[TOPIC 4] Amino Acids and Proteins

Assalamualaikum w.b.t.

To be very honest, I don't really like learning about amino acids and proteins but you know that one quote 

"You'll never know unless you try"

There are 20 essential amino acids and Dr. Amalia told us to try memorise it. I don't want to! Haha. I'm trying to accept the fact that it's inevitable. I am bounded to amino acids and proteins if I were to pursue this course; or maybe as my career, who knows~

Hence, I will try my best to memorise them. Wholeheartedly. x'D

For this topic, we learnt mostly about the structures of the amino acids. Including the structures of all the 20 amino acids. 

What's interesting about the amino acids is that they each have their own letter code. I'm not sure whether we have to memorise this too or not. Ha ha. (dry laugh) 

Other than the structures, the chemical properties of the amino acids were also focused. The amino acids are grouped in four main groups which is polar, non-polar, acidic and basic. 

Actually, if we know the structure of the amino acids well, we can guess the chemical properties of them already. 

For example, the presence of amine group in the amino acids indicates that the amino acid is basic. Or the presence of sulphur or hydroxyl group which is known to be high in electronegativity indicates that it is polar; it can form bonds with other polar molecules. 

It can be concluded that the chemical properties depends on the side group present on the amino acids. 

#I'm not sure if I have been told about this before but I just knew today that physiological pH is actually pH 7.4; neutral pH. 

Other than that, we have to know the structure and significance of the alpha helix and beta pleated sheet and what bonds contribute in the structures. (It's hydrogen bond!).

One of the new thing I learnt during this topic is that structures or components known as 'turns' and 'loops' help to reverse the direction of the polypeptide chain. 

#The difference between loop and turn is that loop is used for long amino acid chains while turn is used for short amino acid chains. 

In conclusion, if you fully understand the structure and chemical properties as well as the functions of some structures. You can answer questions like 'what bonds connect the amino acids?' 'why the amino acid is acidic/basic?' 'what structure help to change the direction of the amino acid chains?'. 

The current topic seems a bit off topic from the usual stuff we learn about microbes. I miss the names of the microbes already. 

Let's study well, ok. We're all in this together after all. Hehe. 

Later! 

:)

[TOPIC 3] Intracellular Structures of Prokaryotes

Assalamualaikum w.b.t. 

Last topic was covered on the external part of the prokaryotes. Hence, now we will focus on the internal part of the prokaryotes. It is no other than the organelles of prokaryotes! Actually for this topic, since we were a bit lagging behind due to public holiday etc, Dr Wan made us did peer teaching instead of her teaching us. 

Every group was assigned on one or two organelles to be presented to the class. My group have to cover the inclusions that exists as granules which is sulphur granules, metachromatic granules and polysaccharide granules. 

After each presentation, the listeners which is our own classmates/lecturemates have to ask some questions regarding our presentation. And we have to find the answers, no matter how hard or easy the question(s) is~ 

What I learned from this topic is that it is important to know the functions of each substance because let's say if an organelles are absent in an organism. We can identify the cause of the disability of the organism to function; which is might be due to absence of the organelles required. 

For example, organism that lacks ribosomes will result in the organism unable to synthesise protein. 

Other than that, it is also important to know the inclusions contained in prokaryotes as inclusions have several functions that is essential for some bacteria. 

For instance, gas vessicles are crucial for photosynthetic bacteria in order to attain enough sunlight to carry out photosynthesis. The gas vessicles will provide buoyancy to the cell and make them float near the surface of water instead of submerged or sink to the bottom of the water source. 

In addition, formation and functions of endospore should be well understood as only prokaryotes can produce endospores. However, only some bacteria such as Clostridium and Bacillus can produce endospores. There are also some diseases related to endospore that can be fatal such as tetanus and gangrene gas. 

This new semester, a new information was added on the endospore part. Before this we were only exposed to the cycle of the endospores and functions but now the components and structures of the endospores are also included; which is the most inner part of endospore consist of inner core followed by cortex, spore coat and the outermost part is exosporium. 

