Lecture Week 6: Viruses, Viroids, and Prions PDF

Viruses, Viroids, and Prions tiny but deadly. Learning objectives week 6 Explain to me what the different parts of a virus are and the functions of these parts. Explain how viruses replicate and how this is different from bacterial growth. Understand how cancer forms and explain how m...

Viruses, Viroids, and Prions tiny but deadly. Learning objectives week 6 Explain to me what the different parts of a virus are and the functions of these parts. Explain how viruses replicate and how this is different from bacterial growth. Understand how cancer forms and explain how mutations and viruses are important for this process.  So why should we care about viruses? Influenza virus – the flu 1918-1920 75,000,000 died HIV – 35,000,000 died last ~30 years Dengue fever – 50,000,000-100,000,000 infections per year. Outline: What are viruses, viroids, and prions Viral diseases and viral anatomy Viral replication and release Viral culturing and study Viroids and prions Outline: What are viruses, viroids, and prions Viral diseases and viral anatomy Viral replication and release Viral culturing and study Viroids and prions Viruses, Viroids, and Prions tiny but deadly.  So what are viruses, viroids, and prions? Acellular--- meaning that compared to even bacteria, they are very simple Composed of one or a few different biomolecules Cannot reproduce independently Cannot grow or respond to the environment. There are more bacteria than human cells in a human body and researchers think there are even more viruses than bacteria. Half of the human genome is made of DNA thought to be viral in origin. Cause many human diseases  So what are viruses, viroids, and prions? Acellular--- meaning that compared to even bacteria, they are very simple Composed of one or a few different Chicken Pox biomolecules Cannot reproduce independently Cannot grow or respond to the environment. There are more bacteria than human cells in a human body and researchers think there are even more viruses than bacteria. Half of the human genome is made of DNA thought to be viral in origin. Cause many human diseases Outline: What are viruses, viroids, and prions Viral diseases and viral anatomy Viral replication and release Viral culturing and study Viroids and prions  Viruses– cause most of the diseases that plague the industrialized world Cannot carry out any metabolic pathway Neither grow nor respond to the environment Cannot reproduce independently Recruit the cell’s metabolic pathways to increase their numbers No cytoplasmic membrane, cytosol, organelles (with one exception) Have extracellular and intracellular state Some of the diseases caused by viruses  Most viruses infect only particular host cells May be so specific they infect only particular kind of cell in a particular host Viral surface proteins have affinity for specific proteins on host cell Generalists – infect many kinds of cells in many different hosts Viruses live in both Extracellular and Intracellular states. Extracellular State Called virion Protein coat (capsid) surrounding nucleic acid Nucleic acid and capsid also called nucleocapsid Some have phospholipid envelope Outermost layer provides protection and recognition sites for host cells Intracellular State Capsid removed Virus exists as nucleic acid Viruses have 2 main parts a genome and capsid. The genome is just like any other genome, composed of nucleic acid Cannot replicate on its own, needs a host cell’s replication machinery. Capsid is the viruses body, comprised of protein and arranges in a symmetrical manner around the virus. Different viruses can have genomes made of different types of nucleic acids. Partial genome Viral Show more variety in of E. coli genome nature of their genomes than do cells Primary way scientists categorize and classify viruses May be DNA or RNA, but never both dsDNA, ssDNA, dsRNA, ssRNA Linear and segmented or single and circular Much smaller than Capsids are the outer protein coat of the virus Provide protection for viral nucleic acid Means of attachment to host’s cells Composed of protein subunits called capsomeres Capsomere made of single or multiple types of proteins Viruses come in three basic shapes Helical,  The viral envelope covers the capsid and genome and is acquired from the host during replication or release. Composed of phospholipid bilayer and proteins Envelope is portion of membrane system of host Some proteins are virally coded glycoproteins (spikes) Envelope’s proteins and glycoproteins Take home messages Viruses are small and deadly. Different types of viruses infect different types of cells. Viruses are composed of a capsid which is made of protein and a nucleic acid