Microbiology microorganisms prokaryotes and viruses notes




Microbiology microorganisms prokaryotes and viruses notes


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Microbiology microorganisms prokaryotes and viruses notes


Microbiology Notes A

Microorganisms: Prokaryotes and Viruses

Can you guess what organisms are pictured here? Are they fat green worms on a red leaf? Here’s a clue: There are more organisms like these than any other on Earth. Here’s another clue: Each organisms consists of a single cell without a nucleus.

The organisms are bacteria called Salmonella. If the word Salmonella rings a bell, that’s probably because Salmonella causes human diseases such as food poisoning. Many other types of bacteria also cause human diseases. But not all bacteria are harmful to people. In fact, we could not survive without many of the trillions of bacteria that live in or on the human body. You will learn why when you read this chapter.





  • antibiotic drug

  • antibiotic resistance

  • Archaea

  • Bacteria

  • biofilm

  • cyanobacteria

  • endospore

  • extremophile

  • flagella

  • genetic transfer

  • Gram-negative bacteria

  • Gram-positive bacteria

  • plasmid

  • vector


No doubt you’ve had a sore throat before, and you’ve probably eaten cheese or yogurt. If so, then you’ve encountered the fascinating world of prokaryotes. Prokaryotes are single-celled organisms that lack a nucleus. They also lack other membrane-bound organelles. Prokaryotes are tiny and sometimes bothersome, but they are the most numerous organisms on Earth. Without them, the world would be a very different place.

An overview of bacteria can be seen at http://www.youtube.com/user/khanacademy#p/c/7A9646BC5110CF64/16/TDoGrbpJJ14.


Evolution and Classification of Prokaryotes

Prokaryotes are currently placed in two domains. A domain is the highest taxon, just above the kingdom. The prokaryote domains are Bacteria and Archaea. The third domain is Eukarya. It includes all eukaryotes. Unlike prokaryotes, eukaryotes have a nucleus in their cells.

The Three Domains of Life. All living things are grouped in three domains. The domains Bacteria and Archaea consist of prokaryotes. The Eukarya domain consists of eukaryotes.

Prokaryote Evolution

It’s not clear how the three domains are related. Archaea were once thought to be offshoots of Bacteria that were adapted to extreme environments. For their part, Bacteria were considered to be ancestors of Eukarya. Scientists now know that Archaea share several traits with Eukarya that Bacteria do not share. How can this be explained? One hypothesis is that Eukarya arose when an Archaean cell fused with a Bacterial cell. The two cells became the nucleus and cytoplasm of a new Eukaryan cell.

Comparison of Bacteria, Archaea, and Eukarya






Unique to Bacteria

Unique to Archaea

Unique to Eukarya

Cell Membrane

Unique to Bacteria

Like Bacteria and Eukarya

Unique to Eukarya

Protein Synthesis

Unique to Bacteria

Like Eukarya

Like Archaea


Absent in most



Peptidoglycan (in cell wall)


Absent in most



Domain Bacteria

Bacteria are the most diverse and abundant group of organisms on Earth. They live in almost all environments. They are found in the ocean, the soil, and the intestines of animals. They are even found in rocks deep below Earth’s surface. Any surface that has not been sterilized is likely to be covered with bacteria. The total number of bacteria in the world is amazing. It’s estimated to be 5 × 1030, or five million trillion trillion. You have more bacteria in and on your body than you have body cells!

Bacteria called cyanobacteria are very important. They are bluish green in color because they contain chlorophyll. They make food through photosynthesis and release oxygen into the air. These bacteria were probably responsible for adding oxygen to the air on early Earth. This changed the planet’s atmosphere. It also changed the direction of evolution. Ancient cyanobacteria also may have evolved into the chloroplasts of plant cells.

Cyanobacteria Bloom. The green streaks in this lake consist of trillions of cyanobacteria. Excessive nutrients in the water led to overgrowth of the bacteria.

Thousands of species of bacteria have been discovered, and many more are thought to exist. The known species can be classified on the basis of various traits. One classification is based on differences in their cell walls and outer membranes. It groups bacteria into Gram-positive and Gram-negative bacteria.

Classification of Bacteria. Different types of bacteria stain a different color when stained with Gram stain. This makes them easy to identify.

Domain Archaea

Scientists still know relatively little about Archaea. This is partly because they are hard to grow in the lab. Many live inside the bodies of animals, including humans. However, none are known for certain to cause disease.

Archaea were first discovered in extreme environments. For example, some were found in hot springs. Others were found around deep sea vents. Such Archaea are called extremophiles, or “lovers of extremes.” The picture below describes three different types of Archaean extremophiles. The places where some of them live are thought to be similar to the environment on ancient Earth. This suggests that they may have evolved very early in Earth’s history.

Extremophile Archaea. Many Archaea are specialized to live in extreme environments. Just three types are described here.

