Cell wall and membrane structure of prokaryotes (Part I)

1) Glycocalyx
- Gelatinous polysaccharides
- Protect from phagocytosis by allowing the bacterium to attach itself to inert (chemically inactive) surface like teeth or rocks
- Source of nutrient and energy to microbes (Example: Streptococcus mutans which colonizes the teeth ferment glucose in glycocalyx and acid by products contribute to tooth decay)
- Protect from dehydration
- If it is loosely attached to the cell wall, it is known as slime layer
- Capsules is firmly attached to the cell wall

2) Flagella

Arrangement of flagella

 

Structure of flagella

 

• Flagella consists of filament, hook and basal body.
• Flagella is made up of protein flagellin, which is arranged in several intertwined chain that form a helix around the hollow core.
• Hook is made up of 120 copies of a single protein, FlgE
• Basal body anchors the flagellum to the cell wall and plasma membrane
• Gram positive bacteria has two rings while gram negative bacteria has four rings as shown in diagram above.
• Flagella contributes to motility
• Motility can be directly observed under light microscope through hanging drop in cavity slide and wet mount preparation
• True motility show propelling action towards definite direction.
• False motility show zigzag movement and directionless. It might seems true movement due to bombardment of water molecules
• Movement towards nutrient, sunlight and magnetic force is known as chemotaxis, phototaxis and magnetotaxis repectively.
• During inoculation, motility of bacteria can be seen through turbidity (cloudiness) of medium
• One of the importance of bacterial locomotion is that it can help the bacteria to move away from unfavourable condition such as accumulation of chemicals



Difference between prokaryotes and eukaryotes flagella

 

 

Flagella and bacterial motility


3) Axial filaments
- Also known as endoflagella
- Wrap around the cell
- Present in spirochetes



Intracellular structures of prokaryotes

1) Plasma membrane

•  Anchoring to cytoskeleton to provide shape to the cell
• Similarities between simple diffusion and facilitated diffusion

 

Similarities between simple diffusion and facilitated diffusion
·       Down the concentration gradient ·       No energy is required
Simple diffusion	Facilitated diffusion
·       Through the phospholipid bilayer	·       Through the transport protein
·       Happens to the small and non polar particles	·       Happens to large and polar particles

• Condition of cells in different type of solutions

	Hypertonic solution	Isotonic solution	Hypotonic solution
Animal cell	Shrink	No net movement of water	Burst
Red blood cell	Crenation	No net movement of water	Haemolysis
Plant cell	Plasmolysis	No net movement of water	Deplasmolysis

 - Application of osmosis in our body:

• Osmoregulation in Amoeba sp. and Paramecium sp.
• Plant wilting (excess fertiliser cause hypertonic soil, water diffuse from root cell to the soil, plasmolysis occur)
• Food preservation (salted fish and pickles)

- Group translocation

• Active transport.
• A mechanism utilised by bacteria to transport a compound into their cell by allowing the compound to bind with protein in plasma membrane, altering its chemical structure during passage across the membrane.
• Example : Phosphotransferase system (PTS) , method used by bacteria for sugar uptake and the source of energy is from phosphoenolpyruvate
• PTS include enzyme I and enzyme II which is substrate specific.
• Modified carbohydrate in the cytoplasm is chemically different compare to carbohydrate outside. Hence carbohydrate will be always transported down the concentration gradient.

