Chapter 19 - Viruses - Biology 202 PDF

BIO 202 Chapter 19 Viruses https://www.sciencedirect.com/topics/immunology-and-microbiology/virus https://www.smithsonianmag.com/science-nature/worlds-largest-virus-was-just-res urrected-34000-year...

BIO 202 Chapter 19 Viruses https://www.sciencedirect.com/topics/immunology-and-microbiology/virus https://www.smithsonianmag.com/science-nature/worlds-largest-virus-was-just-res urrected-34000-year-old-permafrost-180949932/ Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved  https://www.vector4free.com/free-vector-virus-cartoon-31477, https://www.shutterstock.com/image-vector/corona-virus-cartoon-doo dle-illustration-isolated-1629893215 Copyright © 2019, 2016, 2013 Pearson Education, Inc. All Rights Reserved Figure 19.1a A human immune cell (blue) infected by a human immunodeficiency virus (HIV) is releasing more H IV viruses (gold dots), which will go on to infect other cells. Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved Figure 19.1b How does a virus make more viruses? Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved  CONCEPT 19.1: A virus consists of a nucleic acid surrounded by a protein coat A virus is an infectious particle consisting of genes packaged in a protein coat Viruses are much simpler in structure than even prokaryotic cells Viruses can cause a wide variety of diseases They cannot reproduce or carry out metabolism outside of a host cell Viruses exist in a shady area between life-forms and chemicals, leading a kind of “borrowed life” Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved  The Discovery of Viruses: Scientific Inquiry Tobacco mosaic disease stunts growth of tobacco plants and gives their leaves a mosaic coloration In the late 1800s, researchers hypothesized that unusually small bacteria might be responsible Later work suggested that the infectious agent did not share features with bacteria (such as the ability to grow on nutrient media) In 1935, Wendell Stanley confirmed this latter hypothesis by crystallizing the infectious particle, now known as tobacco mosaic virus (TMV) https://www.shutterstock.com/search/tobacco-mosaic-virus Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved Figure 19.2 Inquiry: What causes tobacco mosaic disease? Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved  Structure of Viruses Viruses are not cells A virus is a very small infectious particle consisting of nucleic acid enclosed in a protein coat and, in some cases, a membranous envelope The simple structure of viruses make them a useful biological system https://www.immunology.org/public-information/bitesized-immunology/pathogens-disease/viruses-introduction Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved Viral Genomes Viral genomes may consist of either – double- or single-stranded DNA or – double- or single-stranded RNA Viruses are classified as DNA viruses or RNA viruses The genome is either a single linear or circular molecule of the nucleic acid Viruses have between 3 and 2,000 genes in their genome Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved  Capsids and Envelopes (1 of 3) A capsid is the protein shell that encloses the viral genome Capsids are built from protein subunits called capsomeres A capsid can have a variety of structures; associated viruses may be referred to as helical or icosahedral viruses https://www.sciencedirect.com/topics/medicine-and-dentistry/virus-capsid Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved Figure 19.3 Viral structure Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved  Capsids and Envelopes (2 of 3) Some viruses have accessory structures that help them infect hosts Viral envelopes (derived from membranes of host cells) surround the capsids of influenza viruses and many other viruses found in animals Viral envelopes contain a combination of viral and host cell molecules https://www.sciencedirect.com/topics/medicine-and-dentistry/virus-capsid Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved  Capsids and Envelopes (3 of 3) Bacteriophages, also called phages, are viruses that infect bacteria They 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 https://www.whatisbiotechnology.org/index.php/science/summary/phage-therapy/phage-therapy-uses-viruses-that-attack-bacteria-to-t reat Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved , https://www.researchgate.net/figure/The-structural-sketch-of-bacteriophage_fig1_333754342 CONCEPT 19.2: 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 species that it can infect Some viruses have broad host ranges, while others are able to infect only one species For example, measles virus only infects humans Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved  General Features of Viral Replicative Cycles The viral genome enters the host cell in a variety of ways 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 Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved Figure 19.4 A simplified viral replicative cycle Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved Animation: Simplified Viral Replicative Cycle Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved Replicative Cycles of Phages Phages are the best understood of all viruses Phages have two alternative reproductive mechanisms: the lytic cycle and the lysogenic cycle Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved 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 Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved Figure 19.5 The lytic cycle of phage T4, a virulent phage Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved  Animation: Phage Lytic Cycle Clear plaque fashioned