PCAT Microbiology

What you will learn about in this part...

  • Microorganisms
  • Infectious disease prevention
  • Medical microbiology
  • Immunology  

An important and often over looked aspect of biology concerns really small organisms. By really small we don't mean the difference between an elephant and a mouse, but between a mouse and something so small you cannot see it with the naked human eye, welcome to the wonderful world of microbiology...


Microbiology is defined as the biology of microscopic organisms and its key focus is on minuscule organisms called microbes. But where did all these small things come from? Well, from time immemorial this has always been the number one question on scientists' minds. Whether it is creation from a primordial soup, or an asteroid landing on earth and seeding the planet with the first extraterrestrial organism we are none the wiser.

Evolution from the first replicate

One thing we do know is that it all started out with something very elementary which could replicate itself. This humble beginning could be as small as 3 molecules or a little bit more complex like an amino acid, this "replicant” had the ability to create one and then create an exponential rise of duplicates of itself. This theory is was first put forward by Richard Dawkins in his book "The selfish Gene” which is virtually a precursor to Darwin's theory of evolution.

These small replicants soon became bigger and bigger and soon the first "microorganism” (an organism of microscopic size) were created. This gives you a bit of perspective about size, where an elephant is large to a mouse a microbe is large in comparison to the first replicants. As mentioned in the previous chapter, microorganisms can be classified into two distinct groups (eukaryotes and prokaryotes see figure 9-1). Expanding on this, these groups, in turn can be subdivided into seven subgroups often called "Kingdoms” these include - bacteria, archaea, protists, animals, fungi, plants and possibly viruses (more on this later). Separating organisms into different class is called taxonomy, which is a developing science as new advances come up in biology all the time and organisms are classified and reclassified into different Kingdoms.


Figure 9-1: The different kingdoms.

Bacteria and archaea

There are typically 40 million bacterial cells in a gram of soil and over a million bacterial cells in just one milliliter of drinkable water. In all, it has been estimated that there are about 5 × 1030(5 nonillion) bacteria on Earth with a total weight equaling that of all plants and animals. Strangely enough there approximately 10 times as many bacterial cells in human body (on your skin, in your gut...) as there are human cells in your body. But don't worry, these bacteria are usually harmless and are actually beneficial to your immune system and help you stave off certain infectious diseases.

Be familiar with the word flora, it doesn't mean a floral bouquet! It means the bacteria, which cohabit the human body in our gut and on our skin; they are often referred to as "friendly bacteria”.

There are lots of different classifications of bacteria; an important feature which differentiate certain bacteria is how they use oxygen. Like you and me, we need oxygen to survive, is not a choice it's an obligation or we die, and so to do some bacteria called obligate aerobes if they are starved of oxygen they will die. However, there are some bacteria, which don't need oxygen - obligate anaerobes (and are sometime poisoned by it) and some who are indifferent facultative anaerobes.

The other differentiating criteria for bacteria which the PCAT examiners love to ask questions is how they obtain their energy, luckily enough these can be classified into four main types:

  • Photoautotrophs: Look at the word here photo- meaning light and -auto like autonomous. These are a type of bacteria that produce their own nutrients through the process of photosynthesis, using carbon dioxide from the environment.
  • Photoheterotrophs: Again, look at the word here photo- meaning light and -hetero like heterozygous meaning other. Photoheterotroph bacteria are those, which perform photosynthesis but cannot use carbon dioxide from the environment. In order to get the carbon needed for photosynthesis (which normally comes from carbon dioxide), they extract carbon from a variety of other sources.
  • Chemoautotrophs: So the -photo part here has been replaced with chemo- meaning they get their energy from chemicals around them. So chemoautotrophs get their energy from inorganic compounds, and their carbon needs are obtained from carbon dioxide.
  • Chemoheterotrophs: This type of bacteria obtained their energy from inorganic substances while they get their carbon from a variety of sources other than carbon dioxide. These species are further subdivided based on the source of carbon they use. Some species can extract carbon through parasitic or symbiotic interactions with a host or through the decomposition of other organisms.

The Germ Theory of Disease

The germ theory of disease is termed a "theory” but is the basis of infectious disease medicine. The theory refers to the discovery in the late 19th century that some infectious diseases are caused by small organisms (microorganisms) too small to see without magnification, that invades the host.

The theory arose from a guy called John Snow who lived in Victorian London England (like Sherlock Holmes). At the time the local residents in his area were suffering from a disease called cholera. By talking to local residents, he identified the source of the outbreak as the public water pump on the road where he lived. Although Snow's chemical and microscope examination of a water sample from the Broad Street pump did not conclusively prove its danger, his studies of the pattern of the disease were convincing enough to persuade the local council to disable the well pump by removing its handle. This action has been commonly credited as ending the outbreak.

This was an important step in the progression of cell theory as it proved that small microorganisms can transmit and cause disease in humans and therefore cemented its importance.

The reason Germ Theory is important to a pharmacist working in a pharmacy is that it underpins on of the most common ailments seen in community pharmacy - an infection. This may be fungal, bacteria or viral and can cause a wide range of conditions treated everyday by your common pharmacist. Most commonly, these include ringworm, candidiasis, conjunctivitis and many more!


Bacteria constitute one of the largest domains of the prokaryotic group. They are typically a few micrometers in length and have a wide range of shapes. Bacteria were actually one of the first forms of life to appear on earth and they can live in a wide range of environments from the extreme to the benign, the can be found almost everywhere, such as in soil, water, acidic hot springs or even radioactive waste!

Bacteria and archaea lack a nucleus (there DNA is contained in plasmids) and other membrane-bound organelles (key differentiating feature between bacteria and eukaryotes), they usually live in multicellular colonies, which are individual bacteria group together for safety in numbers. Another characteristic of bacteria and archaea is that they are surrounded by cell walls, which provides rigidity and strength and to their structure. When they are in their optimum environment the can replicate extremely quickly, this can be as much as doubling their population in as little as 20 minutes.

