Tueday, 14th October 2014, 10th Microbiology class "Worries"

As you can see from the title itself, "Worries", the class was indeed... Quiet. It was chest-tightening if I must say myself. And to be honest, I'm not worried during that class because of our SKP exam to be held that evening. Instead, I was worried of Microbiology itself x'D I was disturbed by the fact that our poster haven't gone too far yet or in other word, not much is done yet. Yep, I was deeply disturbed by that. Thinking when will we be recording the video and finalise everything. At least, thats' what I was worried about. I don't know about the others though (◔(ｪ)◔) 
And also because... I haven't searched yet the notes for algae. I have searched for fungi notes though, but today, we were actually going to learn about algae first. That made me restless. Haha. I was afraid if Dr. Wan suddenly asked me about algae (which I have no notes on it nor read anything about it beforehand) so... I'm deeply terrified if i was asked. Hehe. And it was all because... the night before, I used all night to study for my SKP test x'D So I guess I am worried about my SKP after all~~

Today we continue our lesson with algae. And to be in class without reading the notes first is so not cool. By 'not cool', I mean I am not able to discuss about it with the whole class since everyone seemed to have read about it and I don't. I was completely clueless. Hmmm. So I will be updating this blog while learning about algae all over again. By the end of the blog I should have understand about algae, and what you guys are actually talking about during class x'D

GENERAL CHARACTERISTICS OF ALGAE 

• Eukaryotes 
• Most algae are photosynthetic (carry out photosynthesis) and some are chemoheterotrophic (obtain energy from chemical reactions and nutrients from preformed organic matters). 
• Can be unicellular or multicellular. 
• Can occur in salt or fresh water, or on the surfaces of moist soil or rocks. 
• Reproduction in algae occurs in both sexual and asexual forms. 
• Major suppliers of food and oxygen within the aquatic communities. 
• Algae form the base of aquatic food chain. 

Algae covering water surface. 

Volvox ; a type of algae 

Algae covering surface of rocks. 

GROUP OF ALGAE

Chlorophyta (Green algae) 

• Occurs in freshwater and some live in the sea. 
• Most are single cells and microscopic. 
• Consists about 7,000 species. 
• Store food in the form of starch.
• Contains primary pigments : chlorophyll a and b, accessory pigments : carotenoids and xanthophyll. 
• Example : Ulva (sea lettuce), Codium sp. (dead man's finger) 

         

Ulva 

Codium sp.

Phaeophyta (Brown algae) 

• Found in marine environment. 
• Made up of holdfast (base used to attach to rock or bottom), pneumatocyst (air bladder to aid buoyancy) and stipe (supporting stalk) and blade (leaflike structure that floats on the surface to collect sunlight for photosynthesis).
• Cell walls made up of cellulose and polysaccharides called "alginic acid". 
• Store food in the form of "laminarin". 
• Consists about 1,500 species. 
• Contains primary pigments : chlorophyll a and c, accessory pigments : xanthophyll and fucoxanthin.
• Example : Fucus spp. and Sargassum spp.

Structure of brown algae 

Sargassum spp. 

Fucus spp.

Rhodophyta (Red algae) 

• Mainly live in shallow waters and deep tropical seas. Few occurs in freshwater. 
• Most common in warm-temperate and tropical climates.
• Consists about 4,000 to 6,000 species. 
• Lack flagella.
• Store food in the form of "floridean starch". 
• Cell walls are made up of cellulose and polysaccharides such as agar and carrageenin. 
• Contains primary pigments : chlorophyll a and d, accessory pigments : carotenoids, xanthophylls, phycobilins. 
• Example : Porolithin sp., Kappaphycus

Kappaphycus

Porolithin sp.

Euglenaphyta (euglenoids) 

• Occurs in freshwater. 
• Protozoa-like algae. 
• Flagellated. 
• Store food in the form of "paramylon". 
• Some are photosynthetic and some are heterotrophic. 
• No cell wall. 
• Contains primary pigments : chlorophyll a and b, accessory pigments : carotenoids and xanthophylls. 

