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Notes on Genetics of Viruses Discuss whether viruses are living or non-living organisms and explain why viruses are

e obligate parasites o A virus is a sub-microscopic infectious particle composed of a protein coat and a nucleic acid core (contains either DNA or RNA but NOT both, can be double stranded or single stranded) and, in some cases, a membranous envelope o Viruses carry genetic information encoded in their nucleic acid, undergo mutations and can reproduce but they cannot carry out metabolism on their own, cannot produce energy, cannot reproduce on their own and do not possess the characteristics of living things (movement, feeding, excretion, growth and sensitivity) o Viruses are not considered alive o Viruses are obligate intracellular parasites Viruses must invade a host in order to replicate and multiply Within the host, their genetic elements can replicate independently of a hosts chromosomes o Viruses are characterized by having an extracellular state Enables them to be easily transmitted from one host to another Each virus has a host range, a limited number of host cells that it can infect This extracellular state enables some viruses to replicate themselves in a way that is destructive to the host cell. This destructive replication makes viruses agents of disease o Viruses are biological particles and technically are not considered to be living organisms o Virus particles (virions) are produced from the assembly of pre-formed components whereas other organisms grow from an increase in the integrated sum of their components and reproduce by division o Viruses lack the genetic information which encodes apparatus necessary for generation of metabolic energy or protein synthesis. Therefore, viruses are dependent on the host cell for this function. Living characteristics of viruses Non-living characteristics of viruses can grow and reproduce at a fantastic rate, but acellular, contain no cytoplasm or cellular organelles only in living host cells can mutate do not carry out metabolism on their own and must replicate using the host cells metabolic machinery Possess DNA or RNA but never both (except cytomegalovirus which possesses both DNA core and several mRNA segments) Biologically inert, unable to replicate its genes or regenerate its own supply of ATP Classification of viruses o RNA viruses can be classified according to the sense of polarity of their RNA (negative sense, positive sense) o Positive sense = viral RNA is identical to viral mRNA and thus can be immediately translated by the host cell o Negative sense = viral RNA is complementary to mRNA and thus must be converted to positivesense RNA by RNA polymerase before translation Describe the structural components of viruses o Viruses have both extracellular and intracellular states o Extracellular state: Called virion (virus particle)

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Virion contains nucleic acid encased in a protein coat and in some cases a membranous envelope Virion is metabolically inert and does not carry out respiratory or biosynthetic functions o Intracellular state: Initiated where virus infected a host cell o Structures of virions are quite diverse: helical, icosahedral (near symmetrical, near spherical) , membranous envelope, complex Viral genome Molecule of nucleic acid (either DNA or RNA) that functions as the genetic material May be single or segmented, circular or linear, single-stranded or doublestranded Virus is called a DNA virus or RNA virus. RNA viruses lack proofreading abilities and thus leads to a very rapid rate of evolution of RNA ciruses The genome codes for the synthesis of the viral components and viral enzymes required for replication Capsid Protective protein coat enclosing the viral genome Formed from structural subunits called capsomere (proteins) arranged in a precise and highly repetitive pattern around the nucleic acid Small genome size of most viruses restricts the number of different viral proteins making up the capsid Information for proper assembly of proteins into capsomeres is contained within the structure of the proteins themselves and they can self-assembly For many viruses, this self-assembly process is assisted by molecular chaperones, proteins that assist in folding and assembly but that themselves are not part of the final structure Serves to protect and introduce the genome into the host cells Some viruses consist of only a genome surrounded by a capsid and are called nucleocapsid or naked viruses Envelope (present only in some viruses) Complex membranous structures surrounding the polyhedral or helical nucleocapsid Viruses with envelope are called enveloped viruses Enveloped viruses are common in the animal world but some enveloped bacterial viruses are also known Composed of phospholipids and glycoproteins Mostly derived from host cell membranes (plasma membrane, Golgi membrane, nuclear membrane) by process budding Although the envelop is usually of host origin, the virus does incorporate proteins of its own, often appearing as glycoprotein spikes into the envelope o These virus-origin glycoprotein spikes function in attaching the virus to receptors on susceptible host cells (recognition) Describe the reproductive cycles of bacteriophages o Bacteriophages are viruses that only infect bacteria o Some bacteriophages are structurally more complex with unique tail structure composed of base plate, tail fibers and a contractile sheath o Typical structure: Genome: dsDNA