Other differentiating features, which can be seen in Figure 9-2 can be summarized as below:

  • Capsule or Slime layer - some bacteria have a sticky outer layer, which helps them adhesively attach to their environment. Although this feature is not ubiquitous, the chosen few usually have a capsule or slime layer which resides outside of their cell wall.
  • Flagella - these are like little propellers, which rotate to move bacteria through their environment. Not all bacteria have this feature but when they do, bacterial flagella differentiate bacteria from other eukaryotes because it bacterial flagella are hollow.
  • Pili - similar to a flagella, but looks more like a hair sticking out of the bacteria backside. All pili are primarily composed of oligomeric pilin proteins and they are antigenic meaning the human immune system uses them to identify an infectious agent.
  • Spores - think of bacterial spores as bacterial eggs, they lay them when times are bad, i.e. there is a lack of nutrients in the environment, and the spores then germinate when better conditions arise. Bacterial spores are exclusively produced by Actinobacteria and Azotobacter species of bacteria.

In addition to these characteristic structures, bacteria have characteristic shapes to their cells such as cocci, which are rounded, spheres, spirilli, which are spirals and bacilli that are, elongated rods.

bacterial structure

Figure 9-2: Common bacterial structure.

Archaea vs Bacteria

Archaea are very similar to bacteria in that they also are single cellular organisms that lack nuclei. Throughout scientific history archaea and bacteria have been classified as the same type of organism i.e. as bacteria. However, in the past couple of decades a three-tiered domain system has been developed which classifies archaea into a distinct group.

The top three differentiating characteristic between bacteria and archaea include:

  • Biochemical differences. An example of this is that bacterial cell membranes are made from phosphoglycerides with ester bonds, whereas archaea membranes are made of ester lipids. Some archaea are photosynthetic but do not use chlorophyll. Photosynthesis in bacteria (and eukaryotes) is primarily chlorophyll based. In simpler terms bacteria, which photosynthesize, are green because of the chlorophyll they contain whereas photosynthesizing archea are usually not green due to lack of chlorophyll.
  • Genetic mechanics differences. The difference lies in their RNA polymerases and thus in their protein synthesis, the base "thymine" is not present in tRNA of archaea but present in bacteria.
  • Antibiotic sensitivity. Sensitivity to many antibiotics, such as chloramphenicol, rifampicin, kanamycin and anisomycin are different when comparing archea and bacteria. Also, archaea are sensitive to the diphtheria toxin and bacteria are not.

Fungi (known to some as Mushrooms)

You know those grey little mushrooms in the convenience store? Well, although they are usually in the vegetable section, which mainly comprises of plants; mushrooms actually represent their own taxonomic group called fungi.

Fungi are a distinct group within the eukaryotes; they include common yeasts, like those you use to make bread and beer, molds. The main characteristics that differentiate fungi from other eukaryotes is that they have cell walls, which contain chitin, unlike plants, which contain cellulose. Fungi are so unlike other biological organisms they have their own name for the science of studying them, mycology.

Fungi are extremely important to Earth's ecology; their most important job is to break down and recycle dead matter, but they can also act symbiotically, helping other plants and animals grow. Mushrooms were previously considered to be part of the Plant Kingdom because of similarities in their lifestyle and that fact that they are also immobile. Fungi can be classified into seven broad subtypes:

  • Yeasts: the simplest forms of fungi as they only have a single cell they reproduce by splitting in two in a process known as budding.
  • Ascomycetes: the largest subgroup of fungi commonly known as the sac fungi, they are called this, as their defining feature is a microscopic sexual structure, which looks like a sac, in which non-motile spores, called ascospores, are formed.
  • Basidomycetes: often referred to as the "Higher fungi” which comprises of the Ascomycetes and Basidiomycetes. They are club-shaped fungi that contain haploid spores. The group contains many of the well-known edible species such as, puffballs, boletes, bracket fungi, jelly fungi, chanterelles, earthstars and much more!
  • Zygomycetes: the name of this group comes from the zygosporangia, which is a structure where resistant spherical spores are formed during sexual reproduction.
  • Chytrids: this means "little pots” in Greek; they are called this as this fungi group has little structures that look like pots, which contain unreleased spores.
  • Deuteromycetes: this group comprises of everything else, mushrooms are so genetically diverse, it is difficult to have distinct criteria to group them together.
  • Lichens: often found in extreme conditions around the world, lichens are composite organisms, which are formed between a fungus, and a photosynthesizing plant. Lichens are symbiotic with plants, which get their energy from light and are therefore termed photobionts.


Although there are many structural similarities between fungi and the other taxonomic groups, there are some characteristics, which are unique to fungi. Microscopically, these include some fungi species, which grow as single-celled organisms and reproduce by budding or binary fission. A key feature you should know for the PCAT is that the fungal cell wall is comprised of glucans and chitin and not cellulose.

Macroscopically, what is usually deemed as a "mushroom” i.e. the familiar stems and caps that you find in the forest are actually only part of the entire fungi organism, see figure 9-3. Most of the fungi resides underground in the form of root structures called hyphae. Hyphae branch and fork out to develop into mycelium, which is an interconnected network of hyphae. The cap and stem develops from this and its main purpose is to spread spores, yes ladies and gentlemen your mushroom is a fungi sex organ!

