Duke University

Germs and the Immune System

Paper 3

Benjamin C. Lawrence

Math 89S: Mathematics of the Universe

Professor Hubert Bray

December 6, 2016

Abstract

Germs are everyone. They are on the ground, in food, and even inside our own bodies.

The main purpose of this paper is to analyze the four main types of germs, bacteria, viruses,

fungi, and protozoa, and how are body naturally counteracts them using our immune system.

This paper will also contain some information on both the positive and negative impact of the

presence of germs.

Bacteria

Bacteria is one of the more well-known and older forms of microorganisms. Bacteria can

be found almost everywhere, such as in soil, radioactive waste, water, plants, animals, the

earth’s crust, organic material, glaciers, hot springs, the atmosphere, and in the depths of the

oceans. For the most part, the only places bacteria don’t exist are those sterilized by humans

[3]. Before, analyzing how bacteria interact with the human body, it is important to understand

their structures, life-cycles, and functions.

As can be seen above, there are three basic forms of bacteria: the cocci, or spherical like

bacteria; the bacilli, or rod shaped bacteria; and spirilla, or spiral shaped bacteria. Although the

cocci and bacilli can sometimes connect together, as seen in the image, all forms of bacteria are

single-cellular prokaryotic organisms. This means that in addition to functioning as individual

cells, they also contain no nucleus or organelles. Instead, bacteria have a cell wall that functions

as a thin membrane holding their DNA, cytoplasm, plasma membrane, and ribosomes inside. In

addition, the spirilla and bacilli have a basal body that attach their flagella to the cell [3].

There are three main methods by which bacteria reproduce. The first is binary fission.

This is an asexual reproduction process in which bacteria clones itself into two daughter

bacteria. Binary reproduction is a four step process that first requires the replication of a

bacterium’s DNA, then causes the DNA to move to opposite sides of the cell, dividing the

cytoplasm into two pieces, before finally splitting into the two offspring. Overall, this is an

efficient method of reproduction sense it does not require a pair to reproduce. However, the

issue with this is that there is little to no genetic variation from one generation to the next. This

is where the next two forms of reproduction come in. Bacterial recombination is the use of

conjugation, the passing of genetic material between bacteria using pili, or transformation, the

obtaining of DNA from a usually dead bacterium, to create genetic variation among offspring.

Therefore, bacterial recombination is a less efficient, but a more secure way of insuring that a

bacterium’s descendants are resistant to threats such as antibiotics. The final method of

bacterial reproduction is transduction. This is when a virus infects a bacterium, but instead of

causing the bacterium to create more viruses, it accidently causes the bacterium to create

viruses with the bacterium’s DNA inside. Therefore, when these new viruses infect other

bacteria, they end the virus’s reproduction cycle, but double the amount of genetic information

in the new bacteria [3].

The final part of bacteria that is necessary to understand is there function in the world.

One major function of bacteria is extracting nitrogen from the air. Plants require nitrogen to

survive, but they acquire it from the ground not the atmosphere. As a result, bacteria are

necessary in keeping plants alive because they take atmospheric nitrogen and expel it into the

soil in a form which plants can use. Also, bacteria are necessary parts of the human digestive

system. There are a number of materials that are too large for the human digestive track to

break down but that contain nutrients necessary for survival. Therefore, humans need bacteria

in their intestines to break down these materials, allowing for the absorption of nutrients. The

final, and most infamous, function of bacteria is causing disease. Bacteria are the sources of

diseases such as cholera, diphtheria, pneumonia, typhoid, and tuberculosis [3]. These diseases

are either caused by the bacteria themselves entering the body or by the release of toxins they

produce [4].

Viruses

The idea of a virus first came from Friedrich Loeffler and Paul Frosch who in 1898 found

that livestock were being contaminated by means smaller than any known bacteria [5].

However, it was not until 1931, when German scientists Ernst Ruska and Max Knoll developed

the electron microscope were scientists able to visually confirm the existence of viruses [6].

As with bacteria, in order to fully understand viruses, their structure and function must

be fully known. In this case, it is not necessary to understand a virus’s “life-cycle,” because they

are not living organisms. Viruses have no ability to self-replicate or make their own energy, so

they are not classified as biological living things.

