General Biology/Classification of Living Things/Viruses
Viruses are the smallest biological particle (the tiniest are only 20 nm in diameter). However, they are not biological organisms so they are not classified in any kingdom of living things. They do not have any organelles and cannot respire or perform metabolic functions. Viruses are merely strands of DNA or RNA surrounded by a protective protein coat called a capsid. Viruses only come to life when they have invaded a cell. Outside of a host cell, viruses are completely inert.
Since first being identified in 1935, viruses have been classified into more than 160 major groups. Viruses are classified based on their shape, replication properties, and the diseases that they cause. Furthermore, the shape of a virus is determined by the type and arrangement of proteins in its capsid. Viruses pathogenic to humans are currently classified into 21 groups.
Viruses can also attack bacteria and infect bacterial cells. Such viruses are called bacteriophages.
Viral Replication 
As previously stated, viruses are not a biological life form so they cannot reproduce by themselves. They need to take over a functioning eukaryotic or prokaryotic cell to replicate its DNA or RNA and to make protein coat for new virus particles.
In order to enter a cell, a virus must attach to a specific receptor site on the plasma membrane of the host cell. The proteins on the surface of the virus act as keys which fit exactly into a matching glycoprotein on the host cell membrane. In some viruses, the attachment protein is not on the surface of the virus but is in the capsid or in the envelope.
There are two forms of viral replication: the lytic cycle and the lysogenic cycle.
Lytic Cycle 
- Attachment: The virus binds to specific receptors on the host cell.
- Entry: There are two ways in which a virus can enter cells. Firstly, the virus can inject its nucleic acid into the host cell. Secondly, if a virus is contained in an envelope, the host cell can phagocytosise the entire virus particle into a vacuole. When the virus breaks out of the vacuole, it then releases its nucleic acid into the cell.
- Replication: The virus's nucleic acid instructs the host cell to replicate the virus's DNA or RNA.
- Assembly: New virus particles are assembled.
- Lysis and Release: The virus directs the production of an enzyme which damages the host cell wall, causing the host cell to swell and burst. The newly formed virus particles are now released.
Lysogenic Cycle 
- Attachment: Similar to Lytic Cycle
- Entry: Similar to Lytic Cycle
- Incorporation: The viral nucleic acids is not replicated, but instead integrated by genetic combination (crossing over) into the host cell's chromosome. When integrated in a host cell this way, the viral nucleic acid as part of the host cell's chromosome is known as a prophage.
- Host Cell Reproduction: The host cell reproduces normally. Subsequent cell divisions, daughter cells, contain original father cell's chromosome embedded with a prophage.
- Cycle Induction: Certain factors now determine whether the daughter cell undergoes the lytic or lysogenic cycle. At any time, a cell undergoing the lysogenic cycle can switch to the lytic cycle.
The reproduction cycle of viruses with RNA and no DNA is slightly different. A notable example of a RNA-based virus is HIV, a retrovirus.
Retrovirus reproductive cycle 
- The retrovirus force RNA into cell, by either one of the two methods of entry (See above).
- In the retrovirus are reverse transcriptase enzymes, which catalyses the synthesis of a DNA strand complementary to the viral RNA.
- Reverse transcriptase catalyses a second DNA strand complementary to the first. With these two strands, the double-stranded DNA can be created.
- DNA is then incorporated into the host cell's chromosomes. Similar to the concept of a prophage, this incorporated DNA is called a provirus. However, the provirus never leaves the host cell, unlike a prophage.
- The infected host cell undergoes the lytic or lysogenic cycle.
Viral Genome 
The genome of a virus consists of DNA or RNA, whose size and configuration vary. The entire genome can exist as a single nucleic acid molecule or several nucleic acid segments. Also, the DNA or RNA may be single-stranded or double-stranded, and either linear or circular.
Not all viruses can reproduce in a host cell by themselves. Since viruses are so small, the size of their genome is limiting. For example, some viruses have coded instructions for only making a few different proteins for the viruses' capsid. On the other hand, the human genome codes for over 30,000 different proteins. Therefore, the lack of coded instructions cause some viruses to need the presence of other viruses to help them reproduce themselves. Such viruses are called replication defective.
Lastly, it is worthy to note that 70% of all viruses are RNA viruses. As the process of RNA replication (with enzymes and other organelles of the host cell) is more prone to errors, RNA viruses have much higher mutation rates than do DNA viruses.
Viruses Practice Questions 
- As the name implies, the Tomato Spotted Wilt Virus targets tomatoes. Would it be possible for this virus to target other fruits as well? Explain.
- If a DNA and a RNA virus both infected somatic cells, which virus would be more difficult to detect?
- Many people have had cold sores, which are caused by infection with the herpes simplex virus. One characteristic of cold sores is that after a period of inactivity, they will reappear many times during the course of a person's life. Which cycle would the herpes simplex virus undergo?
- Chicken pox is a common, non-fatal disease usually acquired in adolescence and caused by the varicella zoster virus. In adulthood, many people suffer from shingles, an altered form of the varicella zoster virus. Which cycle would the varicella zoster virus have undergone?
- Would an antibiotic work for a person suffering from a cold of flu? Explain.