VIRUSES There are three main properties distinguishing viruses from other micro organisms: • Small size: viruses

are smaller than other organisms, although they vary considerably in size, from 10nm to 300nm (we do not need to know exact values) In contrast, Erythrocytes (that’s red blood cells) are 7500nm in diameter and Bacteria are 1000nm in diameter. • Genome: the genome of viruses may be either DNA or RNA; viruses only contain only one kind of genome (while humans have both DNA and RNA). • Metabolically inert: viruses have no metabolic activity; they do not possess active ribosomes or protein-synthesizing apparatus, although some contain enzymes within them (HIV contains 3 enzymes in its envelope) Viruses can multiply only inside living cells. Inside these susceptible cells, the virus redirects the cell’s synthesizing machinery to the manufacture of new virus components (it basically uses the cells contents to make more viruses). It does this by transcription of the virus genome or nucleic acid into virus specific messenger RNA (mRNA). This viral mRNA (vmRNA) then directs the cell to the replication of new virus particles, which then form the new viruses. VIRUS STRUCTURE Viruses consist basically of a core of nucleic acid – the genome – surrounded by a protein coat. The protein coat protects the genome from inactivation by adverse environmental factors (like an extreme of pH or temperature) The protein coat is antigenic and responsible for stimulating the production of protective antibodies. The structures that make up a virus particle are: • Virion: the intact virus particle • Capsid: the protein coat • Capsomeres: the protein structural units of which the capsid is composed • Nucleic Acid Genome: either DNA or RNA. • Envelope: the particles of many viruses are surrounded by a lipoprotein envelope containing viral antigens, but also partly derived from outer membrane or nuclear membrane of the host cell. VIRUS CLASSIFICATION (Page 1 of lecture notes) Viruses are categorized using the difference in host, genome, envelope and arrangement. All viruses contain a viral genome enclosed in a Capsid protein. • Viruses’ hosts differ between plants, bacteria and animals. • Their genome differ too:  Negative single strand RNA, which is a complementary strand that acts as a template for viral mRNA for replication.  Positive single strand RNA acts directly as mRNA in host cells, and directly codes for proteins.  Retrovirus acts as a template for DNA.

Viruses can be categorized by whether they have a lipid envelope or not. Viruses, such as Herpes, have a lipid envelope taken from the host after a virus leaves the cell. • A viruses arrangement also categorizes a virus:  The most basic being the icosahedral form, in which the virus is a 3D polyhedron made of 20 triangular faces.  The helical arrangement involves the virus’ genome being helically shaped and covered in a cylindrical protein coat.  The complex arrangement of viruses is the icosahedral arrangement as a head with protein legs branching from it, allowing attachment to the host membrane. When looked through an electron microscope, a virus’s genome will appear black while its protein fold appears white around it. THE EFFECT OF TEMPERATURE AND PH ON VIRUSES. All Viruses are coated by a protein coat; and it is this protein coat that is most important in determining the shape of the virus. Any condition that affects proteins will therefore have a direct effect on viruses. An extreme change in pH ionises the side chains of monomers in the polypeptide chain and therefore will change the structure of these monomers. This change in structure will have an overall effect on the shape of the virus. At extreme temperatures, the viruses will also be inactive. GENOMICS OF VIRUSES (Page 9 of Lecture notes) Viruses, such as Hepatitis B, have a genome unlike humans as they can their genome code for many different proteins. It can do this by using same information from DNA, but reading it differently. This is illustrated on page 9 of the lecture notes The virus uses this ability, to read DNA this way, during replication. During replication, the DNA goes through transcription to make early mRNA, which makes early proteins. These proteins are enzymes that are needed to make even more mRNA. So this mechanism is used by the virus to make its own enzymes, which are needed for replication to occur, using the same strand of DNA. VIRAL ENTRY INTO THE CELL (Page 5 of Lecture Notes) There are many ways in which a virus can enter a cell: • An un-enveloped virus may simply travel through the lipid bi-layer into the cytoplasm. • An unenveloped virus may use its protein sub-units to act as receptors, which then bind to the plasma membrane receptors. Once attached, the cell membrane will surround the virus, forming an endosome, which then is released into the cytoplasm. • An enveloped virus’ receptors attach onto the plasma membrane receptors and once attached, the virus’s lipid envelope will integrate itself with the plasma membrane, releasing the nucleocapsid into the cytoplasm. • An enveloped virus’ receptors attach onto the plasma membrane receptors and once attached, the plasma membrane will surround the virus’ lipid envelope,

