WEEK 9

BMY3201-1 BASIC MICROBIOLOGY TECHNIQUES

WHAT HAVE I LEARN?

We enter Part 4 of experiment, which is the cultivation of microorganisms: nutritional and physical requirements, and Enumeration of Microbial Populations. This week we have to do two experiment. 

Experiment 12: Nutritional requirements: Media for the Routine Cultivation of Bacteria. We add Escherichia coli, Alcaligenes faecalis and Streptococcus mitis inorganic synthetic broth, glucose salts broth, nutrient broth and yeast extract broth. The next day, we use the spectrophotometer to measure the turbidity at 600nm wavelength. We can see that the E. coli have the most numbers in the yeast extract broth compare to other medium. However, A. faecalis and S. mitis is more in nutrient broth compare to other medium.

Experiment 13: Use of differential, Selective, and Enriched Media
There are many special- purpose media is used in isolation of bacterial types. The selective media including Phenylethyl alcohol agar, crystal violet agar and 7.5% sodiul chloride agar used to isolate specific groups of bacteria by inhibiting the growth of one type of bacteria while permitting of another. Differential and also selective media act as to distinguish morphologically related groups of bacteria. Media included Mannitol salt agar, MacConkey agar and Eosin- methylene blue agar.Last one is the enriched media, which is the blood agar. This is used to cultivate fastidious microorganisms which have special nutritional needs. We can see the hemolytic properties of streptococcus, which classify into gamma hemolysis, alpha hemolysis and beta hemolysis.  Beta hemolysis is complete destruction of hemoglobin which causes clear zone to be seen surrounding colonies. Hemolysis is produced by streptomycin O and streptomycin S. It's really interesting because there is many different colour change of colonies formed on the bacteria and also surrounding the bacteria. For example, the E. coli appear to be blue black, green sheen on eosin- methylene blue agar after incubation. 

This is spectrophotometer

Cuvette which used to contain culture before put into spectrophotometer

Staphylococcus shows clear yellow zone surrounding the growth

WEEK 9

BMY3101-1 MICROBIOLOGY I

WHAT HAVE I LEARN?

This week we learn about FUNGI. We have seniors who is taking Mycology this sem to form group discussion with us in the class. Seniors in our group are very friendly, they gives examples on fungi and explain about some interesting fungi. They also allow us to ask questions in order to understand in this chapter. 

Senior share with us a special fungi named Ophiocordyceps unilateralis, the zombie ant. They will disperse spore onto the ant and effect neuron systems. When the spore mature, ants will go to the tree.

  http://www.reed.edu/biology/courses/BIO342/2015_syllabus/2014_WEBSITES/khsite/ontogeny.html 

http://earthsky.org/earth/research-zombie-ant-fungus-doesnt-invade-ants-brains

A task to discuss about a fungi is given by Dr. We have chosen Cryptococcus neoformans as our fungi.

Kingdom: Fungi
Phylum: Basidiomycota
Class: Tremellomycetes
Order: Tremellales
Family: Tremellaceae
Genus: Cryptococcus
Species: Cryptococcus neoformans
Cryptococcus neoformans is a fungus that lives in the environment throughout the world. People can become infected with C. neoformans after breathing in the microscopic fungus, although most people who are exposed to the fungus never get sick from it. C. neoformans infections are extremely rare in people who are otherwise healthy; most cases occur in people who have weakened immune systems, particularly those who have advanced HIV/AIDS.

Few fungi are pathogenic to humans. Cryptococcus neoformans is a basidiomycetous fungus that is ubiquitous that can be found in soil and association with certain trees. They undergo both sexual and asexual reproduction. Asexual reproduction is either by budding or by haploid fruiting in response to nutrient deprivation or exposure to the mating pheromone a factor. Sexual reproduction occurs when cells of opposite mating types come together to form a heterokaryon produce basidia and basidiospores. Infection occurs when the fungal particles are inhaled and enter the alveolar space. In most immunocompetent individuals, this infection will develope when the immune is imbalance. Cryptococcus neoformans has emerged as an important cause of mortality in immunocompromised patients, especially those with AIDS. C. neoformans also the most common life-threatening cause of fungal infection. In severe cases, cryptococcal infection progresses to a meningoencephalitis that is fatal if left untreated.