That's pretty much the conclusion for this topic. 

Until then! 

[TOPIC 2] Cell Wall and Membrane Structure of Prokaryotes

Assalamualaikum w.b.t. 

For this topic, I think it is crucial to be able to differentiate between Gram-positive and Gram-negative organism's cell wall properties. 

Other than knowing the difference of the two type of cell walls, it is also important to know the functions and significance of each substances contained in the cell walls. For instance, teichoic acid in Gram-positive organisms and LPS in Gram-negative organisms actually have the same function in which the components contribute to the cell's antigenic specificity. 

Other than knowing the difference and functions of Gram-positive and Gram-negative cells, this topic also covers on the difference between bacteria and archaea. 

So, how to remember the cell wall visual? 
Remember the spaghetti and meatballs picture! :D 

You don't remember? 

Wait. 

I was talking about the above picture! :D 

Why are we focusing on distinguishing bacteria from archaea? 

I would say that it is because this two organisms are in the category of prokaryotes (because they do not have true nucleus and membrane bound organelles) while the other group of microbes are eukaryotes. 

Some of the differences between the two organisms that I think I should note on are : 
- The presence of peptidoglycan 
- The amino acid contained in them 
- The glycosidic bond between the sugars 
- Ester/Ether link 

Other than that, I also learned some new terms. What are they, you ask? 

It's spheroplast and protoplast! 

Protoplast is a cell that has be lysed but it is still capable of carrying out metabolism processes. 

Spheroplast is a cell that have not been completely lysed, thus some of the components of cell wall still remains. 

How do they formed? 

Spheroplast are constructed when the the cell wall has been acted on by the lysozyme, but it is not completely hydrolysed. 

Below are some of the questions that were discussed in class throughout the lesson : 

1. How does glycocalyx act as a source of nutrients?
--> What I found on the net is an example of organism, Streptococcus mutans use glycocalyx as its source of nutrient when energy storage is low. This organism has glycocalyx in the form of capsule and it will break down the glycocalyx and utilise the sugar since glycocalyx is made up of sugars called EPS. 

2. Movement of bacteria towards nutrients or a particular substance is called 'chemotaxis'. 

3. The conjugation of pili is a process where transfer of DNA occurs. However, it does not contribute to the production of new daughter cells. Instead, the plasmid contains specific genes such as resistance to a certain antibiotic and ability to produce enzyme. Thus, the recipient of the DNA transfer will obtain the traits of the donor. 

#Do remember that the transfer of DNA can only occur between the same species! 

4. How is cell wall serve as a site of action for antibiotics? 
Antibiotics have a certain mechanism to attack cells such as attacking the cell wall, nucleic acid, ribosome etc. When antibiotics attack the cell wall, the cell wall will lyse or rupture causing the content to leak out and the organisms will die. 

That's all from me~ 

[TOPIC 1] Introduction To Prokaryotes

Assalamualaikum w.b.t. 

This e-Portfolio 'format' has changed from per week to per topic. I like per week better to be honest so that I don't forget what we have learnt but it's ok, I will manage. Hehe. 

It was a short chapter and it mainly comprised of the past semesters lecture notes. Some of the slides though, not all. 

To me, it was like a refresh or a revision to remind us again (again and again and again and it goes on. Haha) about prokaryotes; their characteristics, types, functions and the differences between bacteria and archaea.

The last time we learn about prokaryotes; which is also the 'first' time, was during first semester if I'm not mistaken. I have to admit, I do remember some of it and forgot some~

This topic shows a sneak peak on what will be discussed more in the following topics. 

Since only bacteria and archaea are grouped as prokaryotes, it is important to know the traits of the two organisms in order to distinguish them. 

Archaea is known as the organism that can survive in extreme conditions; which is also known as extremophile. There are halophiles, thermophiles, acidophiles etc based on the environment they are living. 

