1. Viruses
AP Biology

2. Viruses Viruses are not cells.
They are infectious particles consisting of nucleic acid encased in a protein coat, and, in some cases, a membranous envelope.
Viruses range in size from only 20 nm in diameter to that barely resolvable with a light microscope

3. Viral Genomes
The genome of viruses includes other options than double-stranded (ds) DNA.
Viral genomes may consist of double-stranded DNA, single-stranded DNA, double-stranded RNA, or single-stranded RNA, depending on the specific type of virus.
The viral genome is usually organized as a single linear or circular molecule of nucleic acid.
The smallest viruses have only four genes, while the largest have several hundred.

4. Viral Structure
The capsid is a protein shell enclosing the viral genome.
Capsids are made of a large number of protein subunits called capsomeres, but with limited diversity.
The capsid of the tobacco mosaic virus has over 1,000 copies of the same protein.
Adenoviruses have 252 identical proteins arranged into a polyhedral capsid

5. Some viruses have viral envelopes- membranes cloaking their capsids.
These envelopes are derived from the membrane of the host cell.
envelopes also have some viral proteins and glycoproteins.

6. Virus Reproduction Viruses are obligate intracellular parasites.
They can reproduce only within a host cell.
An isolated virus is unable to reproduce - or do anything else, except infect an appropriate host.
Viruses lack the enzymes for metabolism or ribosomes for protein synthesis.

7. Most viruses of eukaryotes attack specific tissues.
Each type of virus can infect and parasitize only a limited range of host cells, called its host range.
Viruses identify host cells by a “lock-and-key” fit between proteins on the outside of virus and specific receptor molecules on the host’s surface.
Some viruses (like the rabies virus) have a broad enough host range to infect several species, while others infect only a single species.
Most viruses of eukaryotes attack specific tissues.
Human cold viruses infect only the cells lining the upper respiratory tract.
The HIV virus binds only to certain white blood cells.

8. Viral infections
A viral infection begins when the genome of the virus enters the host cell.
Once inside, the viral genome takes over its host, reprogramming the cell to copy viral nucleic acid and manufacture proteins from the viral genome.
The nucleic acid molecules and capsomeres then self-assemble into viral particles and exit the cell.

9. Lytic vs. Lysogenic Cycles in Bacteriophages (phages)
In the lytic cycle, the viral reproductive cycle culminates in the death of the host.
In the last stage, the bacterium or host cell lyses (breaks open) and releases the viruses produced within the cell to infect others.
Virulent phages reproduce only by a lytic cycle.
Phage T4 is a virulent phage

11. Defense against phages in bacteria
While phages have the potential to wipe out a bacterial colony in just hours, bacteria have defenses against phages.
Natural selection favors bacterial mutants with receptor sites that are no longer recognized by a particular type of phage.
Bacteria produce restriction enzymes that recognize and cut up foreign DNA, including certain phage DNA.
Modifications to the bacteria’s own DNA prevent its destruction by restriction enzymes (sequences that restriction enzymes recognize are methylated)

12. The Lysogenic cycle
In the lysogenic cycle, the phage genome replicates without destroying the host cell.
Temperate phages, like phage (lambda) , use both lytic and lysogenic cycles.
Within the host, the virus’ circular DNA engages in either the lytic or lysogenic cycle.
During a lysogenic cycle, the phage genome is replicated without destroying the host cells
During a lytic cycle, the viral genes immediately turn the host cell into a virus-producing factory, and the cell soon lyses and releases its viral products.

13. During the lysogenic cycle, viral DNA is incorporated by genetic recombination into a specific site on the host cell’s chromosome.
In this prophage stage, one of its genes codes for a protein that represses most other prophage genes (the prophage remains silent during this stage).
Other genes that change the phenotype of the bacteria may also be present – expression of a lysogenic prophage is what causes the toxic E. coli to cause infection (unlike the beneficial E. coli in our intestines)
Every time the host divides, it also copies the viral DNA and passes the copies to daughter cells.
Occasionally, the viral genome exits the bacterial chromosome and initiates a lytic cycle.
This switch from lysogenic to lytic may be initiated by an environmental trigger.

15. Viruses in animal cells
Many variations on the basic scheme of viral infection and reproduction are represented among animal viruses.
One key variable is the type of nucleic acid that serves as a virus’ genetic material.
Another variable is the presence or absence of a membranous envelope.