2) Cytoplasm

• Act as a buffer to protect genetic material of cell
• Prokaryotes does not have cytoskeleton

3) Plasmid

• Extrachromosomal genetic material which are not contain of important genes for metabolism
• Example: Gene for drug resistance
• Can be transferred to another bacteria through conjugation

4) Ribosomes

•  Comparison of ribosome between prokaryotes and eukaryotes

Prokaryotes	Eukaryotes
N- formylmethionine as starter for amino acid	Methionine as starter for amino acid
50 S + 30 S = 70 S	60 S + 40 S = 80 S

• Svedberg unit refer to sediment coefficient, in other words speed of centrifugation.
• In prokaryotes, both 50S and 30 S subunit exist separately in cytoplasm until the small subunit recognize and bind to specific mRNA. The larger subunit is now come and form a complete ribosome.
•  Suspended in cytosol is known as freely ribosome
• Bound to endoplasmic reticulum is known as attach ribosome

5) Metachromatic granules

• Also known as volutin
• Function: Storage for inorganic phosphate for generation of energy
• Large
• Found in eukaryotes as well

6) Sulphur granules

• Appear as bright, slightly yellow spherical area in cell
• Energy reserve
• Common in bacteria that use hydrogen sulphide or thiosulphate as electron source

7) Carboxysomes

• Two types: alpha carboxysomes and beta carboxysomes
• Contain two enzyme: ribulose-1,5-biphosphate carboxylase and carbonic anhydrase 
• Used for carbon dioxide fixation during photosynthesis
• The structure is made up of many layer to prevent the carbonic anhydrase diffuse out of the carboxysomes

8) Magnetosomes

• Contain iron oxide which is also known as magnetite
• Allow the bacteria to orient and navigate along the magnetic field
• Lastest finding of a new bacteria BW-1 can produce both greigite and Magenetite

9) Why the smaller the gas vesicles, the lesser the buoyancy, the stronger the cell?

• This is because the lesser the buoyancy, the cell will sink more deeply in the lake.
• The deeper it sink, the greater pressure that it withstand, the stronger it is.

10) Lipids inclusions

• Also known as lipocytes and fat cells
• Two types: White fat cells and brown fat cells

structure of adipocyte

White fat cell	Brown fat cell
Single lipid droplet	Small lipid droplet
No mitochondria	High number of iron containing mitochondria
Cannot generate heat but it does insulate the body	Generate heat by burning calories
Found under the skin	Deposits around vital internal organ and along back and sternum



Difference between brown adipose tissue and white adipose tissue



White fat cells

 

11) Endospore

structure of endospore

Structure	Function
Exosporium	-          Outermost layer -          Additional glycoprotein layer -          Cover spore coat
Spore coat	-          Made up of protein -          Provides chemical and enzymatic resistance
Cortex	-          Needed for dehydration of the spore core, which aids in resistance to high temperature
Germ cell wall	-          This layer of peptidoglycan will become the cell wall of the bacterium after the endospore germinates
Core	-          Exist in a very dehydrated state -          Houses DNA of cell
Small acid soluble proteins (SASPs)	-          Tightly bind and condense the DNA -          Change the conformation of DNA into Z conformation -          Responsible for resistance to UV light, desiccation and DNA damaging chemicals

Introduction to Prokaryotes

Prokaryotes is divided into two domains, one is bacteria while the other one is archaea. Proteobacteria is a large group of gram negative bacteria and includes wide variety of pathogens. They are either facultative anaerobe or obligate anaerobe, meaning they do not depend on oxygen to live. Furthermore, proteobacteria is defined based on the rRNA.

Below are six classes of proteobacteria and their respective examples:

• Alphaproteobacteria     (Brucella, Rhizobium for nitrogen fixation, Wolbachia)
• Betaproteobacteria       (Bordetella that cause whooping cough, Neisseria, Nitrosomonas)
• Gammaproteobacteria  (Escherichia, Shigella, Salmonella, Vibrio, Pseudomonas)
• Deltaproteobacteria      ( Desulfovibrio, Geobacter, Bdellovibrio)
• Epsilonproteobacteria  (Helicobacter the causative agent of peptic ulcer, Wolinella)
• Zetaproteobacteria       (Mariprofundus ferrooxydans)

On the other hand, gram positive bacteria that can form endospore are Bacillus sp. and Clostridium sp.. Streptomyces sp. produce antibiotic called streptomycin.