**Spits out Portobello mushroom burger**

Mushroom structure

Figure 9-3: A generalized structure of fungi

The function of the mushroom cap is to create and disperse its seeds, called mushroom spores. Mushroom spores contain the same genetic material as the original mushroom, this then dispersed in the wind and then land on soil and germinate new mycelium.  This process is essentially cloning, because the daughter cell is identical to the parent, therefore this is deemed asexual reproduction. Mushrooms however, do undergo some sexual reproduction by fusing gametes to create a diploid cell although this is quite rare and only happens when the environment is not providing the right nutrients for the fungi to properly survive.

Top Three Differentiating Features

  • Fungal cells contain membrane -bound nuclei and organelles - unlike prokaryotes.
  • Fungi are not green as they lack chloroplasts  - unlike plants.
  • Fungi possess chitin cell walls and also vacuoles - unlike animals.


Which of the following structural characteristics makes fungi different from all other taxonomically categorized organism?

(A)   Chloroplasts

(B)   Ribosomes

(C)   Mitochondria

(D)   Chitin cell walls

Answer: D


Chitin cell walls - fungi are the only known organisms to contain a cell wall that comprises of chitin. Others organisms such as plants have cell walls but they are made of made of cellulose. Ribosomes and mitochondria are common features to most organisms and therefore do not differentiate fungi. Chloroplasts are a differentiating feature of plants, which photosynthesize, not fungi that get their energy from decaying matter.


Plants can be either microorganisms or multicellular organisms, which include things like flowering plants, ferns and mosses. It is thought that on earth, there are about 300,000 different species of plants.

PCAT examiners love to ask questions about the cellular structure of plants, so make sure you pay attention!

Plants characteristically obtain their energy from sunlight by utilizing a process known as photosynthesis to convert light (photons) into stored chemical energy.


You can thank photosynthesis for every breath of air you take into your lungs. In fact, biochemically, photosynthesis is probably the most important process on the planet. Not only does photosynthesis pump oxygen into the atmosphere, it where all the energy behind our food and almost all the power and heat we use, humans could not live without it although we only use it indirectly.

Plants and some bacteria are autotrophs, meaning they use simple inorganic substance such as carbon dioxide and light to create the energy they need plus a few byproducts. This is achieved by splitting water into hydrogen and oxygen and then combining these molecules with carbon dioxide to produce the sugars we all need to live.

The best way to imagine photosynthesis is as a sequential chain. The process of photosynthesis is as follows:

1.    A photon is absorbed by chlorophyll and passed to the reaction center the chlorophyll uses the photons energy to spit out an electron.

2.    This electron moves down a chain of molecules until it is used to convert carbon dioxide into a carbohydrate a process known as carbon fixation.

3.    This reaction chain is then reset with a new electron stripped out of water, which replaces the initial electron.

All this chemistry, from light absorption to the synthesis of carbohydrates, occurs in a structure called a chloroplast. Chloroplasts have two membranes. The smooth outer membrane holds the entire structure together. The inner membrane is folded into a series of stat discs called thylakoids that contain the pigments and protein complexes required to capture solar energy and release oxygen.


Plants like other organisms are comprised of cells, which have specific distinguishing features (shown in Figure 9-4) these, include:

  • Vacuoles are large, water filled membrane bound organelles, which are central to the cell. Vacuoles are used by plants for a wide range of purposes, including containing water, waste products, maintaining acidic internal pH and maintaining internal hydrostatic pressure and turgor.
  • Chloroplastscontain chlorophyll, which is responsible for photosynthesis and energy provision within the cell. Chloroplasts store energy in the form of ATP and NADPH while freeing oxygen from water.
  • Rigid cell wall made up of cellulose and pectin, located outside the cell membrane. The cell wall offers mechanical support, a filtering system, retention of pressure and prevention of over expansion.

Figure 9-4: Plant cell structure you need to know for the PCAT Exam


Protists are believed to be the eukaryotic organisms, which were the precursors to plants animal and fungi. The best way to think of them is that they are very primitive un-evolved organisms, which lack any complex organelle structures. There are four general subgroups of protists:

  • Unicellular algae almost 75% of all the oxygen in our atmosphere is created by these guys, they play an extremely important role in earths ecology.
  • Protozoameans "first animals”. Protozoa has been found in almost every kind of environment from arid desert to peat bogs.
  • Slime molds are often gelatinous and look like slime.
  • Water molds are always found in wet environments.


As Protists are eukaryotic cells they have organelles and structures common to this kind of cell (see figure 9-5) i.e. things like endoplasmic reticula, Golgi apparatus, digestive vesicles, ribosomes, mitochondria, nucleus with genetic material, karyotheca, etc. All these elements are found dispersed throughout the cytoplasm. A key feature that Protists lack is that they do not have cell walls.

Protist structure

Figure 9-5: The protist structure.


Protists are heterotrophs, meaning they do not make their own food and thus they need to search for it in the environment. Protists have developed several locomotion mechanisms and they actively move towards food. The subsequent digestion for all Protists is intracellular digestion, which means like you and I, organic material is internalized and degraded inside the cell.


Virus, what a horrible word, these little things seem to always do more harm than good. They also hit the headlines, who hasn't heard of these top ten viruses:

1.    Influenza - common seasonal.

2.    Small pox - nearly eradicated.

3.    Typhoid - "Typhoid Mary”.

4.    Bubonic plague - Black Death.

5.    Cholera - massive diarrhea.

6.    Anthrax - as a biological weapon.

7.    Malaria - mosquito transmitted.

8.    SARS - acute respiratory syndrome.

9.    Ebola - 50-89 percent fatal.

10.   HIV - immune disease.

The reason why we have listed viruses at the end of this microorganism classification section, is that viruses aren't defined as microorganisms, well in the classical sense anyway. Viruses do not exhibit characteristics of other living species and are often described as "non-living”. However, for ease-of-use we have included this section here for quicker reference.