The structure of viruses varies, but the above image shows a standard image for what

one might look. At the top of the virus, there is a capsule. This holds the inner nucleic acid core,

which is where the DNA or RNA is stored. Some viruses also have a second envelope layer on

the outside of this for extra protection. Attached to the capsule is the tail which has the end

plate and tail fibers. The tail fibers are what are used to attach to a host cell and the viral

genetic material is released through the tail plate [5].

The main function of a virus is to reproduce and this is done by delivering DNA or RNA to

a host cell [6]. There are four main methods that viruses use to inject their genetic material into

a cell, as can be seen in the above image. The first method, as can be seen on the far left, is via

fusion. Here, the virus fuses directly with its host cell allowing its genetic material to flow

directly into the cytosol. The image directly to the right shows how an influenza virus uses its

tail fibers to activate the cell membrane in such a way that it engulfs the virus. Once engulfed,

the virus can release its genetic material into the cytosol. The third type of virus, here

demonstrated by a polio virus, is a “nonenveloped virus” [7]. In this case, the virus itself never

enters the cytosol, but instead creates a shell from the cell membrane from which to eject its

genetic material. The final method of delivering genetic material is slightly more complicated.

Here, the virus starts out the same way as the nonenveloped virus before, but instead of

releasing its DNA or RNA into the cytosol, it moves straight to the nuclear envelope to deliver its

genetic material to the nucleus [7].

Given the above information, it is easy to see that all naturally occurring viruses are not

good for humans. However, modern science is now allowing doctors to use artificial viruses as

means of delivering genetic information. Research is being done to see if viruses could be used

to deliver genetic material to cancer cells and harmful bacteria.

Fungi

Fungi are the third form of germ and the only one that can be seen by the naked eye.

Also, fungi are a unique form of germ because they can be either single cellular or multicellular.

For the most part, fungi live in soil and plant material and are divided up based on life cycles,

presence and structure of fruiting bodies, and spore structure. The three main types of fungi

are multicellular filamentous molds (MFM), macroscopic filamentous fungi (MFF), and single

celled microscopic yeasts [8].

As can be seen in the above image, MFM are made of very fine threads called hyphae.

These hyphae grow at the tip and branch out to form a network called a mycelium. The tips of

the hyphae have digestive enzymes that break down the organic material in the soil to use as

food. Most of the hyphae grow down into the ground, as is shown in the figure. However, a few

grow up out of the ground to release spores. Since the fungus has no way of moving the spores

on its own, it relies on wind, rain, or insects to spread to new locations [8].

MFF works in a similar fashion to MFM in that it produces a mycelium below the surface

of the earth. The two fungi differ the that MFF produces visible fruiting bodies, commonly

called mushrooms or toadstools. MFF uses the gills under the caps of the mushrooms to hold its

spores until they can be spread [8].

The final form of fungus is yeast. Yeast is the only single celled of these three fungi.

Yeasts are about the same size as red blood cells and undergo asexual reproduction in the same

manner as bacteria [8].

Overall, fungi are similar to bacteria in that they can serve both good and bad purposes.

Mushrooms are essentials in cooking and brewing alcohol would not be possible without

yeasts. But on the other hand some mushrooms are deadly to eat and some yeasts infect our

body to causes diseases such as Candida which hurts people with weak immune systems by

making them even weaker against other diseases [8].

Protozoa

Protozoa are the final group of germs that infect the human body. This germ is a

subkingdom of the kingdom Protista and fossil records show that protozoa have existed all the

way since the Pre-Cambrian Era. On the other hand, the first visual evidence of protozoa was

discovered by Anton van Leeuwenhoek who observed them using a microscope he developed

[10].

Protozoa are very small by nature with the ones living in humans to be smaller than 50

micrometers in diameter. Also, like bacteria, protozoa are unicellular. However, they are

eukaryotes instead of prokaryotes. This means that they have internal organelles and structures

such as a nuclear membrane to house their DNA. The plasma membrane of a protozoa covers

the cytoplasm and pseudopodia (“a temporary protrusion of the protoplasm, as of certain

protozoans, usually serving as an organ or locomotion” [11]). In some other cases, protozoa

move using cilia or a flagellum, also similar to that of bacteria [10].

The reproduction system of protozoa is strange in that it can be either asexual or sexual.

The asexual reproduction process is the same as the binary fission process described for

bacteria. The sexual reproduction process, however, is much more complicated. First, protozoa

form gametes which are then fertilized into zygotes. The zygotes are then encapsulated into a

membrane creating an oocyst. This oocyst is then used to protect the fertilized egg until it can

be transferred to a new host for reproduction [10].

