Semester 3 Microbial physiology Topic 3

Topic 3: Intracellular structures of prokaryote

Notes:
1) The intracellular structure found in prokaryote are plasma membrane, cytoplasm, the nuclear area, ribosomes, inclusions and endospore.

• Plasma membrane

- Function: selectively permeable barrier, synthesize cell wall components, assists in DNA replication, carries on respiration and captures energy as ATP.

- The movement of materials across membrane: simple diffusion, facilitated diffusion, osmosis, active transport and group translocation.

- Simple diffusion, facilitated diffusion and osmosis do not require energy where active transport and group translocation belong to active transport.

- Group translocation are molecules that chemically modified during passage across cytoplasmic membane. 

• Cytoplasm

- Cytoplasm refers to the substance of the cell inside the plasma membrane,

- contains proteins, carbohydrates, lipids, inorganic ions, DNA, ribosomes and inclusions.

- lacks of cyoskeleton

• The nuclear area

- Single long circular molecule of double-stranded DNA

- do not include histones and not surrounded by nuclear envelope

- In addition to the bacterial chromosome, bacteria often contain small circular, double stranded DNA molecule called plasmid.

• Plasmid

- small circular, double stranded DNA

- do not contain genetic material essential for growth

- contain features that enhance survivability such as gene for drug resistance can be transfer from one bacterial to another

- The characteristic of plasmid: not connected to bacterial chromosome and replicate independently of chromosomal DNA

• Ribosomes

- for protein synthesis

- 70S ribosome

- small subunit - 30S and large subunit - 50S

- Each subunit consists of protein and RNA called ribosomal RNA ot rRNA.

- Cells that have high rates of protein synthesis, have a large number of ribosomes.

• Inclusions

- divided into granules and vesicles

- Metachromatic granules are large inclusion. Volutin granules are an intracytoplasmic (inside the cytoplasm of a cell) storage form of complexed inorganic polyphosphate, the production of which is used as one of the identifying criteria when attempting to isolate Corynebacterium diphtheriae on Löffler's medium. They appear red when stained with methylene blue and gives a metachromatic effect.

- Sulfur granules serve a an energy reserve, derive energy by oxidising sulfur and sulfur-containing compounds. The bacteria that contain sulfur granules is sulfur bacteria.

- Carboxysomes contain the enzyme ribulose 1,5 - diphosphate carboxylase. It used for carbon dioxide fixation during photosynthesis.

- Magnetosomes contain iron oxide that act like magnets. Their main function is to protect the cell against hydrogen peroxide accumulation.

- Lipid inclusions store polymer poly-beta-hydroxybutric acid. It revealed by Sudan eyes and the example of bacteria that contain lipid inclusion is Mycobacterium, Bacillus, Azotobacter and Sprillum.

- Gas vesicles are normally found in photosynthetic group such as cyanobacteria, proteobacteria and green sulfur bacteria. The function of gas vesicle is to provide buoyancy for aquatic prokaryotes and to receive sufficient amount of oxygen, light and nutrients.

• Endospores

- resting structure formed by some bacteria for survival during adverse environemental conditions

- germination results in leaving the dormant stage and once again becoming a typical, multiplying cell (vegetative cell)

- high resistant differentiated bacterial cell

- enable the organism to endure extreme environmental conditions

- The structure of spore is more complex than vegetative cell:

- The presence of dipicolinic acid which located in core wall give the resistance properties of endospore because intercalate in DNA and stabilizing it to prevent heat denaturation.

- Genus Bacillus and Clostridium are two common disease causing bacteria that produce endospores as needed.

My own explorace：

1) In group translocation, the substance is chemically altered during transport, preventing it from escaping the cell after it is transported inside. This process requires high-energy phosphate compounds like phosphoenolpyruvic acid (PEP) to phosphorylate the ransported molecule, preventing its movement out of the cell. 

2) The magnetotactic bacteria can be subdivided into two categories, according to whether they produce particles of magnetite or of greigite, although some species are capable of producing both. Magnetite possesses a magnetic moment three times that of greigite.

