Nitrogenous Base

Nitrogenous Base Definition

Several chemicals with a similar cyclic structure, each known as a nitrogenous base, play several important roles in biology. Not only is a nitrogenous base the building blocks for genetic information carrying molecules like DNA and RNA, but different forms of the nitrogenous base serve in various cellular roles from signal transduction to growing microtubules.

In DNA and RNA, a nitrogenous base forms a bond with a 5-sided carbon sugar molecule, which forms a “backbone” for the entire molecule. A nitrogenous base plus this sugar backbone is known as a nucleotide, and forms the building blocks of DNA and RNA.

Nitrogenous Base within Nucleic Acids

Purines and Pyrimidines

When talking about a nitrogenous base in the context of DNA or RNA, it is important to note that there are two base classes of nitrogenous base. Every nitrogenous base shares one feature: a six-sided ring with 4 carbon atoms and 2 nitrogen atoms. A purine has an additional 5-sided ring, created by 1 more carbon and 2 more nitrogen atoms. A pyrimidine nitrogenous base has only 1 six-sided ring. Each nitrogenous base has unique bonds, which makes it function in a unique way within the DNA or RNA. Each base can be seen in the image below.

Purines and Pyrimidines

Deoxyribonucleic Acid (DNA)

The image below shows the structure of DNA. DNA has a “backbone” of deoxyribose, shown here as the colorless molecules with a 5’ and 3’ end. These numbers refer to the exposed carbons in the sugar chain, which gives DNA its directionality and readability. This allows various proteins to read and process the DNA efficiently.

DNA chemical structure

Each colored molecule represents a nitrogenous base. Note how each nitrogenous base pairs with the nitrogenous base across from it. This is called base pairing, and is an important part of DNA replication, repair, and maintenance. Seen here in a proper configuration, each pyrimidine pairs with a purine, allowing several hydrogen bonds to be formed. These bonds, the dashed lines in the image above, hold the DNA in a regular spiraling shape, as well as protect the DNA from having a nitrogenous base accidentally break off.

Enzymes which repair and maintain the DNA can “sense” malformations caused by a lack of hydrogen bonding. If, for example, two purines tried to pair they would not be able to form hydrogen bonds. A repair enzyme would find a “bulge” or irregularity in the DNA. Certain enzymes can then slice out and replace the incorrect base.

Ribonucleic Acid (RNA)

There are two noticeable differences between RNA and DNA. The first is in the name itself. Where DNA is built on deoxyribose, RNA is built on ribose. The only difference between ribose and deoxyribose is an oxygen atom.

The second difference between DNA and RNA is that RNA uses a slightly different set of nitrogenous bases. Seen in the image below, an RNA molecule substitutes uracil for thymine. The reasons for this are not fully understood, although RNA is generally a shorter lived molecule. Further, RNA often exists as a single-strand, rather than a double-strand with hydrogen bonds. This is not always the case, as seen in double-stranded RNA viruses, but RNA is typically single stranded in most animals.

RNA structure

Regardless of whether the nucleic acid is DNA or RNA, the basic formula is the same. Take a nitrogenous base, add on a 5-carbon sugar with a phosphorous group, and bind together. The bonds formed between the phosphorous group and the oxygen of the next 5-carbon ring are called a phosphodiester bond, and form the backbone of both RNA and DNA.

How a Nitrogenous Base Carries Genetic Information

Each nitrogenous base carries little information itself. Rather, each nitrogenous base is read as a unit, with two other bases. These three-base information packets are called codons. Each codon specifies a certain amino acid. Put together in proper order and folded into shape, a chain of amino acids creates a protein. These proteins then carry out the functions of life, including everything from growth to reproduction.

It takes around 3,000,000,000 base pairs to create a functioning human. This means that there are around 6,000,000,000 individual bases in each cell of your body. While this may seem like an enormous amount, your body is constantly processing and replicating your DNA. This is probably the main and most important function of a nitrogenous base for any organism.

Nitrogenous Bases in Other Cell Functions

Energy Transfer

Genetic information storing is not the only task of a nitrogenous base. Many are used in the transfer of energy between food molecules like glucose and the energy needs of proteins within the cell. The most recognized of these molecules is adenine triphosphate, more commonly known as ATP. While biology textbooks often refer to this molecule as the cell’s universal energy transfer molecule, it is important to note that it is based on adenine, the nitrogenous base.

While ATP is widely recognized in a number of cellular reactions, it is not the only nitrogenous base that serves in cellular energy transfer. Another molecule, guanine triphosphate (GTP), is used in a number of cellular functions. GTP opens protein channels, aids in the formation of microtubules, and even energizes the import of important proteins into the mitochondria. This in turn helps produce more ATP via aerobic respiration, which powers the cell’s growth.

Cell Signaling

A nitrogenous base can also serve important roles in cell signaling, a process known as signal transduction. The general scheme involves a number of chemical messengers acting on various proteins within a cell to send a signal. A pancreas cell may measure the blood glucose, transduce a signal to release insulin, and disperse the insulin into the blood stream. This process is integrated and coordinated by a number of factors involving a nitrogenous base.

ATP and cyclic adenine monophosphate play important roles in intracellular signaling such as this. Their ratio drives various chemical reactions to different equilibrium points, which in effect drives the activies of the cell. GTP is implicated in a number of pathways from growth and metabolism to signaled cell death (apoptosis).

Quiz

1. How much information does a nitrogenous base carry?
A. One-third of one amino acid
B. None
C. One amino acid

Answer to Question #1

B is correct. While you may have guessed (A), the answer is actually nothing. There are only 5 nitrogenous base molecules, yet there are over 20 amino acids which can be called for. By itself, a single base does not have enough information to specify any one of these. With two other base molecules, it can specify exactly which of the amino acids is called for.

2. Which of the following is NOT a nitrogenous base?
A. Adenine
B. Thymine
C. Ribose

Answer to Question #2

C is correct. Ribose is a sugar molecule which forms the backbone of RNA. From this backbone various nitrogenous base molecules attach and convey genetic information to the ribosomes, which can use the information to build proteins.

3. A scientist is creating synthetic DNA in a laboratory. At first, he decides to use only two synthetic nitrogenous base molecules. Both of them resemble purine molecules. Which of the following problems will the scientist experiment?
A. Nothing, it should work fine.
B. The DNA will not be double stranded.
C. The DNA will twist too much.

Answer to Question #3

B is correct. The DNA will not be double stranded because the double-stranded nature of DNA is due specifically to the opposite attractive nature of purine nitrogenous bases with pyrimidines. Here, without an opposite to pair to, opposing strands of artificial DNA will not attract to each other and form hydrogen bonds. The scientist must create 2 pyrimidine nitrogenous base molecules for the purines to attract to.

References

• Hartwell, L. H., Hood, L., Goldberg, M. L., Reynolds, A. E., & Silver, L. M. (2011). Genetics: From Genes to Genomes. Boston: McGraw Hill.


• Lodish, H., Berk, A., Kaiser, C. A., Krieger, M., Scott, M. P., Bretscher, A., . . . Matsudaira, P. (2008). Molecular Cell Biology (6th ed.). New York: W.H. Freeman and Company.


• Nelson, D. L., & Cox, M. M. (2008). Principles of Biochemistry. New York: W.H. Freeman and Company.

Nitrogenous Base

Paraphyletic

Paraphyletic Definition

Paraphyletic is a term used in evolutionary biology to describe a group of animals which contains a common ancestor and some, but not all, of the descendants. Describing a group of organisms as a paraphyletic group implies that for some reason, some members of the natural group have been placed into another group. There are many reasons this could happen.

Reasons a Group is Paraphyletic

New Understanding

Sometimes, organisms which look incredibly different are actually closely related. Look at the graph below, describing the phylogenetic relationships between different groups of animals.

Traditional Reptilia

This cladogram shows different groups of animals, with the green shaded area representing reptiles, or the taxonomic group “Reptilia”. As is made clear by the picture, reptiles include a group of animals which is paraphyletic. This is a paraphyletic group because it excludes the mammals (“Mammalia”) and the birds (“Aves”). Both of these groups are descendants of the first animals with amniotic development, the “Amniota”. The Amniota, as a group, would include both the birds and the mammals, and would be monophyletic.

Many groups which we consider natural groups, like the reptiles, are actually paraphyletic. While they include many related animals and their ancestors, these paraphyletic groups fail to take into account the whole picture and the diversity of life. While many of these classifications were made in the days when animals were judged solely by their looks. When modern techniques like DNA analysis were able to inform the relationships between animals, new patterns were observed.