The interesting thing about viruses (termed virions) is they require living organisms to replicate within, viruses cannot replicate by themselves. Once it infects a susceptible cell, however, a virus can direct the cell own biochemical machinery to produce more viruses. Viruses have been known to be able to replicate within all of the previously mentioned taxonomic groups. A useful way to think of viruses is that they are simple machines, which have one goal, replication.

Virions fall into one of three categories: special enzymes needed for viral replication; inhibitory factors that stop host-cell DNA, RNA, and protein synthesis; and structural proteins used in the construction of new virions. These last proteins generally are made in much larger amounts than the other two types. After the synthesis of hundreds to thousands of new virions has been completed, most infected bacterial cells and some infected plant and animal cells rupture, or lyse, releasing all the virions at once. In many plant and animal viral infections, however, no discrete lytic event occurs; rather, the dead host cell releases the virions as it gradually disintegrates.

These events -- adsorption, penetration, replication, and release -- describe the lytic cycle of viral replication. The outcome is the production of a new round of viral particles and death of the cell. Adsorption and release of enveloped animal viruses are somewhat more complicated processes. In this case, the virions "bud” from the host cell, thereby acquiring their outer phospholipid envelope, which contains mostly viral glycoproteins.


In comparison to other organisms, viruses are extremely simple in structure and often only consists of two or three parts:

1.    Genetic material - made up of the DNA or RNA, this contains all of the genetic information for the virus to be able to replicate itself and perform key functions. The nucleic acid may be single- or double-stranded. The entire, physical virus particle, is called a virion, consists of the nucleic acid and an outer shell of protein. The simplest viruses contain only enough RNA or DNA to encode for just four proteins. The most complex can encode 100 - 200 proteins.

2.    A protein coat or capsid - acts as a shield, which protects the viruses internal, precious genetic material. A capsid plus the enclosed nucleic acid is called a nucleocapsid. Viruses have developed so that there are two basic ways of arranging the multiple capsid protein subunits with associated ligands (binding sites) and the viral genome into a nucleocapsid. The simpler structure is a protein helix with the RNA or DNA protected within. Tobacco mosaic virus (TMV) is a classic example of the helical nucleocapsid. In TMV the protein subunits form broken disk-like structures, like lock washers, which form the helical shell of a long rod-like virus when stacked together.

3.    Phospholipid envelope - this is a bilayer envelope which surrounds the protein coat when outside of cell. This is not a ubiquitous feature and only present in some viruses. The phospholipids in the viral envelope are usually nearly identical to those in the plasma membrane of an infected host cell, which helps with penetration into a new host. The viral envelope is, in fact, derived by budding from that membrane, but contains mainly viral glycoproteins.

The Virus structure you need to know for the PCAT Exam

Figure 9-6: The structure of a common virus.

Transmission and replication

The spread of viruses occurs in many different ways. One of the key methods of transmission is via a disease-bearing organism called a vector. Vectors can be either mechanical or biological. Both types of vectors act as a middlemen for the virus; carrying the virus from one place to another. The difference between a mechanical and biological vector is that the biological vectors harbor the virus inside its body whereas the mechanical vector has the virus on the outside body. For instance, common biological vectors are mosquitoes, which spread malaria. A female mosquito bites a human and ingests their blood, this brings the virus into their system. The next mosquito victim is bitten and the virus is transferred. In contrast, an example of a mechanical vector is a housefly, which lands on cow dung, contaminating its external body parts with bacteria from the feces and then lands on a victim's food just before they eat it. These are just two examples of transmission; there are many others that you are probably familiar with:

  • Influenza viruses are spread by coughing and sneezing, and enter a host via sputum (phlegm).
  • Norovirus and Rotavirus are viruses that are transmitted by the fecal-oral route entering via food or water.
  • HIV is one of several viruses transmitted through sexual contact and through exposure to infected vectors such as blood.

Once the virus has been transmitted to a new host, the surface of virus, which includes multiple copies of one type of protein that helps the virus bind or adsorb, specifically to multiple copies of a receptor protein on a host cell. Then, via an array of different mechanisms, depending on which virus, the viral DNA or RNA crosses the plasma membrane into the cytoplasm. The entering genetic material may still be accompanied by inner viral proteins, although in the case of many bacteriophages, all capsid proteins remain outside an infected cell. The genome of most DNA-containing viruses that infect eukaryotic cells is transported (with some associated proteins) into the cell nucleus, where the cellular DNA is, of course, also found. Once inside the cell, the viral DNA interacts with the host's machinery for transcribing DNA into mRNA. The viral mRNA that is produced then is translated into viral proteins by host-cell ribosomes, tRNA, and translation factors. This then ends up in new copies of the virus, which replicate so much the burst out of the cell, this is called lytic replication.

Another form of replication, which a virus undergoes, is call lysogenic replication. This follows the same initial steps as lytic replication but differs in that the virus actually integrates its DNA directly into the host cell genome; this is called a progeny (like a virus-host hybrid). Then once suitably activated the progeny creates new virions and viral replication enters the lytic stage.

Use in everyday activity - food, water...

All the microbiological (microbes) agents mentioned in this chapter are often associated with disease. When this occurs the agent is called a pathogen, basically meaning that it has the ability to transmit diseases. However, this is not always the case, as many microbes are used for an array of beneficial processes such as medicine production, cloning and industrial fermentation. With out microbes we wouldn't have:

  • Alcohol
  • Vinegar
  • Dairy products
  • Antibiotics
  • Certain plastics

Microbes, in particular bacteria, play a crucial role in sewage-treatment, they breakdown waste matter into its basic constituents and reduce toxic effects to fish and other organisms. In agriculture, nitrogen-fixing bacteria including:

  • Cyanobacteria, e.g. the highly significant Trichodesmium
  • Green sulfur bacteria
  • Azotobacteraceae
  • Rhizobia
  • Frankia

Azotobacteraceae are super important as they are often introduced to plant species to increase their crop yield as plants are notoriously poor in being able to obtain nitrogen from their environment.