Structure of euglenoids

Examples of euglenoids

Chrysophyta (golden algae)

• Occur in both marine and freshwater. 
• Flagellated. 
• Cell walls are made up cellulose and pectin (which often filled with silica).  
• Store food in the form of "leucosin" and also in oil droplets. 
• Contains primary pigments : chlorophyll a and c, accessory pigments : carotenoids, fucoxanthin, xanthopylls. 

A colony of golden algae. 

Dinoflagellates (Phylum Pyrrophyta) 

• Occurs in both marine and freshwater. 
• Some are photosynthetic, some are heterotrophic. 
• Have two flagella. (whip, turn and maneuver in water).
• Store food in the form of starch. 
• Some species of dinoflagellates emit blue light when disturbed, called bioluminescence. 
• Some species of dinoflagellates are toxic and can cause red tides and shellfish poisoning.
• Contains primary pigments : chlorophyll a and c, accessory pigment : carotenoids
• Example : Noctiluca scintillans, Pfiesteria piscicidia

Noctiluca scintillans

Pfiesteria piscicidia (SEM)

Bioluminescent algae 

Red tides (a type of harmful algal bloom)

Bacillariophyta (diatom)

• Occurs in freshwater, salt water, moist soil and moist surface of plants. 
• Often regarded as the most beautiful algae. 
• cell walls are made up of glass that is very finely etched with a species-specific pattern of dots and lines. 
• Store food in the form of chrysolaminarin (oily carbohydrate). 
• Contains primary pigments : chlorophyll a and c, accessory pigments : carotenoids, fucoxanthin. 

USES OF ALGAE 

Algae are used in food, animal feed, cosmetics, pharmaceuticals, and biofuels. They can also be used for carbon sequestration and bioremediation of waste and waste water. (this is what I found when I Google for the uses of algae). 

While... These are the points when we discussed in class that day. Algae are used as food (seaweed), fuel, collagen (cosmetics), fertilisers, polisher, filtration and dye for textiles (clothes). 

#FUNFACT 

> Why protist is not classified as "Plantae"? 

Because they don't have vascular system like in plants. 

> Why protist is not classified as "Animal"?

Because they are autotroph (photosynthetic).

Soooo, like I said before, by the end of the blog. I should have learned something about algae. And... I did learnt something (about algae) while finishing this journal! ฅʕ•̫͡•ʔฅ 

P/S Somehow this update is more about me learning about algae instead of what I did in class that day. I'm so sorry. x'D 

Until next class. Hehe.

And happy holiday~~~ 

Adieu!

Friday, 10th October 2014, 9th Microbiology Class "Exam"

Today I arrived quite late to the exam venue. At... If I'm not mistaken, 8.35am. Fortunately, when we arrived the others were also going into the room where our very first Microbiology examination will be held. Yes. We had our examination today!! Haha. The examination is done in 1 hour and 30 minutes. 

And... I got correct for the question on what is the function for pili. Actually, we have to match the organelle with it's function. And there are some that was quite confusing and I'm not so sure about their function. 

(By the way, the answer for what's the function of pili for today's exam is ---> infecting other organisms) 

Afterwards, Dr Wan said that after she observed how we... answered our Microbiology paper today. She got quite worried, i guess? Haha. And that when she asked us why didn't we remember what's the function of pili. Some of us told her that they don't remember but Dr Wan said that that's not the case. The real reason on why we couldn't remember is... We are not supposed to memorise all the organelle and it's function but it is because we do not understand what we learn during class. 

So, for today's lesson which is on Topic 5 "Protozoa", she assigned us a group work. Discuss with our groupmates on what is the best way to remember or study this topic. Such as by doing mind map, watching videos or search for additional informations on the net. After deciding on the best method, share it with the class by presenting today's topic with the method that we have chosen. 

It was veryyy interestin to see how each how each group present it with their own preferred way. Hmm, Farah Alia's group and Megat's group use the mind map method by constructing a mind map online.