C. neoformans virulence is mediated by  polysaccharide capsule that surrounds its cell wall causing multiple effects on the host immune system. This structure act as a physical barrier from phagocytosis and clearance by the immune system. Capsule components inhibit the production of proinflammatory cytokines, deplete complement components and reduce leukocyte migration to sites of inflammation.  The components of the capsule can be detected in the bloodstream and it can be visualized with light microscopy by using India ink staining. The capsule excludes the ink particles and forms clear halos. ( image from: http://gizabethshyder.blogspot.my/2017/05/cryptococcus-neoformans.html)

Photo with seniorssss

WEEK 8

BMY3201-1 BASIC MICROBIOLOGY TECHNIQUES
WHAT HAVE I LEARN?

This week we will be doing the last experiment, experiment 11 which under bacterial staining. Differential staining for visualization of bacterial cell structures including spore staining and capsule stain. 

PART A: Spore stain
The aerobic genera Clostridium and Desulfotomaculum and aerobic genus Bacillus are organisms which can produce spore. The spore can either exist in the bacterial cell or outside the bacterial cell, which called as free spore. Endospore is produced when the environmental condition become unfavorable for the bacterial cell on vegetative cellular activities. If the bacterial cell return to favorable environment, the free spore may revert back to vegetative cells through germination. The spore is seen to be green in colour with pink colour vegetative cells. We can clearly see that there is green colour spore outside the vegetative cell which is the free spore. 

Bacillus cereus spore stain

PART B: Capsule stain
Capsule is gelatinous outer layer secreted by cell which surrounds and adheres to cell wall of bacteria. Not necessary every bacterial have capsule. Capsule contribute in virulent and disease. The capsule can protect the bacterial cell from normal phagocytic activities of host cells. Beside using crystal violet, we can also replace by using negative stain. We also try on staining the bacterial cells using nigrosin. Our group failed to get good result, this may cause by some error while conducting the stain procedure. Only some classmates able to see the transparent capsule surround the purple bacterial cells. Both Klebsiella pneumoniae and Enterobacter aerogenes contain capsule.

Enterobacter aerogenes Capsule stain 

WEEK 8

BMY3101-1 MICROBIOLOGY I

WHAT HAVE I LEARN?

This week we continue on the internal structure of prokaryotes. We are given time to discuss a game on this topic among ourselves. In the end, our group come out question with puzzle. After discussion, the whole class play on the game which designed by each group. On friday, we continue on the games created by classmates. Then, we all given a task to find out an journal article that relates to the internal structure in prokaryote. We discuss among ourselves in group to the organelle given. We choose to take Endoplasmic Reticulum (ER). We read few journal and come out with a conclusion. But, what we found is not really meet the request that dr want, so we have to redo. This is the new article we found, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3949406/?report=reader . This journal article is about The ER quality control and ER associated degradation machineries are vital for viral pathogenesis. 

(image from: https://www.news-medical.net/life-sciences/The-Endoplasmic-Reticulum-and-Golgi-Body-Whate28099s-the-Difference.aspx)

WEEK 7

BMY3201-1 BASIC MICROBIOLOGY TECHNIQUES
WHAT HAVE I LEARN?

This week is we will be doing gram staining and acid- fast staining. Both of them are related to the cell wall composition. The time control of gram staining and acid- fast stain is very important as a little bit change will influence the results. Gram stain is under differential staining which require need of four chemical reagents. Primary stain used in gram staining are Crystal's violet, is to impart colours to all cells. Next is the mordant, Gram's iodine which used to intensify colour of primary stain. To establish a colour contrast, decolorizing agent is used which may or may not remove the primary stain. Decolorizing agent used is 95% ethyl alcohol. The last one is counterstain, safranin has a contrasting colour to that of primary stain. Gram- positive cells have thick peptidoglycan which appear blue in gram staining while gram- negative cells have thin peptidoglycan which appear pink in gram staining. 