Undiscovered Species

Often, we don’t even know that a group we are discussing is paraphyletic. Many species in the world remain undiscovered, which makes them unable to be placed in a phylogeny. If a group doesn’t include all of the existent species, it is a paraphyletic group. A paraphyletic group is not necessarily wrong, as it does show the relationship between organisms and their descendants. However, in analyzing paraphyletic groups, scientists cannot get a full view of the relationships between animals.

Language

Often, the common language for animals outweighs any scientific names ascribed to them. While this is extremely beneficial for average people trying to communicate about various animals, it is often a pain for scientists trying to describe the complex relationships between animals. Consider the word “wasp”. What does that mean to you? It probably means an insect, with wings, a thin abdominal section, and a sharp stinger. While that definition is enough to understand what someone means when they say the word “wasp”, it doesn’t tell you nearly enough if you are an entomologist. Consider the paraphyletic phylogenetic tree below.

Wasps are Paraphyletic

Here, you can clearly see that what laypeople call “wasps” are actually a paraphyletic group which excludes the ants and the bees. When you think about it, it is easy to see how these insects are related to wasps, but it is still wrong to call an ant or a bee a wasp. Yet, according to genetic relationships between the animals, they should all be a part of the same phylogenetic grouping.

Language is a common barrier for evolutionary biologists, and creates many paraphyletic groupings. This is often done unconsciously, as we simply inherit our language from our parents and have to learn how to use it best. For example, while it is now recognized that ants and bees are actually a subset of the paraphyletic wasp grouping, we will always call them ants and bees. Ants will not be called “wingless wasps”, nor will bees become “hairy wasps”. Language has a tendency to stick, making paraphyletic groups more or less a requirement when discussing evolution and the relationships between species.

Quiz

1. A researcher studying the evolution of flying animals groups a bat and a butterfly, and labels them “Things which fly”. What kind of group is this?
A. Paraphyletic
B. Polyphyletic
C. Monophyletic

Answer to Question #1

B is correct. This group, while its members can all fly, did not inherit the trait from a common ancestor. Therefore, instead of sharing a homology, the animals share a homoplasy. This makes the grouping invalid, in terms of the animals actually being related.

2. The advent of modern DNA analysis techniques revealed many paraphyletic groups within the classification schemes backed by science. Why is DNA more revealing than other traits animals have?
A. DNA is unlikely to have a homoplasy.
B. DNA cannot produce mistaken phylogenies.
C. DNA is not more revealing than other methods.

Answer to Question #2

A is correct. A homoplasy, or “false homology”, is a trait which looks the same in two species, but was actually inherited through convergent evolution. When similar environment put similar pressures on different species, they tend to evolve similar adaptations. While DNA analysis can be mistaken, a similar strand of DNA is much more likely to arise through a common ancestor, than through the actual DNA being identical. This is because two proteins which have the same function can have very different amino acids, and come from different DNA. The resulting effect is that DNA shows clearly which animals evolved traits through descent, and which traits simply arose through convergent evolution.

3. In the lab, a scientist goes through pain-staking efforts to create an entirely synthetic species of bacteria. Although the synthetic bacteria looks and functions like a regular bacteria, it is composed of entirely synthetic, non-natural parts. Even the DNA is composed of unique nucleotides, not found in the animal kingdom. The scientist claims that the new bacteria is in a monophyletic group of its own. Is the scientist correct?
A. No, the group is paraphyletic
B. Yes
C. No, there could be other species

Answer to Question #3

B is correct. Yes, in this case the scientist is absolutely correct. The new species, having no ancestors, represents a descendant and all of its ancestors. Unlike other groups of natural animals, it is unrelated to anything else. While it looks like bacteria, it is simply a product of convergent evolution. The group cannot be paraphyletic because there are no more species which could possibly add to the group.

References

• Brusca, R. C., & Brusca, G. J. (2003). Invertebrates. Sunderland, MA: Sinauer Associates, Inc.


• Feldhamer, G. A., Drickamer, L. C., Vessey, S. H., Merritt, J. F., & Krajewski, C. (2007). Mammology: Adaptation, Diversity, Ecology (3rd ed.). Baltimore: The Johns Hopkins University Press.


• Hartwell, L. H., Hood, L., Goldberg, M. L., Reynolds, A. E., & Silver, L. M. (2011). Genetics: From Genes to Genomes. Boston: McGraw Hill.

Paraphyletic

Density Dependent Factors

Density Dependent Factors Definition

Density dependent factors affect a population through increasing or decreasing birth and death rates, in a way that is directly related to the density of the population. Unlike density independent factors, which are not tied to the population density, density dependent factors change how they affect the population as the population changes in size. Like density independent factors, density dependent factors are unique for every population, and density dependent factors for one species or population may not be the same for all populations.

Typically, density dependent factors are biological factors used by the population as a resource. These can be things like food, shelter, or other limited resources. Density dependent factors cause variable changes in the population as its density changes. When the population is small, these factors typically favor increased birth rates and lower death rates, allowing the population to expand. When the population is large and dense, these factors become limited and decrease the birth rate while raising the death rate. This tends to make populations experiencing density dependent factors to show logistic growth, like in the graph below.

Logistic curve

As the graph shows, the population increases rapidly for a time. But, as the density dependent factors change their effects on the population, the growth slows and the population size tends to level off. The various factors which cause this leveling off in the population are density dependent factors. There are usually many density dependent factors involved for a given population. Below are some good examples.

Examples of Density Dependent Factors

Watching Grass Grow

While the saying “watch the grass grow” is often used as a euphemism for boredom, scientists have actually done just that. What they found was a perfect example of density dependent factors affecting the growth rates of an organism.

At first, the scientists had and empty field, freshly tilled with no plants in it. They seeded the field carefully, placing seeds far apart to simulate a low population density. At first, the plants grow exponentially. For several generations, they had all the space and nutrients they needed to grow as fast as they could. Over time, the spaces between the plants filled in, until the field represented a high population density.

At this point, various density dependent factors in the environment switched from positively affecting the plants to negatively affecting them. While nothing changed in the factors themselves, the population became to dense and the resources became source. Consider the resources a plant needs: sunlight, moisture and nutrients. For a plant, all of these resources are tied to the area a plant has access to. If a plant has sole access to a large area, it will receive more nutrients, water and sunlight. As the plants start to crowd in on each other, each plant will have limited access to these valuable resources. At this point, the growth and reproduction of all plants in the population is slowed, and the population gets close to the point of equilibrium, all other things remaining equal.

Fish in a Tank

Likewise, a fish tank is no different than a patch of grass. There are certain density dependent factors which will limit and affect the population size of the organisms in the tank. In a fish tank, the factors are slightly different. Fish need food, oxygen, and a way to detoxify water of their own wastes. These factors are density dependent because they will become drastically more limiting as more fish are added to the fish tank.

In a tank with a low density of fish, each fish has its own space, and has plenty of oxygen. The filter and aerator add oxygen to the water as fast as the fish can consume it, so there is plenty. Likewise, the fish require little food as a collective group, and produce little waste. Their waste can easily be filtered out by the filter, and the owner of the tank can easily distribute food to all the fish. Because there is plenty of room and food, the fish can all get some.

Now consider a tank with an extremely high density of fish, and you can see how these density dependent factors now negatively affect the population growth. In this case, each fish will barely have any space. The amount of oxygen in the water will be depleted, as the filter and aerator cannot keep up with the number of gills in the tank. This reduces the energy and vigor each fish has, reducing their chances of surviving and reproducing. Further, as the fish are so crowded, it doesn’t matter how much the owner feeds them, some fish simply do not get fed. The waste produced by the fish, along with the fish which die from starvation, are too much for the filter to handle and the tank will soon become a stinky mess. The density dependent factors in this case ensure that the population cannot exceed certain limits.

Parasites and Hosts

A well-studied example of density dependent factors comes in the form of parasites and their hosts. When a parasite infects a host, it uses the host’s resources and injures the host. With one parasite, most host’s are fine. It is in the parasite’s best interest to not kill the host, as it can live longer and reproduce more. However, it is also in other parasites’ interest to invade the host. As more and more parasites invade a single host, the host has less and less of a chance of survival. Thus, the parasites are limited by the density dependent factors which keep their host alive. This can be seen in the graph below.

Blackfly life expectancy

This graph shows the life expectancy of a certain species of fly after it ingests different amounts of parasites. As the graph clearly shows, the flies which ingest the fewest parasites live the longest, with a steep drop-off as more parasites enter the system. The flies have a certain amount of energy, nutrients, and damage tolerance. As more parasites enter the system, these density dependent factors don’t necessarily curtail the population density of the parasites. Rather, they kill the host destroy the entire population of parasites. Parasites are opportunistic organisms, and tend to push the limits of their environment in favor of breeding the most.

