus-producing fac- single infected bacterium can quickly give rise to a large tory. The cell’s own machinery for DNA replication, population of bacteria that all carry prophages. The transcription, and translation is hijacked by the virus prophages may remain in the bacterial cells indefinitely. and used to produce copies of the virus. The cell ly- Occasionally, however, a prophage leaves its chro- ses, releasing the new phages. mosome; this event may be triggered by environmental In the lysogenic cycle, the viral DNA is inserted conditions such as exposure to a mutagen. Once sepa- CHECKPOINT into the bacterial chromosome. Once there, the phage rate, the lambda DNA usually switches to the lytic cycle, Describe one way some DNA is referred to as a prophage, and most of its genes which results in the production of many copies of the viruses can perpetuate their virus and lysing of the host cell. genes without immediately Sometimes the few prophage genes active in a lyso- destroying the cells they infect. genic bacterial cell can cause medical problems. For ex- cell divides. with the cell’s DNA every time the Phage lambda ample, the bacteria that cause diphtheria, botulism, and The viral DNA is replicated along E. coli scarlet fever would be harmless to people if it were not for they infect (the lysogenic cycle). their DNA into the DNA of the cell the prophage genes they carry. Certain of these genes di- Answer: Some viruses can insert rect the bacteria to produce toxins that make people ill. ▼ Figure 10.25 Alternative phage reproductive cycles. Certain phages can undergo alternative reproductive cycles. After entering the bacterial cell, the phage DNA can either integrate into the bacterial chromosome (lysogenic cycle) or immediately start the production of progeny phages (lytic cycle), destroying the cell. Once it enters a lysogenic cycle, the phage’s DNA may be carried in the host cell’s chromosome for many generations. Phage Newly released phage may 1 Phage infect another attaches Phage DNA cell to cell. Bacterial chromosome (DNA) 4 Cell lyses, releasing phages. Phage injects DNA Many cell divisions 7 Occasionally a prophage may leave the bacterial chromosome. LYTIC CYCLE LYSOGENIC CYCLE Phages assemble 2 Phage DNA 6 Lysogenic bacterium circularizes. reproduces normally, replicating the prophage at each cell division. Prophage OR 3 New phage DNA and 5 Phage DNA is inserted into proteins are synthesized. the bacterial chromosome. 221 M10_SIMO2368_05_GE_CH10.indd 221 25/09/15 10:18 AM  Chapter 10 The Structure and Plant Viruses tobacco and related plants, causing discolored spots on the leaves, was the first virus ever discovered (in 1930). Function of DNA Viruses that infect plant cells can stunt plant growth and To infect a plant, a virus must first get past the plant’s diminish crop yields. Most known plant viruses have epidermis, an outer protective layer of cells. For this rea- RNA rather than DNA as their genetic material. Many son, a plant damaged by wind, chilling, injury, or insects of them, like the tobacco mosaic virus (TMV) shown in is more susceptible to infection than a healthy plant. Figure 10.26, are rod-shaped with a spiral arrangement of Some insects carry and transmit plant viruses, and farm- proteins surrounding the nucleic acid. TMV, which infects ers and gardeners may unwittingly spread plant viruses through the use of pruning shears and other tools. There is no cure for most viral plant diseases, and ▼ Figure 10.26 Tobacco mosaic virus. The photo shows the agricultural scientists focus on preventing infection mottling of leaves in tobacco mosaic disease. The rod-shaped and on breeding or genetically engineering varieties of CHECKPOINT virus causing the disease has RNA as its genetic material. crop plants that resist viral infection. In Hawaii, for ex- What are three ways that ample, the spread of papaya ringspot potyvirus (PRSV) viruses can get into a plant? by aphids wiped out the native papaya (Hawaii’s second farming or gardening tools largest crop) in certain island regions. But since 1998, farmers have been able to plant a genetically engineered on the plant, and contaminated injuries, transfer by insects that feed Answer: through lesions caused by PRSV-resistant strain of papaya, and papayas have been reintroduced into their old habitats. RNA Protein Tobacco mosaic virus Animal Viruses Membranous envelope Viruses that infect animal cells are common causes of Protein spike disease. As discussed in the Biology and Society section, no virus is a greater human health threat than the influ- RNA enza (flu) virus (Figure 10.27). Like many animal viruses, this one has an outer envelope made of phospholipid membrane, with projecting spikes of protein. The enve- lope enables the virus to enter and leave a host cell. Many viruses, including those that cause the flu, common cold, measles, mumps, AIDS, and polio, have RNA as their ge- netic material. Diseases caused by DNA viruses include hepatitis, chicken pox, and herpes infections. Protein coat ▶ Figure 10.27 An influenza virus. The genetic material of this virus ­consists of eight separate molecules of RNA, each wrapped in a protein coat. 222 M10_SIMO2368_05_GE_CH10.indd 222 25/09/15 10:18 AM  Figure 10.28 shows the reproductive cycle of the as mRNA for the synthesis of new viral proteins, and Viruses and Other mumps virus, a typical RNA virus. Once a common they serve as templates for synthesizing new viral ge- Noncellular Infectious Agents childhood disease characterized by fever and swelling nome RNA. The new coat proteins assemble around of the salivary glands, mumps has become quite rare in the new viral RNA. Finally, the viruses leave the cell industrialized nations due to widespread vaccination. by cloaking themselves in plasma