The genus Mycobacterium are visualised more clearly by acid- fast method. They have thick, waxy ( lipoidal) wall that makes penetration by stains extremely difficult. Primary stain used carbol fuchsin that is soluble in lipoidal materials can penetrate Mycobacterium and is retained. Application of heat in Ziehl- Neelsen method can drives carbol fuchsin throught lipoidal wall and into cytoplasm. Acid- fast cell able resistant to decolorization od acid- alcohol since primary stain is more soluble in cellular waxes. Counterstain used methylene blue to stain previously decolorized cells. Acid- fast cells retain red of primary stain while non- acid- fast cells stained and become blue in colour. 

WEEK 7

BMY3101-1 MICROBIOLOGY I

WHAT HAVE I LEARN?

We were asked to prepare for Prokaryote ( internal) before entering the class. The class started with quiz. We are all sited in groups and have to answer the questions given within one minutes .We are allowed to discuss among ourselves in the group to get the correct answer. The quiz covers all the topic we have learnt before and also the new topics. In the end, our group manage to get the second highest marks among all the other groups. The other day, Dr explained the topic Prokaryote ( internal) with us. 

Extra knowledge ↴
Photosynthetic bacteria: Cynobacterium

• They have bacterium chlorophyll
• found on surface of aqueous ( because they need sunlight for photosynthesis)
• produce oxygen
• recycle nutrients
• contribute to aqueous food chain

Terminal end acceptor 

✔ oxygen ➝ aerobic respiration

❌oxygen ( inorganic acid, hydrogen)  ➝ anaeorobic respiration

INTRACELLULAR
PLASMA MEMBRANE

• Structure = phospholipid bilayer with proteins embedded in and attached to the inner ( intracellular) and outer ( extracellular) surfaces.
• Fuction:

1. Selectively permeable
2. Synthesis cell wall components
3. assists in DNA replication
4. carries on respiration
5. captures energy as ATP

Phospholipid bilayer function as Fluid Mosaic

↳ to ensure composition of extracellular fluid is not same as composition of intracellular fluid.

↳ water soluble substances can pass with aid of proteins
↳ lipid can pass through directly the bilayer

Fluid Mosaic model:
lipid bilayer with floating proteins
↳ amphipathic lipids 
   - polar ends ( hydrophilic head ) → interact with water
   - non- polar ends ( hydrophobic tails ) → insoluble in water
↳ membrane protein

Destruction of plasma membrane

• Disinfectants: alcohols, quaternary ammonium compounds 
• to disinfect/ strelize/ prevent from contamination
• causes leakage of intracellular contents 
• plasmolysis: cells shrink
• lysis: cells burst
• plasma membrane is the first structure to be destroyed due to detergent or antibiotic

Uptake of nutrients 

1. Through barrier

• Macroelements ( macronutriets)

↳ C, O, H, N, S, P

   Found in organic molecule such as proteins, lipids, carbohydrates, and nucleic acids

↳ K, Ca, Mg and Fe 

   Cations and serve in variety of roles including enzymes, biosynthesis

↳ require in large amount

• Micronutrients ( trace elements)

↳ Mn, Zn, Co, Mo, Ni and Cu

↳ require in small amounts

↳ often supplied in water or in media components

↳ ubiquitous in nature

↳ serve as enzymes and cofactors

• unique substances 

     2. Passive process

→ Molecules corss the membrane from an area of high concentration to an area of low concentration

→ Concentration gradient not energy dependent

• Simple diffussion

↳ movement of molecules or ions from high to low concentration until equilibrium

• Facilitated diffusion

↳ need transporters ( carrier proteins /proteins) from high to low concentration

↳ uses membrane bound carrier molecules ( permeases)

↳ more prominent in eukaryotic cells than in bacteria or archaea 

• Osmosis

↳ movement of water molecule from high to low concentration

     3. Active process

→ energy dependent systems :

→ ATP or proton motive force used

ABC Transporters

• Primary active transporters use ATP
• ATP- biding cassette (ABC ) transporters
• Observed in Bacteria, Archaea, and eukaryotes 
• Consists of 
• → 2 hydrophobic membrane spanning domains
• → 2 cytoplasmic associated ATP- binding domains
• → Substrate binding domains