Algae are playing an ever more important role in everyday industry. One reason for this is that they have high nutritional value and are commercialized and consumed as human food, mainly in Asia. Jelly compounds are extracted from some algae, like glues and pastes for industrial and commercial use. Agar, used as a medium for biological culture in laboratories and in medicines, are extracted from rhodophyte algae. Diatom algae deposited on the bottom of the sea form diatomites, used in the production of filters, refractories, thermal isolation and cement. Some algae are used as agricultural fertilizers.

A fascinating area, which is currently in development and hasn't come to full fruition is the use of viruses as medicines. Aside from being the causative agents of many diseases, viruses are important tools in cell biology research. This may seem like an oxymoron, when thinking of the malevolent virus, but virologists have engineered viruses which can be used to go into cell nucleuses and snip out bits of bad DNA and replace them with good functional bits. i.e. genetically modified viruses can carry foreign DNA into a cell and replace the host cell DNA with its own. This approach provides the basis for an ever-increasing list of experimental gene therapy treatments.

Infectious diseases

In the previous part to this chapter we explored microorganisms and mainly concentrated on what they were doing, when they were doing good. However, as you may well know bacteria and viruses are often seen as baddies and there is a very good reason for this, which we will explore in this part.

There are almost an infinite variety of different microorganisms on the planet. Many of these are benign and actually contribute to a healthy well being. However, there are a select, naughty few, which can cause infectious diseases. Infectious disease (a.k.a transmissible disease) is a clinical diagnosed illness, which results from an infection from a pathogenic biological microorganism.

The top four infectious pathogens, in order of pathogenicity (how good they are at being a pathogen) viruses, bacteria, fungi, protozoa and lastly prions. When are pathogen goes out control among a populace it is defined as:

  • Epidemic - occurs when new cases of a certain disease, in a given human population, and during a given period, substantially exceed what is expected based on recent experience: "a flu epidemic".
  • Pandemic - similar to an epidemic but more wide spread infecting more people across a wider geographical area.

Transmission of infectious diseases

Transmission of a disease always happens from one source to another. By defining the means of transmission it is an important part in understanding the nature of the infectious agent. There are many different modes of transmission of infectious diseases, for instance meningitis and many respiratory diseases are transmitted via droplets, which are spread by talking, kissing, coughing and sneezing. Sexually transmitted infections (STI's) are often acquired through the exchange off bodily fluids. Gastrointestinal diseases are often acquired by eating and drinking contaminated food and water.

Before and infectious microorganism can enter the body, it must first overcome certain physical and biological barriers that operate on the bodies external and internal surfaces. The largest body surface, and actually the largest organ of the human body is the skin. The skin is usually thought of as a permeable barrier to infectious agents however sometimes this barrier is breached. In general though, many bacteria do not live long on the surface of the skin because of fatty acids and lactic acid, which is present in sweat that is secreted by skin glands. These secretions often lowered the skins pH, which renders it inhabitable to infectious agents.

Transmission of disease

Figure 9-7: Different modes of interspecies transmission.

Figure 9-7 details out the different modes of transmission of infectious agents. An anthroponose, is an infectious disease in which a disease-causing agent carried by humans is transferred to other animals. If this occurs the other way around i.e. a disease, which an animal carries, which is transferred to humans this transmission is called zoonotic.

Inside the body, such as in the intestinal tract or in the lungs, again secrete thick mucus that act as a mechanical barrier which inhibits bacteria from sticking to the surface of the cells. Think of this almost like a thick oil coating a can of soda, anything that lands on the surface of the oil cannot penetrate to where the metal of the can is as it is mechanically impeded. The only problem is that when the microorganism is stuck in this thick mucus layer then how does the body get rid of it? The answer to this is money surfaces within the skin have tiny protruding parts which act on microscopic level to move this mucus towards an exit such as the mouth, where is coughed and sneezed out. There are also many other mechanical strategies for the body to physically get rid of possible invading microorganisms such urine, saliva and tears. These mechanical factors also sometimes have my microbicidal factor to them for instance in the gastric tract, secreted gastric juices are often highly acidic and there is are certain antimicrobial properties of semen.

Funnily enough, another important defense on the surface of the body are actually bacteria themselves. You've properly heard the term "friendly bacteria” which are present in many probiotic yoghurts, this is not to say that every time you meet them they say hello and dip the hat! Friendly bacteria means that certain bacteria such as Stapholococcus Aureus take up vital space and nutrients on the surface of your body which stops other "unfriendly” bacteria from colonizing and potentially causing a detrimental disease-causing infection. These bacteria, which colonize the gut and the skin often produce their own types of antibiotics called Colicins or certain acids.

The baddies

Viruses, bacteria, fungi, protozoa and multicellular parasites can all turn the rogue once they have penetrated the outer layer of the skin. In many cases, these can cause disease, and if they are left to their own devices they will eventually kill their host. The top seven most deadly infectious diseases include:

  • Acute respiratory infections - mainly bacterial.
  • AIDS - a retrovirus.
  • Diarrheal diseases - mainly caused by bacteria.
  • Tuberculosis - bacterial infection.
  • Measles - a viral infection.
  • Hepatitis B - caused by a virus.

Most infectious diseases in normal individuals are self-limiting and leave little to no damage in their wake. Since microorganisms come in a variety of shapes and forms a wide range of immune responses is required to deal with each type of infection.

Once the microorganism has penetrated the outer layer, the nest stage of defense kicks in to action. This is where the immune system recognizes an invading pathogen (an infectious microorganism) by dispatching the bodies defense system - white blood cells to look for a molecule on the microorganisms surface called an antigen.