Lyme disease

1. Lyme disease is a infectious disease caused by the bite of a tick infected with Borellia burgdorferi.
2. After biting, an expanding of bull's eye rash develops on skin.
3. This disease is not contagious from affected person to someone else.
4. The symptoms are joint swelling and muscle pain.
5. Preventions are wearing long sleeved shirt and long pants tucked into socks, special care in handling outdoor pets and avoid tick habitats such as brushy or overgrown grass habitats.
6. Treatment with antibiotic at early stage is applicable. Example of antibiotics are deoxycycline, amoxicillin and cefuroxime.

Syphilis disease

1. A sexually transmitted disease caused by Treponema pallidum.
2. Antibiotic is available for early stage.
3. Often, syphilis does not have any symptoms.
4. Condom can be used to prevent spreading of syphilis disease.

Purple sulphur bacteria

1. Proteobacteria.
2. Habitat: stagnant water or place with high concentration of hydrogen sulphide.
3. Anaerobic or microaerophilic.
4. Use hydrogen sulphide as reducing agent.
5. Genera: Chromatium sp., Ectothiorhodospira sp.
6. Anoxygenic photosynthesis, which means no oxygen is produced after photosynthesis.

Purple non sulphur bacteria

1. In stead of using hydrogen sulphide, they use hydrogen as reducing agent.
2. High concentration of sulphur will kill them compare to purple sulphur and green sulphur bacteria.
3. Too much hydrogen sulphide is toxic to them.
4. Anoxygenic photosynthesis as water is not used as electron donor.
5. Example: Rhodospirillum sp., Rhodobacter sp., Rhodobium sp.

Green sulphur bacteria

1. Obligate anaerobic photoautotrophic bacteria.
2. Also known as Chlorobiacaee.
3. Non motile.
4. Require reduced sulphur compounds like sulphide.
5. Habitat: Volcanic hot spring, deep in freshwater lake
6. Genera: Chlorobium sp., Prosthecochloris sp., Chloroherpeton sp.
7. Anoxygenic photosynthesis

   

   Comparison between archaea, bacteria and eukaryotes

    

 



Difference of membrane lipid of bacteria and archaea

1st week. 13.9.2015

Hey it's sem three! I thought it will be a relax one since it is just the beginning of the sem. However, there are already many assignments, lab report and tutorial waiting for me. Besides than academic, there is one internal chinese debate competition and hot science exhibition for my weekends. Let's talk about today's hot science exhibition at Petroscience, KLCC.

In the morning I went to KLCC with Megat (Sorry Dr we were late). After that the person in charge brief us for the exhibition. She asked us to try using  simple words to explain the scientific term in microbiology for example pathogen, vaccines and so on as some of the visitors might not from science background. Also, she gave each of us the free ticket for the admission to 'Illusion', the new exhibition which talks about optical illusion. Sometimes the thing that you see and what your brain interpret might not be the same and therefore you will not believe from what you observe.

Basically there are three types of virus, Ebola virus, Corona virus and Bacteriophage. A memory game is conducted in the middle of the exhibition as well to attract the attention of kids. (The memory cards contain the shape of bacteria!) From 10.30 am to 12.00pm, there are only a few visitors coming in and we start explaining to them. After observing my explanation, one of the person in charge gave me feedback that sometimes in stead of just telling them, I should question them first to have two way of communication. At the beginning when the visitors came I will just tell them 'this is Ebola virus', but then after that I will start of with ' Have you heard about Ebola?' 'Do you know MERS, the middle east respiratory syndrome? It is actually caused by Corona virus!' I found it is useful as some of the people may start thinking and wanted to know more. The person in charge told me that Malaysian nowadays are just listening and keep quiet, but most of the time we wouldn't know whether they really understand or not. Thank you and I appreciate the feedback. :)