• Active transport

↳ substances are moved by transporter proteins from low to high concentration

↳ cell has to expend energy for this to happen

• Group tanslocation

↳ molecules are chemically modified during passage across cytoplasmic membrane

↳ energy is expended

CYTOPLASM

• substance of the cell inside the plasmIa membrane
• about 80% water
• contains proteins ( enzymes) , carbohydrates, lipids, inorganic ions and many low molecular weight compound
• Thick, aqueous, semitransparent and elastic
• Major strucure: DNA, ribosomes, inclusions

Intracytoplasmic membranes:

• plasma membrane infolding

↳ observed in many photosynthetic bacteria

↳ observed in many bacteria with high respiratory activity

• Anammoxosome in Planctomycetes

↳ organelle - site of anaerobic ammonia fixation

↳  is a significant component of the biogeochemical nitrogen cycle

Nuclear area:

• Single long circular molecule of double- stranded DNA → bacterial chromosome
• bacterial chromosome do not include histones and not surrounded by nuclear envelope
• contain double- stranded DNA molecules → plasmid 

Plasmid:

• small, circular, double stranded- DNA
• Extrachromosomal genetic elements:
•  →  not connected to bacterial chromosomes
•  → replicate independently of chromosomal DNA
• 🗙 genetic material essential for growth ( limited)
• features that enhance survivability
•  →  eg: gene for drug resistance
•  → Transferable from one bacterial to another

RIBOSOMES

• Sites of proteins synthesis
• 70S ribosomes
• small subunit - 30s
• large subunit - 50s  ( s refer to Svedberg unit )
• each subunit consists of protein and RNA called ribosomal RNA or rRNA
• can be inherited by certain antibiotics
• cells  →  high rates of protein synthesis = large number ribosomes
• antibiotic work by inhibiting proteins synthesis on prokaryotic ribosomes:
•  →  Streptomycin and gentamicin attach to 30S subunit
•  →  Erythromysin and chloramphenicol attach to 50s subunit

extra notes:

The Bacterial Ribosome

The bacterial ribosome is a cytoplasmic nucleoprotein particle whose main function is to serve as the site of mRNA translation and protein synthesis. The ribosome has a mass of about 2.5 MDa, with RNA accounting for 2/3 of the mass. It consists of two subunits denoted 30S (small subunit) and 50S (large). When joined, the ribosome has a sedimentation coefficient of 70S as opposed to 80S due to tertiary structure. The subunits' shape and arrangement are illustrated below: 

In eukaryotes, scientists have seen and identified the 60-S (large) and 40-S (small) subunits. Even though ribosomes have somewhat slightly different structures in different species, there functions areas seems all very similar.

reference: http://www.understandbiology.com/2013/03/ribosomes.html

INCLUSIONS

➝ reserve as deposits

➝ basis of identification

➝ store nutrients

• Metachromatic granules

↳ large inclusion

↳ stained red with blue dyes ( methylene blue)

↳ volutin ⟶ interchangeable with metachromatic ( inorganic phosphate- polyphosphate used in synthesis of ATP)

↳ Corynebacterium diphtheriae ⟶ pathogenic microbe that cause diphtherial

↳ found in algar, fungi, protozoa ( eukaryotic)

• Polysaccharide granules

↳ glycogen and starch 

↳ differentiate by using iodine

   reddish brown ⟶ glycogen granules

   blue ⟶ starch granules

• Lipid inclusions

↳ storage material - polymer poly- β- hydrocxybutyric acid

↳ revealed by Sudan dyes ( fat- soluble)

↳ Mycobacterium, Bacillus, Azotobacter

↳ have waxy cell wall ( except Bacillus)

• Sulfur Granules

↳ energy reserve

↳ derive energy by oxidising sulfur and sulfur containing compounds

↳ Thiobacillus - sulfur bacteria

• Carboxysomes

↳ contain enzyme ribulose 1,5- diphosphate  carboxylase

↳ carbon dioxide fixation during photosynthesis

↳ nitrifying bacteria, cynobacteria and thiobacilli - used CO2 as sole source of carbon

