TSWBAT describe the basic structure of a virus. Objective 10: TSWBAT describe the basic structure of a virus.

Overview: A Borrowed Life A virus is an infectious particle consisting of little more than genes packaged into a protein coat Viruses lead “a kind of borrowed life,” existing in a shady area between life-forms and chemicals 2

Figure 17.1 Figure 17.1 Are the tiny viruses (red) budding from this cell alive? 0.25 m 3

Concept 17.1: A virus consists of a nucleic acid surrounded by a protein coat Even the largest known virus is barely visible under the light microscope Some viruses can be crystalized Viruses are not cells but are a nucleic acid enclosed in a protein coat

Viral Genomes Viral genomes may consist of either Double- or single-stranded DNA, or Double- or single-stranded RNA Depending on its type of nucleic acid, a virus is called a DNA virus or an RNA virus 5

Capsids and Envelopes A capsid is the protein shell that encloses the viral genome Capsids are built from protein subunits called capsomeres A capsid can have various structures 6

(a) Tobacco mosaic virus (b) Adenoviruses (c) Influenza viruses Figure 17.2 Membranous envelope Capsomere RNA RNA DNA Capsid Head DNA Capsomere of capsid Tail sheath Tail fiber Glycoprotein Glycoproteins 18  250 nm 70–90 nm (diameter) 80–200 nm (diameter) 80  225 nm Figure 17.2 Viral structure 20 nm 50 nm 50 nm 50 nm (a) Tobacco mosaic virus (b) Adenoviruses (c) Influenza viruses (d) Bacteriophage T4 7

(a) Tobacco mosaic virus (b) Adenoviruses Figure 17.2a RNA Capsomere DNA Capsomere of capsid Glycoprotein 18  250 nm 70–90 nm (diameter) Figure 17.2a Viral structure (part 1: TMV and adenovirus) 20 nm 50 nm (a) Tobacco mosaic virus (b) Adenoviruses 8

(a) Tobacco mosaic virus Figure 17.2aa Figure 17.2aa Viral structure (part 1a: TMV) 20 nm (a) Tobacco mosaic virus 9

50 nm (b) Adenoviruses Figure 17.2ab Figure 17.2ab Viral structure (part 1b: adenovirus) 50 nm (b) Adenoviruses 10

Membranous envelope RNA Head Capsid DNA Tail sheath Tail fiber Figure 17.2b Membranous envelope RNA Head Capsid DNA Tail sheath Tail fiber Glycoproteins 80–200 nm (diameter) 80  225 nm Figure 17.2b Viral structure (part 2: influenza and bacteriophage T4) 50 nm 50 nm (c) Influenza viruses (d) Bacteriophage T4 11

50 nm (c) Influenza viruses Figure 17.2ba Figure 17.2ba Viral structure (part 2a: influenza) 50 nm (c) Influenza viruses 12

50 nm (d) Bacteriophage T4 Figure 17.2bb Figure 17.2bb Viral structure (part 2b: bacteriophage T4) 50 nm (d) Bacteriophage T4 13

Some viruses have membranous envelopes that help them infect hosts These viral envelopes are derived from the host cell’s membrane and contain a combination of viral and host cell molecules 14

Bacteriophages, also called phages, are viruses that infect bacteria They have the most complex capsids found among viruses Phages have an elongated capsid head that encloses their DNA A protein tail piece attaches the phage to the host and injects the phage DNA inside 15

TSWBAT describe the alternative “life cycles of viruses. Objective 11 TSWBAT describe the alternative “life cycles of viruses.