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Capsid: Capsomeres, Sheath, Base plate, Tail fibers No envelope o Lytic bacteriophages replicate through the lytic life cycle o Temperate bacteriophages are capable of replicating through both lytic and lysogenic life cycles Describe bacteriophages that reproduce via a lytic cycle eg T4 phage o Virus would choose to undergo the lytic cycle if there is unlimited host cell as it can produce the max number of new virus, the lysogenic cycle cannot tap the potential of uninfected cells o Virus would also choose lytic if the conditions within the infect bacteria is unfavourable o Virus only capable of replicating using lytic cycle is called a virulent phage (X temperate phage) Step 1: Adsorption Attachment sites on the phage adsorb with tail fibers to receptor sites on the host bacterium Most adsorb to the bacterium cell wall, although some are able to adsorb to the flagella or pili Specific strains of bacteriophages can only adsorb to specific bacteria strains (viral specificity) o Recognized by lock and key fit between viral proteins and bacteria receptors Step 2: Penetration In most cases, phage enzyme drills a hole in the bacterial wall and the phage injects its genome into the bacterial cytoplasm Some phages accomplish this by contracting a sheath which drives a hollow tube into the bacterium. This begins the eclipse period (the bacteria is already infected with virus, but no observable change) Only the phage genome enters the bacterium, the capsid remains on the outside Step 3: Replication nucleic acid and protein synthesis Phage genome encodes enzymes that shut down the bacteriums macromolecular synthesis Phage replicates its genome and use the bacteriums metabolic machinery to synthesize phage enzymes and phage structural components Step 4: Maturation Assembly of virions Phage enzymes assemble around the genomes Step 5: Release and reinfection Usually a phage coded lysozyme breaks down the peptidoglycan in the bacterial cell wall causing osmotic lysis and release of the intact bacteriophages The released bacterial phages are able to inject other bacteria o Whole process take about 30 minutes o On rare occasions, two virulent phage can infect a bacteria at the same time and provide opportunity for recombination! o Bacteria have defenses against the phages eg restriction enzymes tht recognize and cut up certain phage DNA

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T4 phages

Only capable of undergoing the lytic lifecycle Infects E coli Using its tail fibers, T4 phages can attach to the host cell. The tail fibers are hollow, allowing its nucleic acids to pass through into the cell it is infecting during attachment The bacteriophage T4 exists as an inactive virion until its tail fiber comes into contact with the surface of an E coli Sensors on the ends of tail fiber recognize binding sites on E Coli T4 binds to the surface of the host, punctures the cell with its injection tube then injects it own genetic material into the host Viral DNA arriving in the cell is linear but the free ends soon join up to make a circle This genetic information subverts the host cells normal operation and sets the cells biosynthetic machinery to work creating replicas of the virus The newly created viruses escape from the cell and float about until its comes into contact with a new host cell Describe bacteriophages that reproduce via a lysogenic cycle eg lambda o Temperate phages can undergo both lytic and lysogenic cycles o Lysogenic cycle can incorporate its DNA into the bacteriums DNA and become a noninfectious prophage Step 1: Adsorption The phage adsorb to the host bacterium/lysogen and inject its genome into the bacteria The linear phage DNA circularizes (similar to the lytic cycle) Step 2: Penetration Phage does not shut down the host cell Phage DNA inserts into the host bacteriums DNA and become prophage This can cause disease if the genome carried by the prophage in the bacteria codes for toxin proteins. So when the bacterial affects the human/animal host, disease c an result eg scarlet fever. Step 3: Replication with bacterial chromosome Expression of the phage genes is blocked by repressor Phage DNA replicates as part of the bacterium DNA so that every daughter cells now contains the prophage Step 4: Spontaneous Induction

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Phage genes are activated and phage DNA is excised New phages are produced by the lytic life cycle

Describe animal viruses o Animal viruses are viruses that infect animal cells and replicate by the productive life cycle o Animal viruses have varied effects on cells Lytic infection: results in the destruction of the host cell Persistent infection: in the case of enveloped viruses, release of virions through budding may be slow and the host cell may not lysed. The cell may remain alive abd continue to prouduce viruses over a long period of time Latent infection: delay between infection by the virus and the appearance of the symptoms. Latent infections reappear spasmodically. (this is different from the latent period in bacteriophage lysogenic cycle as the virus infection of an animal cell is generally not due to integration of the viral genome) Transformation into a tumor cell: viruses can transform the animal cell to make it a tumor cell (not the same as transformation in bacterial genetics) Cancer is a cellular phenomenon of uncontrolled growth Most cells in mature animal do not divide extensively due to presence of growth inhibiting factors but after undergoing transformation, growth becomes uncontrolled Caused by viruses such as retroviruses, papovavirus, adenovirus and herpes virus groups