• Magnetosomes

↳ Iron oxide ( Fe3O4) acts as magnet

↳ for downward movement until reaching suitable attachment site

↳ protect cell against hydrogen peroxide accumulation

↳ Aquaspirillum magnetotacticum ( gram - bacteria)

• Gas vesicles

↳ hallow cylinders covered by protein

↳ membrane bounded

↳ gas vacuole

↳ appeared bright, refractile areas with an irregular outline in phase microscope

↳ thin membrane surrounding hallow space

↳ found in photosynthetic group:

  cynobacteria

  proteobacteria

  green sulfur bacteria

  heterotropic bacteria

  archaea - Methanogen and halophile

↳ provide buoyancy for aquatic prokaryotes to receive sufficient amounts of o2, light and nutrients

extra knowledge:

Green sulfur bacteria

• Green sulfur bacteria depend on light for life due to their obligate phototrophic metabolism.
• Green sulfur bacteria perform a highly efficient photosynthesis due to the presence of light harvesting organelles, the chlorosomes, which are filled with special bacteriochlorophyll molecules.
• Green sulfur bacteria inhabit the lowermost part of the photic environments due to their efficient light capture.
• Green sulfur bacteria inhabit the lowermost part of the chemocline in the stratified environment due to their sensitivity to oxygen, their high sulfide tolerance and their dependence in light.
• Green sulfur bacteria are important drivers of oxidation of reduced sulfur compounds in the stratified, sulfide‐containing environment receiving low irradiation.

reference: 

Biology of Green Sulfur Bacteria, Johannes F Imhoff, Helmholtz Centre for Ocean Research, Kiel, Germany, Published online: June 2014 http://www.els.net/WileyCDA/ElsArticle/refId-a0000458.html

Green non- sulfur bacteria

Formerly known only as a group of gliding filamentous bacteria capable of anoxygenic photosynthesis, the green nonsulfur bacteria (phylum Chloroflexi) now are also known to comprise numerous chemotrophic bacteria of diverse ecophysiology and phylogeny. The most conspicuous representatives are the green‐ or orange‐coloured thermophilic bacteria which form dense microbial mats in hot springs. They are typical photoorganoheterotrophs and well adapted to their changing environment by their gliding motility, tactic responses and versatile physiology. Culture‐independent studies have revealed a plethora of novel, unknown 16S ribosomal ribonucleic acid (rRNA) gene sequence types, indicating that the diversity of these bacteria in the natural environment is only marginally understood. Nonphotosynthetic members of the Chloroflexi occur in freshwater, soil and decaying organic matter, as well as methanogenic granular sludge and other wastewater treatment systems where they seem to aid in granule formation and participate in carbohydrate turnover.

reference:

Green Nonsulfur Bacteria, Jörg Overmann, Ludwig‐Maximilians‐Universität München, München, Germany, Published online: September 2008 http://www.els.net/WileyCDA/ElsArticle/refId-a0000457.html

Purple sulfur bacteria

The purple sulfur bacteria belong to the phylum Proteobacteria. These bacteria are often found in stagnant waters or where there are high concentrations of Hydrogen Sulfide. In order to conduct photosynthesis, they need anoxic conditions, which mean that they cannot survive where there are high dissolved oxygen concentrations. They take the hydrogen sulfide from the water column and metabolize it into granules of elemental sulfur. These sulfur granules may be oxidized to form sulfuric acid. In high numbers, these bacteria give the water and the floc a pink or purplish tint. Generally, they are indicators of septicity, and in severe cases, the dispersed purple sulfur bacteria can cause high effluent Total Suspended Solids levels. In the Pulp and Paper Mill industry, purple sulfur bacteria can be helpful in identifying septic zones which is no other than an indication of poor dissolved oxygen concentrations in different sections of a wastewater treatment system. Although they can be helpful in identifying certain problems within wastewater treatment systems, purple sulfur bacteria are not principal Biochemical Oxygen Demand (BOD) degraders and makes them more of a problem within the system when present in high numbers. 