genome. The type of nucleic acid in which makes up the viral genome is a convenient way to classify viruses. Some viruses also have an envelope composed of fatty acids. Outline: What are viruses, viroids, and prions Viral diseases and viral anatomy Viral replication and release Viral culturing and study Viroids and prions  Viral replication is dependent upon the hosts organelles and Lytic replication enzymes. Replication cycle usually results in death and lysis of host cell Stages of lytic replication cycle of bacteriophage Attachment Entry Synthesis Assembly Release  Lysogeny is another type of viral replication cycle Infected host cells grow and reproduce normally for Lambda Phage: one of the most us generations before they lyse molecular tools ever. Temperate phages Prophages – inactive phages Lysogenic conversion results when phages carry genes that alter the phenotype of a bacterium  Attachment Prophage Entry in chromosome Lambda phage Lytic Lysogeny cycle Synthesis Release Replication of chromosome Assembly and virus; cell division Induction Further replications and cell divisions Figure 13.11 The lysogenic replication cycle in bacteriophages: phage lambda and E. coli  Viruses are the ultimate replicating machine Number of infective virions is in medium (log scale) by lys Burst size irions e of v Entry Releas Synthesis and assembly Time (minutes) Attachment Burst time E. coli 20 minutes to replicate Yeast 2 hours to replicate Human cells much longer to replicat Figure 13.9 Pattern of virion abundance in lytic cycle  Group Questions Larger viruses typically have a double stranded genome where as smaller viruses have a single stranded genome. Why might this be? If colony of 1 million bacteria was infected by a single phage and each lytic replication cycle produced 200 phage how many replication cycles would it take before all of the bacteria are killed. Assume each bacteria is only infected by a single phage. Replication of animal viruses follows the basic pathway of bacteriophages with a few key differences. Differences between animal and bacteria viruses Presence of envelope around some viruses Eukaryotic nature of animal cells may require additional steps for integration. Virus must get into the nucleus Replication of animal viruses follows the basic pathway of bacteriophages with a few key differences. Differences Presence of envelope around some viruses Eukaryotic nature of animal cells Lack of cell wall in animal cells, so entry into a human cell is different from Replication of animal viruses follows the basic pathway of bacteriophages with a few key differences. Differences Presence of envelope around some viruses Eukaryotic nature of animal cells Lack of cell wall in animal cells, so entry into a human cell is different from Central Dogma of Biology provides some guiding principles for viral replication Viruses must assemble (put themselves together) This means they must 1)Copy their genome 2)Make the proteins that make the capsid How this happens depends upon the type of virus. Messenger RNA = mRNA Different viruses have genomes made of different nucleic acids. Show more variety in nature of their genomes than do cells Primary way scientists categorize and classify viruses May be DNA or RNA, but never both dsDNA, ssDNA, dsRNA, ssRNA Linear and segmented or single and circular  Some Useful definitions: ss = single stranded ds = double stranded + is like messenger RNA can be directly translated into protein - is the opposite so it cannot be directly translated into protein  Synthesis of animal viruses requires different strategies depending on the type of nucleic acid it uses for a genome. DNA viruses can use the RNA viruses often machinery of the cell as they are essentially very very small replicate in the cytoplasm. parts of the mammalian genome. This is more complicated Usually means that they have due to variation of the to go the nucleus in order to type of RNA genome you replicate. can potentially have. DNA replication machinery is +ssRNA, -ssRNA, dsRNA located there.  Synthesis of animal viruses requires different strategies depending on the type of nucleic acid it uses for a genome. Remember the virus must make both more viral genomes and capsids. +ssRNA can act as messengerRNA = mRNA so the viral genome can be translated as any other transcript (capsid) Viral RNA polymerase makes –ssRNA From the –ssRNA more + ssRNA can be transcribed +ssRNA retroviruses are slightly different as they require a DNA intermediate  So what if you are an RNA virus that wants to incorporate into the genome or make more RNA virus? reverse transcriptase is an Reverse transcriptase enzyme used to generate complementary DNA from an RNA template Drugs that inhibit these enzymes can be potent antivirals?  