Chew's group chose to watch videos in order to understand more since we can visualise it and also search for words or terms that we don't understand like... "African sleeping sickness" which is a disease that is caused by flies (at least that's what Mawardah said hehe. I'll look up for it, after writing this blog. hehe). 

Ee Lyn's group gave us few questions, and we have to fill in the blanks. Which really helps! :D 

Mashi's group chose the flash cards method, they agreed that it is easier to read notes that way especially when we are having quizzes. 

And lastly, Choy's group where they presented the "Protozoa" topic by using the capital of the characteristics, like... for example PIPA which stands for Phagocytosis, Ingestion, Pinocytosis, and Absorbtion. (See? Even I remembered it up until now, haha xD) and they even prepared some "short songs" but the lyrics is based on the characteristics for the major group of protozoa. They even made us sing along with them. We were forced to, under Choy's command. Hahaa

And as for my group, we also use the mind map method but we sort the... "biography of protozoa" (Can I even say it like that? xD) by dividing the informations into four main sections which is characteristics, movement, habitat and example. And we also use the icon method. For example, for the point "housed in shell". We presented it by putting a house drawing followed by "in" and a shell drawing. We think that it is more fun that way, suitable for us "youngins". Hehe. 

But we didn't get the chance to present our presentation today because we ran out of time, the class was dragged until 12.30pm when our class was supposed to end at 12.00pm. Hee. And it was our fault anyway; very poor time management. The preparation for the presentation should only be done in 10 minutes only (that's what Dr Wan told us before we started preparing) but apparently we took more that 10 minutes.. Hee. 

Until then, 

Adieu!  

Tuesday, 7th October 2014, 8th Microbiology Class "I don't remember what I'm feeling that day, but I'm sure it's a positive feeling"

 Class started a bit late. 15 minutes late if I am not mistaken. Dr Wan was late by 15 minutes. Hehe. It's okay though, not that I mind x'D In addition to it, Dr Wan was late. Yes. But she arrived late while carrying a plastic bag. That sprang to mind at that moment that last friday, on our previous class before we go back for Eid al-Adha, she promised to bring 'Rendang' for us. I didn't know she actually meant it. Hehehe. But she told us afterwards that she was late because she was cooking "rendang" for us but at the last minute, she remembered that some of our class members are allergic to chicken, so she cooked fried rice for the said students. That's so... Sweet and thoughtful of Dr Wan x'D

And classes soon after, on the last section of Topic 3 which covered on Inclusions.

Since today's lesson was a bit short, I shall do the "What I learned today" or "New Things That I Learned Today". Hehe.

New Things That I Learned Today

• Although it is well known that prokaryotes have metachromatic granules, Dr Wan told us that eukaryotes also have metachromatic granules, which is used as food storage.

• Other than as an energy reserve and having for nutrient, sulphur granules is also used to form spore.

• (This is not something that I just knew, but I wanted to put this in the journal too, because I am reminded about it again x'D so it's important too)

• The other name or term used for "carbon fixation" is Kelvin cycle or Kelvin-Benson cycle (Thanks to Dr Wan for reminding us!!)

• Dr Wan asked us what is "microbial nutrition" (what they eat to survive?)

1. Source of carbon
2. Source of energy

• For microbial that uses carbon dioxide and light, it is called "phototrophic microbe" or "photosynthetic".
• While other microbial that use other kinds of chemical (other than dioxide and light), it is called "heterotrophs".

• The function of magnetosomes is to passively align along the Earth's magnetic field lines to direct themselves to the side where there is oxygen.

• Microbes that requires oxygen to survive is called "microaerophile".

• Magnetosomes can be in chain form, diamond or bullet. ONLY ONE or TWO chain!
• Other function of magnetosome is to protect the cell against hydrogen peroxide accumulation.

• Why do the cell want to prevent from hydrogen peroxide? (Chew, one of my classmate asked that to Dr Wan, and Dr Wan asked us back. Haha. But of course we remained silent. Hehe.)