However, there is a bacteria that can withstand extreme condition but it is not an archaea. So how do you differentiate them? That's what we're going to learn. 

In conclusion, we are going to look through the properties that the bacteria have but not present in archaea and vice verca. There is not only one characteristics though, there are a few of them such as their cell wall components and membrane lipids. 

That's all from me~

[14th September 2015] [WEEK 2] "Schedule Change"

Assalamualaikum w.b.t 

I managed to survived Week 1, thankfully. Hehe. 

Other courses are starting to get too much on my plate with the never ending assignments. BMY3103 haven't give us any killer task, yet. (Hehe) 

Me and some of the classmates were late to class this week. Due to some changes in our time table, our Inorganic Chemistry Lab had to take the time slot originally for BMY3103. And our Microbiology class had to be held a little late, and end a little late too, of course. 

Dr. Wan suggested that class start at 11.15am, so that everyone can take their time walking to FBSB. 

I will try to arrive in time next week! 

So this week, we learn a bit of this and that about prokaryotes. Dr. Wan asked us to access Padlet that she had created. The title : "Microbial Physiology" in which Dr. Wan want us to search something; anything! about prokaryotes that may be useful for our knowledge. It can be in any form such as video, articles and journals. 

Our group found something about prokaryotes that is related to their genetics. In which the researches used genetic sequencing to see the diversity of prokaryotes. It turn out that there are few types of prokaryotes that we should know other than the general bacteria and archaea that we already know.

There are bacteroidetes, firmicutes, actinobacteria, proteobacteria and other phyla. 

Other groups had also found interesting informations about prokaryotes such as... Hmmm. One of the group mentioned something about the relation between prokaryotes and weight reducing.

It is basically about how the metabolism of the human body react to the normal flora in the gut. The researches are trying to understand the mechanism of the human body by observing and determining the bacteria that is present in their body. 

It is actually the same concept as isolating cultures from patients with a particular disease and grow them to see what species are the microorganisms that infect the patients; and decide whether it is the cause of a disease or not. In addition to that, we have to determine the most suitable antibiotic that will prevent their growth. The same goes to the weight reducing method using prokaryotes that the researches are trying to come out with. 

After everybody done presenting and explaining why their group picked the articles of their choices, Dr. Wan proceeded with every group have to pick a group of proteobacteria and present it on Monday~ 

In conclusion, today I learnt that other than the characteristics or prokaryotes, it is equally important to know the functions and metabolisms of prokaryotes. It is actually quite vast as their functions not only bound to medicinal value, but also to the environment, genetics and so on. I will anticipate what's more to come in this topic in order to understand more about prokaryotes. 

That's all from me. 

Adieu! :)  

[7th September 2015] [WEEK 1] "Welcome Back!"

Assalamualaikum w.b.t 

Alhamdulillah. We meet again! :D 

My feeling for today's first class was actually partially excited and partially nervous. Yes. It's a mixed feeling. Nervous because I'm afraid I already forgot some of the basic things about Microbiology that we have learnt such as the difference between prokaryotes and eukaryotes. Excited because.... Hmm I don't know what I'm excited for. Haha. Mostly because I get to meet my classmates and lecturers again! 

Oh. I'm also nervous because this semester's courses and schedule are no joke. Of course, it's going to get tougher and maybe harder; the subjects. 

Class was at 10.00am but Dr. Wan told us via WhatsApp that she will be a little late due to a meeting that she had to attend that morning. 

Today we didn't really learn anything. Dr. Wan only went through our course outline and told us that there will be three lecturers for BMY3103 this semester. Besides Dr. Wan, Dr. Amalia and Dr. Suriana (my mentor! :D) will also be teaching us. So many lecturers for one course~

I think it's going to be fun~ Just like last semester where Dr. Sieo Chin Chin taught us for the first few parts of the course (but took quite a long period to cover the topics, though). At least, we are able to see the difference and a variety teaching methods of the lecturers of our faculty. 