Despite the skins effectiveness in excluding infectious agents from getting into the blood, it is not perfect. Some pathogenic microorganisms get access to the circulatory system via cuts or grazes in the surface of the skin. This type of infectious agent is called an "opportunistic microorganism” which takes advantage of vulnerable barriers to entry.

When this occurs the body employee's two main tactics to get rid of them. The first, is a mechanism called phagocytosis, which involves specialized cells to attack the bacteria by engulfing them and swallowing them up. The second mechanism, is for the body to secrete certain bactericidal enzymes and chemical factors that like a poison destroy the infectious agent.

Hygiene and preventative measures

One way to reduce the occurrence of infectious diseases is to stop the transmission of pathogenic microorganisms from one place to another, using hygiene and preventative measures. You have probably seen on TV, doctors in hospitals going from patient to patient, each time washing their hands. This is to reduce the chances of transmission from an infected patient to a non-infected patient. The most widely used disinfectants are alcohol, iodine and chlorhexidine.


The science of studying pathogens, their transmission to humans and the subsequent immune defense is called immunology. As a PCAT student you will need to know a lot about immunology, as it's a key area where things can go wrong with patients. For instance, if the patient has have an organ transplant i.e. one of their organs goes wrong and they have to you get another one from someone else, when they put it into their body the immune system can actually reject it because it thinks it is a foreign antigen. There are medicines now, which can suppress the immune system and stop the body from rejecting new organs.

The goodies and why we need them

We have already discussed the baddies being antigens invading bypassing, the outer layer, entering the blood and hopefully being destroyed by phagocytosis or chemical attack, but not about how this comes about.

There are two main types of phagocytes called "professional” phagocytic cells. A Russian Zoologist categorized the two types, both microscopically, as either large macrophages or the smaller polymorphicgranulocytes. Although they different in size they have much the same function, which is to provide a defense against pus forming bacteria (also known as pyogenic).

Macrophages start their life out as promonosites in bone, these then develop into monocytes in the blood and then finally mature into macrophages which inhabit a wide range of tissues throughout the body, collectively the network of macrophages is called the nuclear  phagocyte system. The polymorphic granulocytes on the other hand, roam freely within the blood and do not have their own energy generating mitochondria as they use glycogen stores to anaerobically respire.  For what polymorphs gain from being mobile they loose out in longevity, due to this lack of mitochondria they are unsustainable and therefore short lived.

The first stage in the way a "professional” phagocyte attacks a microorganism is the detection of the microorganism, it does this using receptors called PAMPs (Pathogen Associated Molecular Patterns). When these receptors are triggered, a signal travels through the phagocyte and starts the actin-myosin contractile system. This complicated sounding mechanism, is really just a big hug. The phagocyte reaches around the infectious agent and brings it inside of itself. Once the microorganism is completely engulfed, cytoplasmic granules contained within the phagocytes vacuole are discharged and then begin to break down the microorganism. This starts with NADP used to transfer energy to oxygen making strong antimicrobial agents such as hydrogen peroxide and hydroxyl radicals, which attack the microorganism's cell membrane causing it to deform.

Sometimes the immune system finds it difficult to use cells like macrophages or other phagocytes to save cells from primary infection. This can often happen when a virus enters the cell, takes it over and uses the innate cellular mechanisms to reproduce itself. When this occurs is at the interest of the host to destroy these infected cells before the virus has time to further replicate and spread to other host cells. For this reason, the immune system has created Natural Killer (NK) cells which have the job of finding infected cells and destroying them i.e. they are cytotoxic (cyte=cell, toxic=poison). NK's are classified large granular lymphocytes (LGLs) that use their lectin-like receptors to attach to glycoproteins on the surface of compromised cells. Think of these glycoproteins as a viral infected cells holding up a flag telling the NK that it is infected and altruistically needs to be destroyed for the greater good of the host (so brave!). NK's not only do this for cells, which are virally infected but any cell that may compromise the host like some cancer cells.

Apart from NK's, macrophages and polymorphic granulocytes, there is another way the immune system elicits this response to invading infectious agents. The immune system can release antibodies, otherwise known as immunoglobulins) which are glycoproteins, shaped like a big "Y”. Antibodies are commonly made up of four basic structural units, too heavy chains and two small light chains. Each antibody contains a paratopewhich is analogous to a lock this lock fits the antigens epitope which is analogous to the key. Using this lock and key mechanism an antigen can tag an invading microorganism so that other parts of the immune system can identify and neutralize it.

Although the top seven infectious diseases mentioned at the beginning of this section are extremely varied, ranging from retroviruses to bacteria, they all have one thing in common; they all contain recognizable structural antigens. Meaning they are recognized by the bodies immune system and dealt with appropriately. The immune system will try and find the entity and try to neutralize the potentially malicious invader by using antibodies secreted from cells called B lymphocytes (the B is for Bone as this is where they originate). Antibodies fit together with antigens almost like pieces of the puzzle, or a lock and key.

Antibody structure of the PCAT Exam

Figure 9-8: The structure of an antibody.

Antigens bind to antibodies at special regions called epitopes (see figure 9-8). Epitopes are the distinct molecular surface features of an antigen capable of being bound by an antibody. For instance imagine too flat services colliding together, they cannot grip one another and would slide pass each other. If these flat surfaces had an epitope, the surface would have ridges them to grip one another and interact together.

Antigens are usually polysaccharides or proteins and are in fact parts of bacteria and viruses that the immune system can recognize such as coats, cell walls, capsules, and flagella. Sometimes however, the body can get confused and innocuous substance can be recognized as antigens such as pollen or egg whites and elicit an erroneous immune response, often called an allergy. i.e. When you suffer from hay fever and start sneezing, this is your body's immune system thinking the pollen in the air is a foreign antigen and must be destroyed and therefore you need to sneeze out the invading allergen.