• Some fact about hydrogen peroxide that was mentioned by Dr Wan that day.

1. Hydrogen peroxide contained in hair dye.
2. Aerobic organism are able to neutralise the toxicity of H
   2O
   2 because they have the enzyme that help degrade H
   2O
   2.
3. On the other hand, bacteria have magnetosome to protect themselves. While bacteria that don't have magnetosomes, have enzyme peroxidase instead.

• When bacteria face a harsh environmental condition, it will trigger the formation of endospores.  (vegetative cell -----> endospore)
• When bacteria face a favourable condition, it will germinate again into vegetative cell.

• When endospore is stained with malachite green (the only stain that can detect endospore), positive result will stained green, while negative result will stained red or pink or white.

• Desiccation = extreme dryness

• Bacteria that can live in extreme dryness is called "xerophilic".

• "Dipicolinic acid" is an acid that prevent from desiccation in bacteria.

• Chew asked Dr Wan if endospore can be destroyed? Dr Wan said that certain radiation can kill it, but only radiation, no chemical can destroy it yet.

That's all for today. This is all what I can tell for today's (Monday class) journal. This is solely what Dr Wan said during class. Haha. Maybe there are some of them I have missed or didn't jot it down. Or maybe I have heard it wrongly... I hope not O_O And I didn't do any further Google-ing because the internet connection is very poor nowadays, here,at college. Hmm I don't think I can even consider it as "poor" but I couldn't even connect to the internet at all x'D We're having a bit of a problem here with the internet connection, I guess. So, there's not much information that I can share.. 

In between class, we stopped for a break. We ate the rendang and fried rice that Dr Wan brought!! It was delicious!! :D :D While on break, she asked us to "submit" what microbe that we have decided to adopt :D So... after searching and also discussing with my older sister (since she studied Medicine before, she studied Microbiology too) and she suggested some microbes but at last I picked Shigella dysenteriae after further research about some of the microbes.

I even considered diatom and volvox, like I said before (wayyy earlier, in my first or second post, maybe? x'D) but Shigella dysentriae won my heart. Keke.

And Dr Wan also introduced us to a new website, "Socrates" for us to answer some questions. It's a "pretty" website!  It's a good method to... attract our interest to answer the questions. Hehe. I'm telling this from my point of view as a student! :D

Oh and also! We can check daily news or updates about microbes on this website 

www.sciencedaily.com

Adieu!

:D

Friday, 3rd October 2014, 7th Microbiology Class "Eid al-Adha"

Everyone was in the mood of going back home today, with their bags (please notice the (s) on the bag hahaha indicating they are carrying more bags than they usually do to class) I wish you Happy Eid al-Adha in advance :) I hope all of you arrived home safely. 

Today's lesson continues from where we last stop last week. Still under the topic of external structures of prokaryotes before proceeding on some of "The Internal structures of Prokaryotes". Despite the "Raya" mood, everybody was cooperating with the lesson as usual. Hehe. And we even had some foods mentioned during class! It's not even related to Raya actually. It's all because we came across the diagrams of peptidoglycan that looks a lot like sausages, Gram negative and Gram positive cell walls that look like spaghetti with meatballs and cytoplasm, due to it's jellylike structure, it reminds everyone of jelly or in malay we called it 'dadih'. Hahahaha. I see all of you are hungry, eh? x'D

"Spaghetti and meatballs" Gram negative and Gram positive cell walls

"Sausages" peptidoglycan 

Today Dr Wan kind of focusing more on the Gram positive and Gram negative cell walls during the end of the lesson. Thus, I shall conclude about these cell walls first.

The two cell walls are different are different by the structure itself. Like the one that I have posted above. 

GRAM POSITIVE CELL WALL 

1. 1- Have many layers of peptidoglycan. 
2. 2- Contains teichoic acid and lipoteichoic acid (which is teichoic acid that attached to plasma membrane) 
3. 3- 90% of the cell wall is peptidoglycan. 
4. 4- Do not contain outer membrane. 