by Escherichia coli phage MSK with Escherichia coli C host (primarily X174 host) lawn on a double-layer agar plate. https://www.researchgate.net/figure/Clear-plaque-fashioned-by-Escherichia-coli-phage-MSK-with-Escherichia-coli-C-host_fig1_3541 00581 Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved The Lysogenic Cycle (1 of 2) The lysogenic cycle replicates the phage genome without destroying the host The viral DNA molecule is incorporated into the host cell’s chromosome Phages that use both the lytic and lysogenic cycles are called temperate phages A temperate phage called lambda is widely used in biological research ( ) Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved Figure 19.6 The lytic and lysogenic cycles of phage lambda, a temperate phage λ, Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved Animation: Phage Lysogenic and Lytic Cycles Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved The Lysogenic Cycle (2 of 2) The integrated viral DNA is known as a prophage Every time the host divides, it copies the phage DNA and passes the copies to daughter cells An environmental signal can trigger the virus genome to exit the bacterial chromosome and switch to the lytic mode Some prophages are expressed during lysogeny, and some cause the host bacteria to secrete toxins that are harmful to humans Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved  Acute and Latent HSV–1 Infection Copyright © 2019, 2016, 2013 Pearson Education, Inc. All Rights Reserved https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2021.644664/full  Bacterial Defenses Against Phages (1 of 4) Bacteria have their own defenses against phages Natural selection favors bacterial mutants with surface proteins that cannot be recognized as receptors by a particular type of phage Foreign DNA can be identified as such and cut up by cellular enzymes called restriction enzymes The bacterium’s own DNA is protected from the restriction enzymes by being methylated https://www.neb.com/en-us/products/r0101-ecori Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved Bacterial Defenses Against Phages (2 of 4) Both bacteria and archaea can protect themselves from viral infection with the CRISPR-Cas system It is based on sequences called clustered regularly interspaced short palindromic repeats (CRISPRs) Each “spacer” sequence between the repeats corresponds to DNA from a phage that had infected the cell Particular nuclease proteins interact with the CRISPR region; these are called CRISPR-associated (Cas) proteins Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved  Bacterial Defenses Against Phages (3 of 4) When a phage infects a bacterial cell that has the CRISPR-Cas system, the phage DNA is integrated between two repeat sequences If the cell survives the infection, it can block any attempt of the same type of phage to reinfect it The attempt of the phage to infect the cell triggers transcription of the CRISP R region The resulting RNAs are cut into pieces and bound by Cas proteins Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved Bacterial Defenses Against Phages (4 of 4) The Cas proteins use the phage-related RNA to target the invading phage DNA The phage DNA is cut and destroyed Natural selection favors phage mutants that can bind to altered cell surface receptors or that are resistant to enzymes The relationship between phage and bacteria is in constant evolutionary flux Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved Figure 19.7 The CRISP R-Cas system: a type of bacterial immune system Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved  Replicative Cycles of Animal Viruses There are two key variables used to classify viruses that infect animals: – An RNA or DNA genome, either single-stranded or double-stranded – The presence or absence of a membranous envelope Whereas few bacteriophages have an envelope or an RNA genome, many animal viruses have both Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved Viral Envelopes (1 of 2) Many viruses that infect animals have a membranous envelope Viral glycoproteins on the envelope bind to specific receptor molecules on the surface of a host cell The viral envelope is usually derived from the host cell’s plasma membrane as the viral capsids exit Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved Figure 19.8 The replicative cycle of an enveloped RN A virus Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved  Viral Envelopes (2 of 2) Other viral membranes form from the host’s nuclear envelope and are then replaced by an envelope made from Golgi apparatus membrane The herpesvirus is an example of this Copyright © 2021, 2017, 2014 Pearson Education, https://www.researchgate.net/figure/The-Lytic-Human-Herpesvirus-Life-Cycle-Step-1-Binding-During-primary-lytic-infection_fig1_351994883 Inc. All Rights Reserved  Viral Genetic Material (1 of 2) 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) https://www.sciencedirect.com/topics/immunology-and-microbiology/human-immunodeficiency-virus Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved  Viral Genetic Material (2 of 2) The viral DNA that is integrated into the host genome is called a provirus Unlike a prophage, a provirus remains a permanent resident of the host cell 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 virus particles released from the cell Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved Table 19.1 Classes of Animal Viruses Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved Animation: HIV Replicative Cycle Animation: Retrovirus (HI V) Replicative Cycle Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved Figure 19.9 