From what I observed, most of the visitors are just nodding their head and walk away without asking more about the virus until I met with one Malay family. They are very friendly and three of them are very interested about virus. The daughter of the family studied human science in Cyberjaya, therefore sometimes she helped me to explain to her parents. For instance, she told her parents that the virus is either reproduce through DNA or RNA and so on. I was so glad to meet with them as there are not much people who really concern about the current issues like MERS and Ebola and wanted to know more about the causes which is by the tiny microorganism that we cant even see or feel in our surrounding. When I am explaining on something, the family will listen and tell me what they know as well. They also ask me some questions like how is the disease transmitted and is there any cure for it. After that, the aunty shook my hand and said thank you. Talking to them is really brighten up my days and I like them very much.

* Megat and I went to the Illusion exhibition, It was amazing and sometimes it make me couldn't believe what I just saw! One of the example is there is a black dot in the middle of picture, when we focus looking at it the colour bars around the dot will fade away and disappear. When you blink your eyes, the colour bars will appear again. There is also a jar where they can put the thing bigger than the opening of the jar into it. Sometimes we just wonder how can it happen. It was indeed an eye opening one!

 How I introduce these virus
Ebola virus

• Early stages - headache, muscle pain, sore throat
• Later stages - Kidney and liver failure, Vomiting and diarrhoea
• Fruit bat is the first organism that transmit the virus.
• Human are infected by closed contact with the blood, secretions of infected animal.( For example, the people ate the infected bat or the fruit that bitten by the bat in Africa because it is a rural area and they stay in the forest)
• Human and human transmission happen through close contact of broken skin or wound.
• It has an outbreak in Africa.
• No cure for Ebola disease 

Corona virus

• Corona virus introduce MERS and SARS (respiratory disease)
• In latin word, 'corona' is known as crown and the naming is based on the appearance.
• Human and human transmission is occurred through closed contact. Normally the health care workers have higher chance to get infected as they spend long time taking care the patients.
• It is the most common causes for common cold.

Bacteriophage

• Virus that kill harmful microorganism
• It is better than antibiotics as antibiotics kill all the bacteria regardless it is good or bad while bacteriophage only infect specific harmful microorganism
• They kill the bacteria through reproducing in the cell, and finally the cell breaks.

****One of the visitors asked me, where will the bacteriophage goes after it burst? I said it will stay in the body, am I right? >,<

Aspects of Biotechnology in Microbial Ecology

Functions of microorganisms in microbial colony

1) Microorganism as pollutants

Salmonella can be found both inside and outside of eggs. Normally, eggs can be infected by fecal contamination when the egg exits the hen's body or by dirt from surroundings. That is why the eggs are washed and sanitized at the processing plant. Bacteria can also be inside an uncracked, whole egg. Contamination of eggs may be due to Salmonella within the hen's ovary or oviduct being transferred into the contents of yolk and white before the shell forms. Over the years, however, scientists have found that Salmonella Enteritidis has the ability to grow both in the egg yolk and white.

Keeping eggs adequately refrigerated prevents any Salmonella present in the eggs from growing to higher numbers, so eggs should be refrigerated until they are needed. Moreover, cooking reduces number of bacteria in eggs due to the use of high temperature.

Symptoms of Salmonella infection: (12-72 hours after consumption of contaminated food)
- Fever
- Abdominal pain
- Diarrhea

Actions that can be taken to reduce Salmonella infection from eggs
- Discard cracked eggs
- Keep eggs from refrigerated
- Avoid consumption of raw eggs.
- Eggs should be fully cooked

2) Microorganism cause of pollution

Methylmercury is a neurotoxin that poses significant health risk to human. It is formed by the action of anaerobic bacteria. They turn inorganic mercury into methyl mercury.

3) Microorganism as indicator of pollution

Dr mentioned that if E. coli is found in water, it has a high possibility that the water is contaminated with faeces.

4) Microorgnism may reduce pollution

For example, Rhodococcus can be used in oil degradation.