Quiz

1. Which of the following is a density dependent factor for humans?
A. Food
B. Hurricanes
C. Solar Flare

Answer to Question #1

A is correct. For many organisms, food is a density dependent factor. At low densities, food is almost always readily available. At high densities, it becomes scarce. As humans become denser on this planet, we will need to develop ways to generate more food in less area to overcome this density dependent factor.

2. A volcano erupts on the island of Hawaii, killing off many local organisms in the path of the lava flow. Which category can the volcano go into?
A. Density Independent Factors
B. Density Dependent Factors
C. Neither

Answer to Question #2

A is correct. Unlike density dependent factors, a volcano affects any organism in its path, regardless of density. The organism could have been the last of its kind, or one of many, but it will still be negatively impacted by the volcano.

3. Many people have forecasted that because of the exponential growth of humans over the last several decades, that the trend will continue and we will overshoot our carrying capacity. Why is this unlikely?
A. It is VERY likely. We’re DOOMED!
B. Density dependent factors drive logistic growth.
C. We will get hit by an asteroid before that time.

Answer to Question #3

B is correct. As the first graph in this section shows, most populations are subject to logistic growth, which levels off as it reaches a certain height. In fact, human statisticians have shown that as populations get denser and people attain greater wealth, they tend to have less babies. This trend is happening world-wide, and most experts agree that the human population is leveling off.

References

• Cain, M. L., Bowman, W. D., & Hacker, S. D. (2008). Ecology. Sunderland, MA: Sinauer Associates, Inc.


• Feldhamer, G. A., Drickamer, L. C., Vessey, S. H., Merritt, J. F., & Krajewski, C. (2007). Mammology: Adaptation, Diversity, Ecology (3rd ed.). Baltimore: The Johns Hopkins University Press.


• Kaiser, M. J., Attrill, M. J., Jennings, S., Thomas, D. N., Barnes, D. K., Brierley, A. S., & Hiddink, J. G. (2011). Marine Ecology: Processes, Systems, and Impacts. New York: Oxford University Press.

Density Dependent Factors

Facultative Anaerobe

Facultative Anaerobe Definition

A facultative anaerobe is an organism which can survive in the presence of oxygen, can use oxygen in aerobic respiration, but can also survive without oxygen via fermentation or anaerobic respiration. Most eukaryotes are obligate aerobes, and cannot survive without oxygen. Prokaryotes tolerate a wide range of oxygen, from obligate anaerobes which are poisoned by oxygen, to facultative anaerobes and obligate aerobes. Some prokaryotes are even aerotolerant, meaning they can survive in oxygen, but use anaerobic pathways for energy.

A facultative anaerobe can experience the best of both worlds. In times of low oxygen, a facultative anaerobe can use fermentation or anaerobic respiration to create ATP for the cells, typically still from the breakdown of glucose. The only real difference in these pathways from aerobic respiration is that they use a different electron receptor at the end of the pathway. Aerobic respiration relies on oxygen to accept electrons at the end of the electron transport chain. A facultative anaerobe can use a variety of other pathways to deal with these extra electrons, as discussed in the examples.

It should be noted that facultative anaerobes are sometimes referred to as facultative aerobes. The terms are generally interchangeable.

Examples of a Facultative Anaerobe

Yeast

A common facultative anaerobe is yeast, used in various cooking applications such as making bread or beer. In either case, this facultative anaerobe must function without oxygen. Yet, the yeast can still survive, and must for these products to come out right.

In bread, yeast is responsible for making the bubbles in the dough. These pockets of air make the bread light and fluffy. Otherwise, the bread would bake into a solid mass more like a cake or brownie. Yeast creates these air pockets through the release of carbon dioxide, a byproduct of converting the glucose in the dough into energy. For a lighter, more airy dough chefs often let the dough “rise”. This term simply means setting the yeast-laden dough in a warm place, and allowing the facultative anaerobe to do its work. Over the course of an hour or so, the yeast will create large amounts of carbon dioxide within the dough, expanding it and making it lighter.

In beer, wine, and other alcoholic beverages, yeast is the key ingredient. The process of fermentation, or the creation of alcohol, occur in yeast when they have plenty of sugar but little oxygen. Brewers and wine-makers use this aspect of the facultative anaerobe to generate the alcohol within their products. Aerobic respiration completely reduces glucose to a few recyclable molecules and carbon dioxide. Fermentation, on the other hand, leaves a final product: ethanol. Beer and wine makers create the ethanol (an alcohol) in their products by strictly controlling the amount of sugar and oxygen in their fermentation tanks. In these conditions any facultative anaerobe will resort to fermentation, and put off ethanol as a byproduct. When the alcohol reaches the proper level in the mixture, the yeast are filtered out and the drink is bottled.

Mollusks

While most think only of small, single-celled facultative anaerobes, several larger groups of animals have evolved the ability to survive without oxygen. One of these, the mollusks, has a group of organisms which have adapted to regularly survive stints without oxygen. Mussels, often found in intertidal areas, experience daily shifts in their access to water. When the tide drops, the mussels become exposed to the air, and must close their shells to avoid drying out. In some areas, the tide can go out for significant periods of time. The mussels cannot open their shells to get oxygen, or risk drying out and dying of dehydration.

To solve their conundrum, mussels like those in the image above have evolved the abilities of a facultative anaerobe. Instead of relying on their normal aerobic respiration when the tide goes out, the mussels switch to a form of energy which breaks down amino acids. This allows the mussel to survive hours, or even days, without getting a fresh source of oxygen.

Quiz

1. Humans muscles rely on aerobic respiration to produce the ATP necessary to work them. However, in times of stress and intense exercise, these muscles often run out of oxygen. In this case, the muscles must resort to a form of fermentation which produces lactic acid. Lactic acid can damage cells when it builds up, so the cells must quickly revert to aerobic respiration if they are to survive. Are humans facultative anaerobes?
A. No
B. Yes
C. Maybe

Answer to Question #1

A is correct. Humans are usually considered obligate aerobes, as we need oxygen pretty much all the time. Although our muscles can survive short bursts without oxygen, our bodies are still actively working on getting oxygen to the muscles. Lactic acid is a temporary, short-term fix that can last only a few minutes. However, the line between facultative anaerobe and obligate aerobe is not clear, as many animals have alternate methods of generating energy when oxygen is low.

2. What is the difference between a facultative anaerobe and an obligate anaerobe?
A. A facultative anaerobe only has anaerobic pathways.
B. An obligate anaerobe can survive the presence of oxygen.
C. A facultative anaerobe can survive and use oxygen.

Answer to Question #2

C is correct. A facultative anaerobe can switch between aerobic and anaerobic metabolisms. An obligate anaerobe does not have this capability. Oxygen, to an obligate anaerobe, is toxic. To a facultative anaerobe, oxygen represents an opportunity to make more ATP than normally possible.

3. While scientists used to believe that facultative anaerobe organisms were typically single-celled remnants of an earlier time, evidence has showed that many gut parasites are often facultative anaerobes. Which of the following provides an explanation of this fact?
A. These organisms have a constant access to oxygen.
B. Often, areas of the gut are anaerobic, forcing these organisms to use an anaerobic pathway.
C. These organisms do not represent a facultative anaerobe.

Answer to Question #3

B is correct. The gut is a dangerous place, for obligate aerobes. The gut of most animals receives little to no oxygen input. Yet, every once in a while animals will swallow small pockets of air or oxygen is present in their food. Gut parasites, hoping to make the most of these conditions, can operate without oxygen. But, when oxygen is present they want to take advantage and produce as much energy as possible.

References

• Brusca, R. C., & Brusca, G. J. (2003). Invertebrates. Sunderland, MA: Sinauer Associates, Inc.


• Muller, M., Mentel, M., Hellemond, J., & Henze, K. (2012). Biochemistry and Evolution of Anaerobic Energy Metabolism in Eukaryotes. Microbiology and Molecular Biology Reviews. doi:10.1128/MMBR.05024-11


• University of Comenius. (2018, October 3). Anaerobic Bacteria. Retrieved from Jfmed.uniba.sk: https://www.jfmed.uniba.sk/fileadmin/jlf/Pracoviska/ustav-mikrobiologie-a-imunologie/ANAEROBIC_BACTERIA.pdf

Facultative Anaerobe

Facultative Anaerobe

Facultative Anaerobe Definition

A facultative anaerobe is an organism which can survive in the presence of oxygen, can use oxygen in aerobic respiration, but can also survive without oxygen via fermentation or anaerobic respiration. Most eukaryotes are obligate aerobes, and cannot survive without oxygen. Prokaryotes tolerate a wide range of oxygen, from obligate anaerobes which are poisoned by oxygen, to facultative anaerobes and obligate aerobes. Some prokaryotes are even aerotolerant, meaning they can survive in oxygen, but use anaerobic pathways for energy.