Protozoa are holozoic organisms. This means that they require organic materials in the

form of particulates or a solution to survive. For the most part this is not problematic because

they are so small that even large numbers of them do not consume very many nutrients. The

problem becomes more apparent when they enter the human body. Protozoa can be digested,

causing them to end up in the intestinal track. When this happens, they can start to consume

the nutrients required by humans. This leads to diseases such as Giardiasis and Malaria [12]. So

while protozoa are for the most part harmless, if allowed to enter the human body, can become

a very serious problem.

The Immune System

The human skin is the first level of the human immune system. The goal of the skin is to

keep germs out of the body, which works in the majority of cases. However, sometimes, in spite

of the skin, germs are able to enter the body. This is done by going through the digestive or

respiratory system (or a small cut in the skin if one is present). Once microbes have passed

through the skin, the human body mounts a second form of protection: antibodies. All the cells

in a single person have markers on them that indicate they are supposed to be there. If a cell

does not have the correct protein markers, then the body will consider it a foreign object. This

is also why a blood donor must have the same blood type as the receiver. In the case of germs,

the microbes do not have valid proteins to be present in the body. As a result, antibodies are

sent out to find and mark any foreign materials. Once “antibodies attach to a bacterium, they

send signals to complement proteins and phagocytic cells to destroy the bound microbes” [13].

In the case of a virus attack, an infected cell will signal it has been invaded by changing the

proteins visible on its surface. This will call the immune system to destroy the infected cell.

Parasites such as protozoa are destroyed by the immune system by signaling an inflammatory

response (swelling of the tissue) and then destroying of the parasite by releasing toxic

chemicals in the swelling area [13].

Conclusion

Overall, germs are a necessary part of the ecosystem. They consume dead organisms,

help provide nutrients to plants, and break down materials in the human digestive system.

While it is true that some can be harmful, the human body has the necessary tools to stop

germs from becoming too dangerous.

WORKS CITED

Author, Name of Article, Website name, URL, Medium, Date[1] Science NetLinks. “What’s a Germ?” Advanced Science. Serving Society.

http://sciencenetlinks.com/student-teacher-sheets/whats-germ/ Web.

[2] Brogan, Ryan. “What are Germs?” Kids Health. http://kidshealth.org/en/kids/germs.html

Web. January 2015

[3] Nordqvist, Christian. “What is Bacteria? What are Bacteria?” Medical News Today.http://www.medicalnewstoday.com/articles/157973.php Web. 11

January 2016

[4] “How Bacteria Cause Disease.” Britannica Kids.http://kids.britannica.com/comptons/article-197141/bacteria Web. 6

December2016

[5] Emiliani, C. “Introduction to the Viruses.” UCMP Berkeleyhttp://www.ucmp.berkeley.edu/alllife/virus.html Web. 1993.

[6] Vidyasagar, Aparna. “What are Viruses?” LiveScience.http://www.livescience.com/53272-what-is-a-virus.html Web. 5 January

2016.

[7] Alberts B, Johnson A, Lewis J. “Four virus uncoating strategies. Molecular Biology

of the Cell, 4th Edition. https://www.ncbi.nlm.nih.gov/books/NBK26833/figure/A4648/?report=objectonly 2002

[8] “Fungi.” Microbiology Online.http://microbiologyonline.org/about-microbiology/introducing-

microbes/fungi Web. 2016.

[9] “Mycelium.” Wikipedia. https://en.wikipedia.org/wiki/Mycelium Web. 4 October 2016.

[10] Yaeger, Robert. “Chapter 77 Protozoa: Structure, Classification, Growth, andDevelopment.” Medical Microbiology, 4th Edition. https://www.ncbi.nlm.nih.gov/books/NBK8325/Web. 1996.

[11] “Pseudopod.” Dictionary.com. http://www.dictionary.com/browse/pseudopod Web.

2016.

[12] “Protozoan Diseases.” Med-Health.net.http://www.med-health.net/Protozoan-Diseases.html Web. 6 December

2016.

[13] US Department of Health and Human Services National Institutes of Health.

“Understanding the Immune System How It Works.” NIH Publication.http://www.imgt.org/IMGTeducation/Tutorials/ImmuneSystem/UK/the_immune_system.pdf Web. September 2003.