forming an endosome, which is then released into the cytoplasm. This endosome has therefore got a nucleocapsid surrounded by two lipid envelopes. VIRAL EXIT/RELEASE FROM THE CELL There are two ways in which a virus can exit a cell: • Lysis: In which the virus exits the cell membrane, and acquire part the host’s cell membrane to form its own lipid envelope. Lysis eventually results in the death of the cell. • Budding: In which viruses acquire their external envelope as a fragment of the host cell membrane using essential proteins, usually the hosts proteins. This method helps the virus leave the cell without lysing the cell, allowing the cell to produce more viruses. LIFE CYCLE OF A DOUBLE STRANDED DNA VIRUS (Page 10) Hepatitis B is a form of double stranded DNA viruses. The diagram below shows the life cycle of the virus with these 6 steps: 1.) The virus enters the cytoplasm of the virus with its lipid envelope binding to the cell membrane through fusion and releasing the virus capsid into the cytoplasm. 2.) The virus travels to the nucleur membrane via a microtubule, and enters into the nucleus through a nucleur pore. 3.) The DNA strand of the Virus Genome goes through transcription to form EARLY mRNA. The mRNA is transported out of the nucleus to the cytoplasm where it goes through translation on ribosomes to form EARLY PROTEINS. These early proteins are enzymes, and are transported into the nucleus to the viral DNA. 4.) The early proteins are used as the viral DNA goes through transcription again to form LATE mRNA. This mRNA has two purposes: • The mRNA is used in REPLICATION to make more viral DNA. • The mRNA is transported into the cytoplasm from the nucleus and undergoes translation to form LATE PROTEINS. 5.) All the materials have been made, and assembly of new viruses occurs. Part of the late proteins are capsid proteins, which surround the newly made DNA to form a new nucleocapsid. The other part are envelope proteins that form on the nucleur membrane. 6.) As the nucleocapsid is complete, it exits the nucleur membrane, taken some membrane with it, which has the envelope proteins. Now the nucleocapsid has a lipid envelope around it, forming a new Hepatitis B virus. This exits out of the cell through a channel.

LIFE CYCLE OF A NEGATIVE SINGLE STRANDED mRNA VIRUS (Pg 12) Rabies and Influenza A are forms of negative single stranded mRNA viruses. The diagram below shows the life cycle of the virus with these 7 steps: 1.) The virus bonds to the cell surface membrane at specific receptors, and is taken up into a membrane-enclosed endosome. This process is known as endocytosis. 2.) Uncoating in the endosome takes place and the viral (-) RNA is released into the cytoplasm and transported into the nucleus. In the nucleus, the viral (-) RNA is used in 3 ways: 3.) The (-) RNA is replicated to produce even more copies of (-) RNA. 4.) The (-) RNA goes through transcription to make (+) RNA, which is mRNA. The mRNA travels out of the nucleus to the cytoplasm and undergoes translation to make viral proteins. These viral proteins enter into the nucleus and wrap around the new copies of (-) RNA and form new nucleocapsids.

5.) The (-) RNA goes through transcription to make (+) RNA, which is mRNA. The mRNA travels out of the nucleus to the cytoplasm and undergoes translation to make viral proteins. These viral proteins travel to the endoplasmic reticulum and further to the golgi body, forming specialised glycoprotein receptors. These receptors assemble themselves on the cell membrane. 6.) The nucleocapsid (on the diagram as the Ribonucleoprotein core) exits the nucleus through pores. 7.) The nucleocapsid recognizes the points where there are viral proteins on the cell membrane and buds off at these points, taking memr ane with it. This forms the lipid envelope and completes replication. LIFE CYCLE OF A RETROVIRUS (Page 13) HIV-1 is a form of Retrovirus. The diagram below shows the life cycle of the virus with these 7 steps: 1.) The virus attaches to the cell membrane at protein receptors and binds to the membrane through fusion. The contents of the virus are released into the cytoplasm with the viral lipid membrane being integrated into the cell surface membrane. 2.) One of the enzymes brought in by the virus, Reverse Transcriptase, uses the RNA strand and creates a complementary DNA strand. This forms a RNADNA double strand. 3.) The RNA strand is removed and only the DNA strand is left. This is then used to make a complementary DNA strand, eventually resulting in a double stranded DNA version of the viral genome. 4.) This DNA is transported via Microtubules to the nucleus and moves into the nucleus. In the nucleus, an enzyme from the virus, INTEGRase, INTEGRATES the virus DNA into the hosts DNA. This forms a ProVirus. 5.) The Provirus undergoes transcription by the host’s enzymes, distinguishing it as if it was its own DNA. This forms Viral mRNA. 6.) The Viral mRNA exits the nucleus and undergoes translation on the ribosomes, creating viral proteins. Some of the viral proteins produced go through the endoplasmic reticulum and golgi body to 7.) Some of the viral proteins produced assemble around the RNA, forming a nucleocapsid. 8.) The nucleocapsid buds out of the cell, taking membrane with the membrane proteins, forming the lipid envelope. As the host cell forms more and more viruses, the cell eventually dies as its resources and membrane are exhausted.

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