CBL  1.1

The information in this introduction/overview is covered in depth in this and later modules.

CLASSIFYING LIVING THINGS: THE THREE DOMAINS

The Three Domain System, developed by Carl Woese in 1990, is a system for classifying biological organisms. Before Woese's discovery of archaea as distinct from bacteria in 1977, scientists believed there were only two types of life: eukarya and bacteria.

The highest ranking previously used had been "kingdom," based on the Five Kingdom system adopted in the late 1960s (based on principles developed by Swedish scientist Carolus Linnaeus, whose system groups organisms based on common physical characteristics.)

The Current System

As scientists learn more about organisms, classification systems change. Genetic sequencing has given researchers a whole new way of analysing relationships between organisms. The current Three Domain System groups organisms primarily based on differences in ribosomal RNA (rRNA) structure.

Under this system, organisms are classified into three domains and six kingdoms.

The domains are:

• Archaea

• Bacteria

• Eukarya (Eukaryotes)

The kingdoms are:

• Eubacteria (Bacteria - true bacteria)

• Archaebacteria (Archaea - ancient bacteria)

• Protista (Protists)

• Fungi

• Plantae (Plants)

• Animalia (Animals)

Scientists use a tool called a phylogenetic tree (see diagrams below) or a “tree of life” to reflect the evolutionary relationships among organisms or groups of organisms. Scientists consider phylogenetic trees to be a hypothesis of the evolutionary past because we cannot go back to confirm the proposed relationships. 

Many phylogenetic trees have a single point at the base, representing a common ancestor. The point where a split occurs, called a branch point, represents where a distinct new line evolved. It is important to note that although they share an ancestor, it does not mean that the groups of organisms evolved from each other. Notice that the three domains— Bacteria, Archaea, and Eukarya—diverge from a single point and branch off. The small branch that plants and animals (including humans) occupy in this diagram shows how recent and tiny these groups are compared with other organisms. 

1. Prokaryotes

Prokaryotes are microscopic, single-celled organisms. In prokaryotes all the water-soluble components, proteins, DNA, and metabolites are located together in the cytoplasm enclosed by the cell membrane, rather than in separate cellular compartments (called organelles). They do not have a distinct nucleus with a membrane, and no other specialised organelles. 

Prokaryotes include both the bacteria and the archaea (pronounced arkey-a). Prokaryote life seems to have started just over 4 billion years ago, feeding off the early carbon dioxide, carbon monoxide, steam, nitrogen, hydrogen, and ammonia atmosphere. 

Typical prokaryotes are minute rods or cocci (spheres) about 0.5–5.0 μm in diameter or length. The category also includes: 

• organisms as small as mycoplasmas, with diameters of only 0.1–0.3 μm and undefined shapes, due to their lack of cell walls

• organisms as large as Epulopiscium, which grows to 300 μm in length. 

The prokaryote classification includes all of the blue–green bacteria or cyanobacteria (previously called blue–green algae).

Archaea were only discovered in the 1970s and classified into a separate domain in 1977. 

a) Bacteria

Bacteria are microscopic, single-celled, prokaryotic organisms that thrive in diverse environments that range from the soil to the ocean and inside the human gut.

Bacteria (singular: bacterium) are classified as prokaryotes because they are single-celled organisms with a simple internal structure that lacks a nucleus, and contains DNA that either floats freely in a twisted, thread-like mass called the nucleoid, or in separate, circular pieces called plasmids. 

Humans' relationship with bacteria is complex. Sometimes bacteria lend us a helping hand, such as by curdling milk into yogurt or helping with our digestion. In other cases, bacteria are destructive, causing diseases like pneumonia and Staphylococcus aureus (MRSA, Golden Staph).

Bacteria can be distinguished by the nature of their cell walls, by their shape, or by differences in their genetic makeup.  There are three basic bacterial shapes: Cylindrical, capsule-shaped ones known as bacilli (singular: bacillus); round bacteria called cocci (singular: coccus),; and spiral bacteria, called spirilla (singular: spirillum).  

b) Archaea

Archaea are a group of microscopic single-cell organisms that were discovered in the early 1970s. There is still much about archaeans that is not known. Many live and thrive under some of the most extreme conditions, such as extremely hot, acidic, or alkaline environments.