16. Viruses equipped with an outer envelope use the envelope to enter the host cell.
Glycoproteins on the envelope bind to specific receptors on the host’s membrane.
The envelope fuses with the host’s membrane, transporting the capsid and viral genome inside.
The viral genome duplicates and directs the host’s protein synthesis machinery to synthesize capsomeres with free ribosomes and glycoproteins with bound ribosomes.
After the capsid and viral genome self-assemble, they bud from the host cell covered with an envelope derived from the host’s plasma membrane, including viral glycoproteins.

17. These enveloped viruses do not necessarily kill the host cell
Enveloped animal viruses include :
Herpes, smallpox, SARS. Yellow fever, hepatitis C, Ebola, influenza, rabies, HIV

18. Herpes Virus
Herpes viruses have envelopes that are not derived from plasma membrane.
The envelope of the herpes virus is initially derived from the nuclear envelope of the host and once it enters the cytoplasm it cloaks itself in an envelope derived from the Golgi.
These double-stranded DNA viruses reproduce within the cell nucleus using viral and cellular enzymes to replicate and transcribe their DNA.
Herpesvirus DNA may become integrated into the cell’s genome as a provirus.
The provirus remains latent within the nucleus of nerve cells until triggered by physical or emotional stress to leave the genome and initiate active viral production.

19. RNA viruses
The viruses that use RNA as the genetic material are quite diverse, especially those that infect animals.
In some with single-stranded RNA (class IV), the genome acts as mRNA and is translated directly.
In others (class V), the RNA genome serves as a template for mRNA and for a complementary RNA.
RNA animal viruses include :
Influenza, HIV

20. Mutation of existing viruses is a major source of new viral diseases.
RNA viruses tend to have high mutation rates because replication of their nucleic acid lacks proofreading.
Some mutations create new viral strains with sufficient genetic differences from earlier strains that they can infect individuals who had acquired immunity to these earlier strains.
This is the case in flu epidemics.

21. Retroviruses Retroviruses have the most complicated life cycles.
These RNA viruses carry an enzyme, reverse transcriptase, which transcribes DNA from an RNA template.
The newly made DNA is inserted as a provirus into a chromosome in the animal cell. (unlike a prophage, the provirus becomes a permanent addition to the cell’s DNA)
The host’s RNA polymerase transcribes the viral DNA into more RNA molecules.
These can function both as mRNA for the synthesis of viral proteins and as genomes for new virus particles released from the cell.

22. One particularly famous retrovirus
Human immunodeficiency virus (HIV), the virus that causes AIDS (acquired immunodeficiency syndrome) is a retrovirus.
The viral particle includes an envelope with glyco- proteins for binding to specific types of white blood cells, a capsid containing two identical RNA strands as its genome and two copies of reverse transcriptase.

23. The reproductive cycle of HIV illustrates the pattern of infection and replication in a retrovirus.
After HIV enters the host cell, reverse transcriptase synthesizes double stranded DNA from the viral RNA.
Transcription produces more copies of the viral RNA that are translated into viral proteins, which self-assemble into a virus particle and leave the host.

24. Why viruses make us sick…
The link between viral infection and the symptoms it produces is often obscure.
Some viruses damage or kill cells by triggering the release of hydrolytic enzymes from lysosomes.
Some viruses cause the infected cell to produce toxins that lead to disease symptoms.
Other have molecular components, such as envelope proteins, that are toxic.
In some cases, viral damage is easily repaired (respiratory epithelium after a cold), but in others, infection causes permanent damage (nerve cells after polio).

25. Or simply…
Many of the temporary symptoms associated with a viral infection results from the body’s own efforts at defending itself against infection.
The immune system is a complex and critical part of the body’s natural defense mechanism against viral and other infections.
Modern medicine has developed vaccines, harmless variants or derivatives of pathogenic microbes, that stimulate the immune system to mount defenses against the actual pathogen.

26. Viroids
Viroids, smaller and simpler than even viruses, consist of tiny molecules of naked circular RNA that infect plants.
Their several hundred nucleotides do not encode for proteins but can be replicated by the host’s cellular enzymes.
These RNA molecules can disrupt plant metabolism and stunt plant growth, perhaps by causing errors in the regulatory systems that control plant growth.

27. Prions Prions are infectious proteins that spread a disease.
They appear to cause several degenerative brain diseases including “mad cow disease”
According to the leading hypothesis, a prion is a misfolded form of a normal brain protein.
It can then convert a normal protein into the prion version, creating a chain reaction that increases their numbers.