[TOPIC 5] Introduction To Microbial Metabolism

Assalamualaikum w.b.t. 

Hi~ 

Since we already know about the formation and structures of amino acids and proteins. The current topic will now discuss on the functions and metabolism of the proteins. 

When I hear or come across the word 'protein', the first thing that comes to mind is 'enzyme'. He he. How about you? 

This topic firstly exposed us on metabolism such as what's the meaning, and the process involved; which is anabolism and catabolism. 

It's important to know what those two words mean. And also identify which process release energy and absorb energy. 

Next, the types of enzymes were also included in the topic. There are six of them. I have already 'met' these six types of enzyme before during our last semester which is included in Biomolecules subject. 

Other than the types of enzymes, the other important thing to know is the properties of enzyme.

This is really important, right! 

Some of the properties of the enzyme are enzymes are specific, can be inhibited by certain conditions and not used up in a chemical reaction. (Make sure you know the other functions too, I only include some of it~). 

In addition to that, it is weird if the mechanism of enzyme is not included, right? So, of course it is crucial to know that too~ 

There are two mechanisms though, the lock and key method and the induced fit method. 

I found a cute and an interesting picture of the lock and key method! So that people can memorise it easier and more fun, in some sort, because it's related to our daily life; the key. Hehe. 

If there is a method on how to make the enzyme works, there should be reasons or conditions on how to disable the enzyme functions, right? 

Yes! 

There are a few factors affecting enzyme's functions which is concentration of substrates enzymes, pH, temperatures and enzyme inhibitors. 

Make sure to know how each factor contribute to inhibit the enzyme's activity. 

Especially on the types of inhibitions. Each of the inhibition; competitive inhibition, non-competitive inhibition have their own mechanisms; where they will interact with the enzyme either at the active or the allosteric site and the effects on the products formation. 

That's all from me~ 

[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~