Synthesis of animal viruses requires different strategies depending on the type of nucleic acid it uses for a genome. -ssRNA have to overcome the fact that –ssRNA can’t be directly used by ribosomes Carry a special enzyme to make +ssRNA Carries a RNA dependent RNA transcriptase in its capsid  Synthesis of animal viruses requires different strategies depending on the type of nucleic acid it uses for a genome. dsRNA viruses use a combination of the strategies mentioned previously The mechanisms of assembly and release of animals viruses depends upon its genetic material. Most DNA viruses assemble in nucleus Most RNA viruses develop solely in cytoplasm Number of viruses produced depends on type of virus and size and initial health of host cell  Three mechanisms of virus release: 1) Lysis: cells break open Cell Lysis and die Naked viruses are released by exocytosis or lysis Exocytosis is when the viruses leave the cell without breaking open the cell. Makes the cells sick but they don’t die so they can still make more viruses.  I. Enveloped viruses Do not usually lyse the host cell and thus cause persistent infections. Similar to exocytosis but in addition the virus wraps itself in the cytoplasmic membrane of the cell. This hides it from the immune system and facilitates entry into a new cell. Figure 13.14 The process of budding in enveloped viruses  Viral Latency (How many of you have heard of Shingles?) More than 3 million US cases per year Preventable by vaccine Short-term: resolves within days to weeks  What is latency? Chicken Pox Latency leads to Shingles later Latency is when animal viruses remain dormant in host cells May be stay there for years with no viral activity Some latent viruses do not become incorporated into host chromosomes Incorporation of provirus into host DNA is permanent Take home messages Viruses can replicate very very quickly. Viruses use much of the host replication machinery in order to replicate as such finding drugs that are effective against them is difficult. Synthesis of animal viruses requires different strategies depending on the type of nucleic acid it uses as a genome. Outline: What are viruses, viroids, and prions Viral diseases and viral anatomy Viral replication and release Viral culturing and study Viroids and prions  Viruses Oncogenes and Cancer Cancer is a group of diseases involving abnormal cell growth with the potential to invade or spread to other parts of the body. Neoplasia Uncontrolled cell division in multicellular animal Mass of neoplastic cells is tumor The difference between benign and malignant tumors is metastasis. Viruses Oncogenes and Cancer: Cancer is a group of diseases involving abnormal cell growth with the potential to invade or spread to other parts of the body. Neoplasia Uncontrolled cell division in multicellular animal Mass of neoplastic cells is tumor So how does a cell get to be The difference between benign and malignant tumors like this and is metastasis. what do viruses have to do with any of this?  There are many different factors that contribute to the activation of oncogenes (genes that can cause cancer when activated) Ultraviolet light Radiation Carcinogens Viruses The one things that link all of these factors is that they damage and thus mutate DNA.  There are many different factors that contribute to the activation of oncogenes Woman who constantly used tanning Ultraviolet light beds shares gruesome selfie Radiation Carcinogens Viruses  There are many different factors that contribute to the activation of oncogenes Ultraviolet light Radiation Carcinogens Viruses  There are many different factors that contribute to the activation of oncogenes Viruses cause 20–25% of human cancers Some carry copies of oncogenes as part of their genomes Some promote oncogenes already present in host Some interfere with tumor repression Specific viruses are known to cause ~15% of human cancers Burkitt’s lymphoma Hodgkin’s disease Kaposi’s sarcoma Cervical cancer The oncogene theory of cancer induction Normal noncancerous state Protooncogene= oncogene that is as Figure 13.16 The oncogene theory of cancer induction Figure 13.16 The oncogene theory of cancer induction I want to study viruses, I want to study cancer, how can I do this? Viruses cause cancer Viruses cause many of the most dangerous diseases We should study viruses  Are Viruses Alive? Some consider them complex pathogenic chemicals Others consider them the least complex living entities Use sophisticated methods to invade cells Have the ability to take control of their host cell Are able to replicate themselves as long as in a host © 2012 Pearson Education Inc.  