Think of the common symptoms of an allergy is not only sneezing but inflammations of the skin and this is just one of the key areas that antibodies bodies are responsible for. When the antibody comes into contact with a foreign antigen, it attaches itself to the surface of the microorganism and then acts as a flag signaling other cell types to eat it via phagocytosis, this results in the inflammation. The second way that antibodies can work, is by blocking interactions of the infectious agent by combining with one of the reacting molecules that it requires to function. For example, an antibody directed against the influenza virus can prevent the virus from attaching itself to a specific receptor on the host cell.

Developmental immunology how to develop your protective army

Although the majority of antibodies have the same basic for constituent parts i.e. two heavy chains and two light chains there are some important differences based on the heavy chains that they possess (see figure 9-9). When these heavy chains come in different forms of the antibody is referred to as a different isotype. There are five different isotypes known in mammals, and they all have different roles and help create bespoke in your responses for different antigens these five include:

  • Immunoglobulin A (IgA) - mainly found in mucosal secretions in the genital tract, gut, and the respiratory track. The main secretions include saliva, breast milk and tears.
  • IgD- mainly act as a receptor sitting on B cells that have not been exposed to antigens. They have them shown to activate mast cells and basophils.
  • IgE- mainly involved in allergy responses. IgE triggers histamine release from mast cells and basophils when bound to an allergen.
  • IgG- has four main forms and provides the main antibody based immunity against invading pathogens. This is the only known immunoglobulin that crosses into the placenta.
  • IgM- present on the surface of B cells and in a secreted form (pentamer). Works in the early stages of B cell mediated (humoral) immunity to eliminate pathogens before there is sufficient IgG. IgM is the main antibody which can undergo agglutination, which is when multiple antibodies of the same subtype group together to create a larger mass which can impede the movement and transmission of infectious agents.

Antibody, biology course for PCAT Exam

Figure 9-9: The different antibody structures.

All immunoglobulins are created by B-cells, which are part of white blood cells, these act as little multi talented factories which identify invading pathogens and secrete appropriate antibodies.

Passive and adaptive immunity

When a microorganism enters the body, there may already be defense systems in place, which has the ability to prevent the development of the infectious agents. These established defenses are called the "innate” immune system. However sometimes the body isn't prepared for an infectious agent and has to create novel defense mechanisms, this is called "adaptive” immunity.

The distinguishing characteristic of adaptive immunity in comparison to in innate immunity is that the response during adaptive immunity creates a specific memory of an infectious agent, which is then imprinted on the innate immune system.

Activated B cells can change into either antibody-producing cells called plasma cells that secrete soluble antibodies or memory cells that can survive in the body for years afterward in order to allow the immune system to remember an antigen and respond faster upon future exposures.

T-Lymphocytes cells

T-Lymphocytes play much the same role as an NK in that it recognizes cells that are infected with an infectious agent and tries to rectify the situation. T-Lymphocytes can actually help macrophages identify intracellular parasites and help macrophages engulf and phagocytose them. T-Lymphocytes do this by recognizing a molecule called the major histocompatibility complex (lets call this MHC for short). MHC is a by-product of a cell, which is in trouble as it is formed form parts of a cell, which are being degraded by an infectious agent.

The lymphatic system

The lymphatic system is composed of a network of vessels throughout the body. The main purpose is to collect unused fluids and return them into the circulatory system. The lymphatic system also contains lymph vessels, lymph nodes, and organs, which help in the absorption of fat (in the villi of the small intestine) and the immune system function.

Lymph vessels are closely associated with the circulatory system vessels. Larger lymph vessels are similar to veins. Lymph capillaries are scatted throughout the body. Contraction of skeletal muscle causes movement of the lymph fluid through valves.

Lymph organs include the bone marrow, lymph nodes, spleen, and thymus. Bone marrow contains tissue that produces lymphocytes. B-lymphocytes (B-cells) mature in the bone marrow. T-lymphocytes (T-cells) mature in the thymus gland. Other blood cells such as monocytes and leukocytes are produced in the bone marrow. Lymph nodes are areas of concentrated lymphocytes and macrophages along the lymphatic veins. The spleen is similar to the lymph node except that it is larger and filled with blood. The spleen serves as a reservoir for blood, and filters or purifies the blood and lymph fluid that flows through it. If the spleen is damaged or removed, the individual is more susceptible to infections. The thymus secretes a hormone, thymosin, that causes pre-T-cells to mature (in the thymus) into T-cells.

Lymphatic system

Figure 9-10: The structural layout of the lymphatic system.

Medical microbiology

The discovery in the 19thCentury that infectious agents were the cause of many diseases was the founding stone of the discipline of medical microbiology. Medical microbiology is the branch of medicine concerned with the prevention, diagnosis and treatment of infectious diseases. You will learn more during the pharmacy graduate program however; there are a few things that will be useful for the PCAT Exam.

A medical microbiologist observes the characteristics of pathogens, their modes of transmission, mechanisms of infection and growth and then uses their knowledge of medicine to control or destroyed the infectious agent.

Increasing importance of emerging antibiotic resistance

As the only sure fire way to kill infectious bacteria is to use antibiotics (anti=against, biotic=living) unfortunately, they are over used. In the US many patients go to their physician with indiscriminate symptoms like a "runny nose” or a temperature and because the physician is not 100% sure of the diagnosis they will often prescribe antibiotics, just in case, i.e. "a cant hurt mentality”. Although it "can't hurt the patient” in the short term, in the long term it can harm the general populace. Furthermore, patients with legitimate bacterial infections who are prescribed antibiotics often do not completely entire course meaning that some bacteria who have been exposed to the antibiotic will escape and be more resistant than other bacteria.