A facultative anaerobe can experience the best of both worlds. In times of low oxygen, a facultative anaerobe can use fermentation or anaerobic respiration to create ATP for the cells, typically still from the breakdown of glucose. The only real difference in these pathways from aerobic respiration is that they use a different electron receptor at the end of the pathway. Aerobic respiration relies on oxygen to accept electrons at the end of the electron transport chain. A facultative anaerobe can use a variety of other pathways to deal with these extra electrons, as discussed in the examples.

It should be noted that facultative anaerobes are sometimes referred to as facultative aerobes. The terms are generally interchangeable.

Examples of a Facultative Anaerobe

Yeast

A common facultative anaerobe is yeast, used in various cooking applications such as making bread or beer. In either case, this facultative anaerobe must function without oxygen. Yet, the yeast can still survive, and must for these products to come out right.

In bread, yeast is responsible for making the bubbles in the dough. These pockets of air make the bread light and fluffy. Otherwise, the bread would bake into a solid mass more like a cake or brownie. Yeast creates these air pockets through the release of carbon dioxide, a byproduct of converting the glucose in the dough into energy. For a lighter, more airy dough chefs often let the dough “rise”. This term simply means setting the yeast-laden dough in a warm place, and allowing the facultative anaerobe to do its work. Over the course of an hour or so, the yeast will create large amounts of carbon dioxide within the dough, expanding it and making it lighter.

In beer, wine, and other alcoholic beverages, yeast is the key ingredient. The process of fermentation, or the creation of alcohol, occur in yeast when they have plenty of sugar but little oxygen. Brewers and wine-makers use this aspect of the facultative anaerobe to generate the alcohol within their products. Aerobic respiration completely reduces glucose to a few recyclable molecules and carbon dioxide. Fermentation, on the other hand, leaves a final product: ethanol. Beer and wine makers create the ethanol (an alcohol) in their products by strictly controlling the amount of sugar and oxygen in their fermentation tanks. In these conditions any facultative anaerobe will resort to fermentation, and put off ethanol as a byproduct. When the alcohol reaches the proper level in the mixture, the yeast are filtered out and the drink is bottled.

Mollusks

While most think only of small, single-celled facultative anaerobes, several larger groups of animals have evolved the ability to survive without oxygen. One of these, the mollusks, has a group of organisms which have adapted to regularly survive stints without oxygen. Mussels, often found in intertidal areas, experience daily shifts in their access to water. When the tide drops, the mussels become exposed to the air, and must close their shells to avoid drying out. In some areas, the tide can go out for significant periods of time. The mussels cannot open their shells to get oxygen, or risk drying out and dying of dehydration.

To solve their conundrum, mussels like those in the image above have evolved the abilities of a facultative anaerobe. Instead of relying on their normal aerobic respiration when the tide goes out, the mussels switch to a form of energy which breaks down amino acids. This allows the mussel to survive hours, or even days, without getting a fresh source of oxygen.

Quiz

1. Humans muscles rely on aerobic respiration to produce the ATP necessary to work them. However, in times of stress and intense exercise, these muscles often run out of oxygen. In this case, the muscles must resort to a form of fermentation which produces lactic acid. Lactic acid can damage cells when it builds up, so the cells must quickly revert to aerobic respiration if they are to survive. Are humans facultative anaerobes?
A. No
B. Yes
C. Maybe

Answer to Question #1

A is correct. Humans are usually considered obligate aerobes, as we need oxygen pretty much all the time. Although our muscles can survive short bursts without oxygen, our bodies are still actively working on getting oxygen to the muscles. Lactic acid is a temporary, short-term fix that can last only a few minutes. However, the line between facultative anaerobe and obligate aerobe is not clear, as many animals have alternate methods of generating energy when oxygen is low.

2. What is the difference between a facultative anaerobe and an obligate anaerobe?
A. A facultative anaerobe only has anaerobic pathways.
B. An obligate anaerobe can survive the presence of oxygen.
C. A facultative anaerobe can survive and use oxygen.

Answer to Question #2

C is correct. A facultative anaerobe can switch between aerobic and anaerobic metabolisms. An obligate anaerobe does not have this capability. Oxygen, to an obligate anaerobe, is toxic. To a facultative anaerobe, oxygen represents an opportunity to make more ATP than normally possible.

3. While scientists used to believe that facultative anaerobe organisms were typically single-celled remnants of an earlier time, evidence has showed that many gut parasites are often facultative anaerobes. Which of the following provides an explanation of this fact?
A. These organisms have a constant access to oxygen.
B. Often, areas of the gut are anaerobic, forcing these organisms to use an anaerobic pathway.
C. These organisms do not represent a facultative anaerobe.

Answer to Question #3

B is correct. The gut is a dangerous place, for obligate aerobes. The gut of most animals receives little to no oxygen input. Yet, every once in a while animals will swallow small pockets of air or oxygen is present in their food. Gut parasites, hoping to make the most of these conditions, can operate without oxygen. But, when oxygen is present they want to take advantage and produce as much energy as possible.

References

• Brusca, R. C., & Brusca, G. J. (2003). Invertebrates. Sunderland, MA: Sinauer Associates, Inc.


• Muller, M., Mentel, M., Hellemond, J., & Henze, K. (2012). Biochemistry and Evolution of Anaerobic Energy Metabolism in Eukaryotes. Microbiology and Molecular Biology Reviews. doi:10.1128/MMBR.05024-11


• University of Comenius. (2018, October 3). Anaerobic Bacteria. Retrieved from Jfmed.uniba.sk: https://www.jfmed.uniba.sk/fileadmin/jlf/Pracoviska/ustav-mikrobiologie-a-imunologie/ANAEROBIC_BACTERIA.pdf

Facultative Anaerobe

Facultative Anaerobe

Facultative Anaerobe Definition

A facultative anaerobe is an organism which can survive in the presence of oxygen, can use oxygen in aerobic respiration, but can also survive without oxygen via fermentation or anaerobic respiration. Most eukaryotes are obligate aerobes, and cannot survive without oxygen. Prokaryotes tolerate a wide range of oxygen, from obligate anaerobes which are poisoned by oxygen, to facultative anaerobes and obligate aerobes. Some prokaryotes are even aerotolerant, meaning they can survive in oxygen, but use anaerobic pathways for energy.

A facultative anaerobe can experience the best of both worlds. In times of low oxygen, a facultative anaerobe can use fermentation or anaerobic respiration to create ATP for the cells, typically still from the breakdown of glucose. The only real difference in these pathways from aerobic respiration is that they use a different electron receptor at the end of the pathway. Aerobic respiration relies on oxygen to accept electrons at the end of the electron transport chain. A facultative anaerobe can use a variety of other pathways to deal with these extra electrons, as discussed in the examples.

It should be noted that facultative anaerobes are sometimes referred to as facultative aerobes. The terms are generally interchangeable.

Examples of a Facultative Anaerobe

Yeast

A common facultative anaerobe is yeast, used in various cooking applications such as making bread or beer. In either case, this facultative anaerobe must function without oxygen. Yet, the yeast can still survive, and must for these products to come out right.

In bread, yeast is responsible for making the bubbles in the dough. These pockets of air make the bread light and fluffy. Otherwise, the bread would bake into a solid mass more like a cake or brownie. Yeast creates these air pockets through the release of carbon dioxide, a byproduct of converting the glucose in the dough into energy. For a lighter, more airy dough chefs often let the dough “rise”. This term simply means setting the yeast-laden dough in a warm place, and allowing the facultative anaerobe to do its work. Over the course of an hour or so, the yeast will create large amounts of carbon dioxide within the dough, expanding it and making it lighter.

In beer, wine, and other alcoholic beverages, yeast is the key ingredient. The process of fermentation, or the creation of alcohol, occur in yeast when they have plenty of sugar but little oxygen. Brewers and wine-makers use this aspect of the facultative anaerobe to generate the alcohol within their products. Aerobic respiration completely reduces glucose to a few recyclable molecules and carbon dioxide. Fermentation, on the other hand, leaves a final product: ethanol. Beer and wine makers create the ethanol (an alcohol) in their products by strictly controlling the amount of sugar and oxygen in their fermentation tanks. In these conditions any facultative anaerobe will resort to fermentation, and put off ethanol as a byproduct. When the alcohol reaches the proper level in the mixture, the yeast are filtered out and the drink is bottled.

Mollusks

While most think only of small, single-celled facultative anaerobes, several larger groups of animals have evolved the ability to survive without oxygen. One of these, the mollusks, has a group of organisms which have adapted to regularly survive stints without oxygen. Mussels, often found in intertidal areas, experience daily shifts in their access to water. When the tide drops, the mussels become exposed to the air, and must close their shells to avoid drying out. In some areas, the tide can go out for significant periods of time. The mussels cannot open their shells to get oxygen, or risk drying out and dying of dehydration.

