Click here for the Virus Student Learning Guide

1. Introduction

Viruses are infectious particles that stand on the border between life and non-life. They’re much smaller and simpler than cells. But, like any living being, they have genes, and that gives them one of the key properties of life: genetic instructions for self-replication. At the same time, viruses lack many of life’s other key properties: they’re not made of cells, and they lack any independent metabolism. Viruses are best described as obligate intracellular parasites, a phrase worth taking apart:

• Parasites are organisms that interact closely with a larger host organism, causing their host harm. While viruses don’t qualify as organisms (an organism is an independent living thing), they certainly prey on a larger host, causing it harm. That host, in some cases, is us. Every time you’ve had a cold, the flu, or another viral infection, you’ve been parasitized by a virus. The COVID-19 pandemic (as we discuss in the next tutorial) was caused by a virus.
• Obligate means “by necessity.” Viruses can’t live on their own. The only way they reproduce themselves is by parasitizing a living cell.
• Intracellular means “within cells.” Viruses are the smallest parasites imaginable, preying upon life at its most basic level: the cell.

While COVID-19 has alerted most people to the importance of viruses, most people aren’t aware of how ubiquitous viruses are. It’s thought that each of Earth’s 9 million or so species is preyed upon by one or more viruses ^{National Library of Medicine}. Humans alone might host over 1000 viruses (over 200 have been identified so far). A study at UC Santa Barbara estimated that every liter of seawater might have ten million bacteriophages  (viruses that attack bacteria). National Geographic has reported that there might be 10³¹ viruses on planet Earth: many more than stars in the universe.

So let’s see how these obligate intracellular parasites work. If it suits your learning style, you can start by viewing my music video, I’m a Virus! Otherwise, just continue with the tutorial below.

2. Viruses: Size

One of the first things to know about viruses is how small they are. The image to the left shows a type of virus called a bacteriophage (or just phage) attached to a bacterial cell.  On the right, you can see a comparison between a single bacteriophage and a bacterial cell. Note that the numbers are right, but that visually, the virus should be even smaller. Just to connect the smallness of viruses with what you might already know, think of it this way. A DNA molecule is about 2 nanometers wide. A virus is only about 15 times bigger than that. When we talk about viruses, we’re practically at a molecular scale

3. Viruses: Structure

Viruses are also much simpler than cells. To the left, you can see an artist’s depiction of the bacterial viruses that are shown above. These bacterial viruses consist of two main parts: a genetic core (1), consisting of DNA or RNA; and a protein coat (2), also known as a capsid. The capsid, in turn, is made of self-assembling units called capsomeres.

On the right, you can see another type of virus, with the same numbering scheme used to indicate the genetic core (1) and the capsid/protein coat (2). An individual capsomere subunit is at “3.” Note that if the capsomere/capsid relationship is making you think about the tertiary and quaternary levels of structure in proteins, you’ve learned a lot about biology. Good job!

In addition to the capsid, there can also be other protein parts.  I’ve always thought that bacteriophages look amazingly similar to NASA’s lunar module, which enabled humans to land on the moon during the Apollo program in the 1960s and 70s. As you can see in the diagram of the bacteriophage above and on the left, this bacteriophage has, on its bottom, what looks like landing gear, and that’s exactly what it is: proteins for attaching to the cells that these viruses parasitize.

Along with landing gear, viruses have various mechanisms for injecting their genes through a cell’s membrane and/or wall, as well as a few other enzymes that the virus will make use of as it attacks its victims.

As we’ll see below and in the next tutorial, some animal-attacking viruses (such as HIV or SARS-CoV-2) have an even more complex structure. But, for now, all you need to remember about viral structure is the genetic core (made of DNA or RNA) and the protein coat (made of self-assembling units called capsomeres). So, with that in hand, let’s see how viruses do their deadly work.

4. The Lytic Cycle

While viruses aren’t alive, their replication cycle is often referred to as a life cycle. The simplest viral life cycle is called the lytic cycle. In your studies of biology, you’ve met the root lyse several times in words like hydrolysis and lysosome. Hydrolysis is a process in which molecules are broken apart. Lysosomes are organelles that enable cells to digest engulfed food particles (or even organisms). What do you think the lytic cycle breaks apart?

Here’s the lytic cycle for a bacteriophage(or “phage”). As discussed above, that’s the name for a virus that attacks a bacterial cell.

1. The cycle begins with a phage (“a”) randomly bumping into its host. Proteins on the phage (the “landing gear” at “b”) enable it to attach to the wall (“d”) of its bacterial host. The host cell’s chromosome is shown at “c.”
2. The phage injects its DNA (“e”) into its victim.
3. The phage then uses the host cell’s molecular machinery (such as DNA polymerases) to copy the phage’s DNA, while simultaneously shutting down the host cell’s DNA.
4. The host’s RNA polymerases and ribosomes are used to create new phage components.
5. Based on molecular complementarity, these phage components assemble themselves into new viruses.
6. At a certain point, the host is so stuffed with phages that it bursts, releasing new phages into the environment.

Got it? Label the diagrams below.