FUN FACT #1

Teichoic acid

• There are two types : wall teichoic acid (WTA) that attached to peptidoglycan and lipoteichoic acid (LTA) that attached to plasma membrane.
• Resistance towards environmetal stresses, low osmolarity, antimicrobial peptides, antimicrobial fatty acids, cationic antibiotics and lytic enzymes produced by the host. 
• Act as receptor for phage particles. 
• Can bind to cationic groups thus providing a reservoir of ions close to the surface of bacteria that may ease the activity of different enzymes. 
• Involved in cell division and cell morphogenesis (a process that concerned with the shapes of tissues, organs and entire organisms and the positions of the various specialized cell types).
• WTA act as the spatial and temporal regulator for peptidoglycan metabolism, controlling the level of cross-linking. The highly cross-linked peptidoglycan showed a higher resistance to enzymatic degradation by lysozyme. 
• Thus, the high resistance helped the bacteria when interacting with host that produce lysozyme as they can defense themselves against bacterial infections. 
• And also, the cell wall does not degrade easily! 
• Hence, that's why most of Gram positive bacteria are not pathogenic; harmless.

GRAM NEGATIVE CELL WALL 

1. Very few layer of peptidoglycan. 
2. Have outer membrane that consists of lipoproteins, lipopolysaccharides (LPS), phospholipids and porins. 
3. 10% of the cell wall is peptidoglycan.

Aside from Gram positive and Gram negative cell wall, there are also atypical cell walls. Which 'atypical' itself means 'unusual'. 

ATYPICAL CELL WALL (Unusual cell wall) 

1. Mycoplasma : Have no cell wall. Instead, they have sterols. (which has the same composition with cholesterol). 
2. Chlamydiaceae : The cell wall contains LPS.
3.  Archaea : Lack of peptidoglycans in their cell walls but have pseudopeptidoglycans. 

THE DIFFERENCE BETWEEN CELL WALL OF AN ARCHAEA AND BACTERIA

As I had mentioned in the previous entry. The difference between archaea and bacteria is the components of their cell wall where peptidoglycan is present in bacteria but not in archaea.

Instead, archaea have pseudopeptidoglycan which is a substance that is quite similar to peptidoglycan.

The difference between peptidoglycan and pseudopeptidoglycan is that in peptidoglycan, the disaccharide molecule is made up of monosaccharides called N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM). The alternating NAM and NAG molecules are linked by β(1,4) glycosidic bonds.

On the other hand, pseudopeptidoglycan in archaea are made up of N-acetylglucosamine (NAG) which is the same as in peptidoglycan, but instead of NAM, it has N-acetyltalosamimuronic acid (NAT).  The alternating NAM and NAT are linked by β(1,3) glysodic bonds.

Next, we proceeded on the “Internal Structures of Prokaryotes”. During this “session”, the class participated more when discussing/learning this topic, there were more response compared to when Dr Wan was teaching us about the “External Structures of Prokaryotes”. It’s obvious that this is all because of our previous assignment Dr Wan assigned us last week -->> Make a mind map for the topic of internal structures of prokaryotes.

The internal structures of prokaryotes consists of

• Plasma membrane
• Cytoplasm
• The nuclear area (Nucleoid and plasmid)
• Ribosomes
• Inclusions
• Endospore

FUN FACT #2

Prokaryotes do carry on respiration. There are two types of respiration which are aerobic respiration and anaerobic respiration.  The plasma membrane is the one who is responsible to carry on the respiration, though. 

PLASMA MEMBRANE

There are two movements of materials across the membrane namely the active process and passive process.

PASSIVE PROCESS

·    The process where molecules move from a region of higher concentration to a region of lower concentration, down the concentration gradient, WITHOUT the aid of energy (ATP).

·   

T   There are three types of passive process which are simple diffusion (The movement of molecules from high to low concentration until equilibrium), facilitated diffusion (the movement of molecules from high to low concentration, WITH the aid of carrier protein), and osmosis (the movement of water from high concentration of water to low concentration of water).