To solve their conundrum, mussels like those in the image above have evolved the abilities of a facultative anaerobe. Instead of relying on their normal aerobic respiration when the tide goes out, the mussels switch to a form of energy which breaks down amino acids. This allows the mussel to survive hours, or even days, without getting a fresh source of oxygen.

Quiz

1. Humans muscles rely on aerobic respiration to produce the ATP necessary to work them. However, in times of stress and intense exercise, these muscles often run out of oxygen. In this case, the muscles must resort to a form of fermentation which produces lactic acid. Lactic acid can damage cells when it builds up, so the cells must quickly revert to aerobic respiration if they are to survive. Are humans facultative anaerobes?
A. No
B. Yes
C. Maybe

Answer to Question #1

A is correct. Humans are usually considered obligate aerobes, as we need oxygen pretty much all the time. Although our muscles can survive short bursts without oxygen, our bodies are still actively working on getting oxygen to the muscles. Lactic acid is a temporary, short-term fix that can last only a few minutes. However, the line between facultative anaerobe and obligate aerobe is not clear, as many animals have alternate methods of generating energy when oxygen is low.

2. What is the difference between a facultative anaerobe and an obligate anaerobe?
A. A facultative anaerobe only has anaerobic pathways.
B. An obligate anaerobe can survive the presence of oxygen.
C. A facultative anaerobe can survive and use oxygen.

Answer to Question #2

C is correct. A facultative anaerobe can switch between aerobic and anaerobic metabolisms. An obligate anaerobe does not have this capability. Oxygen, to an obligate anaerobe, is toxic. To a facultative anaerobe, oxygen represents an opportunity to make more ATP than normally possible.

3. While scientists used to believe that facultative anaerobe organisms were typically single-celled remnants of an earlier time, evidence has showed that many gut parasites are often facultative anaerobes. Which of the following provides an explanation of this fact?
A. These organisms have a constant access to oxygen.
B. Often, areas of the gut are anaerobic, forcing these organisms to use an anaerobic pathway.
C. These organisms do not represent a facultative anaerobe.

Answer to Question #3

B is correct. The gut is a dangerous place, for obligate aerobes. The gut of most animals receives little to no oxygen input. Yet, every once in a while animals will swallow small pockets of air or oxygen is present in their food. Gut parasites, hoping to make the most of these conditions, can operate without oxygen. But, when oxygen is present they want to take advantage and produce as much energy as possible.

References

• Brusca, R. C., & Brusca, G. J. (2003). Invertebrates. Sunderland, MA: Sinauer Associates, Inc.


• Muller, M., Mentel, M., Hellemond, J., & Henze, K. (2012). Biochemistry and Evolution of Anaerobic Energy Metabolism in Eukaryotes. Microbiology and Molecular Biology Reviews. doi:10.1128/MMBR.05024-11


• University of Comenius. (2018, October 3). Anaerobic Bacteria. Retrieved from Jfmed.uniba.sk: https://www.jfmed.uniba.sk/fileadmin/jlf/Pracoviska/ustav-mikrobiologie-a-imunologie/ANAEROBIC_BACTERIA.pdf

Facultative Anaerobe

Density Independent Factors

Density Independent Factors Definition

Density independent factors, in ecology, refer to any influences on a population’s birth or death rates, regardless of the population density. Density independent factors are typically a physical factor of the environment, unrelated to the size of the population in question. Density independent factors vary depending on the population, but always affect the population the same regardless of its size. There are many common density independent factors, such as temperature, natural disasters, and the level of oxygen in the atmosphere. These factors apply to all individuals in a population, regardless of the density.

However, density independent factors are often confused density dependent factors for a number of reasons. First, density independent factors for one population of organisms is not the same for every organism on the planet. While oxygen is a density independent factor for most oxygen breathing organisms, it may be a density dependent factor for some. Image an obligate anaerobe bacteria, for instance. Oxygen is toxic to these organisms. As they grow in density, the bacteria furthest from the nearest source of oxygen is protected. If these bacteria where to grow thick, oxygen would not affect each bacteria, and the effect on the death rate would be lessened. This would make oxygen a density dependent factor for these particular bacteria.

Analyzing each population specifically allows scientists to identify their unique density independent factors. Below are several examples of common density independent factors and how they affect various species.

Examples of Density Independent Factors

Natural Disaster

Natural disaster is a perfect example of a density independent factor. Consider a hurricane, slamming into the coastline. While we often see the devastation of these storms on the news, we rarely consider the impacts of such a storm on wildlife and vegetation in the area. The fact is, hurricanes increase the death rate for many species, while some species see a highly increased birthrate after the destruction.

During a hurricane, winds increase to dangerous speeds, tearing large trees out of the ground. Trees like the one in the image above would survive any regular storm. For many species, a hurricane drastically increases the death rate, as the trees simply cannot withstand the wind and waves. Many animals, such as fish and amphibians, succumb to rapidly rising and falling tides. Many news images show pictures of fish washed up into roadways. These animals and plants die, regardless of how dense their population was. They could have been the last of their species, or one in a billion.

Yet, hurricanes do not only bring death. Consider the area unearthed by the tree in the above image. New, smaller plants will be given an opportunity to grow where they were previously restricted by the shade cast by the large tree. Fungi and insects living on dead plant matter will be able to feast and reproduce on the dead wood. The standing water left from the hurricane provides many insects, such as mosquitos, ample breeding sites. While this is often a nuisance for humans, it increases the food source of birds and bats, possibly increasing their birthrates as well. Yet, the hurricane affects all species and individuals within its path, regardless of how many there were.

Pollution

Like other density independent factors, pollution is a good example of a density independence. While humans are concentrated in cities around the globe, the emissions and chemicals we create are dispersed into the atmosphere. From here, they are carried globally and affect all organisms. Even organisms in the oceans are affected, as pollutants dissolve from the atmosphere into various water sources.

Therefore, whether you are the last pair of endangered clownfish in the ocean or have a huge population like sparrows, your birthrate is still negatively impacted. Density independent factors like these often cause a slow and steady drag on populations over time. Even the human population sees drastic health effects from pollution, from lead poisoning do to drinking water to increased lung diseases.

Honeybees

Instead of looking at density independent factors in general, let’s turn our view to a population of honeybees and the factors that likely affect the size of their population. Density independent factors for honeybees include things like weather and temperature. Regardless of the current size of their population, bees need the temperature and weather to stay within certain ranges. If the weather does not stick to this pattern, many bees will die. For example, if there was suddenly snowstorm in the middle of summer, the bees would be caught off guard and would die in the cold.

However, the bees also face a number of density dependent factors. For instance, their food source and its effects on their population is directly related to the size of their population. If they have a small population, there will be plenty of food for all and the bees will grow. If the population is larger than the amount of food available, bees will starve and the death rate will increase. Food, and other usable biological resources, are density dependent. Density independent factors will affect the bees regardless of how many bees are present.

Quiz

1. In a small garden patch under a small tree, several species of plant are planted in differing numbers. Consider the sunlight as a resource for the plants. Is sunlight one of the density independent factors, or is it density dependent?
A. Density Independent Factor
B. Density Dependent Factor
C. Neither

Answer to Question #1

B is correct. As the plants grow, they will take up a larger and larger area, competing for the sunlight. As the years go by, the tree will get larger, and take up more of the sunlight. If more plants are added to the area, there will be even less sunlight to go around. Density independent factors, such as weather events, will affect the plants regardless of how many are in the garden. Sunlight will be more beneficial to the plants if there are less of them in the garden.

2. Do density independent factors always limit the population? That is, do they always increase the death rate or lower the birth rate?
A. No
B. Yes
C. Only Density dependent factors do that

Answer to Question #2

A is correct. Any factor, density dependent or independent, can be either beneficial or negative. This all depends on the population being affected. Some density independent factors, such as hurricanes, help some species while they hurt other species. Hurricanes are a density independent factor because they generate the same effect regardless of the current population density.

3. A population of field mice increases after a farmer leaves his field unharvested for a season. Which of the following categories does this factor fall into?
A. Density Independent Factors
B. Density Dependent Factors
C. Increased death rate

Answer to Question #3

B is correct. Food is almost always a density dependent factor, because if the population gets too big the food abundance will quickly turn to a food shortage. Density independent factors would be things like temperature and tornadoes, which would affect the mice regardless of their current or future density.

References

• Cain, M. L., Bowman, W. D., & Hacker, S. D. (2008). Ecology. Sunderland, MA: Sinauer Associates, Inc.


• Feldhamer, G. A., Drickamer, L. C., Vessey, S. H., Merritt, J. F., & Krajewski, C. (2007). Mammology: Adaptation, Diversity, Ecology (3rd ed.). Baltimore: The Johns Hopkins University Press.