reference:

http://www.ebsbiowizard.com/resources/micro-gallery/purple-sulfur-bacteria/

Purple non- sulfur bacteria

• Originally named “non-sulfur” because it was thought that they could not use sulfide as electron donor
• Can tolerate small concentrations of sulfur, but much lower than green and purple sulfur bacteria. 
• High Concentrations of H2S are toxic
• Primarily anaerobes, but can carry out respiration in low O2 concentrations
• Purple non-sulfur bacteria grow in where they have access to sunlight and are not in contact with oxygen

reference: 

https://web.stanford.edu/class/cee274s/presentations2012/Machak_Christina_PNS.pptx

ENDOSPORE

• resting structure formed by some bacteria for survival during adverse environmental conditions
• germination results in leaving the dormant stage 
• becoming typical. mutiplying cell ( vegetative cell)
• Bacillus and Clostridium, disease causing bacteria 
• cannot be destroyed easily, even harsh chemicals
• formed internal to bacterial cell membrane
• highly resistant differentiated bacterial cell
• enable organism endure extreme environmental conditions
• high dehydrated strcuture thick walls and additional layers
• contains macromolecules and variety of substances absent from vegetative cells
• spore is formed within cell
• impermeable to dye, stained with Malachite green
• small acid- soluble proteins
• ➝ protect DNA from UV radiation, desiccation and dry heat
• ➝ serve as carbon and energy source during germination
• remain dormant indefinitely but germinate quickly when appropriate trigger is applied
• can form at terminal or middle

Xerophilic microbes

➝ group of microbes that can survive in desiccation & very dry environment

forming of endospores

➝ produce cortex- protect endospore from harsh environment

➝ all water content will be less than 1% in the endospore

source: http://www.biologydiscussion.com/essay/essay-on-bacteria-microbiology/29550

Endospores and infectious disease

➡ harmless themselves until germinate, involve in transmission of disease to human

➡ Bacillus anthracis

➡ Clostridium tetani

➡ Clostridium botulinum

➡ Clostridium perfringens 

Clostridium perfringens 

Clostridium perfringens (C. perfringens) is a spore-forming gram-positive bacterium that is found in many environmental sources as well as in the intestines of humans and animals. C. perfringens is commonly found on raw meat and poultry. It prefers to grow in conditions with very little or no oxygen, and under ideal conditions can multiply very rapidly.  Some strains of C. perfringens produce a toxin in the intestine that causes illness. Clostridial gas gangrene is a highly lethal necrotizing soft tissue infection of skeletal muscle caused by toxin- and gas-producing Clostridium species. The synonym clostridial myonecrosis better describes both the causative agent and the target tissue. The composition of gas is the same as our environment. Serious cases will have to amputate.

source:

https://www.cdc.gov/foodsafety/diseases/clostridium-perfringens.html

https://emedicine.medscape.com/article/214992-overview

WEEK 6

BMY3201-1 BASIC MICROBIOLOGY TECHNIQUES
WHAT HAVE I LEARN?

This week we will learn about the bacterial staining. A stain is an organic compound which containing benzene ring, a chromophore and an auxochrome group. Acidic stains are anionic, which means that on ionization of the stain, the chromogen ( coloured compound) portion which is negatively charged will bind to the positively charged cellular component, protein. For example, picric acid. Basic stains are cationic, which mean that on ionization of the stain, the chromogen portion which is positively charged will has strong affinity for the nucleic acids, negatively charged cellular component. For example, methylene blue, malachite green, crystal voilet and carbolfuchsin. Simple staining is use for visualization of morphological shape and arrangement which differential staining use in separation into groups and also visualization of structure. 

We first start with the bacterial smears. The preparation including the heat fixation which fixed the bacterial proteins on the glass surface by rapid passing the air- dried smear few times over flame of Bunsen burner. Next we go on on simple staining. Simple staining only stained the bacterial smear with single reagent. The bacterial shapes and arrangement can be clearly seen under microscope after staining. Lastly, the negative staining. The negative staining require acidic stain which include India ink or nigrosin. These negatively charged chromogen will not penetrate the cell thus give image of unstained cells viewed against the coloured background which is darker in colour. Negative staining is more to use in determine whether an organism possesses a capsule. 

WEEK 6

BMY3101-1 MICROBIOLOGY I

WHAT HAVE I LEARN?