3) The formation of endospores may help maintain the symbiotic association between these Epulopiscium-like symbionts and their surgeonfish hosts. Since endospore formation coincides with periods in which the host surgeonfish is not actively feeding, the cells do not need to compete for the limited nutrients present in the gut at night. The protective properties of the endospores also allow them to survive passage to new surgeonfish hosts. The fish may also benefit from this relationship because it is able to maintain stable microbial populations that assist in digestion and may receive a nutritional gain from microbial products released during mother cell death and spore germination.

Reflection:

I would like to know the benefit of endospore to the environment.  People always think that endospore maximize the chance of spreading disease. Actually endospore is not just spreading disease, but it help to maintain the symbiotic association between Epulopiscium-like symbionts and their surgeonfish hosts. Besides that, Bacillus subtilis spores are useful for the expression of recombinant proteins and in particular for the surface display of peptides and proteins. Therefore, everything have their good side and bad side include endospore, bacteria or even virus.

Semester 3 Microbial Physiology Topic 2

Topic 2: Cell Wall and Membrane Structure of Prokaryotes

Notes:
1) There are four structure external to the cell wall:

• Glycocalyx

- substances that surround cell

- it is made inside the cell and excreted to the cell surface

- capsule is called if the substance is organised and is firmly attached to the cell wall

- slime layer is called if the substance is unorganized 

- Functions: protection from phygocytosis, attachement to various surfaces, source of nutrients, and protect a cell against dehydration.

• Flagella

- Long filamentous appendages that propel bacteria

- There are four arrangement of flagella: Monotrichious, Amphitrichous, Lophotrichous and Peritrichous. 

- There are three basic parts in a flagellum:

Filament(contain the globular protein flagellin) , Hook, Basal body(gram-negative bacteria contains two pairs of rings and gram-positive bacteria contains only the inner pair)

• Axial Filaments

- bundles of fibrils that arise at the ends of the cell beneath the outer sheath.
- spiral around the cell
- present in the spirochetes group of bacteria
- e.g. Treponema pallidum and Borrelia burgdorferi

• Fimbriae and Pili

- Hairlike appendages that are shorter, straighter and thinner than flagella

-consist of pilin

- used for motility rather than for motility

- There are two types of fimbriae and pili: Fimbriae can occur at the poles, evenly distributed over the entire surface, and can number anywhere from a few to several hunfred per cell.

- Pili are longer than bimbriae and joint bacterial fells in the perparation for the transfer of 

DNA from on cell to another. 

Pili is used for the transfer of extrachromosomal

2) Cell wall component: Gram-negative and gram positive bacteria

Gram-negative and gram positive bacteria are structurally different and this differences cause them to have different characteristics. Gram-negative bacteria are resistant to antibiotics due to the presence of outer membrane.

3) Archaea have cell walls consisting of polysaccharide, glycoprotein but not peptidoglycan.

They contain a substance similar to peptidoglycan called pseudopeptidoglycan (pseudomurein).

Their cell wall type is S layer which protects against osmotic stress, pH and enzymes.

Archaea are naturally resistant to lysozyme and penicillin.

4) The unique feature found in cell wall of archae is the presence of L-amino acid instead of D-amino acid, the presence of N-acetyltalosaminuronic acid but not N-acetylmuramic acid and the presence of beta(1,3) glycosidic bond instead of beta(1,4)glycosidic bond.

My own exlporace：

1) Mycobacterium does not have any glycocalyx because they do not have cell wall or very little cell wall material.

2) Capsules give better protection than slime layer because capsule is organised and is firmly attached to the cell wall.

3) A spheroplast is a cell from which the cell wall has been almost completely removed, as by the action of penicillin. Spheroplasts are osmotically fragile, and will lyse if transferred to a hypotonic solution.

4) Septic shock is what happens as a complication of an infection where toxins can initiate a full-body inflammatory response. It often occurs in people who are elderly or have a weakened immune system. It is thought that the inflammation resulting from sepsis causes tiny blood clots to form, which can block oxygen and nutrients from reaching vital organs. As a result, the organs fail, causing a profound septic shock. 

Reflection:
Although cell wall and membrane structure of prokaryotes have learned in last two semester, there are few terms that I am not familiar with. Septic shock and spheroplast are new for me. I think to differentiate gram negative and gram positive bacteria have to be very specific to avoid any error since this is the important step to identify the bacteria.