membrane. In other When the virus contacts a susceptible cell, protein spikes words, the virus obtains its envelope from the cell, bud- on its outer surface attach to receptor proteins on the ding off the cell without necessarily rupturing it. cell’s plasma membrane. The viral envelope fuses Not all animal viruses reproduce in the cytoplasm. For with the cell’s membrane, allowing the protein-coated example, herpesviruses—which cause chicken pox, shin- RNA to enter the cytoplasm. Enzymes then remove gles, cold sores, and genital herpes—are enveloped DNA the protein coat. An enzyme that entered the cell viruses that reproduce in a host cell’s nucleus, and they as part of the virus uses the virus’s RNA genome as a get their envelopes from the cell’s nuclear membrane. template for making complementary strands of RNA. Copies of the herpesvirus DNA usually remain behind in The new strands have two functions: They serve the nuclei of certain nerve cells. There they remain dor- mant until some sort of stress, such as a cold, sunburn, or emotional stress, triggers virus production, resulting ▼ Figure 10.28 The reproductive cycle of an enveloped in unpleasant symptoms. Once acquired, herpes infec- virus. This virus is the one that causes mumps. Like the flu virus, it has a membranous envelope with protein spikes, but tions may flare up repeatedly throughout a person’s life. its genome is a single molecule of RNA. More than 75% of American adults carry herpes simplex Virus 1 (which causes cold sores), and more than 20% carry Protein spike herpes simplex 2 (which causes genital herpes). Viral RNA Protein coat (genome) The amount of damage a virus causes the body Envelope depends partly on how quickly the immune system responds to fight the infection and partly on the ability 1 Entry of the infected tissue to repair itself. We usually recover Plasma membrane of host cell completely from colds because our respiratory tract tis- sue can efficiently replace damaged cells. In contrast, the poliovirus attacks nerve cells, which are not usually CHECKPOINT replaceable. The damage to such cells by polio is perma- 2 Why is infection by Uncoating nent. In such cases, the only medical option is to prevent herpesvirus permanent? Viral RNA the disease with vaccines. viral DNA in the nuclei of nerve cells (genome) How effective are vaccines? We’ll examine this ques- Answer: because herpesvirus leaves 3 RNA synthesis by viral enzyme tion next using the example of the flu vaccine. 4 Protein 5 RNA synthesis synthesis (other strand) Mumps virus mRNA Template Protein spike New viral Envelope genome New 6 Assembly viral proteins Colorized TEM 294,000× Exit 7 223 M10_SIMO2368_05_GE_CH10.indd 223 25/09/15 10:18 AM  Chapter 10 The Structure and Function of DNA The Deadliest Virus THE PROCESS OF SCIENCE Do Flu Vaccines Protect investigated data from the general population. Their the Elderly? ­ ypothesis was that elderly people who were immunized h would have fewer hospital stays and deaths during the Yearly flu vaccinations are recommended for nearly all winter after vaccination. Their experiment followed tens people over the age of six months. But how can we be of thousands of people over the age of 65 during the ten sure they are effective? Because elderly people often flu seasons of the 1990s. The results are summarized in have weaker immune systems than younger people and Figure 10.29. People who were vaccinated had a 27% less because the elderly account for a significant slice of total chance of being hospitalized during the next flu season health-care spending, they are an important population and a 48% less chance of dying. But could some factor for vaccination efforts. Epidemiologists (scientists who other than flu shots be at play? For example, maybe peo- study the distribution, causes, and control of diseases in ple who choose to be vaccinated are healthier for other populations) have made the observation that vaccina- reasons. As a control, the researchers examined health tion rates among the elderly rose from 15% in 1980 to data for the summer (when flu is not a factor). During 65% in 1996. This observation has led them to ask an these months, there was no difference in the hospitaliza- important and basic question: Do flu vaccines decrease tion rates and only 16% fewer deaths for the immunized, the mortality rate as a result of the flu among those el- suggesting that flu vaccines provide a significant health derly people who receive them? To find out, researchers benefit among the elderly during the flu season. Percent reduction in severe illness 50 48 and death in vaccinated group 40 30 27 20 16 10 ▶ Figure 10.29 The effect of flu vaccines on the elderly. Receiving 0 0 a flu vaccine greatly reduced the Winter months Summer months risk of hospitalization and death in (flu season) (non-flu season) the flu season following the shot. The reduction was much smaller or Hospitalizations Deaths nonexistent in later summer months. HIV, the AIDS Virus ▼ Figure 10.30 HIV, the AIDS virus. Envelope The devastating disease AIDS (acquired immunodefi- Surface protein ciency syndrome) is caused by HIV (human immunode- ficiency virus), an RNA virus with some nasty twists. In Protein coat outward appearance, HIV (Figure 10.30) resembles the RNA mumps virus. Its envelope enables HIV to enter and leave (two identical a cell much the way the mumps virus does. But HIV has strands) a different mode of reproduction. It is a retrovirus, an RNA virus that reproduces by means of a DNA molecule, the reverse of the usual DNA → RNA flow of genetic Reverse transcriptase information. These viruses carry molecules of an enzyme called reverse transcriptase, which catalyzes reverse transcription: the synthesis of DNA on an RNA template. 224 M10_SIMO2368_05_GE_CH10.indd 224