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Topic: Viruses Learners Outcome

a) Discuss whether viruses are living or non-living and explain why they are obligate parasites b) Describe the structural components of viruses c) Describe the reproductive cycles of the following virus types i. Bacteriophages that reproduce via a lytic cycle e.g. T4 phage ii. Bacteriophages that reproduce via lysogenic cycle e.g. lambda phage iii. Enveloped virus e.g. influenza iv. Retroviruses e.g. HIV d) Explain how viral infections cause disease in animals

Virus obligate parasite


Unable to replicate on its own; require a living host or a cell to support their metabolism and replication Able to enter a cell and take over, directing cell to make more virus particles In isolation, viruses have a common hereditary material (DNA/RNA) characteristic of living organisms.

Virus Structure (intact infectious viral particle is called a viron)

Naked viruses just nucleocapsid Enveloped viruses nucleocapsids covered by an envelope Nucleocapsid what an infectious virus particle will contain at minimum Genome Structur e - Single or multiple/segmented - Circular or linear - Either DNA or RNA (but not both) - Single-stranded or doublestranded Capsid - Protein coat that surrounds the genome - Structure determined by viral nucleic acid - Accounts for most of the mass of a virus, especially small viruses - Composed of protein subunits called capsomeres Protect and introduce the genome into host cells

Present in most animal viruses Envelope - An additional outer layer that surrounds the nucleocapsid - Composed of phospholipids and glycoproteins that are arrange to form lipid bilayer.

Function

Codes for synthesis of viral components and viral enzymes for replication and assembly Genes are few in number ranging from 3-100 depending on species. No. of genes degree of complexity displayed by virus

Others

- For most viruses, lipid bilayer derived from host cell membranes by budding (host cells nuclear, vacuolar or plasma membranes) - Although of host cell origin, virus incorporates proteins of its own appear as glycoprotein spikes

* 4 main morphological virus types helical, icosahedral, enveloped, complex (classified based on capsid structure; type of nucleic acid; absence/presence of viral envelope

Viral Replication
Begins with the virus invading the host cell and taking over hosts metabolic machinery. Nucleic acid in a virion contains only a few genes which code for the viral structural components (capsid proteins, viral enzymes involved in viral life cycle) Viral enzymes involved in replication and processing of viral genome. Enzymes involved in protein, ribosome or tRNA synthesis and energy production are supplied by host cell and used for synthesizing viral proteins. A single virion can give rise to many smilar viruses in a single host cell.

(T4) Bacteriophages
Viruses that infect only bacteria Two types: lytic (lytic life cycle), temperate (lysogenic life cycle)

A) Attachment

Attachment sites on tail fibres recognize and attach/adsorb to complementary receptor sites on bacterial surface weak chemical interaction: weak bonds are formed between the attachment and receptor sites Viral specificity: Specific strains of bacteriophages can only adsorb to specific strains of host bacteria Most bacteriophages attach to bacterial cell wall, some can attach to flagella or pili

B) Penetration

Bacteriophage tail releases an enzyme, phage lysozyme, which digest the adjacent bacterial cell wall, allowing molecules to be released through the hole in cell wall. Molecules reach the virus trigger a change in the shape of the base plate initiates a springlike contraction of the bacteriophage tail sheath, thrusting the hollow core tube through the cell wall Tip of core reaches the plasma membrane, DNA from the bacteriophages head passes through the tail core, through the plasma membrane and enters bacterial cell Empty capsid remains outside the cell Genome of phages which attach to the flagella or pili of bacterial cell will enter through these hollow organelles

C) Replication

Free viral nucleic acid is used immediately to synthesize mRNA using host RNA polymerase High virulent phages produce early proteins that completely take control from host cell (host cell DNA degraded into nucleotides within minutes. Nucleotides reused later to synthesize viral DNA. Viral DNA escapes degradation because of methylation of its DNA Enzymes coded by phage genome takes over bacteriums macromolecular synthesizing machinery for its own use Phage uses the host cells nucleotides and several of its own enzymes to synthesize many copies of phage DNA.

Biosynthesis of viral proteins begin phage uses bacteriums metabolic machinery to synthesize phage enzymes and phage structural components *Eclipse period: several minutes following infection, complete and infective virions, but separate components, cannot be found in host cell. D) Maturation Bacteriophage DNA and capsid are assembled to form a DNA-filled head. Tail fibres join with tail, then DNA-filled head attaches to tail E) Release

Lysozyme, which is coded for by a phage gene, is synthesized within cell causes bacterial cell wall to break down Cell membrane of host cell breaks open (lyses) and newly produced bacteriophages are released from host cell to infect other susceptible cells in the vicinity and the viral reproduction cycle is repeated within those cells. Lambda Bacteriophage (only has one short tail fibre) A) Attachment

Attachment site on tail fibre recognize and attach/adsorb to complementary receptor sites on bacterial surface weak chemical interaction: weak bonds are formed between the attachment and receptor sites Viral specificity: Specific strains of bacteriophages can only adsorb to specific strains of host bacteria Most bacteriophages attach to bacterial cell wall, some can attach to flagella or pili

B) Penetration

Bacteriophage tail releases an enzyme, phage lysozyme, which digest the adjacent bacterial cell wall, allowing molecules to be released through the hole in cell wall. Molecules reach the virus trigger a change in the shape of the base plate initiates a springlike contraction of the bacteriophage tail sheath, thrusting the hollow core tube through the cell wall Tip of core reaches the plasma membrane, DNA from the bacteriophages head passes through the tail core, through the plasma membrane and enters bacterial cell Empty capsid remains outside the cell Genome of phages which attach to the flagella or pili of bacterial cell will enter through these hollow organelles