• Kaiser, M. J., Attrill, M. J., Jennings, S., Thomas, D. N., Barnes, D. K., Brierley, A. S., & Hiddink, J. G. (2011). Marine Ecology: Processes, Systems, and Impacts. New York: Oxford University Press.

Density Independent Factors

Obligate Anaerobes

Obligate Anaerobes Definition

Obligate anaerobes are organism which can only live in environments which lack oxygen. Unlike the majority of organisms in the world, these organisms are poisoned by oxygen. Obligate anaerobes are typically bacteria, and live in a variety of places naturally. Many obligate anaerobes live in the human body, in places like the mouth and gastrointestinal tract where oxygen levels are very low. Sometimes, these bacteria can accidentally be deposited where they are not supposed to be, causing serious infection. Some obligate anaerobes include the bacteria which cause gangrene and a number of other infections. Below is a microscope slide showing the Clostridium genus of bacteria, responsible for gangrene, tetanus, botulism, colitis, and other serious infections.

Clostridium acetobutylicum

Why are Obligate Anaerobes Killed in Oxygen?

Unlike obligate aerobes, which require oxygen to survive, obligate anaerobes are actually poisoned by it. Unlike many organisms which thrive in oxygenated environments, obligate anaerobes do not have several key enzymes needed to detoxify oxygen in the cell. Oxygen itself, in the presence of water, produces several byproducts including hydrogen peroxide (H2O2). Hydrogen peroxide is a weak acid, and affects a number of enzymes within anaerobic cells. In high levels of oxygen, the cell becomes so acidic that it can no longer function.

This is why obligate anaerobes typically are only found in areas of little to no oxygen. At this level, their metabolic enzymes are not sufficiently hampered by the changes oxygen causes. Aerobic bacteria and eukaryotes have a number of defense mechanisms against oxygen. These include the enzymes superoxide dismutase, catalase, and peroxidase, which help deal with the byproducts of oxygen by keeping them as oxygen gas or making them into harmless water molecules.

Evolutionary Significance of Obligate Anaerobes

The existence of obligate anaerobes is a significant clue in the theory of the origins of life on planet Earth. While our atmosphere has a significant amount of oxygen now, that may not have always been the case. The presence of obligate anaerobes today suggests that the atmosphere once had much less oxygen, allowing bacteria to survive without oxygen facilitating enzymes. The theory suggests that with the rise of photosynthetic organisms, there also came a rise in the level of oxygen in the environment.

Where Obligate Anaerobes Exist

Today, the obligate anaerobes exist in many environments, all which have a defining quality of low oxygen levels. Many obligate anaerobes exist in the soil, away from the top layers which are highly exposed to oxygen. Other obligate anaerobes can be found in the gut, mouth, and reproductive tracts of animals. In these places, they is little to no oxygen because they are not exposed to blood vessels.

Sometimes, a severe infection can be caused when these bacteria get access to the sterile internal areas of the body. This typically happens when an organism is wounded, allowing the bacteria access to the normally closed-off areas. If the wound gets closed quickly and in a sterile manner, the bacteria will die in the presence of the oxygenated blood that gets to the area. If the wound does not have blood flow and is exposed to obligate anaerobes, it gives them a place to breed and grow. Many of these obligate anaerobes release toxins which destroy regular tissue. This caused the infection to get worse, and allows the bacteria to spread. Many infections caused by obligate anaerobes can be deadly if left untreated.

Finding Obligate Anaerobes

Obligate anaerobes can only be found in environments with low oxygen levels. In a world saturated by oxygen, this may seem like obligate anaerobes may be hard to find. But in fact, the opposite is true. Obligate anaerobes can be found in almost every environment, hidden away from expose to oxygen. To find the obligate anaerobes in any sample a simple experiment like the one below can be conducted.

Anaerobic

The five images shown above represent where different types of bacteria can be found in a sample grown in a loosely capped test tube. The loose cap allows oxygen to saturate the top layer of the growth solution in the tube. Thus, image 1 represents the obligate aerobes, or the organisms which need oxygen. The obligate anaerobes, seen in image 2, are at the complete other side of the test tube.

At this end of the test tube, the oxygen concentration is the lowest. For one, it has to diffuse through the entire column of water to reach the bottom of the test tube. Without being disturbed or aerated in any way, the oxygen level will naturally be the lowest here. Further, the organisms in the tube which use oxygen will tend to congregate towards the top. These organisms will tend to deplete the oxygen within the test tube at all levels. This helps drive the oxygen gradient towards the top of the tube. Therefore, scientists searching for obligate anaerobes simply need to look in the most oxygen deprived portion of any sample. The other images (3-5) represent other kinds of bacteria, such as facultative anaerobes, which can survive in various conditions and may or may not need or use oxygen.

Quiz

1. The following is a list of bacteria and their main metabolic functions. Which of these are obligate anaerobes?

1. A bacterium which uses oxygen to facilitate glucose metabolism


2. A bacterium which tolerates oxygen, but does not use it in metabolism


3. A bacterium which does not tolerate oxygen, and does not use it in metabolism

A. All of the above
B. 2 and 3 only
C. 3 only

Answer to Question #1

C is correct. Obligate anaerobes are obligated to stay in an anaerobic environment. This means they cannot survive oxygen. A bacterium which tolerates oxygen, but doesn’t use it is known as a aerotolerant bacteria.

2. A scientist takes a sample from the bottom of a nearby lake. He divides the sample into three test tubes. In the first test tube, he adds an air pump. In the second test tube, he seals the cap and removes the oxygen. The third tube he leaves unsealed, and undisturbed. Which tubes will NOT grow obligate anaerobes?
A. Tubes 1 and 3
B. Tube 1 only
C. Tube 2 only
D. Tube 3 only

Answer to Question #2

B is correct. Only tube 1 will be saturated with oxygen, making it nearly impossible for anaerobic bacteria to survive. Without the ability to process the byproducts of oxygen metabolism, the bacteria would quickly die due to exposure to oxygen-based toxins.

3. Obligate anaerobes are often spore-forming, meaning that in times of stress the bacteria will store their DNA in a secured package which can whether environmental conditions. Why is it important that obligate anaerobes create spores capable of surviving conditions of high oxygen?
A. It is not important
B. These spores must survive oxygenated environments to colonize low-oxygen areas
C. These spores can use oxygen to help reproduce the bacteria

Answer to Question #3

B is correct. The modern atmosphere consists of mainly of nitrogen, but has around 21% oxygen. This is an extremely high amount for obligate anaerobes, and would typically kill them. The spore secures the DNA from oxygen degradation, and allows it to travel to a favorable environment before growing into a functioning bacteria.

References

• Lodish, H., Berk, A., Kaiser, C. A., Krieger, M., Scott, M. P., Bretscher, A., . . . Matsudaira, P. (2008). Molecular Cell Biology (6th ed.). New York: W.H. Freeman and Company.


• University of Comenius. (2018, October 3). Anaerobic Bacteria. Retrieved from Jfmed.uniba.sk: https://www.jfmed.uniba.sk/fileadmin/jlf/Pracoviska/ustav-mikrobiologie-a-imunologie/ANAEROBIC_BACTERIA.pdf


• Widmaier, E. P., Raff, H., & Strang, K. T. (2008). Vander’s Human Physiology: The Mechanisms of Body Function (11th ed.). Boston: McGraw-Hill Higher Education.

Obligate Anaerobes

Competition

Competition Definition in Biology

Competition is a relationship between organisms in which one is harmed when both are trying to use the same resource related to growth, reproduction, or survivability. Competition stems from the fact that resources are limited. There are simply not enough of some resources for all individuals to have equal access and supply. Competition can occur between organisms of the same species, or between members of different species.

Competition between species can either lead to the extinction of one of the species, or a decline in both of the species. However, this process can often be interrupted by environmental disturbances or evolution, which can change the rules of the game. Competition is often involved when species are limited in their range, often by direct competition from other organisms.

Examples of Competition

Intraspecific Competition

Intraspecific competition is a density-dependent form of competition. “Intra” refers to within a species, as opposed to “inter” which means between. Intraspecific competition can be summed up in the image below.

Intraspecific competition

In this image, two wild dogs known as Dholes fight over a carcass. The carcass is a resource, something both organisms need to survive. Intraspecific competition is density dependent for one reason. The more dholes you have, the less food each one gets. To the individual dhole, food is everything. With very few predators of their own, the most successful dholes (the ones who survive and reproduce the most) often are simply the ones who eat the most.

Thus, while these dholes may have coordinated to take down this deer, they are now competing to see which one will get to eat first. The one that eats first will get more, and be more likely to survive and reproduce. The other one (or the last one if there are many) will not get as much. This will lower its survivability and the chances it will get to reproduce. Since evolution relies mainly on which organisms reproduce, this form of competition can quickly lead to changes in a population if only a few of the individuals are surviving and reproducing.