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While some viruses do not directly cause cancer, they can lead indirectly to an increased risk of cancer by weakening the immune systems ability to detect and destroy transformed cells Describe the productive life cycle of animal viruses o Step 1: Adsorption Binding of attachment sites on the viral surface with receptor sites The virus can only infect a host cell is the host cell have receptors for the virus on its surface that is capable for supporting viral replication These receptors are normal surface molecules involved in routine cellular functions but because a portion of the molecule on the viral surface resembles the chemical configuration of the bodys cellular molecule, it can normally bind to the receptor thus allowing the virus to adsorb to the host cells surface o Step 2: Penetration Enveloped virus enter the host cell through these ways 1. The viral envelope may fuse with the host cell membrane, thus releasing the nucleocapsid into the cytoplasm 2. The whole virus is taken in by endocytosis whereby the host cell cytoplasmic membrane invaginates and pinches off, placing the virus in an endocytic vesicle o Step 3: Uncoating Uncoating is the release of the viral genome from the remainder of the virus done via 1. Fusing with the cytoplasmic membrane during penetration 2. Fusing with the membrane of the endocytic vesicle after endocytosis Viral capsid is then enzymatically removed and the viral genome is relased This occurs in the eclipse period where no intact virions can be detected within the cell o Step 4: Replication Viral genome directs the host cells metabolic machinery (ribosomes, tRNA, nutrients, energy, enzymes etc) to synthesize viral enzymes and viral parts Viral genome is transcribed into viral mRNA that goes to the host cells ribosome where it is translated into viral structural proteins and viral enzymes During early phase of replication, the viral genome is replicated thousands of times During late phase, the viral structural proteins and enzymes are produced. Viral proteins and glycoprotein that are synthesized at the rough ER, coded by the viral genome are incorporated into the host cells membranes During the uncoating and replication stages, the virus is not infectious o Step 5: Maturation Capsid is assembled around the genome o Step 6: Release The host may or may not be lysed Viruses obtain their membranes by budding But prior to budding, the viral proteins and glycoproteins are already incorporated under the replication stage During budding, the host cell membrane (may be the plasma membrane/ Golgi membrane/ nuclear membrane) envaginates and pinches off

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If the membrane is obtained from the Golgi or nucleus, the virus is released by exocytosis via transport vesicles some viruses, capable for cell fusion, may be transported from one cell to the adjacent cell by cell to cell contact o Step 7: Reinfection Describe the reproductive cycles of an enveloped virus eg influenza o Structure of influenza virus Usually spherical or ovoid Is enveloped that derives its lipid bilayer from the plasma membrane of the host cell On the surface of the membrane, there is two different varieties of glycoprotein spike are embedded in the envelope ~80% - hemagglutinin (protein that functions in the attachments of the virus to a host cell and entry of the viral genome into the target cell) ~20% - neurominidase (protein that helps in facilitating the release of newly produced virus particles by cleaving the sugars the bind to the mature viral particles) Within the envelope is the capsid In the capsid is the influenza genome that is organized into 8 pieces of single-stranded RNA (ssRNA) segmented genome each RNA fragment is associated with a protein (Nucleoprotein) and forms ribonucleoprotein RNP Because it Is a rare virus that has its genome in separate segments, influenza virus has a much higher potential for recombinants to form that contributes to the rapid development of new flu strains in nature. In the lab, such recombinant technique is used to develop vaccine strains o Life cycle of influenza virus Step 1: Adsorption Hemagglutinin (glycoprotein spike0 binds to the sialic acid (glycoprotein receptor) on the cell membrane Step 2: Penetration and Uncoating The cell surface invaginates and the virus particle is taken in by endocytosis Protein Clathrin forms a netlike structure beneath the docking virus. It acts as an external scaffold causing the cell membrane to invaginate and finally form the vesicle. Environment in the endosome is more acidic thus modifying the haemagglutinin spikes The altered spikes draws the membranes of the virus and the endosome together thus fusing them, creating a hole where the viral contents are released These include: M1 viral matrix protein and nucleocapsid Step 3: replication The virus dispatches its genetic material and internal proteins to the nucleus of the cell

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In the nucleus, the viral genome acts a template for the synthesis of complementary RNA strands o Serve as template for the synthesis of new viral genome RNA. The new viral genomic RNAs becomes associated with nucleoproteins o Serve as mRNA for the synthesis of new viral proteins At the same time, haemagglutinin and neuramindase are incorporated into the cell membrane Step 4: maturation Helical nucleocapsid formed Around the nucleocapsid, matrix proteins collect beneath the cell membrane Step 5: Release Virus particles begin to take shape and bud from the cell surface Cell membrane envelopes around the nucleocapsid and matrix protein becomes the viral envelope already incorporated with the H and n spikes The original sialic acid of the host cell membrane is removed by neuramindase to prevent clumping of virus particles Describe the reproductive cycles of retroviruses eg HIV o Retroviruses have ss RNA genome but are generally not considered RNA virus because they use DNA intermediates to replicate o Retroviruses are able to carry reverse transcription o HIV is a virus with viral latency (ability of the pathogenic virus to lie dormant within a cell) o viral latency is a result primarily from the lack of production of specific host cell proteins that are required for the activation of the viral genes o this may be caused by either viruses remaining latent within the cytoplasm of the cell or virus having inserted their DA into the host cells chromosomes forming a provirus o Depending on the extracellular stimuli, the virus may later choose to activate the viral genes leading to a burst of viral replication via the productive life cycle o HIV causes latency by forming provirus. It may choose to either directly proceed into the productive life cycle upon infection or remain latent in the host cells chromosomes o Structure of HIV virus 2 copies of single-stranded RNA which is enclosed by a conical capsid Within the capsid are two molecules of enzyme reverse transcriptase (which transcribe RNA to DNA) + integrase Outside the capsid in the matrix is protease Has an envelope with gp120 and gp41 (glycoprotein spikes) o Life cycle of HIV virus Step 1: Binding and fusion The virus binds to the outside of the T lymphocyte (wbc0 to be infected through the interaction between gp120 and gp41 on the CD4 receptor on the cells surface Virus enters the cell by fusing its membrane with the cells membrane, pushing its viral proteins into the cytoplasm (ie everything else other than the envelope) Step 2: uncoating and reverse transcription

