Microbiology is the study of microscopic organisms that have no cells, and includes fungi, viruses, and bacteria (discussed ). Pathogenic microbes are microbes which cause human disease.

Fungi is a kingdom (defined ). Examples of phyla (again, defined ) of fungi include ascomycota, basidiomycota, and zygomycota, all of whom end in “myocota” from Greek “mykes” meaning “mushroom”. Although oomycetes were originally a division of fungi, they are now considered protists, which are a diverse group of eukaryotic microorganisms, which do not fit into other kingdoms.

Fungi is unique as their cell walls contain resilient chitin, as supposed to plants whose cell wall contain cellulose.

Whereas plants produce energy from nutrients taken from its surrounding, and is known as autotrophy; fungi cannot and instead obtain energy by consuming other organisms, known as heterotrophy. Fungi are exo-digesters, meaning they digest food outside their bodies by excreting enzymes, then absorb digested material through the cell walls. Fungi are commonly [but not necessarily] saprophytic, meaning they feed on dead or decaying matter.

Most fungi grow as hyphae, which are thread-like structures. The interconnected network of hyphae is known as mycelium. Fungi typically have a haploid nuclei (single set of chromosomes, discussed ), but [also] have a diploid stage. Fungi is able to reproduce by sexual or asexual means. Sexual reproduction is preferred when rapid population growth is required (no partner is required so it’s quicker) in favorable environments, whilst sexual reproduction is preferred when rapid genetic diversity is required for adaptation to unfavorable environments. Many fungi also produce haploid spores for asexual reproduction. Spores are reproductive structures.

An example of a fungus is yeast, which are a single-celled organism, which reproduce most commonly by budding, but some also by fission. Budding is a form of asexual reproduction where a new organism develops as a bud out of another one. Yeasts are facultative anaerobes, which are organisms that make ATP by aerobic respiration if oxygen is present, but is also capable of switching to fermentation [into ethanol] if oxygen is absent.

Formative learning activity	Maps to RK3.B
What are fungi?

Viruses are so small, most can’t be seen with an optical microscope, and are about 1/100 the size of the average bacteria, thereby being able to infect bacteria, known as bacteriophage. Viruses are not alive, and hence don’t belong to a kingdom. Life involves the ability to metabolize macronutrients to create energy. Viruses are infectious agents that must be parasitic, meaning it requires a host cell’s metabolic process and enzymes to reproduce. Viruses are parasitic, as they don’t have cellular structure [of organelle and nucleus], and thus can’t replicate via cell division. The complete virus particle, from outside to in, contains:

• Lipid envelope, which is acquired from the host cell membrane, and surrounds the virion to protect itself when outside. Envelopes are found in many animal viruses
• Capsid, which is a protective coat of protein. Capsids are classified according to structure, and are usually either helical or icosahedral. Icosahedral is a shape with 20 sides
  • Viroids are RNA molecules that aren’t classified as virions, because they lack a protein coat. Viroids are pathogenic to plants
• Inner content, including:
  • Nucleic acid, which is either DNA or RNA [but not both], which contains genetic information. Irrespective of whether DNA or RNA, nucleic acids can be either single or double-stranded. Single strands can be either plus strand, which is similar to mRNA and thus can be directly translated [into protein]; or minus strand, which is complementary to mRNA, and hence must be transcribed into a plus strand [mRNA] before being translated [into protein]. Retrovirus is an RNA virus that replicates using the enzyme reverse transcriptase to produce DNA from its RNA genome (i.e. does the reverse of transcription), and incorporates the DNA into the host genome. An example of retrovirus is HIV. Prions are infectious protein molecules that don’t contain DNA or RNA, but are able to replicate even without a genome. For example, prions are responsible for mad cow disease
  • Proteins, in particular enzymes required for viral replication

Formative learning activity	Maps to RK3.B
Describe the structure of viruses?

The viral life cycle involves:

• Attachment, where the virus binds to a particular protein on the host cell. This particularity requirement explains why viruses can only infect a limited range of species. Viruses though, can be carried, without causing pathogenic response. For example, the flu is harbored in a ducks’ gastrointestinal system, who may have no apparent symptoms, but transmit to humans by bird droppings
• Penetration, where virions enter the host cell, by, as in bacteriophages (viruses able to infect bacteria, discussed ), injecting its gene into the cell. Alternatively, the virus tricks the cell into performing endocytosis (discussed ), engulfing the virus inside a phagosome (also discussed ) and taking it into a cell. The viral capsid is first removed, known as uncoating, then both capsid and viral genetic material is released from the phagosome by exocytosis
• Replication, where the host’s machinery is tricked into thinking the viral genetic material is its own, thereby duplicating the virus. This includes either:
  • Lytic cycle, where the virus takes over the cell’s machinery, and reproduces inactive virions, and self-assembles into complete viruses. The cell swells with viruses, until it bursts, known as lysis. The new viruses are now free to infect other cells
  • Lysogenic cycle, where the viral nucleic acid is incorporated into the host cell’s genome. As the viral nucleic acid is not expressed, the viral genes are able to be replicated with the host cell genome, known as prophage, until such time that the virus enters into the lytic cycle
• [Self-]assembly, where the viral genetic material is used to create viral proteins
• Release, where viruses are released from the host

Formative learning activity	Maps to RK3.B
Describe the viral life cycle?

Bacteria is a domain (which consists of different kingdoms), with sizes between the virus and eukaryotic cell. Bacteria are prokaryotes.