C) Replication Original linear phage DNA forms a circle

Circular DNA can multiply and be transcribed production of new phage and to cell lysis (via lytic cycle) OR, circular DNA can integrate into and become part of circular bacterial DNA non-infectious prophage (lysogenic cycle) Most of prophage genes are repressed by repressor proteins that are products of phage genes stop transcription of all other phage genes that would direct synthesis and release of new virions. Every time host cells machinery replicates bacterial chromosome, it replicates the prophage DNA prophage found in all progeny cells, where it remains latent

D) Spontaneous induction One of every million-billion bacteria containing a prophage

Induction occurs spontaneously but frequency is enhanced by irradiation with UV light or exposure to agents that damage DNA destroys repressor protein by increased protease activity. Prophage is no longer repressed but is excised and its genome replicated.

E) Maturation Phage components are produced using host bacteriums metabolic machinery Bacteriophage DNA and capsid are assembled to form a DNA-filled head. Tail fibre join with tail, then DNA-filled head attaches to tail F) Release

Lysozyme, which is coded for by a phage gene, is synthesized within cell causes bacterial cell wall to break down Cell membrane of host cell breaks open (lyses) and newly produced bacteriophages are released from host cell to infect other susceptible cells in the vicinity and the viral reproduction cycle is repeated within those cells.

*Lysogenic cells - Immune to reinfection by same bacteriophage - May exhibit phage conversion new properties following integration of prophage into host genome - Capable of specialized transduction

Influenza

Size/ Shape 80 to 120nm diameter Spherical / Ovoid

Genome - 8 segments of single stranded (-) RNA (viral genome is complementary to viral mRNA) - RNA is packaged with protein into a helical nucleoprotein form, with three polymerase peptides (form an enzyme complex which functions in rep and trascrp of viral genome) for each RNA segment.

Capsid Antigenic protein lining on inner side of envelope

Envelope - Derives lipid bilayer from plasma membrane of host cell - Two kinds of glycoprotein spikes: haemagglutinin and neuraminidase, embedded in envelope. - Different types of H and N give rise to different strains of influenza virus

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A) Attachment

Protruding glycoproteins bind to specific receptor molecules on surface of host cell. (Haemmagglutinin sialic acid in humans)

B) Penetration and Uncoating

Enters by endocytosis. The host plasma membrane invaginates and pinches off, placing virus in an endocytic vesicle. Vesicle will fuse with lysosome causing its pH to drop. Within the vesicle, low pH environment stimulates viral envelope to fuse with lipid bilayer of vesicle membrane nucleopcasid released into cytoplasm. Capsid is degraded by cellular enzymes nucleoprotein (protein and nucleic acid complex) enters nucleus of cell

C) Replication

Viral genome used as template to synthesis mRNA strands in turn acts as template for synthesis of new viral RNA genome

mRNA strands exit nucleus to cytosol and RER where they are translated into viral structural components capsid proteins in cytosol, glycoproteins for viral envelope at ER

D) Maturation Vesicles from ER transport viral glycoproteins to be incorporated into plasma membrane Capsid proteins then associate with glycoproteins at plasma membrane

Viral genome associates with proteins to form nucleoprotein interacts with capsid proteins at plasma membrane of host cell initiates budding process

E) Release Each new virus buds from cell (evagination) Acquires host membrane with viral glycoproteins embedded With enveloped virsus, host cells may or may not be lysed Facilitated by neuraminidase

Human Immunodeficiency Virus (retrovirus)


Size/ Shape 120nm in diameter Spherica l Genome - 2 copies of single-stranded (+) RNA (viral genome has same sequence as viral mRNA) - RNA is enclosed by proteins known as nucleocapsid proteins Capsid - Usually conical-shaped - Made of another type of proteins different from nucleocapsid proteins - Within: 2 molecules of reverse transcrp enzyme, integrase and protease Envelope - Derives envelope lipid bilayer from host-cell plasma membrane - Glycoproteins protrude through envelope - gp120, gp41 have a specific conformation that allows virus to attach itself to certain receptors (CD4) on T4 helper cells

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Virus Core

A) Attachment Virus particle bumps into a cell that carries on its surface a CD4 protein. Glycoprotein gp120 on virus particle surface interacts with CD4 with the help of a co-receptor. B) Penetration and Uncoating With the help of gp41, viral envelope will fuse with host cell membrane and capsid is released into the

cell, leaving the envelope behind. Capsid is then degraded, releasing enzymes and RNA into cytoplasm.

C) Replication Reverse transcriptase enzyme will catalyze conversion of viral RNA into DNA. First catalyze synthesis of DNA strand complementary to viral RNA strand to form RNA-DNA hybrid RNA strand is then degraded Second DNA strand complementary to first is synthesized to form a double stranded DNA molecule

Viral DNA enters host cell nuclues where it is integrated into genetic material of host, catalyzed by enzyme integrase integrated viral DNA may persist in latent state for many years Activation of host cell will result in transcription of viral DNA into mRNA mRNA translated into viral polyproteins (3 polyproteins are coded from HIV genome) Viral polyproteins are cleaved into smaller function proteins by enzyme protease Envelope glycoproteins gp120 and gp41 are made in ER and vesicles will transport them to the plasma membrane Viral RNA forms genetic material for next generation of viruses

D) Maturation Vesicles from ER transport viral glycoproteins to be incorporated into plasma membrane Capsid proteins then associate with glycoproteins at plasma membrane E) Release

Following assembly, virus buds off from cell and is released to infect another cell.

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