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Once in the cell the viral core uncoats and releasing its genetic material and enzymes into the cytoplasm Reverse transcription transcribes the ss viral RNA genome into ss DNA and then the complementary DNA that makes the ssDNA into dsDNA, which is compatible with the cellular DNA Step 4: Integration of DNA DNA copy of the viral genome is transported to the nucleus DNA copy enters the cell and viral enzyme integrase integrates the DNA into the cells chromosomal DNA, forming a provirus The inserted viral DNA stay dormant until it is activated (unlike prophage, provirus remains permanently inside the host cell) For the formation of new HIV virus, occasionally the provirus is transcribed into viral RNA which function as both the viral genome and mRNA for viral proteins and new HIV virus can be formed. This integration can be a cause of cancer Step 4: Transcription When activated the virus uses host enzyme RNA polymerase to transcribe its viral genome back to RNA which functions as mRNA for the synthesis of proteins and genomes for the next viral generation Step 5: Translation, assembly and budding Viral mRNA undergoes translation The resulting viral protein chains are cut into small pieces by the viral enzyme protease Assembly also begins as the freshly cut proteins and viral RNA assemble into separate copies of the original viral core Step 6: budding The assembling viral cores migrate to the cell surface and begin to bud (sometimes the assembly of the viral cores may not be complete as they bud, but if not complete, they can just complete the assembly in the separate daughter virus) Each viral copy takes away with it a tiny section of the cells membrane to make up the envelope Explain how viral infection cause disease in animals eg mammals through the disruption of host tissue and functions (eg HIV and T helper cells, influenza and epithelial cells of the respiratory tract) o Viruses may damage or kill cells by the release of hydrolytic enzymes from lysosomes o Viruses may cause infected cells to produce toxins that lead to disease symptoms o Viruses may induce some changes in the host cells called cytopathic effects which refers to degenerative changes in cells resulting from the multiplication of certain viruses Eg altered shape, detachment from substrate, membrane fusion, altered membrane permeability o Most virus infection result in death of the host cell (by cell lysis, alterations to the cells surface membrane and apoptosis (programmed cell death). This lead to cessation of normal activities.

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Some viruses cause no apparent changes to the infected cell. Cells in which the virus is latent and inactive show few signs of infection and often function normally. This causes persistent infections and virus is often dormant for many months or years. How influenza cause disease Influenza virus have ability to evade the hosts immune system by changing its surface antigens heamagglutinin and neuramindase Epidemic (small scale): influenza virus can have antigenic drift which are mutations that cause a gradual change in the antigens. This gives rise to new strains of influenza virus every 1-2 years by point mutation Pandemic (worldwide): caused by antigenic shift where the influenza virus obtain a new genome segment from an influenza virus capable to infecting other animals such as ducks or swine through genetic reassortment. This cause major change in the H and N antigens Influenza virus cause cytopathic effects at te columnar epithelial cells in the respiratory duct Results in changes in host cells morphologies causing acute disease of lung and airways Can also lead to cell damage induced by inhibiting normal host cell protein synthesis and apoptosis (programmed cell death) Influenza virus can cause fever Infected spithelial cells of the respiratory tract activate the bodys immune system to develop fever Influenza virus can lead to increased risk of secondary infections Damage to columnar epithelial cells which disrupt epithelial cell barrier Decrease in clearance of mucus by ciliated cells How HIV causes AIDS Acquired Immune Deficiency Syndrome Infection with HIV results in progressive destruction of CD4 T lymphocytes As no. of T lym decrease, the bodys immune system becomes compromised The body is unable to produce humoral and cell-mediated immune responses Person becomes susceptible to infections and cancer that cause death The individual would experience opportunistic infections (infections that normally does not induce illness in people, but because of the compromised immune system at that point in time, they get ill) eg PCP, pneumocystis pneumonia (lung infection)

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