Archaea are now known to live just about everywhere on Earth. They are particularly numerous in the ocean. Archaea in plankton may be one of the most abundant types of organisms on the planet. Archaea are also thought to play important roles in the carbon and nitrogen cycles. For these reasons, Archaea are now recognized as a major aspect of life on Earth.


Prokaryote Structure

Most prokaryotic cells are much smaller than eukaryotic cells. Although they are tiny, prokaryotic cells can be distinguished by their shapes. The most common shapes are helices, spheres, and rods.

Prokaryotic Cell Shapes. The three most common prokaryotic cell shapes are shown here.

Plasma Membrane and Cell Wall

Like other cells, prokaryotic cells have a plasma membrane. It controls what enters and leaves the cell. It is also the site of many metabolic reactions. For example, cellular respiration and photosynthesis take place in the plasma membrane.

Most prokaryotes also have a cell wall. It lies just outside the plasma membrane. It gives strength and rigidity to the cell. Bacteria and Archaea differ in the makeup of their cell wall. The cell wall of Bacteria contains peptidoglycan (composed of sugars and amino acids). The cell wall of most Archaea lacks peptidoglycan.

Prokaryotic Cell. The main parts of a prokaryotic cell are shown in this diagram. The structure called a mesosome was once thought to be an organelle. More evidence has convinced most scientists that it is not a true cell structure at all. Instead, it seems to be an artifact of cell preparation. This is a good example of how scientific knowledge is revised as more evidence becomes available. Can you identify each of the labeled structures?

Cytoplasm and Cell Structures

Inside the plasma membrane of prokaryotic cells is the cytoplasm. It contains several structures, including ribosomes, a cytoskeleton, and genetic material. Ribosomes are sites where proteins are made. The cytoskeleton helps the cell keeps its shape. The genetic material is usually a single loop of DNA. There may also be small, circular pieces of DNA, called plasmids. The cytoplasm may contain microcompartments as well. These are tiny structures enclosed by proteins. They contain enzymes and are involved in metabolic processes.

Prokaryotic DNA. The DNA of a prokaryotic cell is in the cytoplasm because the cell lacks a nucleus.

Extracellular Structures

Many prokaryotes have an extra layer, called a capsule, outside the cell wall. The capsule protects the cell from chemicals and drying out. It also allows the cell to stick to surfaces and to other cells. Because of this, many prokaryotes can form biofilms. A biofilm is a colony of prokaryotes that is stuck to a surface such as a rock or a host’s tissues. The sticky plaque that collects on your teeth between brushings is a biofilm. It consists of millions of bacteria.

Most prokaryotes also have long, thin protein structures called flagella (singular, flagellum). They extend from the plasma membrane. Flagella help prokaryotes move. They spin around a fixed base, causing the cell to roll and tumble. Prokaryotes may have one or more flagella.

Bacterial Biofilm. The greatly magnified biofilm shown here was found on a medical catheter (tubing) removed from a patient

Variations in the Flagella of Bacteria. Flagella in prokaryotes may be located at one or both ends of the cell or all around it. They help prokaryotes move toward food or away from toxins.


Many organisms form spores for reproduction. Some prokaryotes form spores for survival. Called endospores, they form inside prokaryotic cells when they are under stress. The stress could be UV radiation, high temperatures, or harsh chemicals. Endospores enclose the DNA and help it survive under conditions that may kill the cell. Endospores are commonly found in soil and water. They may survive for long periods of time.

Prokaryotic Endospores. The red shapes are bacterial cells. The blue-green shapes are endospores.


Prokaryote Metabolism

Like all living things, prokaryotes need energy and carbon. They meet these needs in a variety of ways. In fact, prokaryotes have just about every possible type of metabolism. They may get energy from light (photo) or chemical compounds (chemo). They may get carbon from carbon dioxide (autotroph) or other living things (heterotroph). The table below shows all the possible types of metabolism. Which types of prokaryotes are producers? Which types are consumers?

Metabolism in Prokaryotes

Type of Energy

Source of Carbon: carbon dioxide

Source of Carbon: other organisms




Chemical Compounds



Most prokaryotes are chemoheterotrophs. They depend on other organisms for both energy and carbon. Many break down organic wastes and the remains of dead organisms. They play vital roles as decomposers and help recycle carbon and nitrogen. Photoautotrophs are important producers. They are especially important in aquatic ecosystems.


Prokaryote Habitats

Prokaryote habitats can be classified on the basis of oxygen or temperature. These factors are important to most organisms.

  • Aerobic prokaryotes need oxygen. They use it for cellular respiration. An example is the bacterium that causes the disease tuberculosis (TB). It infects human lungs.

  • Anaerobic prokaryotes do not need oxygen. They use fermentation or other methods of respiration that don’t require oxygen. In fact, some cannot tolerate oxygen. An example is a bacterium that infects wounds and kills tissues, causing a condition called gangrene.


Like most organisms, prokaryotes live and grow best within certain temperature ranges. Prokaryotes can be classified by their temperature preferences, as shown below.