Interspecific Competition

Interspecific competition is between individuals which are different species. This could be between any two species, as long as they are competing over a resource. An interesting example of interspecific competition is found in coastal marine environments, like the coral reef in the picture below.

In this picture, there are dozens of species. There are several species of fish. Behind them, as a backdrop many people would ignore, is a canvas of dozens of species of coral. Coral, while it may look like some sort of rock or plant, is actually a colony of tiny animals. These tiny animals filter organic material from the water, and use stored bacteria to photosynthesize sunlight for additional energy. Thus, each coral species is competing with not only the other corals, but also with the fish for available nutrients and sunlight.

While corals might not seem like a competitive bunch, they are actually directly competitive with other corals. When an enemy coral is encroaching on their space, they can deploy chemical warfare to counter their rival. Often, coral fights end in one of the corals being killed by the other. While the corals are not predators of each other, the competition still ends in the death of one of the corals. The victorious coral was simply fighting for the resources it needs.

Direct and Indirect Competition

There is also another aspect of competition that can be applied to scenarios of limited resources, and that is the idea of direct vs indirect competition. Direct competition is like both of the scenarios above, and there are many more examples of it. Any time two or more animals fight or have a symbolized confrontation, this is probably some sort of competition for a resource.

However, indirect competition is when the two animals do not interact, but the presence of both animals in the same territory causes the competition. Think of the fish in the example above. If those fish feed on the same resources used by the corals, then the fish are in competition for the limited resources. Coral, being more or less anchored to the ocean floor, have little chance of directly attacking the fish. Instead, this would be referred to as an asymmetrical indirect competition. The fish eat as much of the food as they want, and the coral are limited to scraps. The coral have no way of competing. Luckily for most coral reef systems around the world, the ocean has plenty of food for most.

Outcomes of Competition

Competition is not a static process. Once set in motion, it can go a number of different ways. While the models may show that it will eventually drive one species to extinction, in reality a number of things can happen. First, an environmental disturbance, such as a fire or large wave, can upset the ecosystem and destroy the advantage the best competitor had. Typically, a pinewood forest is made mostly of pine trees because they are the best competitors in the environment. However, after a forest fire the most populous plants are small, opportunistic plants that grow quickly. The fire causes a change in the environment, which completely changes the dynamics of competition.

Further, most competition is also an evolutionary pressure on both parties. Animals from both sides that compete the best are able to survive and reproduce. Thus, over time the competition tends to resolve itself. More often than not, the competition can devolve as the species adapt to use different resources or change the way it uses a resource. This is known as character displacement. It is most well-documented in finches. When two different species of finch live on separate islands, their beaks are the same size because they prefer similar seeds. When they occupy the same island, one of their beaks gets smaller while the other gets larger. This separates the resources they consume and alleviates the competition.

Quiz

1. Which of the following represents competition?
A. Two swans (male and female) doing a mating dance
B. A lion defends its kill from a pack of hyenas
C. A lion stalks a buffalo, ready to pounce

Answer to Question #1

B is correct. In this case, the lion’s kill represents the resource. It needs the food to survive and reproduce. But so do the hyenas. Because they are fighting for it, it makes it direct competition. When the lion was stalking the buffalo that would be predation, which is different than competing for a resource. Two swans doing a ritualistic dance would be a form of intraspecies communication.

2. What is the difference between intra- and interspecific competition?
A. Intraspecific is between members of the same species
B. Interspecific is between members of the same species
C. They are the same

Answer to Question #2

A is correct. While the different forms of competition can be about similar resources, they are often carried out in different ways. Intraspecific competition often occurs when the resource is within the species, such as access to females. Interspecific competition is easiest remembered as different predators fighting over the same piece of meat.

3. A bald eagle is flying over a field, and sees a smaller hawk. The hawk has a fresh kill, but the bald eagle swoops in, threatens the hawk, and steals it. Which term best describes this scenario?
A. Predation
B. Intraspecific, indirect competition
C. Interspecific, direct competition

Answer to Question #3

C is correct. In this case, the bald eagle directly attacks and steals a resource from another species. If the species of hawk could no longer compete, because the eagles had already eaten all of the prey, that would be indirect competition. There are many other forms of indirect competition, but in this case the animals compete for the food directly.

References

• Cain, M. L., Bowman, W. D., & Hacker, S. D. (2008). Ecology. Sunderland, MA: Sinauer Associates, Inc.


• Feldhamer, G. A., Drickamer, L. C., Vessey, S. H., Merritt, J. F., & Krajewski, C. (2007). Mammology: Adaptation, Diversity, Ecology (3rd ed.). Baltimore: The Johns Hopkins University Press.


• Kaiser, M. J., Attrill, M. J., Jennings, S., Thomas, D. N., Barnes, D. K., Brierley, A. S., & Hiddink, J. G. (2011). Marine Ecology: Processes, Systems, and Impacts. New York: Oxford University Press.

Competition

Lytic Cycle

Lytic Cycle Definition

The lytic cycle is named for the process of lysis, which occurs when a virus has infected a cell, replicated new virus particles, and bursts through the cell membrane. This releases the new virions, or virus complexes, so they can infect more cells.

As seen in the graphic above, the lytic cycle is often accompanied by the lysogenic cycle in many bacteria viruses, known as bacteriophages. After the virus injects its DNA or RNA into the host bacteria, the genetic material can enter either the lytic cycle or the lysogenic cycle.

In the lysogenic cycle, the bacteriophage DNA lies practically dormant. However, whenever the bacteria divides, the DNA of the virus is inadvertently copied. In this way, the virus can continue replicating within its host. As long as the bacteria are successful, the virus may remain dormant. At a certain point, conditions may change, and the virus will enter the lytic cycle.

In this cycle, the viral DNA or RNA is expressed by the host organism’s cellular mechanisms. In other words, the viral genes use the proteins within the cell to replicate themselves and produce viral proteins. These proteins and copies of the DNA will become new virions. The cell, helpless to its viral hijacker, simply waits until the pressure of these new virions is too high. Then, the cell membrane breaks. This lysis of the cell releases the virions created in the lytic cycle. Their final destination is a new cell, in which the lytic cycle can take place again. If conditions are favorable and the cell is dividing, the virus may stay in the lysogenic cycle for a time. Ultimately, to infect a greater number of cells, more virus genomes will enter the lytic cycle and produce thousands or millions of copies of themselves in a shorter amount of time.

Steps of the Lytic Cycle

Bacteriophage lysogenic and lytic cycle

Adsorption and Penetration

Adsorption is the process through which a bacteria gets its DNA or RNA into the host cell. This is labeled as 1 in the image above. The capsid, or protein coat around the viral genome, consists of very specific proteins. This sheild of proteins not only comes together to protect the viral genes, it serves as a sort of “key” to unlock a cell. The surface of the proteins are shaped to interact with proteins on the surface of the host cell.

When the “lock and key” align, the virion is bound to the cell membrane. When this happens, it also changes the shape of the capsid. This tears a hole or injects the viral DNA into the host cell. Here, it may travel into the nucleus or replicate in the cytoplasm. This depends on the virus itself, what type of genome it has, and the conditions of the cell.

Replication

During the lytic cycle, the replication of viral genes is carried out a number of times by a hijacked cellular system. Remember that the virus itself has imported few, if any, supporting proteins. Thus, the viral DNA must produce these in order to hijack the cell’s processes. The first proteins created are often created as the cell reads its own DNA and produces proteins. The viral genes simply sneak into the process. This creates what are called viral early proteins.

These early proteins have important functions (to the virus) of commandeering the cell’s machinery. They clear the cell’s normal metabolic agenda, and turn many of its activities toward the replication of viral genes and the production of viral proteins. The virus uses the raw products the cell has assembled (amino acids and nucleic acids) as building blocks for the parts it needs.

While this may seem like an overly complex process for such a small virus genome, consider first that there are really only a handful of proteins. Most viruses produce and code for only a handful of proteins. Unlike cells, a virus doesn’t need the complex proteins required to metabolize energy. As obligate parasites, a virus is dependent upon its host cell’s ability to provide raw materials. This makes it one of the most efficient forms of DNA replication that we know of.

Assembly and Release

As these parts are built, their natural evolutionary shapes help them come together in the proper way. Since most of the components are proteins, they have formed over evolutionary time to be able to come together with very little outside influence. The assembly of new virions is a hallmark of the lytic cycle. The other viral life cycle does not include producing and assembling new virions.