Not all bacteria are created equally; they have similar genes but they are all uniquely different in very small ways. Some reproduce faster than others and some are more susceptible to poisons in the environment than others. An antibiotic is similar to a poison, but is more specific as it selectively kills bacteria and not humans. Some bacteria will be more resistant to antibiotics than others. If you keep using antibiotics that kill susceptible bacteria and just leave the bacteria, which are immune to replicate, soon you will have a lot of immune bacteria. This is what happens in a clinical scenario, if you use antibiotics indiscriminately you will breed "super bugs” which are resistant to whatever you throw at them. A recent example of this is Methicillin Resistant Staphylococcus Aureus (we will call it MRSA for short!). Staphylococcus Aureus is a bacteria and Methicillin is an antibiotic, this bacteria has had so many antibiotics thrown at it has become resistant to a wide range of antibiotics including methicillin and as a result is very hard to kill. This has become a problem in the medical field because if you were to become infected with MRSA the doctors treating you haven't got a lot of options when trying to kill the invading bacteria. The process of a bacteria changing to become more resistant to an antibiotic is called bacterial transformation. These transformations have actually lead to new species of bacteria which are resistant to certain antibiotics, this goes so far that a lot of bacteria and now classified on the basis of their antimicrobial resistance.

For instance, a famous gasification of bacteria is either Gram negative or Gram positive. Both gram-positive and gram-negative bacteria have a cell wall made up of peptidoglycan and a phospholipid bilayer with membrane-spanning proteins, so they are very similar. However, gram-negative bacteria have a unique outer membrane, a thinner layer of peptidoglycan, and a periplasmic space between the cell wall and the membrane. In the outer membrane, gram-negative bacteria have lipopolysaccharides (LPS), porin channels, and murein lipoprotein all of which gram-positive bacteria lack. As opposed to gram-positive cells, gram-negative cells are resistant to certain lysozymes and forms of penicillin (one of the first and most overly used antibiotics). The gram-negative outer membrane, which contains LPS, an endotoxin, blocks antibiotics, dyes, and detergents protecting the sensitive inner membrane and cell wall.

How to test for certain bacteria: The Petri Dish

It would be great if microbiologists could point a device at some bacteria and like a tricorder in Star Trek, it would tell them exactly what species of bacteria it is. Unfortunately, the technology is not at this point yet. We are somewhat limited; you may remember in school you may have done laboratory work where you use an agar jelly (made from seaweed) in a plastic saucer to grow some bacteria. To control the growth of cultures, sometime antibiotics or other substances are added to the agar. A sample is then added to the medium-nutrient mixture and cell culture growth is observed. As it is known that certain bacteria are resistant to certain antibiotics; by placing a range of antibiotics on the petri dish you can make an educated guess about the species of that bacteria by looking at where the bacteria grows.

PCAT Practice Questions

1. Which of the following antibodies is mainly found in bodily secretions?

A. IgB

B. IgG

C. IgM

D. IgA

2. AIDs is caused by which of the following?

A. A retrovirus

B. A bacteria

C. A fungal infection

D. An amoebic infection

3. Which of the following infectious agents is transmitted via the oral fecal route?

A. Tubercle bacillus


C. Norovirus

D. Hepatitis B virus

4. Viruses usually do not contain which of the following?

A. Genetic material

B. Protein coat

C. Capsid

D. Glycoprotein coat

5. Which of the following is not a distinguishing feature of plants?

A. Vacuole

B. Chloroplasts

C. Rigid cellulose cell wall

D. Ribosomes

6. Which of the following terms defines bacteria which get their energy from inorganic chemicals in their environment without the use of light?

A. Photoautotrophs

B. Photoheterotrophs

C. Chemoautotrophs

D. Chemoheterotrophs

Answers and explanations

1. D

The correct option here is option D. IgA is mainly found in mucosal secretions in the genital tract, gut, and the respiratory track. The main secretions include saliva, breast milk and tears.

2. A

The best answer here is option (A), HIV is caused by retrovirus. A retrovirus is an RNA virus that replicates in a host cell using cellular machinery to make copies of itself.

3. C

Norovirus and Rotavirus are viruses which are transmitted by the fecal-oral route. The viruses are transmitted by fecally-contaminated food or water; by person-to-person contact and via aerosolization of the virus and subsequent contamination of surfaces.


The best option here is option D as viruses usually have a phospholipid coat instead of a glycoprotein coat. All viruses must possess some genetic material so that they can replicate themselves so option (A) should be immediately ruled out. Options (B) and (C) can be ruled out because viruses usually have a coating which is either a capsid or a protein coat.


Option (B) here is the odd one out, as many other types of organisms contain ribosomes to convert genetic material into proteins, and therefore is not distinguishing feature of plants. Option (A) Vacuole is a differentiating feature of plants as they are used by plants for a wide range of purposes, including containing water, waste products, maintaining acidic internal pH and maintaining internal hydrostatic pressure and turgor. One of the most distinguishing features of plants is that their green and therefore contain chlorophyll within chloroplasts so Option (B) can be ruled out. Lastly, although other organisms have cell walls such as fungi, fungi cell walls are made of chitin, so option C can be ruled out.


Interior which use chemicals to obtain their energy without the use of photons are called Chemoautotrophs, which is option (D). You can actually figure this out as you can by ruling out option (A) and (B) as the words contain the -photoin it which means light. The difference between heterotrophs and autotrophs, is that heterotrophs get their energy from inorganic substances and autotrophs get energy from organic compounds.

Last modified: Friday, 2 August 2013, 01:08 PM
Last modified: Friday, 3 March 2017, 4:39 AM