Extra information

- If we want to increase the production of microbes, bioreactor is used which the volume is up to 1000L.


- Pesticide such as DDL is toxic in high concentration. It function through interfering the synthesis of chitin. Thus it will disturb the development of insects such as grasshopper since the head, thorax and body is mostly made up by chitin.

- Superbug is resistant to antibody

-Thiram is a fungiside. It is used to prevent fungal disease in seed and crops. Besides, it also acts like an animal repellent to protect fruit trees and ornamental( plant that is grown for its beauty and decorative value) from damage by rabbits and rodents.

Water related disease

- What is Methaemoglobinemia? 
Reduction of ability of blood to carry oxygen due to reduced level of haemoglobin.

- Who will be the victim?
Infants are most infected. They may seem healthy, but show the sign of blueness around the mouth, hands and feets. This is why they are given the name 'Blue baby syndrome'.

- What are the syndrome?
These children will have breathing difficulties,continuous vomiting and diarrhoea.

- What is the cause?
High concentration of nitrate in drinking water, especially in bottle fed infants and water from well in rural areas. The source of nitrate comes from manure and fertiliser on agriculture land.

- How does it work?
In human body, nitrates will be converted to nitrites. Nitrites is then react with haemoglobin in red blood cell to form methaemoglobin, affecting the body's ability to carry oxygen.

Biogeochemical cycles

 Carbon cycle

1)      Reduced form of carbon: CH₄, Organic matter [ presence of H]

       Oxidized form of carbon: CO, CO₂ [To ease my memorising, there is presence of O]

 

 

 2) Organic matter undergo respiration to release CO₂.

      Organic matter undergo fermentation to become CH₄, CO₂, H₂.

 

3) Carbon dioxide will be fixed into organic matter again by plants and photosynthetic bacteria such as cyanobacteria and green algae.

 

4) Organic matter includes cellulose, lignin, hemicellulose from plant cell wall, starch, hydrocarbon and lipids from animals.

 

 

Nitrogen cycle

 

3 major process:

1) Nitrification (Oxidation)

Ammonium ion (NH₄⁺)     -------------->   Nitrite (NO₂⁻) --------------> Nitrate (NO₃⁻)

2) Denitrification

 

Nitrate (NO₃⁻) -----------> Nitrogen gas (N₂) / Nitrite (NO₂⁻)

 

Reduction of nitrate to ammonium ion by several bacteria such as Geobacter sp. , Clostridium sp. , Desulfovibrio sp.

 

Nitrate (NO₃⁻) -----------> Ammonium ion (NH₄⁺)

 

3) Nitrogen fixation (Reduction)

 

Nitrogen gas (N₂) ----------> Ammonium ion (NH₄⁺)

 

Sulfur Cycle

1) Mineralization of organic sulphur to the inorganic form, hydrogen sulphide (H₂S is toxic)
2) Oxidation of sulphide (H₂S)  and elemental sulphur (S) to sulphate (SO₄⁻)
3) Reduction of  elemental sulphur (S) /sulphate (SO₄⁻) to sulphide (H₂S) (dissimilatory)
4) Reduction of sulphate (SO₄⁻) to organic sulphur. (assimilatory)

 Iron cycle

Oxidation (Aerobic condition)

Ferrous ion (Fe²⁺) --------> Ferric ion ( Fe ᶟ⁺)

Reduction (Anaerobic condition)

Ferrous ion (Fe²⁺) <-------- Ferric ion ( Fe ᶟ⁺)

Ferric ion ( Fe ᶟ⁺) --------> Fe₃O ₄by magnetotactic bacteria

Manganase cycle

Oxidation
Mangnase ion (Mn²⁺)-------->  Manganic ion (MnO₂)(Mn ⁴⁺ )

Reduction
Mangnase ion (Mn²⁺) <--------  Manganic ion (MnO₂)(Mn ⁴⁺ )