Well I’ve decided to check out some Krebs cycle videos to see who could explain it the simplest and I’ve found this video done by “brightstorm2” unfortunately the guy who does these videos never introduces himself before beginning, so I never got his name 😦 Thats my first criticism to his video. Well before I begin here is the link for the video:

I never liked learning about the Krebs cycle because it’s normally boring and confusing if you don’t understand the reactions taking place.

What I love about his videos is that he is teaching using a television to show diagrams, pictures and videos to help us see what is happening. What I like about the diagrams he uses is that its really simple an easy to just watch and understand exactly what is happening. He explains the work well and he simplifies the reactions in a way that it is easy to remember. Another thing I like about his videos is that it is short and to the point. So if you need to quickly review the Krebs cycle you can do so in under 6minutes 🙂 He communicates well with his viewers and keeps them engaged and thinking. His speech was clear and well understandable. I enjoyed his video and he was not boring at all. I normally get bored and lost for this topic 😦

A summary of the video

a) Krebs cycle ccurs in matrix of mitochondria.

b) Only occurs if O2 present.

c) Link Reaction: Pyruvate moves into matrix & loses 1 carbon as 1 CO2. 1 more NADH is made.

d) The remaining 2C molecule enters the Krebs Cycle.

In several steps,

e) energy & hydrogens are removed from the 2 carbons and changed to more NADH & FADH2. These migrate to Electron Transport.

f) 1 more ATP is made. The cell can use this.

g) each remaining carbon is removed as CO2 & released to air.

What occurs in one turn of the Krebs cycle:

1. 2 Carbon molecule enters the cycle & joins a 4C molecule.
2. In a series of steps, the remaining H and high energy electrons are removed from the 2 C.
3. Three NAD+ are converted into 3 NADH & 3H+.
4. One FAD is converted into 1 FADH2.
5. One ATP is made.
6. Two CO2 are released.
7. At the end of the cycle, nothing remains of the original glucose molecule.



So today I will be commenting on a youtube vidoe, on a topic done in class. I’m choosing to do an enzymes video today. This one was done by Mr Jason Matthews my biochem lecturer.

This is the vid:

This video is very effective as it is a combination of both audio and visual. Therefore it engages the visual learners as well as it appeals to the people who must listen to learn. The video is also interactive, where Mr JM asks you questions on the topic. I really enjoy his videos because of his communication style, I feel like I’m in his class and I’m wide awake. As a visual learner I am able to better understand a topic from his videos than from reading a text book, although I still have to ;).  All the diagrams, graphs, bright colours and pictures help me in understanding and seeing clearly what is being taught. What I really appreciate about this video is the simplicity in which Mr JM explains the work. It is broken down to ABC and it really helps especially if your a slow learner. Everything is easier to remember if you understand it first, so I know I’ll b ready for exams watching these videos. I think all teachers should break down the complicated work into an easy way to learn it, like the way Mr JM does it.

albert einstien

Some wise words from the boss. Teachers take note.

Well I actually summarized this video already, in my blog post: ENZYMES!!!!

So in this excellent video Mr JM talks about the importance of enzymes, how life can not exist without enzymes. He goes on to explain how the enzyme works and touches a little on all the hypotheses on how an enzyme work. The most popular being the ‘LOCK & KEY FIT’ and the ‘INDUCED FIT HYPOTHESIS’. He talks about the 6 major classes of enzymes and also how to name the enzymes. He introduces us to Holoenzymes, which is an active, complex enzyme consisting of an apoenzyme and a coenzyme. Then finally he compared inorganic catalyst with biological catalyst. Biological catalyst are complex proteins, these are very specific and when involved in a reaction, no wasteful bi-products are formed. Whereas, inorganic catalyst are simply inorganic molecules which are not regulated easily and is not as specific as biological catalyst. 

My only wish is that Mr JM would make these wonderful videos on everything, then maybe I’ll have a shot at getting all AAAAs 😉

Keep up the excellent work Sir!



So today’s class was about Lipids. Yep thats right, all about the fats!!

Well eating too many  lipids can make you fat 😦 but is that all to lipids???

Lipid is a fatty or waxy organic compound that is readily soluble in nonpolar solvent but not in polarsolvent. Its major biological functions involve energy storage, structural component of cell membrane, and cell signaling.