Ways they are like bacteria:

• they are single-celled prokaryotes, meaning they lack membrane-bound organelles, including a nucleus

• they have a typical prokaryotic cell anatomy:  plasmid DNA, cell wall, cell membrane, cytoplasm, and ribosomes

• some also have long, whip-like protrusions called flagella, thread-like structures that allow organisms to move by propelling them through their environment  

• they come in a variety of shapes including cocci (round), bacilli (rod-shaped), and irregular shapes. 

Ways they are different from bacteria:

Archaeans were originally thought to be bacteria until DNA analysis showed that they are so very different that scientists had to come up with a new classification group. 

• The genetic code of rRNA is very different from bacteria, reflecting differing evolutionary paths. (This still needs to be confirmed by sequencing the 16s rRNA of more organisms.)

• They have very different genes encoding their flagella, and these are made of different proteins.

• Their genes resemble eukaryotes more than they do bacteria.

• The cell wall in bacteria contains peptidoglycans (a molecule composed of both protein and sugar rings), but archaea do not have this compound in their cell walls.

• Cell division in archaea involves processes not found in bacteria.

• Bacteria can form spores that lie dormant for years, until a proper habitat is found in which they can grow, but Archaea haven't been found to do that.

2. Eukaryotes

Eukaryotes can be unicellular (the Protists) or multicellular organisms (fungi, plants and animals). Virtually all the life we see each day belongs to the third domain, Eukaryota. 

Eukaryotic cells are more complex than prokaryotes. The DNA is linear and found within a nucleus. Eukaryotic cells boast their own personal "power plants", called mitochondria. These tiny organelles in the cell  produce chemical energy. 

a) Protists

Protists are  very diverse, but they are typically unicelluar and less complex in structure than other eukaryotes.   Protists do not share many similarities, but are grouped together because they do not fit into any of the other kingdoms. Some protists are capable of photosynthesis; some are single celled; some are multicellular or form colonies; some are microscopic; some are enormous (giant kelp); some are bioluminescent; and some are responsible for a number of diseases that occur in plants and animals. Protists live in aquatic environments, moist land habitats, or even inside other eukaryotes. 

As eukaryotes, they have a nucleus that is surrounded by a membrane. In addition to a nucleus, protists have additional organelles, eg mitochondria, in their cytoplasm.  Some types include ciliates, flagellates, pseudopods.

b) Fungi

Fungi (singular: fungus) are a kingdom of eukaryotic organisms that are heterotrophs (cannot make their own food) and have important roles in nutrient cycling in an ecosystem. Some fungi are single-celled (yeast), while others are multicellular. As eukaryotes, fungi cells have a membrane-bound nucleus and organelles. Some fungi are responsible for diseases in humans eg fungal nail infection (#4), tinea (#5) and Candida (#6)

Click arrow to progress images. 

c) Plants

d) Animals

Many people animals are only the mammals, like people and lions as the only animals. But the animal kingdom includes many diverse organisms such as worms and moths and spiders and starfish, as well as fish and snakes and birds. 

A cell is the smallest structural and functional unit of an organism. [Cells are made from atoms, so they are larger than molecules, macromolecules and viruses] 

Our bodies are made up of many millions of cells, usually a combination of different types of cells having different functions (specialisations).

The most basic cell is made up of:

• a nucleus (the part of the cell that controls all its functions)

• cytoplasm (the jellylike substance that surrounds the nucleus)

• organelles (smaller cell structures that perform a specific cell function; organelles means "little organs")

• a cell membrane (the  'wall' through which materials pass in and out of the cell). 

Reminder: there are two main classes of cells: prokaryotic cells (prokaryotes) and eukaryotic cells (eukaryotes). 

PROKARYOTIC CELLS (bacteria, archaea)

Generally, unicellular organisms are prokaryotes. 