In this way, the lytic cycle resembles a small virus factory. All of the parts of the virus are produced independently, then assembled, and finally released into the environment. While the image above shows only 3 assembled virions at stage 6, in reality there would be millions. Compare the lytic cycle to the lysogenic cycle below it, in which an accurate 2 copies are shown after 1 bacterial division.

Quiz

1. Which of the following represents the lytic cycle?
A. Viral DNA is replicated as the host cell divides.
B. The viral genome takes over the host cell, and creates a virus factory.
C. The viral genome is mostly dormant.

Answer to Question #1

B is correct. Remember that the lytic cycle is like a factory. It takes over the cell and tries to make as many virions as fast as possible. Eventually, this overwhelms the cell and causes it to lyse, or break open. This is the reason it is called the lytic cycle. The lysogenic cycle is a much more dormant version of the viral life cycle. It is a passive state in which the viral genes get replicated as a byproduct of cell division.

2. Which life cycle, the lytic cycle or the lysogenic cycle, produces the most virions?
A. It depends
B. The lytic cycle
C. The lysogenic cycle

Answer to Question #2

A is correct. While the lytic cycle is a factory for new virions and is a clear answer, the question did not specify a time frame. If a virion infects a cell, instantly enters the lytic cycle and kills the cell, then it has only produced a million virions and now needs a new host. A bacteriophage genome which enters the lysogenic cycle may be inadvertently copied into millions of cells itself. Then, if even only a few of these enter the lytic cycle, that bacteriophage will far outnumber the previous example. In other words, it depends entirely on how long the lysogenic cycle is allowed to continue.

3. Based on what you now know about the lytic cycle, why is it so hard to eradicate the common cold?
A. It shouldn’t be!
B. The virus changes too much.
C. In targeting the mechanisms viruses use, you target the mechanisms every cell uses.

Answer to Question #3

C is correct. In most forms of medicine, a basic treatment to a disease is to take away the underlying cause. However, because viruses use the same machinery your healthy cells use, there is no way to target them specifically. If we did, we might accidently destroy all the cells in our body. I would rather get a cold.

References

• Brusca, R. C., & Brusca, G. J. (2003). Invertebrates. Sunderland, MA: Sinauer Associates, Inc.


• Lodish, H., Berk, A., Kaiser, C. A., Krieger, M., Scott, M. P., Bretscher, A., . . . Matsudaira, P. (2008). Molecular Cell Biology (6th ed.). New York: W.H. Freeman and Company.


• McMahon, M. J., Kofranek, A. M., & Rubatzky, V. E. (2011). Plant Science: Growth, Development, and Utilization of Cultivated Plants (5th ed.). Boston: Prentince Hall.

Lytic Cycle

Lytic Cycle

Lytic Cycle Definition

The lytic cycle is named for the process of lysis, which occurs when a virus has infected a cell, replicated new virus particles, and bursts through the cell membrane. This releases the new virions, or virus complexes, so they can infect more cells.

As seen in the graphic above, the lytic cycle is often accompanied by the lysogenic cycle in many bacteria viruses, known as bacteriophages. After the virus injects its DNA or RNA into the host bacteria, the genetic material can enter either the lytic cycle or the lysogenic cycle.

In the lysogenic cycle, the bacteriophage DNA lies practically dormant. However, whenever the bacteria divides, the DNA of the virus is inadvertently copied. In this way, the virus can continue replicating within its host. As long as the bacteria are successful, the virus may remain dormant. At a certain point, conditions may change, and the virus will enter the lytic cycle.

In this cycle, the viral DNA or RNA is expressed by the host organism’s cellular mechanisms. In other words, the viral genes use the proteins within the cell to replicate themselves and produce viral proteins. These proteins and copies of the DNA will become new virions. The cell, helpless to its viral hijacker, simply waits until the pressure of these new virions is too high. Then, the cell membrane breaks. This lysis of the cell releases the virions created in the lytic cycle. Their final destination is a new cell, in which the lytic cycle can take place again. If conditions are favorable and the cell is dividing, the virus may stay in the lysogenic cycle for a time. Ultimately, to infect a greater number of cells, more virus genomes will enter the lytic cycle and produce thousands or millions of copies of themselves in a shorter amount of time.

Steps of the Lytic Cycle

Bacteriophage lysogenic and lytic cycle

Adsorption and Penetration

Adsorption is the process through which a bacteria gets its DNA or RNA into the host cell. This is labeled as 1 in the image above. The capsid, or protein coat around the viral genome, consists of very specific proteins. This sheild of proteins not only comes together to protect the viral genes, it serves as a sort of “key” to unlock a cell. The surface of the proteins are shaped to interact with proteins on the surface of the host cell.

When the “lock and key” align, the virion is bound to the cell membrane. When this happens, it also changes the shape of the capsid. This tears a hole or injects the viral DNA into the host cell. Here, it may travel into the nucleus or replicate in the cytoplasm. This depends on the virus itself, what type of genome it has, and the conditions of the cell.

Replication

During the lytic cycle, the replication of viral genes is carried out a number of times by a hijacked cellular system. Remember that the virus itself has imported few, if any, supporting proteins. Thus, the viral DNA must produce these in order to hijack the cell’s processes. The first proteins created are often created as the cell reads its own DNA and produces proteins. The viral genes simply sneak into the process. This creates what are called viral early proteins.

These early proteins have important functions (to the virus) of commandeering the cell’s machinery. They clear the cell’s normal metabolic agenda, and turn many of its activities toward the replication of viral genes and the production of viral proteins. The virus uses the raw products the cell has assembled (amino acids and nucleic acids) as building blocks for the parts it needs.

While this may seem like an overly complex process for such a small virus genome, consider first that there are really only a handful of proteins. Most viruses produce and code for only a handful of proteins. Unlike cells, a virus doesn’t need the complex proteins required to metabolize energy. As obligate parasites, a virus is dependent upon its host cell’s ability to provide raw materials. This makes it one of the most efficient forms of DNA replication that we know of.

Assembly and Release

As these parts are built, their natural evolutionary shapes help them come together in the proper way. Since most of the components are proteins, they have formed over evolutionary time to be able to come together with very little outside influence. The assembly of new virions is a hallmark of the lytic cycle. The other viral life cycle does not include producing and assembling new virions.

In this way, the lytic cycle resembles a small virus factory. All of the parts of the virus are produced independently, then assembled, and finally released into the environment. While the image above shows only 3 assembled virions at stage 6, in reality there would be millions. Compare the lytic cycle to the lysogenic cycle below it, in which an accurate 2 copies are shown after 1 bacterial division.

Quiz

1. Which of the following represents the lytic cycle?
A. Viral DNA is replicated as the host cell divides.
B. The viral genome takes over the host cell, and creates a virus factory.
C. The viral genome is mostly dormant.

Answer to Question #1

B is correct. Remember that the lytic cycle is like a factory. It takes over the cell and tries to make as many virions as fast as possible. Eventually, this overwhelms the cell and causes it to lyse, or break open. This is the reason it is called the lytic cycle. The lysogenic cycle is a much more dormant version of the viral life cycle. It is a passive state in which the viral genes get replicated as a byproduct of cell division.

2. Which life cycle, the lytic cycle or the lysogenic cycle, produces the most virions?
A. It depends
B. The lytic cycle
C. The lysogenic cycle

Answer to Question #2

A is correct. While the lytic cycle is a factory for new virions and is a clear answer, the question did not specify a time frame. If a virion infects a cell, instantly enters the lytic cycle and kills the cell, then it has only produced a million virions and now needs a new host. A bacteriophage genome which enters the lysogenic cycle may be inadvertently copied into millions of cells itself. Then, if even only a few of these enter the lytic cycle, that bacteriophage will far outnumber the previous example. In other words, it depends entirely on how long the lysogenic cycle is allowed to continue.

3. Based on what you now know about the lytic cycle, why is it so hard to eradicate the common cold?
A. It shouldn’t be!
B. The virus changes too much.
C. In targeting the mechanisms viruses use, you target the mechanisms every cell uses.

Answer to Question #3

C is correct. In most forms of medicine, a basic treatment to a disease is to take away the underlying cause. However, because viruses use the same machinery your healthy cells use, there is no way to target them specifically. If we did, we might accidently destroy all the cells in our body. I would rather get a cold.

References

• Brusca, R. C., & Brusca, G. J. (2003). Invertebrates. Sunderland, MA: Sinauer Associates, Inc.


• Lodish, H., Berk, A., Kaiser, C. A., Krieger, M., Scott, M. P., Bretscher, A., . . . Matsudaira, P. (2008). Molecular Cell Biology (6th ed.). New York: W.H. Freeman and Company.


• McMahon, M. J., Kofranek, A. M., & Rubatzky, V. E. (2011). Plant Science: Growth, Development, and Utilization of Cultivated Plants (5th ed.). Boston: Prentince Hall.

Lytic Cycle