Structures of some common lipids

The main functions of lipids:

ØStructuring cell membranes. The cell membrane constitutes a barrier for the cell and      controls the flow of material in and out of the cell.


ØEnergy storage. Triglycerides are an efficient form of energy storage that can be mobilized when fuel is needed.



ØTransmission of information in cells (signal transduction). Lipid hormones, like steroids and eicosanoids, also mediate communication between cells.


ØCellular metabolism. The fat-soluble vitamins A, D, E, and K are required for metabolism, usually as coenzymes.




[Fatty Acids]


The terms saturatedmono-unsaturated, and poly-unsaturated refer to the number of hydrogens attached to the hydrocarbon tails of the fatty acids as compared to the number of double bonds between carbon atoms in the tail. Fats, which are mostly from animal sources, have all single bonds between the carbons in their fatty acid tails, thus all the carbons are also bonded to the maximum number of hydrogens possible. Since the fatty acids in these triglycerides contain the maximum possible amouunt of hydrogens, these would be called saturated fats.


Oils, mostly from plant sources, have some double bonds between some of the carbons in the hydrocarbon tail, causing bends or “kinks” in the shape of the molecules. Because some of the carbons share double bonds, they’re not bonded to as many hydrogens as they could if they weren’t double bonded to each other. Therefore these oils are called unsaturated fats. Because of the kinks in the hydrocarbon tails, unsaturated fats can’t pack as closely together, making them liquid at room temperature.

Essential fatty acids

EFAs are fatty acids which the body can not make but it is required for good health, therefore we must obtain them from our diet. The term “essential fatty acid” refers to fatty acids required for biological processes but does not include the fats that only act as fuel.

Only two fatty acids are known to be essential for humans: alpha-linolenic   acid (an omega-3 fatty acid) and linoleic acid (an omega-6 fatty acid). Some other fatty acids are sometimes classified as “conditionally essential,” meaning that they can become essential under some developmental or disease conditions; examples include docosahexaenoic acid (an omega-3 fatty acid) and gamma-linolenic acid (an omega-6 fatty acid).  


Omega-3 fatty acids (also known as n-3 fatty acids) are polyunsaturated fatty acids that are essential nutrients for health. We need omega-3 fatty acids for numerous normal body functions, such as controlling blood clotting and building cell membranes in the brain, and since our bodies cannot make omega-3 fats, we must get them through food. Omega-3 fatty acids are also associated with many health benefits, including protection against heart disease and possibly stroke. New studies are identifying potential benefits for a wide range of conditions including cancer, inflammatory bowel disease, and other autoimmune diseases such as lupus and rheumatoid arthritis.

Well I hope this post made you understand lipids a little better 🙂

Make sure and check out this vid on lipids by my lecturer

see you soon…:)




So last blog was about how you get pryruvate from glucose. Well now that you have pyruvate what happens with it????

Well we are going to discuss the fate of pyruvate today 🙂

What happens with pyruvate all depends on the presence or absence of oxygen. Recall: oxygen is needed in respiration to break down glucose to energy. If ample amount of oxygen is present then aerobic respiration occurs, pyruvate will be converted to acetyl CoA and enter the kreb cycle. However, if the body is not getting enough oxygen then anaerobic respiration occurs, the pyruvate could either be converted to lactate or ethanol.


Pyruvate is converted to Acetyl CoA by the enzyme Pyruvate dehydrogenase.

Acetyl CoA enters the kreb cycle where its main functio is to convey the carbon atomes within the acetyl group to the citric acid cycle (krebs cycle) to be oxidized for energy production. Here is a summary of the reactions occurring in the krebs cycle


Pyruvate could either be converted to latate or ethanol here.


Pyruvate is converted to Lactate by the enzyme Lactate dehydrogenase.  In this reaction  NAD+ is regenerated.


Pyruvate is first converted to Acetaldehyde by the enzyme Pyruvate decarboxylase, then converted to Ethanol by the enzyme Alcohol dehydrogenase. This is a summary of the reactions taking place.

I know this blog post didn’t give you too much detail into each reaction. This was a summary of the reactions occurring with the conversion of pyruvate to energy, lactate or ethanol.