During today's class, Dr. Wan asked us what will we be learning. And few voices answered "physiology of microbiology" which is, yes, our course name for this semester. And Dr. Wan said "my kids can answer that too!". Hehe.

I searched on the net and it says that physiology of microbiology is the study of how the microbial cell functions biochemically.

I sometimes misunderstand the word "physiology" and "physically". They sound kind of the same, isn't it? 

Dr. Wan further elaborated that we will be focusing on prokaryotes' organelles such as the carboxysome, magnetosomes etc. I guess we will be learning about the organelles in greater depth than we did previously. 

Other than went through the course outline, Dr. Wan also briefed us about the upcoming Amazing Microbe Carnival. She already told us about the carnival through our WhatsApp group during the semester break. We will be doing something that involved 3D printing. Ha ha. I don’t even know how it will looks like, not before Dr. Wan told us today and even showed us few pictures of the posters with 3D props and also the machinery itself. I learned a new device today! 

I can’t wait to see the outcome! I mean how our 3D printing going to look like. It’s going to be a whole new experience for me~

That’s all for this week.

No class on Wednesday though, because Dr. Wan had to be at another place that morning.

Adieu! :)

14/14!

1^st June 2015, Monday

Assalamualaikum w.b.t and a very good day to you :D 

Today was the last class for BMY3102. It was held at BMF which is also where our first meeting with Dr. Wan took place. He he he.

However, today’s lesson was a bit… dull because everybody is… sleepy? Everybody was quite quiet during the whole lesson. Except when Dr. Wan was talking about something that is non-related to the lesson, only then everybody was talking and looked animated again. Haha.

Today we learnt the last two topics in BMY3102 which is Biogeochemical Cycle and Aspects of Biotechnology in Microbial Ecology.

As for Biogeochemical Cycle, there are five major cycle which involved elements that are important to the environment. There are carbon cycle, nitrogen cycle, sulphur cycle, iron cycle and manganese cycle.

I wonder if there are other element’s cycle? Hmm. I will look up about it on the Net and tell you by the end of this post. He he he.

Or I will just tell you now. Haha.  

Other than the five well-known cycles, there are also other cycles such as phosphorus cycles, oxygen cycle, water cycle and hydrogen cycle. These are all important elements in our lives and ecology. 

So.. Here are some new information I managed to obtain during class today :

• Methanogens/ methanotrophs are abundant in Klang and Banting (in Malaysia). For example : Oil palm farms

• What organisms that involved in carbon fixing? What kind of bacteria? --> Photoautotroph

• Organelles involved in carbon fixations are carboxysome and also magnetosome in magnetotactic bacteria. 

• There are few processes involved during nitrogen fixation. Other than biological fixation which is done by microbes that we have learnt in this topic, nitrogen can also be fixed by lightning which is also called atmospheric fixation. There are also industrial fixation. 

Industrial fixation : 

"Under great pressure, at a temperature of 600°C, and with the use of a catalyst, atmospheric nitrogen and hydrogen (usually derived from natural gas or petroleum) can be combined to form ammonia (NH₃). Ammonia can be used directly as fertilizer, but most of its is further processed to urea and ammonium nitrate (NH₄NO₃)."

- Retrieved from http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/N/NitrogenCycle.html 

• Why do we need nitrogen cycle? To be used in fertilizers to give nutrients to plants. 

• Other than Nitrosomonas, Nitrococcus and Nitrobacter. Nitropyra can also fix nitrogen.

• Prokaryotes that can fix nitrogen is called “rhizotroph”.

• Manganese is one of the trace elements.

 What important about biogeochemical cycles is that there are elements that  needed to be recycle and broken down in order for the organisms to obtain nutrients. If you think about, if there are no microorganisms that can break down this nutrients, the nutrients will remain in the surrounding or environment and non-usable. 

Thus, when this happen, the organisms cannot obtain the much required nutrients to carry out certain reactions or to grow healthily. 