Classification of Prokaryotes by Temperature


Type of Prokaryote

Preferred Temperature

Where It Might Be Found


above 45°C (113°F)

in compost


about 37°C (98°F)

inside animals


below 20°C (68°F)

in the deep ocean


Reproduction in Prokaryotes

Prokaryote cells grow to a certain size. Then they divide through binary fission. For a discussion of exponential growth and bacteria see http://www.youtube.com/watch?v=-3MI0ZX5WRc (10:43).

Binary Fission

Binary fission is a type of asexual reproduction. It occurs when a parent cell splits into two identical daughter cells. This can result in very rapid population growth. For example, under ideal conditions, bacterial populations can double every 20 minutes. Such rapid population growth is an adaptation to an unstable environment. Can you explain why?

Genetic Transfer

In asexual reproduction, all the offspring are exactly the same. This is the biggest drawback of this type of reproduction. Why? Lack of genetic variation increases the risk of extinction. Without variety, there may be no organisms that can survive a major change in the environment.

Prokaryotes have a different way to increase genetic variation. It’s called genetic transfer. It can occur in two ways. One way is when cells “grab” stray pieces of DNA from their environment. The other way is when cells directly exchange DNA (usually plasmids) with other cells. Genetic transfer makes bacteria very useful in biotechnology. It can be used to create bacterial cells that carry new genes.


Bacteria and Humans

Bacteria and humans have many important relationships. Bacteria make our lives easier in a number of ways. In fact, we could not survive without them. On the other hand, bacteria can also make us sick.

Benefits of Bacteria

Bacteria provide vital ecosystem services. They are important decomposers. They are also needed for the carbon and nitrogen cycles. There are billions of bacteria inside the human intestines. They help digest food, make vitamins, and play other important roles. Humans also use bacteria in many other ways, including:

  • Creating products, such as ethanol and enzymes.

  • Making drugs, such as antibiotics and vaccines.

  • Making biogas, such as methane.

  • Cleaning up oil spills and toxic wastes.

  • Killing plant pests.

  • Transferring normal genes to human cells in gene therapy.

  • Fermenting foods.

Fermented Foods. Fermentation is a type of respiration that doesn

Bacteria and Disease

You have ten times as many bacteria as human cells in your body. Most of these bacteria are harmless. However, bacteria can also cause disease. Examples of bacterial diseases include tetanus, syphilis, and food poisoning. Bacteria may spread directly from one person to another. For example, they can spread through touching, coughing, or sneezing. They may also spread via food, water, or objects.

Another way bacteria and other pathogens can spread is by vectors. A vector is an organism that spreads pathogens from host to host. Insects are the most common vectors of human diseases.

Bacterial Disease Vectors. Ticks spread bacteria that cause Lyme disease. Deerflies spread bacteria that cause tularemia.

Humans have literally walked into some new bacterial diseases. When people come into contact with wild populations, they may become part of natural cycles of disease transmission. Consider Lyme disease. It’s caused by bacteria that normally infect small, wild mammals, such as mice. A tick bites a mouse and picks up the bacteria. The tick may then bite a human who invades the natural habitat. Through the bite, the bacteria are transmitted to the human host.

Controlling Bacteria

Bacteria in food or water usually can be killed by heating it to a high temperature (generally, at least 71°C, or 160°F). Bacteria on many surfaces can be killed with chlorine bleach or other disinfectants. Bacterial infections in people can be treated with antibiotic drugs. For example, if you ever had “strep” throat, you were probably treated with an antibiotic.

Antibiotics have saved many lives. However, misuse and over-use of the drugs have led to antibiotic resistance in bacteria. The diagram below shows how antibiotic resistance evolves. Some strains of bacteria are now resistant to most common antibiotics. These infections are very difficult to treat.

Evolution of Antibiotic Resistance in Bacteria. This diagram shows how antibiotic resistance evolves by natural selection.


Lesson Summary

  • Prokaryotes include Bacteria and Archaea. An individual prokaryote consists of a single cell without a nucleus. Bacteria live in virtually all environments on Earth. Archaea live everywhere on Earth, including extreme environments.

  • Most prokaryotic cells are much smaller than eukaryotic cells. They have a cell wall outside their plasma membrane. Prokaryotic DNA consists of a single loop. Some prokaryotes also have small, circular pieces of DNA called plasmids.

  • Prokaryotes fulfill their carbon and energy needs in various ways. They may be photoautotrophs, chemoautotrophs, photoheterotrophs, or chemoheterotrophs.

  • Aerobic prokaryotes live in habitats with oxygen. Anaerobic prokaryotes live in habitats without oxygen. Prokaryotes may also be adapted to habitats that are hot, moderate, or cold in temperature.

  • Prokaryotic cells grow to a certain size. Then they divide by binary fission. This is a type of asexual reproduction. It produces genetically identical offspring. Genetic transfer increases genetic variation in prokaryotes.

  • Bacteria and humans have many important relationships. Bacteria provide humans with a number of services. They also cause human diseases.


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