Viruses cannot be grown outside of a host, so to study them scientists must grow them in some other cell. Inside a mature organism bacteria, plant, or animal Fertilized eggs Cell culture Bacterial la Viral plaqu n allow the researcher to estimate the number of viruses Viruses cannot be grown outside of a host so to study them scientists must grow them in some other cell. Inside a mature organism bacteria, plant, or animal Fertilized eggs Cell culture Growing viruses in plants or animals leads to a whole host of ethical and technical issues.  A wide variety of sites suitable for viral inoculation make eggs especially useful in Air sac Injection into culturing viruses chorioallantoic Injection into membrane chorioallantois Injection into Figure 13.18 embryo Inoculation sites for the culture of viruses in embryonated chicken eggs Injection into Injection into amnion yolk sac  Culturing Viruses in Cell (Tissue) Culture can be simpler than maintaining animals Consists of cells isolated from an organism and grown on a medium or in a broth Two types of cell cultures Diploid cell cultures (100 generations max) these are just normal cells taken from our bodies Continuous cell cultures derived from tumors so  Henrietta Lacks (HeLa cells) are cells from a cervical cancer. Henrietta died in the 1950’s her cells are still being used a standard of human cell culture. Neither Lacks nor her family gave her physician permission to harvest the cells. At that time, permission was neither required nor customarily sought. The cells were later commercialized. In the 1980s, family medical records were published without family consent. Genome sequence was published without their consent. Group questions 1) List some challenges of studying viruses that infect humans. 2) Describe how viral infection can cause cancer. Why do we not get cancer every time we get a virus? potentially helpful videos on viral replication https:// www.youtube.com/watch?v=uIut0oVWC Eg https://www.youtube.com/watch? v=J4BN4dARpio Take home messages Viruses can cause cancer by mutating areas of the genome that in turn allow for unregulated cell growth. Many other factors can contribute to oncogene activation. Viruses require a host cell to replicate. In order to study viruses researchers grow them inside other cells. Combinations of viral biology and cancer biology has lead to development of some of the most powerful tools in biology. Outline: What are viruses, viroids, and prions Viral diseases and viral anatomy Viral replication and release Viral culturing and study Viroids and prions  Viroids are extremely small circular infectious pieces of RNA that infect plants. Genome of bacteriophage T7 PSTV Viroids can have grave economic consequences They infect many important crops. Are thought to be relics of the RNA world which is something we will discuss in more detail in the coming weeks.  Prions are single proteins that when undergo a structural change can cause disease. Proteinaceous infectious agents Cellular PrP protein Made by all mammals Normal structure with -helices called cellular PrP Prion PrP Disease-causing form with -pleated sheets called prion PrP Prion PrP changes shape of cellular PrP so it becomes prion PrP  Prions act like bad influences, they take well behaved proteins and make them pathogenic. They only cause disease in mammals Three different Prion Diseases Normally, nearby proteins and polysaccharides force PrP into its correct shape (cellular Prp) PrP mutations result in formation of prion PrP Fatal neurological degeneration, fibril deposits in brain, and loss of brain matter Large vacuoles form in brain Characteristic spongy Prion diseases are horrible, but they are relatively rare. No treatment Fatal Are spread through ingestion of infected material or through membrane protein contact. Prions only destroyed by incineration or autoclaving in 1 N NaOH Take home messages Viroids are small infectious pieces of RNA that generally infect plants. Prions are infectious proteins that have structurally changed such that they can cause healthy proteins to change structure as well. Prions cause neurodegenerative diseases but luckily they are relatively rare. Prions are virtually indestructible Group Questions 1) Why might it be beneficial for a virus not to kill a cell? 2) Describe the main difference between + and – strand RNA virus replication. 3) Is single stranded DNA normally found in human cells that have not been infected with a ssDNA virus.  Tiny holes found in the thalamus caused by a prion that is genetically inherited. Thalamus is responsible for allowing you to fall into deep sleep. http://www.cnn.com/2017/09/19/health/fatal-insomnia-family-curse-somethings- Prion Overview video