ACTIVE PROCESS

·    The process where molecules move from a region of lower concentration to a region of higher concentration, against the concentration gradient, WITH the aid of energy (ATP).

·   
     There are two types of active process which are active transport (molecules are moved by transporter protein from low to high concentration, with the aid of energy) and group translocation (where the transport protein change shape when transporting the molecules, with the aid of energy).

CYTOPLASM

This is where we were all reminded to “dadih” due to the jelly-like structure of the cytosol. Haha!

The major substances of cytoplasm are DNA, ribosomes and inclusions.

NUCLEAR AREA

Consists of the nucleoid and plasmid.

NUCLEOID

·    Nucleoid is a single, long circular molecule of double stranded DNA (in prokaryotes, we called it “bacterial chromosome”).

PLASMID

•      Small, circular, double-stranded DNA.
•      An extrachromosomal genetic elements.
•      There are five types of plasmid with their own specific functions which are virulence plasmid, Col plasmid, fertility plasmid, degradative plasmid and resistance plasmid.

The functions of each type of plasmid

•     They are transferable from one bacteria to another bacteria. (same species only!!)

Functions of the plasmid :

1.     To carry antibiotic resistant genes and spread them. Thus, many diseases can be prevented or treated.
2.    To carry genes that involved in metabolic activities.
3.     Capable of producing antibacterial proteins. 

And there are also other functions of plasmid. 

RIBOSOMES

In my opinion, ribosome is an organelle that is very well known to everyone.  For  “everyone” that previously studied Biology/Science in secondary school, that is. Hehe.

The function of ribosome is as the site of protein synthesis. And they are one of the major components of cytoplasm, as I had mentioned earlier. In eukaryotes, some ribosome are membrane bound (where they are attached to the rough endoplasmic reticulum (RER) and some are boundless, and floating around in the cytosol). Since there are no RER in prokaryotes, the ribosomes are pretty much boundless.

There are 70S (S = Svedberg unit) ribosomes which consists of two subunits, small subunits = 30S and large subunits = 50S).

If you’re wondering why 30S and 50S doesn’t make up a total of 80S but instead of the stated 70S. I did wonder about that too, but sadly I didn’t do any initiatives to look up for it. Hee. I’ll be more productive and curious after this. I will!! And. Ah. Actually Dr Wan asked us during today’s class. “Anybody searched for why it 70S and not 80S?” but nobody answered. Hehe. 

Dr Wan said that it is because during centrifugation, there are some ribosomes that are lost, that’s why the number of ribosomes are not enough (80S).

In conclusion, cells that have a high rates of protein  synthesis, obviously have a large number of ribosomes inside them. Thus, several antibiotics will get into action in order to inhibit protein synthesis of ribosomes.

Some examples of the antibiotics are :

•      Aminoglycoside antibiotic (streptomycin, gentamicin, azithromycin, telithromycin etc) 
•      Macrolide antibiotics (Erythromycin, clarithromycin etc….)

FUN FACT #3

Macrolides are primarily bacteriostatic, that is by binding to 50S subunits of the ribosome, they inhibit bacterial protein synthesis. 

"Bacteriostatic" = Capable of inhibiting the growth or reproduction of bacteria. 

And today’s class ended!! Three days of holiday, is quite long…  I mean, Dr Wan said that it is long.. I… have no comment on that. Hahaha. What I do know is, I can’t wait to go home! Salam Eid al-Adha everyone! 

P/S  Although today’s lesson went well, and I understand most of it but there are some that I don’t understand, especially on the Gram positive and Gram negative part. Since there are Gram positive and Gram negative cell walls for both bacteria and archaea. It is quite confusing at first, i didn’t know that there are also Gram positive and Gram negative archaea too!! I’m surprised when I found out that in the lecture notes. Haha.. I will read more on that, read carefully. Real careful. Hmm but come to think of it, it’s not that I don’t understand. I’m confused. Hehe...