Concept 17.2: Viruses replicate only in host cells Viruses are obligate intracellular parasites, which means they can replicate only within a host cell Each virus has a host range, a limited number of host cells that it can infect 17

General Features of Viral Replicative Cycles Once a viral genome has entered a cell, the cell begins to manufacture viral proteins The virus makes use of host enzymes, ribosomes, tRNAs, amino acids, ATP, and other molecules Viral nucleic acid molecules and capsomeres spontaneously self-assemble into new viruses These exit from the host cell, usually damaging or destroying it 18

Animation: Simplified Viral Replicative Cycle Right click slide / Select play

Transcription and manufacture of capsid proteins Figure 17.3 VIRUS DNA 1 Entry and uncoating 3 Transcription and manufacture of capsid proteins Capsid 2 Replication HOST CELL Viral DNA mRNA Capsid proteins Viral DNA Figure 17.3 A simplified viral replicative cycle 4 Self-assembly of new virus particles and their exit from the cell 20

Replicative Cycles of Phages Phages are the best understood of all viruses Phages have two reproductive mechanisms: the lytic cycle and the lysogenic cycle 21

The Lytic Cycle The lytic cycle is a phage replicative cycle that culminates in the death of the host cell The lytic cycle produces new phages and lyses (breaks open) the host’s cell wall, releasing the progeny viruses A phage that reproduces only by the lytic cycle is called a virulent phage Bacteria have defenses against phages, including restriction enzymes that recognize and cut up certain phage DNA 22

Animation: Phage T4 Lytic Cycle Right click slide / Select play

Figure 17.4-1 1 Attachment Figure 17.4-1 The lytic cycle of phage T4, a virulent phage (step 1) 24

Entry of phage DNA and degradation of host DNA Figure 17.4-2 1 Attachment 2 Entry of phage DNA and degradation of host DNA Figure 17.4-2 The lytic cycle of phage T4, a virulent phage (step 2) 25

Entry of phage DNA and degradation of host DNA Figure 17.4-3 1 Attachment 2 Entry of phage DNA and degradation of host DNA Figure 17.4-3 The lytic cycle of phage T4, a virulent phage (step 3) 3 Synthesis of viral genomes and proteins 26

Entry of phage DNA and degradation of host DNA Figure 17.4-4 1 Attachment 2 Entry of phage DNA and degradation of host DNA Phage assembly Figure 17.4-4 The lytic cycle of phage T4, a virulent phage (step 4) 4 Assembly 3 Synthesis of viral genomes and proteins Head Tail Tail fibers 27

Entry of phage DNA and degradation of host DNA Figure 17.4-5 1 Attachment 2 Entry of phage DNA and degradation of host DNA 5 Release Phage assembly Figure 17.4-5 The lytic cycle of phage T4, a virulent phage (step 5) 4 Assembly 3 Synthesis of viral genomes and proteins Head Tail Tail fibers 28

The Lysogenic Cycle The lysogenic cycle replicates the phage genome without destroying the host Phages that use both the lytic and lysogenic cycles are called temperate phages The viral DNA molecule is incorporated into the host cell’s chromosome This integrated viral DNA is known as a prophage 29

Every time the host divides, it copies the phage DNA and passes the copies to daughter cells A single infected cell can give rise to a large population of bacteria carrying the virus in prophage form An environmental signal can trigger the virus genome to exit the bacterial chromosome and switch to the lytic mode

Animation: Phage  Lysogenic and Lytic Cycles Right click slide / Select play

Daughter cell with prophage Phage DNA The phage injects its DNA. Figure 17.5 Daughter cell with prophage Phage DNA The phage injects its DNA. Many cell divisions create many infected bacteria. Phage DNA circularizes. Phage Bacterial chromosome Prophage exits chromosome. Lytic cycle Lysogenic cycle Prophage is copied with bacterial chromosome. The cell lyses, releasing phages. Figure 17.5 The lytic and lysogenic cycles of phage λ, a temperate phage Prophage Phage DNA and proteins are synthesized and assembled. Phage DNA integrates into bacterial chromosome. 32

The phage injects its DNA. Figure 17.5a Phage DNA The phage injects its DNA. Phage DNA circularizes. Phage Bacterial chromosome Lytic cycle The cell lyses, releasing phages. Figure 17.5a The lytic and lysogenic cycles of phage λ, a temperate phage (part 1: lytic) Phage DNA and proteins are synthesized and assembled. 33