Make sure to check out this vid will help you so much 😉


Untill next time


Published Paper #1

N-terminal and Central segments of the Type 1 Ryanodine Receptor (RyR) Mediate its Interaction with FK506 Binding Proteins.


Tanya Girgenrath, Mohana Mahalingam, Bengt Svensson, Florentin R. Nitu, Razvan L.Cornea and James D. Fessenden. 2013. N-terminal and central RyR1 segments mediate FKBP binging. Accessed April 13, 2013.

The receptor ryanodine (RyR) is a Ca release channel which is involved in muscle excitation-contraction (EC) coupling. There are two types of isoforms of RyR, that is RyR1 and RyR2 which instructs EC coupling in cardiac muscle and skeletal muscle. When the homotetrameric proteins in the sarcoplasmic reticulum (SR) is activated, Ca 2+ is realeased causing muscle contraction. Mutations with RyR1 can cause muscle disorders such as malignant hyperthermia (MH). It is unknown as to the reasons why the amino acid substitution changes the structure of RyR1. One hypothesis suggest that the N-terminal and central part of RyR1 touches and this forms a domain switch, which causes uncontrollable release of Ca 2+. 12 kDa  is a binding protein for immunosuppressant drug FK506. The protein FKBP12 encourages the RyR1 close state and inhibits Ca 2+ leakage in reastin muscle as a result. To determine the sequence of the RyR1 protein , FRET, was used to make 5 single-Cys FKBP variants along with Alex Fluor 488. The D-FKBP’s were targeted to full length RyR1 containing deca-histidine. Tags were placed within the N-terminal to amino acid residues 76 to 619 ot central to amino acid residues 2157 to 2777 of the RyR1 protein. The FRET acceptor called Cy3NTA binds specifically and saturably to the deca-histine tags. This allows for distance analysis for FRET, measuring from D-FKBP to Cy3NTA. The results indicate that the D-FKBP binds proximal to both the N-terminal and the central domains of RyR1 which suggest that the FKBP binding site is made up of determinants from both regions. Furthermore, the RyR1 N-terminal and central domains are proximal to each other, and a core premise of the domain-switch hypothesis of RyR function. From observations it was seen that FRET from GFP  fused at position 620 within the N-terminal domain to the central domain deca-histine tagged sites gives evidence for the hypothesis. Therefore, it was concluded that the N-terminal and the cental domain elements were closely apposed to the FKBP binding site within the RyR1 structure.  

This publish paper helped me to understand enzymes and proteins better. Reading a real life example of how they work helped me to grasp the concepts of enzymatic activities and the way in which inhibitors affects enzymes.


lets see how much you remembered in glycolysis


1)  In glycolysis, after one molecule of glucose is converted to 2 molecules of pyruvate, the net gain of ATP and NADH is:

A.  2ATP nad 2NADH

B. 4ATP and 2NADH

C.2ATP and 2NADH

D. 2ATP and 2NAD+

E. 4ATP and 2NAD+

Select the correct multiple answer using one of the keys A, B, C, D or E as follows,to answer question 2:

A. 1, 2 and 3 are correct

B. 1 and 3 are correct

C. 2 and 4 are correct

D. only 4 is correct

E. all are correct

2. Which enzymes are involved in glycolysis between glucose 6-phosphate and Fructose 1,6-bisphosphate:

1. heokinase

2. phosphohexose isomerase

3. triose phosphate

4. phosphofructokinase-1

 Well I hope this test was easy. If not, Keep clam and try again 🙂



Today we started glycolysis and I must confess its a lot of reactions to remember! While my lecturer was teaching this I was like…

but at the end of class I realized there was noting to be afraid of. It was easy stuff..

So lets get started…..

Glycolysis is series of reactions where one glucose molecule is split into two molecules of pyruvate, using ten enzymes.




Well this was a summary of the all the reactions in glycolysis. Pay attention to the placement of each one of the enzymes in the whole glycolysis summary equation. I hope this didn’t make u feel like…

If it is not clear at first, no problem, learn at  your  own pace, im sure you can do it 🙂 Good luck!

Gylcolysis vid by my lecturer

Don’t fear there will be another blog post on glycolysis 🙂