5. The Lysogenic Cycle

In the lysogenic cycle, viral genes incorporate themselves into the chromosomes of their hosts. As you can see in image 1 (on the upper right side of the diagram to your left), the cycle begins just as the lytic cycle does: with the virus (B) injecting its genes (C) into its host (D).

But in step two, things start to differ. Here, the viral DNA (in red) incorporates itself into its host’s chromosome (at “E,” in blue). Once there, the viral DNA is called a provirus (or a prophage, if it’s a bacterial virus).

From this point on, as you can see in part II of the diagram (images 3, 4, and 5) the provirus becomes part of (and benefits from) the host cell’s reproductive cycle. In other words, every time the cell replicates itself, the cell will also replicate the provirus. Since bacteria can reproduce themselves very quickly (E. coli can reproduce itself every 20 minutes under ideal conditions), lysogenic incorporation can be an effective reproductive strategy for lysogenic viruses.

At certain moments, however, proviruses can break out of their dormancy, excise themselves from their host chromosome, and re-enter the virulent, lytic cycle. It’s possible that certain environmental stimuli, such as exposure to ultraviolet light, induce this change ^{Encyclopedia Britannica}. The consequences of this break-out are seen in the top half of the diagram: in # 6, viral genes are synthesized. In # 7, viral proteins are translated. In # 8, self-assembly of viral parts occurs, leading to lysis in step 9.

Use what you’ve learned above, plus your knowledge of biology, to label the diagram below.

6. HIV: Structure and Life Cycle

“HIV” is an acronym for Human Immunodeficiency Virus. Infection with HIV, if untreated, causes AIDS: acquired immunodeficiency syndrome. Let’s look at that term:

• Acquired: you have to be infected with the virus to get AIDS. In other words, unlike some other disorders of the immune system, it’s not inherited.
• Immunodeficiency. Your immune system is how your body fights off invading disease-causing organisms such as bacteria or fungi, as well as viruses. If you’re immunodeficient, you lack all or some of your body’s capacity to fight off these invaders.

Here’s a description of how HIV causes AIDS from HIV.gov

HIV attacks the body’s immune system, specifically the CD4 cells (T cells), which help the immune system fight off infections. If left untreated, HIV reduces the number of CD4 cells (T cells) in the body, making the person more likely to get infections or infection-related cancers. Over time, HIV can destroy so many of these cells that the body can’t fight off infections and disease. These opportunistic infections or cancers take advantage of a very weak immune system and signal that the person has AIDS, the last state of HIV infection.

In terms of our AP Biology course, one of the key things to understand about HIV is that it’s a retrovirus. Retroviruses have RNA genes, and then use an enzyme called reverse transcriptase to make a DNA transcript of their RNA. Note that this is the opposite of what usually happens during transcription, during which DNA is transcribed into RNA: that’s why this is reverse transcription, and why HIV is a retrovirus. This DNA then lysogenizes, entering into the nuclear DNA of its host, the helper T cell.

Let’s start by looking at the key parts of HIV’s structure, and then we’ll go through its life cycle.

“1” is HIV’s RNA genome. Surrounding the genes (at “2”) is a capsid. “3” is reverse transcriptase, an enzyme whose function is described immediately above. “4” indicates the glycoproteins (proteins with an attached carbohydrate) that enable HIV to bind with and inject its genes and enzymes into its host. These glycoproteins are embedded in a phospholipid bilayer (“5”). As we’ll see below, these phospholipids are stolen from the infected helper T cell as HIV oozes out of its victim in a process that closely resembles exocytosis. “6” is another enzyme called “protease.” Protease modifies some of the viral polypeptides that HIV forces its host to synthesize, creating mature viral proteins that can be assembled into new viruses.

Let’s now look at HIV’s life cycle. The letter “a” represents HIV in an infected person’s bloodstream. The glycoproteins on HIV’s surface enable it to bind with membrane proteins on the surface of HIV’s target, the Helper T cell (“d”). Binding leads to the fusion of HIV with the Helper T, allowing viral RNA (“c”) and reverse transcriptase (“b”) to enter the cell.
The function of reverse transcriptase is to convert the information in viral RNA into DNA. Using HIV’s RNA as a template, reverse transcriptase creates a hybrid DNA/RNA molecule (shown at “e”), which is then converted to a molecule that is purely viral DNA (at “f”). This viral DNA then enters the Helper T cell’s nucleus (“g”), where it becomes incorporated into the T cell’s chromosomal DNA as a provirus (“H”). Once in the nucleus, HIV’s DNA will be transcribed into RNA (“j”). The cell’s ribosomes (“k”) will translate the viral RNA into viral proteins (“i”), which will self-assemble into new viruses (“m”) that bud off from the helper T cell’s membrane (“l”), to be released into the blood or lymph.

Take this quiz to make sure you’re understanding how HIV works.

9. A virus quiz

If you understand 1) viral structure, 2) the lytic cycle, 3) the lysogenic cycle, 4) the life cycle of retroviruses like HIV, and 5) how viruses act to increase variation both within themselves and their hosts, then you know everything about this topic that’s required for an AP Biology course. To test your understanding, take the quiz below (which mostly focuses on the diagrams above).

10. Next Steps

Continue on to Understanding SARS-CoV-2, the next tutorial in this module.