Prokaryotes are organisms whose cells don’t have a membrane-enclosed nucleus, and don’t have complex membrane-bound organelles. Prokaryotes though, do have organelles, including the ribosome (which translates genes into protein, discussed ). Prokaryotes have 70S ribosomes, consisting of a 30S small, and 50S large subunit. In contrast, eukaryotes have 80S ribosomes, consisting of 40S small, and 60S large subunit. Bacteria have a continuous stretch of [double stranded]DNA in a circular shape. Most bacteria is spherical, known as cocci; or rod-shaped, known as bacilli. Bacilli can also be a rigid spiral-shaped, known as spirilli; or a flexible helical coil, known as spirochetes.

Protoplast is a bacterial cell, with its cytoplasm and plasma membrane (discussed ), but without its cell wall. Cell wall is distinct from, and found outside the plasma membrane, in plants, bacteria, and fungi. Glycocalyx (from “glycol” meaning “sugar”, and “kalyx” meaning “coat”) is a polysaccharide coat of glycolipids and glycoproteins, immediately outside the cell wall, [or in animals who don’t have a cell wall] on the surface of its plasma membrane. Glycocalyx is used by the immune system to distinguish between a body’s own healthy tissues and outside organisms. For example, changes in glycocalyx in cancerous cells prevent contact inhibition, which is the natural process of arresting cell growth when two or more cells come in contact with each other. Bacterial cell walls are made of peptidoglycan. Peptidoglycan (aka murein) is a polymer of sugars and amino acids, such that the peptides (links of amino acids) are cross-linked to other peptide chains. Bacteria can be classified by Gram staining, such that Gram positive stains dark purple, as the thick peptidoglycan cell wall stains purple; whilst gram negative stains pink, as [their peptidoglycan layer is thinner, and] they have an outer membrane on the outside of the peptidoglycan layer, which prevents penetration of the stain. Many gram negative bacteria have fimbria or pili, which are hair-like structures on the cell surface, which assists bacteria to attach to a surface.

Capsules or slime layers may be found on the further outside, produced by bacteria to surround their cells, to protect cells from phagocytosis, desiccation, and bacteriophages. Phagocytosis is engulfing solid particles to form a phagosome (see ). Desiccation is extreme dryness.

Bacteria can also produce endospores, which can survive extreme heat and chemical stresses. For example, botulism is caused by a bacterium, whose endospores are able to survive under high temperatures of the canning process.

Bacteria can move using bacterial flagella, which is a helix, made up of the globular protein flagellin. Bacterial flagellum is driven by a proton pump. When flagella is rotated in one direction, the bacteria runs straight; but when rotated in the opposite direction, the bacteria tumbles thereby permitting change of direction. Bacteria decide direction by chemotaxis, which is movement based on chemical concentration gradients.

“You know, Jamie,” Emily started, “movement by flagella reminds me of John 3:8 when it talks about the Spirit being like the wind which blows wherever it pleases.”

“Just like the ‘resident Christian bad boy’ who does whatever he pleases ,” Mandy giggled, winking and clicking her fingers at Jamie.

“More like the pretend-to-be bad boy ,” Blaire said.

“Augustine wrote ‘Sum si fallor’ (I am because I err), 1200 years before Descartes wrote the famous ‘Cognito, ergo sum’ (I think therefore I am),” Mandy remarked, “Spirit filled bad boys are because they do… not think!”

“But seriously,” Mandy continued, “I once had a theological professor, who said that the reason why we teach our kids how to follow the law, is because it’s easier, than teaching them to follow the Spirit. We ourselves are scared where the wind may blow.”

“Follow concentration gradient,” Emily said, “trust in God, and shoot for the stars, because you are a star!”

“So Disney,” Mandy replied cynically, “but yes babe.”

“That’s actually biblical,” Emily remarked, “Philippians 2:14-15 says ‘Do everything without grumbling or arguing, so that you may become blameless and pure, children of God without fault in a warped and crooked generation. Then you will shine among them like stars in the sky.’ So there you have it, we are to be a star!”

Bacteria reproduce by binary fission, which is a form of asexual reproduction. Asexual reproduction is where offspring arise from a single parent, and therefore inherit the genes of that parent only. Binary fission is the splitting of a cell into two identical clone daughter cells. Bacteria however, can undergo genetic recombination, by:

• Conjugation, which is the bacterial equivalent of sex, as it involves exchanging genetic material. The donor bacterium [with an F-plasmid, known as F-plus], produces a sex pilus, which attaches to the recipient bacterium [without the F-plasmid, known as F-minus]. F-plasmid is a ring of DNA. The F-plasmid is an episome, meaning it is a plasmid that can integrate into the circular DNA of bacteria. The plasmid then transfers a single strand from the donor into the recipient, both cells then synthesize a complementary strand to reproduce a double stranded circular plasmid, to create two new donors
• Transformation, which is genetic alteration resulting from direct uptake of naked DNA from surroundings
• Transduction, which is the transfer of genetic information from one bacterium to another, by a viral vector

Bacteria can be classified into its nutritional requirements based on:

• Source of energy, which can be from sunlight, known as phototrophs; and from chemicals, known as chemotrophs
• Source of carbon, which can be organic, known as heterotroph (from “hetero” meaning “others”, and “troph” meaning “nutrition”, eating others for nutrition); or inorganic, known as autotroph (via carbon fixation)
• Source of electron donors [for growth], can be inorganic, known as lithotroph; or organic, known as organotroph

[img]bacterial-conjugation.png[/img]

Formative learning activity	Maps to RK3.B
What are the shapes of bacteria?