That is why microbes play a big role in our ecology as well as biogechemical cycles.

Try to imagine our life without microbes to help carry out all this cycles! (°□°)

For second part of the lecture, we went on with Aspects of Biotechnology in Microbial Ecology. The last lesson!

 Points that I managed to jot down during lecture~ :

• Why do the farmers burn the residues of the farms after harvesting? --> To prevent growth of fungal pathogen. Although it is the fastest way to get rid of crops residues, it is also the most un-environmental friendly and actually harmful to our biosphere. 

• Instead of burning the crops residues, we should bury them. It is more environmental friendly that way.

• Where can we find Salmonella?  --> In raw meat or poultry (chicken) and eggs.

• What is “eutrophication”? --> It is a condition in which the nutrients are high especially in lakes and ponds that can cause pollution such as algae bloom and red tide.

• Mercury is also a heavy metal.

• Methyl mercury can also cause cancer.

• Microorganisms act as an indicator in pollution. For example : when E. coli are present, it indicates that the water source is contaminated with stools. This can be due to the water not properly treated.

• How to culture microorganisms in big amount/scale? --> Using a tank called “bioreactor”. It functions to produce a large scale of microbes. Dr. Wan even suggested that we go for a trip to visit the bioreactor sometime during third semester where everybody happily agreed aside from the continuous request to go to a chocolate factory too but countered by Dr. Wan when she asked “Tell me what microbes involved in production of chocolate?”. Haha. I myself do not know.

Actually there are microbes involved! I searched about it. Just now. He he he. 

"Chocolate Products

Microorganisms are also used in the production of finished chocolate products. Alpha amylase obtained from Aspergillus is used to hydrolyze starch for chocolate syrup and invertase from Saccharomyces is used to hydrolyze sucrose in filling mixtures to make soft-centered chocolate-covered candies."

- Retrieved from http://www.smccd.edu/accounts/case/chocolate.html 

Microbes involved in production of chocolates are yeast, lactic acid bacteria, acetic acid bacteria, aerobic spore forming bacteria and filamentous fungi. In which the microbes have their respective functions. 

Yeast -> important to enhance fermentation by bacteria. They convert sugars, such as sucrose, glucose, and fructose, into ethanol and CO2, decrease the acidity of the pulp by using up citric acid, and produce aromatic compounds, which contribute to the chocolate aroma and are important to development of flavor.
Lactic acid bacteria -> The Bacillus spp. found during the aerobic phase of fermentation have been found to be responsible for the flavoring of chocolate.

- Retrieved from http://microbewiki.kenyon.edu/index.php/Chocolate 

• Biodegradation --> Breakdown of big molecules to small molecules.

• Oil-degrading bacteria are bacteria that can produce mycolic acid.

• Recalcitrant --> Molecule compound that cannot be degraded.

• "Blue baby" syndrome is a disease caused by high number of nitrogen in haemoglobin.

"Blue baby" syndrome 

"Potentially fatal blood disorder in infants under six months of age which is also called methemoglobinemia in which there is a reduction in the oxygen-carrying capacity of blood."

• As we all know, bioremediation is a process where we use living organisms to enhance the degradation of pollutants. Thus, the organisms that are going to be used must be ensured that they are not contaminated. For example : a pure culture or mixed cultures that its’ identities are known.

• “Superbug”? --> Microorganisms that are resistant to drugs and antibiotics.

In conclusion, microorganisms are everywhere around us and they are important in our lives and to the environment. Based on this topic, I can see that they are very important to our ecology because there are some microbes that are the cause of pollution (pollutants) but they arealso some of them that can detect the pollution such as lichen. Even so, microbes are also the ones who can reduce pollution! 

Hence, it is important to know the microorganisms’ capabilities in order to have the best solution to ensure pollution are at low levels. 

It's a wrap! See you guys in next semester. In shaa Allah. :D 

P/S Pray for our success in the upcoming final examination!