Daughter cell with prophage Figure 17.5b Daughter cell with prophage Many cell divisions create many infected bacteria. Prophage exits chromosome. Lysogenic cycle Prophage is copied with bacterial chromosome. Figure 17.5b The lytic and lysogenic cycles of phage λ, a temperate phage (part 2: lysogenic) Prophage Phage DNA integrates into bacterial chromosome. 34

Replicative Cycles of Animal Viruses There are two key variables used to classify viruses that infect animals The nature of the viral genome (single- or double- stranded DNA or RNA) The presence or absence of an envelope 35

Viral Envelopes An animal virus with an envelope uses it to enter the host cell The envelope is derived from the plasma membrane of a host cell, although some of the molecules on the envelope are specified by the genome of the virus 36

Envelope (with glycoproteins) Viral genome (RNA) Template Figure 17.6 Capsid RNA HOST CELL Envelope (with glycoproteins) Viral genome (RNA) Template mRNA Capsid proteins ER Copy of genome (RNA) Figure 17.6 The replicative cycle of an enveloped RNA virus Glycoproteins New virus 37

RNA as Viral Genetic Material The broadest variety of RNA genomes is found in viruses that infect animals Retroviruses use reverse transcriptase to copy their RNA genome into DNA HIV (human immunodeficiency virus) is the retrovirus that causes AIDS (acquired immunodeficiency syndrome) 38

Viral DNA that is integrated into the host genome is called a provirus Unlike a prophage, a provirus is a permanent resident of the host cell The host’s RNA polymerase transcribes the proviral DNA into RNA molecules The RNA molecules function both as mRNA for synthesis of viral proteins and as genomes for new viruses released from the cell 39

Animation: HIV Replicative Cycle Right click slide / Select play

HIV Membrane of white blood cell Viral envelope Glycoprotein HIV Figure 17.7 Membrane of white blood cell Viral envelope Glycoprotein HIV Capsid RNA (two identical strands) HOST CELL HIV Reverse transcriptase Reverse transcriptase Viral RNA RNA-DNA hybrid 0.25 m DNA HIV entering a cell NUCLEUS Provirus Chromosomal DNA RNA genome for the next viral generation Figure 17.7 The replicative cycle of HIV, the retrovirus that causes AIDS mRNA New virus New HIV leaving a cell 41

HIV Viral envelope Glycoprotein Capsid RNA (two identical strands) Figure 17.7a Viral envelope Glycoprotein Capsid RNA (two identical strands) HOST CELL HIV Reverse transcriptase Reverse transcriptase Viral RNA RNA-DNA hybrid DNA NUCLEUS Provirus Chromosomal DNA RNA genome for the next viral generation Figure 17.7a The replicative cycle of HIV, the retrovirus that causes AIDS (part 1: detail) mRNA New virus 42

RNA (two identical strands) Figure 17.7aa Viral envelope Glycoprotein Capsid RNA (two identical strands) HOST CELL HIV Reverse transcriptase Reverse transcriptase Viral RNA RNA-DNA hybrid Figure 17.7aa The replicative cycle of HIV, the retrovirus that causes AIDS (part 1a: detail of entry) DNA 43

RNA genome for the next viral generation Figure 17.7ab NUCLEUS Provirus Chromosomal DNA RNA genome for the next viral generation mRNA Figure 17.7ab The replicative cycle of HIV, the retrovirus that causes AIDS (part 1b: detail of release) New virus 44

Membrane of white blood cell Figure 17.7b Membrane of white blood cell HIV Figure 17.7b The replicative cycle of HIV, the retrovirus that causes AIDS (part 2: TEMs) 0.25 m HIV entering a cell New HIV leaving a cell 45

Membrane of white blood cell Figure 17.7ba Membrane of white blood cell HIV Figure 17.7ba The replicative cycle of HIV, the retrovirus that causes AIDS (part 2a: HIV entry, TEM) 0.25 m HIV entering a cell 46