This week we move on to next topic that is the Introduction to Prokaryotes. We have covered the whole chapter in 1 hour 30 minutes. With some addition explanation from Dr, i am able to understand more about this chapter. We study about the external structure in this class before going to the internal structure of prokaryote. Dr gives some external knowledge before the class start. For sterilization,  we use UV, autoclave or Bunsen burner and also filter sterilize technique. Filter sterilize technique uses substances filter through membrane filter of 0.25- 0.45 micrometer. For example the antibiotic. Antibiotic is added into medium to ensure that there is no growth of bacteria. When we grow fungus but there is contamination of bacteria, antibiotic is added to control.

Prokaryotes are group of organisms that lack of nucleus ( = karyon) and other membrane bounded organelles. Bacteria and archeae are prokaryote. 

Size 

0.2 to 2.0 micrometer in diameter and 2 to 8 micrometer in length.

Shapes

Coccus  - sphere
Bacillus - rod shaped
Spiral    

Arrangement

Cocci: diplococci,staphylococci and streptococci

Bacilli: diplobacilli and streptobacilli

Spiral: vibrio, spirillum and spirochete

There are also addition shape:

Unusual

- star-shaped

- square

- triangular

Pleomorphic

- within  a population, they can dorm various shapes

- they can change shape to adapt the extreme temperature

No fixed shape

- cellwall-less : mycoplasma/ ureaplasma

* microorganisms which have a larger size:

- bigger adaptivality to environment 

- store more food 

mycoplasma are the smallest bacteria, 0.3 microns.

Cell structure of bacteria

Cell wall and membrane structure of prokaryote 

Structure external to the cell wall

• Glycocalyx
• flagella
• axial filaments
• fimbriae and pili

GLYCOCALYX

• surrond the cell
• made inside the cell and excreted to cell surface
• polysaccharides, polypeptides or both
• made of sugars called an extracellular polysaccharides ( EPS)                                *most of bacteria can produce EPS. Example: biofilm attach to surface in form of matrix, stick to each other

Function

• protection from phagocytosis
• attachment to various surface
• source of nutrients
• protect a cell against dehydation
• maintain the shape

Two cell surface layers

• capsules

- organized and firmly attach to cell wall

- distinct and gelatinous 

- antiphagocytic 

- protect from dehydration

• slime layer

- unorganized and loosely attached to the cell wall

FLAGELLA

• Treadlike, locomotor appendages extending outward from plasma membrane and cell wall
• made of protein flagellin and consistes of a filament and basal region

Function

• motility and swarming behavior
• attachment to surfaces
• may be virulence factors

Arrangement of flagella

Flagella strcuture 

Gram + organisms have 2 rings ( 1 in cell wall, 1 in cell membrane)

Gram - organisms have 4 rings ( 2 in cell wall, 2 in cell membrane )

Types of motility

- when there is harmful to bacteria ( antibiotic, chemical), they have to run away

• "run" or "swim"

Moves in one direction for a length of time

• 'tumbles"

runs interrupted by periodic abrupt, random changes in direction

# when hit smtg

• "swarm"

rapid wavelike movement

AXIAL FILAMENT ( endoflagella)

• Bundles of fibrils that arise at the ends of the cell beneath the outer sheath
• spiral around the cell
• present in a spirochetes group of bacteria 
• eg: Treponema pallidum and Borrelia burgdorferi 

FIMBRIAE AND PILI

• Hairlike appendages that are shorter, straighter and thinner than flaggela
• consists of pilin
• used for attachment

Fimbriae 

• occur at poles of bacterial cell
• evenly distributed over entire surface of cell
• few to hundred per cell

Pili

• longer than fimbriae
• one or two per cell
• for preparation of transfer of DNA 
• sex pili ( transfer of plasmid)

Cell wall

• surround cytoplsmic membrane 
• not regulatory structure
• ❌ selectively permeable
• can fit and pass through
• composed of macromolecular network called peptidoglycan ( murein)
• peptidoglycan consists of repeating dissacharides
• dissacharides: N- acetylglucoseamine (NAG) and N- acetylmuramic acid (NAM)
• alternating NAM and NAG linked in row - by glycosidic ( 𝞫 1,4) bonds                                                                             adjacent - by peptide bonds