Semester 3 Microbial physiology Topic 1

Topic 1: Introduction to Prokaryotes

Notes:

1) Prokaryotes divided into two domains which are bacteria and archaea.
2) Definition of prokaryote: Organisms that lack a cell nucleus or any other membrane-bound organelles.
3) They are unicellular, but a few prokaryotes such as myxobacteria have multicellular stages in their life cycles.
4) Prokaryotic diversity include proteobacteria, cyanobacteria, gram positive bacteria, spirochetes with unique morphology, green sulfur and green nonsulfur bacteria.

- Proteobacteria are a major group (phylum) of gram-negative bacteria.
a. Alphaproteobacteria - They grow at very low nutrient area and are agriculturally important because they able to induce nitrogen fixation.
b. Epsilonproteobacteria - They are microaerophilic and they are the most common cause in stomach cancer.
c. Gammaproteobacteria - They are medically important and a large group of pathogen belong to this group such as Salmonella spp.
d. Betaproteobacteria - They play a role in nitrogen fixation in various types of plants, oxidizing ammonium to produce nitrite.
e. Deltaproteobacteia - They are predators on other bacteria and are important contributors to the sulfur cycle.

- Cyanobacteria are aquatic and photosynthesic. They have live on earth for 3.5 billion years. Therefore, they important in shaping the course of evolution and ecological change throughout earth's history.
- Gram positive bacteria have specifc membrane structure. Their structure consist of thick peptidoglycan layer, teichoic acids and gram-positive bacteria are more receptive to antibiotics than gram-negative, due to the absence of the outer membrane.
- Spirochetes are helical in shape They are tightly coiled, and so look like miniature springs or telephone cords.These filaments run along the outside of the protoplasm, but inside an outer sheath; they enable the bacterium to move by rotating in place. Spirochetes causes syphilis and lyme disease.
- Green sulfur bacteria and green nonsulfur bacteria are autotrophs. They produce energy from light and are named for their green pigment, usually found in photosynthetic bodies called chlorosomes.
- Deinococcus radiodurans are extremophilic bacteria where they can survive cold, dehydration, vacuum and acid. Deinococcus radiodurans has a unique quality in which it can repair both single- and double-stranded DNA. When a damage is apparent to the cell, it brings it into a compartmental ring-like structure, where the DNA is repaired and then is able to fuse the nucleoids from the outside of the compartment with the damaged DNA. They are the toughest bacterium in the world.

5) Archaea, the another domain of prokaryote. They are known as extremophiles, halophiles and thermoacidophiles. Their can survice in harsd environement because of their specific cell structure. They are chemotrophic and chemolithotrophics. The example of archaea is Pyrolobus and Halobacterium.

The differences between Bacteria and Archaea:



My own Explorace:
1)  Deinococcus radiodurans can withstand large amounts of radiation, can live in a vacuum for up to six weeks and live, can live dehydrated, and live through fluctuations in pH. This bacteria is so special that it was the first be in the phylum "Deinococcus". This is one of the only organisms in the world that can withstand 5,000 GYs of radiation. It can repair itself completely within 12-24 hours and can survive on Mars.

2) Crenarchaeota are Archaea that have been classified as a phylum of the Archaea kingdom.The Crenarchaeota were thought to be sulfur-dependent extremophiles but recent studies have identified characteristic Crenarchaeota environmental rRNA indicating the organism may be the most abundant archaea in the marine environment. Until recently all cultured Crenarchaea had been thermophilic or hyperthermophilic organisms, some of which have the ability to grow at up to 113 °C. These organisms stain Gram negative and are morphologically diverse having rod, cocci, filamentous and oddly shaped cells.

3) E. coli O157:H7’s ability to induce injury in humans is a result of its ability to produce numerous virulence factors, most notably Shiga toxin, which is one of the most potent toxins known to man.

4) Shiga toxin has multiple variants and acts like the plant toxin ricin by inhibiting protein synthesis in endothelial and other cells. Endothelial cells line the interior surface of blood vessels, and are known to be extremely sensitive to E. coli O157:H7, which is cytotoxigenic to these cells.

Reflection:
Deinococcus radiodurans are such a strong bacteria, I can't imagine how they can withstand so high radiation that even can't stand by a person. This is my first time heard proteobacteria in the class. Proteobacteria are gram negative bacteria but it has divided into five classes.