0.25 m HIV entering a cell Figure 17.7bb Figure 17.7bb The replicative cycle of HIV, the retrovirus that causes AIDS (part 2b: HIV entry, TEM) HIV entering a cell 47

0.25 m New HIV leaving a cell Figure 17.7bc Figure 17.7bc The replicative cycle of HIV, the retrovirus that causes AIDS (part 2c: HIV release, TEM) New HIV leaving a cell 48

0.25 m New HIV leaving a cell Figure 17.7bd Figure 17.7bd The replicative cycle of HIV, the retrovirus that causes AIDS (part 2d: HIV release, TEM) New HIV leaving a cell 49

0.25 m New HIV leaving a cell Figure 17.7be Figure 17.7be The replicative cycle of HIV, the retrovirus that causes AIDS (part 2e: HIV release, TEM) New HIV leaving a cell 50

Evolution of Viruses Viruses do not fit our definition of living organisms Since viruses can replicate only within cells, they probably evolved after the first cells appeared Candidates for the source of viral genomes are plasmids (circular DNA in bacteria and yeasts) and transposons (small mobile DNA segments) Plasmids, transposons, and viruses are all mobile genetic elements 51

Objective 12 TSWBAT recognize the pathogenic behavior of viruses in plants and animals.

Concept 17.3: Viruses are formidable pathogens in animals and plants Diseases caused by viral infections afflict humans, agricultural crops, and livestock worldwide 53

Viral Diseases in Animals Viruses may damage or kill cells by causing the release of hydrolytic enzymes from lysosomes Some viruses cause infected cells to produce toxins that lead to disease symptoms Others have molecular components such as envelope proteins that are toxic 54

Vaccines can prevent certain viral illnesses A vaccine is a harmless derivative of a pathogen that stimulates the immune system to mount defenses against the harmful pathogen Vaccines can prevent certain viral illnesses Viral infections cannot be treated by antibiotics Antiviral drugs can help to treat, though not cure, viral infections 55

Emerging Viruses Viruses that suddenly become apparent are called emerging viruses HIV is a classic example The West Nile virus appeared in North America first in 1999 and has now spread to all 48 contiguous states 56

In 2009 a general outbreak, or epidemic, of a flu-like illness occurred in Mexico and the United States; the virus responsible was named H1N1 H1N1 spread rapidly, causing a pandemic, or global epidemic

1 m (a) 2009 pandemic H1N1 influenza A virus Figure 17.8 Figure 17.8 Influenza in humans 1 m (a) 2009 pandemic H1N1 influenza A virus (b) 2009 pandemic screening 58

1 m (a) 2009 pandemic H1N1 influenza A virus Figure 17.8a Figure 17.8a Influenza in humans (part 1: SEM) 1 m (a) 2009 pandemic H1N1 influenza A virus 59

(b) 2009 pandemic screening Figure 17.8b Figure 17.8b Influenza in humans (part 2: screening) (b) 2009 pandemic screening 60

Three processes contribute to the emergence of viral diseases The mutation of existing viruses, which is especially high in RNA viruses Dissemination of a viral disease from a small, isolated human population, allowing the disease to go unnoticed before it begins to spread Spread of existing viruses from animal populations; about three-quarters of new human diseases originate this way

Strains of influenza A are given standardized names The name H1N1 identifies forms of two viral surface proteins, hemagglutinin (H) and neuraminidase (N) There are numerous types of hemagglutinin and neuraminidase, identified by numbers

Viral Diseases in Plants More than 2,000 types of viral diseases of plants are known; these have enormous impacts on the agricultural and horticultural industries Plant viruses have the same basic structure and mode of replication as animal viruses Most plant viruses known thus far have an RNA genome and many have a helical capsid 63

Plant viral diseases spread by two major routes Infection from an external source of virus is called horizontal transmission Herbivores, especially insects, pose a double threat because they can both carry a virus and help it get past the plant’s outer layer of cells Inheritance of the virus from a parent is called vertical transmission 64

Figure 17.UN01 Figure 17.UN01 In-text figure, infected squash, p. 341 65