Function

• prevent from rupturing when water pressure inside is greater than outside
• contribute pathogenicity
• classification
• maintain shape - rigid wall compensades for flexibility of membrane
• provide rigid platform ( a point of anchorage ) for surface appendages ( flagella, pili, cilia emanate from wall and extend beyond)
• counters effects of osmotic pressure → strength of cell wall keep cell from bursting when osmotic intracellular > extracellular

Gram positive 

• have thick layer of peptidoglycan
• lies between plasma membrane and cell wall is smaller than gram - 
• periplasm have only few protein
• enzyme secreted called exoenzyme → aids in degration of large nutrient

Teichoic acid

• primarily of an alcohol ( such as glycerol or ribitol) & phosphate 
• negatively charged (-)
• provide much more of wall's antigen specificity
• make gram positive acidic
• cell walls ❌ degrades easily

2 types → lipoteichoic acid ( spans the peptidoglycan layer & linked to plasma membrane)

             → wall teichoic acid ( link to peptidoglycan layer)

↝ DON'T HAVE OUTER MEMBRANE

Gram negative

• one, less layers peptidoglycan → more susceptible to mechanical breakage
• peptidoglycan bonded to lipoprotein
• ❌ teichoic acid

peptidoglycan ↪ 10% of cell wall

                       ↪ bonded lipoprotein

                       ↪ located btw outer membrane and cytoplasmic membrane ( periplasmic                                   area) 

Periplasmic space

• high concentration of degrating enzyme
• large amount of transport proteins
• 20%- 40% of cell volume

↝ HAVE OUTER MEMBRANE 

• consists of lipoproteins, lipopolysaccharides ( LPS) , phospholipids and porins
• strong negative charge → evade phagocyctosis
• provide barrier for antibiotic ( penicillin ), lysozyme, detergent, heavily metals, bile salts, certain dyes.
• porins from channel permit passage of molecules such as nucleotides, dissacharides, peptides, aminoacids, vitamin B12 and iron

LPS

• ↦ polysaccharides portion called O polysaccharides ( composed by sugar)
• function as antigen
• useful for distinguish gram -
• role same as teichoic acid
• ↦ lipid portion called lipid A
• endotoxin
• toxic when in host's bloodstream or glastrointestine tract - cause fever and toxic shock

source: https://www.slideshare.net/shaniapasaoa/gram-positive-and-gram-negative

Unusual features of peptidoglycan 

↷ D- alanine & D- glutamic acid used

↷ N- acetylmuramic acid & diaminopimelic acid found in bacteria ( archeae or eukarya ❌)

↷ diaminopimelic ( DAP) found in gram - bacteria

↷ peptidoglycan layer are porous, unlike membrane

Atypical cell walls

• mycoplasma

↬ no cell wall, have very little wall materials

↬ membrane contains sterols - impart rigidity to membrane and protect them from osmotic        lysis

↬ smallest bacteria

↬ can pass through most bacterial filters

↬ eg: Mycoplasma pneumoniae  

• Chlamyddiaceae 

↬ 2 membrane ( like gram -)

↬ some genes for peptidoglycan synthesis found in genome

↬ obligate intracellular parasites

↬ non- replicative elementary body ( EB) form have extensive cross- linking in outer                  membrane proteins; analogous to spore 

Archaea

• lack peptidoglycan 
• some have cell walls consisting polusaccharides, glycoprotein or protein
• contain pseudopeptidoglycan ( psedomurein )
• most common wall type - paracrystalline surface layer ( s- layer)
• resistant to lysozyme and penicillin 

Pseudopeptidoglycan 

• 𝞫 ( 1,3 ) glycosidic bonds ( lysozyme insensitive )
• N- acetylglucosamine (NAG) & N- acetyltalosaminuronic acid (NAT)

S- layer

• surface / outermost layer forming " lipidless membrane"
• G+, G-
• composed of repeating subunits of protein or glycoprotein ( with hexagonal symmetry)
• protects against osmotic stress, PH and ezyme 
• aid in attachment
• inhibit phagocytosis