Prokaryotic cells: 

• lack a true nucleus that isolates genetic material (DNA/RNA) from its organelles

• DO NOT have membrane-bound organelles (ie organelles do not have a membrane as the outer layer)

• contain ribosomes (for protein synthesis)

The diagrams below are of a prokaryotic cell.

EUKARYOTIC CELLS

Generally, multicellular organisms are made up of eukaryotic cells. Eukaryotic cells are the more evolved version of prokaryotic cells. 

Eukaryotic cells have:

• membrane- bound organelles (eg mitochondria) 

• a true nucleus that isolates DNA material from the rest of the organelles in the cytoplasm  (The nucleus is basically the ‘brain’ of the cell. It stores all the DNA and transmits  information for the cell activities to be carried out. This includes controlling the process of protein-synthesis.)

• mitochondrion that creates energy for the cell to use

• lysosome that processes waste material

• rough endoplasmic reticulum where many different types of proteins are processed and put together in processes called transcription and translation

• smooth endoplasmic reticulum that manufactures lipids and metabolises sugars and other materials for the cell to use later

• ribosomes that create proteins

• chromatin, the cell's genetic material, that is kept in the nucleus. 

Eukaryotic cells are much more complex than prokaryotes.  The cell diagram below is of an animal cell, which is a eukaryotic cell.  

ORGANELLES

A significant difference between prokaryotes and eukaryotes, and between eukaryotic plants and animals, arises from the absence or presence of organelles. 

An organelle is a membrane-bound (surrounded by a 3-D membrane) structure found within a cell  - think of organelles as smaller rooms within a factory, with specialised conditions to help these rooms carry out their specific task (like a pantry stocked with food). These organelles are found in the cytoplasm, a viscous (flowing) liquid found within the cell membrane that houses the organelles and is the location of most of the action happening in a cell. Below is a table of the organelles found in eukaryotic cells. 

NOTE: There are more than just organelles in the cytoplasm. There are other substances such as amino acids, dissolved mineral ions, sugars, enzymes (proteins) that are essential for cell activities in the cytoplasm of the million of cells that makes up a multicellular organism.

Plant and Animal Cells

Although plants and animals are both composed of eukaryotic cells, there are important differences in some of their organelles, and in the structure of their cells.

The inner structures, and through those some insights into the functions, of cells began with the development of the microscope.

Light Microscopes

The light microscope, often referred to as the optical microscope, uses visible light and a system of lenses to magnify images of small objects. Optical microscopes are the oldest design of microscope. 

Simple light microscope

Has a single lens, found in the eyepiece. 

Compound microscope

A compound light microscope is a microscope with more than one lens and its own light source. In this type of microscope, there are ocular lenses in the eyepiece and objective lenses in a rotating nosepiece closer to the specimen. 

This produces a greater degree of magnification compared to the single lens of the simple microscope.

The compound microscope provides enough magnification power to observe cell structures that cannot be seen using a simple microscope.

Introduction and use of the electron microscope:

Electron microscope employs beams of electrons and is used to:

• analyse the surface of a specimen, providing information regarding the surface landscape and chemical composition

• observe the complex, internal structure of cell specimens and their organelles: eg the discovery of the structural similarities between the endoplasmic reticulum and peroxisomes led to the understanding of how these organelles allowed proteins to travel between these organelle and led to the  identification of peroxisome biogenesis disorder (disease)

• locate and track molecules and compounds in the body to further our understanding on chemical reaction pathways

Biologist reporting to others sometimes need to represent diagrams of what they are seeing under the microscope. It is important when they do this to accurately represent size, just as cartographers do on a map. They use scaled diagrams. 

There are 3 aspects to drawing scaled diagrams of cells:

1. determining magnification used when viewing under a microscope, and distinguishing it from resolution

2. determining size of an object seen under a microscope using field of view and magnification

3. drawing diagrams to scale 

2. Field of View:

• Field of view is the size of the viewing area you can see when looking through a microscope.

View Videos:

• Field of View https://www.youtube.com/watch?time_continue=253&v=iNh3FatqAAY [8.30 mins] 

• Microscopes & Field of View https://www.youtube.com/watch?v=x_4I3WZ4eqI [15.01 mins]