The replicative cycle of HIV, the retrovirus that causes AIDS Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved Evolution of Viruses (1 of 2) Viruses do not fit our definition of living organisms Since viruses can replicate only within cells, they probably evolved as bits of cellular nucleic acid Candidates for the source of viral genomes include plasmids and transposons Plasmids, transposons, and viruses are all mobile genetic elements Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved  Evolution of Viruses (2 of 2) The largest virus identified about 20 years ago is the size of a small bacterium Its genome encodes proteins involved in translation, DNA repair, protein folding, and polysaccharide synthesis There is controversy about whether this virus evolved before or after cells In the past decade several even larger viruses have been identified; how these evolved is an unresolved question Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved CONCEPT 19.3: Viruses and prions are formidable pathogens in animals and plants Diseases caused by viral infections affect humans, agricultural crops, and livestock worldwide Smaller, less complex entities called prions also cause disease in animals Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved Viral Diseases in Animals (1 of 2) 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 Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved Viral Diseases in Animals (2 of 2) 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, such as smallpox, rubella, mumps, and others Viral infections cannot be treated by antibiotics!!! Antiviral drugs can help to treat, not cure, viral infections by inhibiting synthesis of viral DNA and by interfering with viral assembly Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved  Emerging Viral Diseases (1 of 8) Emerging viruses are those that suddenly become apparent HIV, the AIDS virus, is a classic example COVID-19 very quickly turned from an emerging infectious disease to a global pandemic The genome of COVID-19 is a positive-sense, single-stranded RNA. https://shs.cairn.info/revue-confluence-2022-1-page-29?lang=fr, https://www.nature.com/articles/s41565-020-0732-3, https://www.rochester.edu/newscenter/covid-19-rna-coronavirus-research-428952/#:~:text=%E2%80%9CThe%20genome%20of%20 the%20virus,sense%2C%20single%2Dstranded%20RNA Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved  COVID-19 is a ss(+) RNA virus Life cycle of positive‐ and negative‐sense single‐stranded RNA (ssRNA) viruses. A, B, Flowchart of RNA synthesis by RNA‐dependent RNA polymerase (RdRP) of positive‐sense (A) and negative‐sense (B) ssRNA viruses. Small circles at the 5′‐ends of positive‐sense RNA denote m7G‐cap structures, which occur in most of viral mRNAs https://www.researchgate.net/figure/Life-cycle-of-positive-and-negative-sense-single-stranded-RNA-ssRNA-viruses-A-B_fig1_343955 700 Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved Emerging Viral Diseases (2 of 8) The Ebola virus is one of several emerging viruses that cause hemorrhagic fever, an often a fatal illness In 2014, a widespread outbreak (epidemic) of Ebola virus occurred In 2017, 2018, and 2019, smaller outbreaks occurred in the Democratic Republic of the Congo Other examples of emerging viruses include the chikungunya virus and the recently emerging Zika virus (2015) COVID - 2019 Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved  Human coronavirus 229E, magnified to x60,000 via negative contrast electron microscopy https://www.microscope.com/coronavirus-under-an-electron-microscope Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved  Emerging Viral Diseases (3 of 8) One cause of rapidly emerging viral disease in humans is mutation of existing viruses into new ones that can spread more easily A second cause is the spread of a viral disease from a small, isolated human population A third cause is the spread of existing viruses from other animals – It is estimated that about three-quarters of new human diseases originate in this way Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved  Emerging Viral Diseases (4 of 8) Flu epidemics are caused by type A influenza viruses; these infect a wide variety of animals including birds, pigs, horses, and humans Strains of influenza A are given standardized names based on the viral surface proteins hemagglutinin (HA) and neuraminidase (NA) As of 2017 18 types of HA, and 11 types of neuraminidase, have been identified Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved  Emerging Viral Diseases (5 of 8) The H5N1 strain is quite deadly, because it is very different from influenza strains circulating among people for a long time It is thus difficult for people to mount an effective immune response to this strain However, it has not caused an epidemic because it is not transmitted from person- to-person The diagram show the virus structure consist of Neuraminidase (NA), Hemagglutinin (HA), Lipid layer (envelop), Capsid consist of M1 matrix protein that give the virus rigidity and contain the RNA, and Nucleoprotein (RNA). Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved https://www.researchgate.net/figure/The-diagram-show-the-virus-structure-consist-of-Neuraminidase-NA-Hemagglutinin-HA_fig1_344026200  Emerging Viral Diseases (6 of 8) A deadly strain of H1N1, originally called the swine flu, was not actually transmitted to humans from pigs Instead, the story was more complex, H1N1 was a unique combination of swine, avian, and human influenza genes An epidemic of H1N1 occurred in 2009, reaching 207 countries, infecting over 600,000 people and killing almost 8,000 A global epidemic like this is called a pandemic COVID-19: Last updated: April 13, 2024, 01:00 GMT - 7,010,681 deaths https://www.worldometers.info/coronavirus/coronavirus-death-toll/ Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved Emerging Viral Diseases (7 of 8) Influenza viruses have nine RNA segments in their genome, leading to many new genetic combinations They also have a high rate of mutation Normal seasonal flu viruses are not considered emerging viruses because variants of these viruses have been circulating among humans for a long time However, these viruses still undergo mutation and reassortment Variations thought to be most likely to occur each year are selected to generate vaccines Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved Emerging Viral Diseases (8 of 8) Changes in host behavior or the environment can increase the spread of viruses responsible for emerging diseases New roads into a remote area may increase spread of viral diseases The use of insecticides and mosquito nets may help prevent the spread It is possible that global climate change may allow mosquitoes that carry viruses to expand their range Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved Figure 19.11 Netting as protection against virus- carrying mosquitos Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved  1918 Influenza Pandemic (Spanish Flu) What caused the 1918 influenza pandemic (Spanish flu)? The 1918 flu pandemic was caused by a form of influenza A virus (H1N1). Experts think it might have started as an avian influenza. Researchers think the first cases in humans started in early 1918, possibly in military camps in the U.S. How many people got the flu during the 1918 pandemic? Experts estimate that 500 million people — or a third of the world’s population at the time — were infected with the flu during the 1918 pandemic. How many people died during the 1918 pandemic (Spanish flu)? About 50 million people worldwide died from the flu between 1918 and 1919. Some experts estimate the number to be as high as 100 million. About 675,000 people died in the U.S. https://my.clevelandclinic.org/health/diseases/21777-spanish-flu Copyright © 2019, 2016, 2013 Pearson Education, Inc. All Rights Reserved  Viral Diseases in Plants (1 of 2) More than 2,000 types of viral diseases of plants are known and cause spots on leaves and fruits, stunted growth, and damaged flowers or roots Most known plant viruses have an RNA genome Many have a helical capsid, while others have an icosahedral capsid Plant viruses constitute a major cause of plant diseases with an estimated economic impact of more than USD 30 billion annually (!) https://pubmed.ncbi.nlm.nih.gov/33348905/ Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved Figure 19.12 Immature tomato infected by a virus Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved  Viral Diseases in Plants (2 of 2) Plant viruses spread disease by two major routes: – Horizontal transmission, entering through damaged cell walls – Vertical transmission, inheriting the virus from a parent – Viroids are small, single-stranded, circular RNAs that can infect plants and cause specific diseases, even though they do not have the ability to code for proteins – Cause millions if not billions of dollars in damage each year https://www.sciencedirect.com/topics/neuroscience/viroid#:~:text=Viroids%20are%20small%2C%20single%2Dstranded,their%20stru ctural%20and%20functional%20properties Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved , https://norgenbiotek.com/blog/Viroids-An-Agriculturists-Worst-Nightmare Prions: Proteins as Infectious Agents (1 of 2) Prions are infectious proteins that appear to cause degenerative brain diseases in animals Scrapie in sheep, mad cow disease, and Creutzfeldt-Jakob disease in humans are all caused by prions Prions are incorrectly folded proteins, can be transmitted in food, act slowly, and are virtually indestructible Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved Prions: Proteins as Infectious Agents (2 of 2) Prions are somehow able to convert a normal form of a protein into the misfolded version Then several prions aggregate into a complex that can convert more proteins to prions, which join the chain Prions might also be involved in diseases such as Alzheimer’s and Parkinson’s disease There are many outstanding questions about these small infectious agents Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved  Figure 19.13 Model for how prions propagate https://www.semanticscholar.org/paper/Prion-protein-disease-and-neuropathology-of-prion-Pl essis/de97d4031880b54761f814b813c1461f1955cace/figure/0 Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved Figure 19.UN04 Summary of key concepts: lytic and lysogenic cycles Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved Figure 19.UN05 Test your understanding, question 8 (growth curves) Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved Copyright This work is protected by United States copyright laws and is provided solely for the use of instructors in teaching their courses and assessing student learning. Dissemination or sale of any part of this work (including on the World Wide Web) will destroy the integrity of the work and is not permitted. The work and materials from it should never be made available to students except by instructors using the accompanying text in their classes. All recipients of this work are expected to abide by these restrictions and to honor the intended pedagogical purposes and the needs of other instructors who rely on these materials. Copyright © 2021, 2017, 2014 Pearson Education, Inc. All Rights Reserved