A picture is worth a thousand words…

Dear biochemians, it’s been fun but all good things come to an end. I literally have minutes left before the deadline so this is my farewell post. Words cannot adequately express how much I admire Mr. Matthew. He is a brilliant educator who is passionate about what he does as well as his students. Passion like that will take you far and I aspire that one day I become an inspiration to others as Mr. Matthews is to me. I may be some what of a delinquent but that doesn’t mean I’m not aware of Mr. Matthew’s genuine efforts to revolutionize the learning experience. I appreciate everything we have learnt from this wise man and like they say, a picture is worth a thousand words… 🙂

hokage1

These words are just a few of the things I have learnt from the Hokage himself and there are a few praises hidden in between. The further away u are from the screen the more clearly you will see that these words form a picture of the most brilliant UWI lecturer I have come across thus far. 🙂

good bye citizens of Biochem Nation, until we meet again… 🙂

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By tjchadee

Multiple choice…. again -_-

So there is a lot of controversy concerning how many exam questions we are actually supposed to do. Originally I did two which you will find in a previous post because that was my interpretation of what Mr. Matthew meant in the blog manual. However to be on the safe side I am including 2 more questions, besides a little multiple choice never hurt nobodyyyyyy 😛

multi

Admit it. You’ve done this before.Heck! you do this for every exam!! LOL

Select the correct multiple answer using ONE of the keys A,B,C,D or E as follows:

1. Oxidoreductase

2. Lipase

3. Glucokinase

4.Transferase

5. Lyase

Which of the following are Major classes of enzymes?

A. 2 and 3 only.

B. 1, 2 and 3 only.

C 1, 4 and 5 only.

D.2, 4 and 5 only.

E. All are correct.

Single answer MCQ

Which of the following is the storage Polysaccharide in animals?

A. Glucagon.

B.Starch.

C.Glycogen.

D.Chitin.

E.Cellulose.

Jeopardy….Biochemian edition of course! :D

So I was inevitably infected by the biochem game show bug and couldn’t just stop at who wants to be a millionaire. As such dear biochemians, I present to you JEOPARDY! the biochemian edition 😀 This game is designed to be played aloud with a group of friends. You can divide yourselves up into teams and play just like on tv, I’m assuming you all are going to be playing with monopoly money unless you all have enough dollar bills to make it rain 😛 I think this would be great fun for a group study session but if you like by all means attempt to answer the questions on your own and see how much money your left with 😛 So give it a try people and have fun with it! 😀

jeopardy

http://jeopardylabs.com/play/biochem-jeopardy

By tjchadee

Who wants to be a millionaire? Biochemian edition! :D

Greetings to all citizens of biochem nation. So i am extremely excited about this blog post! Exams are approaching and I am always on the hunt for fun ways to learn. So i thought to myself what could make learning biochemistry more entertaining? I am a big game show fanatic and thought to myself it would be so cool if i could create my very own online game that mimics television game shows but is based on material learnt in my BIOL 1362 course. And so I came up with the brilliant idea to make a who wants to be a millionaire the biochem edition! I’m sure you will love it and it’s fun and engaging way to learn biochemistry. All the life lines even function just like on tv! So are you feeling like you’re going to be a millionaire today? Follow the link and find out for yourself 😀

who wants

http://www.superteachertools.com/millionaire/online/game1365605018.php

By tjchadee

Published Paper review, numero dos… Brown adipose tissue and it’s benefits on glucose metabolism, glucose tolerance and body weight.

Obesity is a medical condition whereby the accumulation of  excess body fat has reached an extent to which it may have adverse effect on health or even lead to death. Obesity is also known to increase the risk of diseases such as Diabetes. Both diabetes and Obesity affect an alarming percentage of people in the world and in modern times of fast food and reduced physical activity the numbers keep on rising. Scientists are constantly on the hunt for improved treatments for these types of disorders. Upon conducting my research I was presently surprised when I stumbled upon several published papers stating the positive effects of brown adipose tissue on glucose tolerance, metabolism and body weight.

New treatments for Diabetes are on the horizon because scientists have shown that brown adipose tissue (BAT) positively affects metabolism, glucose tolerance and body weight. Brown adipose tissue burns fat to produce heat unlike white adipose tissue which stores fat. Brown adipose tissue has a tissue rich in mitochondria which use glucose and fatty acids as fuel. Obesity is associated with increase in the mass of adipose tissue. Brown adipose tissue may have an integral role in maintaining a metabolically healthier, slimmer phenotype.

Researchers are studying whether BAT is involved in glucose metabolism and its effect on metabolism and weight loss. A study involves transferring BAT from male mice into the visceral cavities of mice that had been fed a diet high in fat. After a period of time the BAT transplant mice were fed a normal diet and exhibited an improvement in glucose tolerance, increased insulin sensitivity , a decrease in fat mass and weight loss. Three controls groups including mice with white adipose tissue transplant and a glass bead implant and surgery sans transplantation showed no improvement in metabolism. The study suggests that BAT is an endocrine organ which can improve whole body and tissue glucose homeostasis. The BAT transplantation even  alleviated the dangerous effects of a high fat diet. Even though the transplanted BAT actively took up glucose, this effect may be comparatively small compared with larger effects observed in other tissues.

A note worthy finding of the study was the ability of the BAT transplants to regularize glucose levels in the mice that consumed high fat diets. The beneficial effects observed  seemed to be due to the circulation of IL-6 which was increased in these mice. Increase in IL-6 is associated with glucose metabolism and this indicates that BAT can be targeted for treatment of obesity linked diseases including diabetes, metabolic syndrome and insulin resistance.

reference:

http://www.jci.org/articles/view/62308

Published paper review, numero uno…Leigh Syndrome- A mitochondrial DNA related disease.

So I must express how much I disliked doing this published paper review. My reason being is that many publish papers that I could sourced online were not free and also those that I did manage to have access to were very long and complex to interpret and comprehend. I decided to base my review on an organelle associated disease when I came across an article on Leigh syndrome. Before my conducting my research I had actually never heard of Leigh syndrome. I must say however, I am genuinely depressed after reading about how young children are affected by this disorder.I hope that my review on Leigh syndrome enlightens my readers and inspires you to do more research and truly hope that maybe one of the biochemians reading this blog becomes the scientific savior to discover the cure for such a terrible disease.

Leigh Syndrome is also known as juvenile subacute necrotizing encephalopathy and is associated with  Mitochondrial DNA mutation. It is a severe neurological disease that usually arises between 3 to 12 months of age and often occurs after viral infection.  This disease is associated with psychomotor regression as well as gradual loss of mental ability. Close to half of all affected individuals perish before age three due to respiratory or cardiac failure. Very few individuals develop this disorder in their adulthood.

Characteristic symptoms of Leigh’s disease include dysphagia (difficulty swallowing) and  persistent vomiting. Hyperventillation or irregular respiration , hypothermia and hyperthermia may be caused by brain lesions. The muscles of individuals suffering with Leigh syndrome are usually negatively affected. The individual may develop hypotonia or weak muscle tone, dystonia or involuntary muscle contractions as well as axtaxia or movement and balance problems. Peripheral neuropathy characterized by weakness or loss of sensitivity in limbs is common with affected individuals hence their ability to move is impaired.The eyes of the affected individual can also be affected and they may experience eye movement disorders and retinitis pigmentosa.

Cardiac ailments such as hypertrophic cardiomyopathy, hepatic disorders and renal disorders such diffuse glomerulocystic kidney damage are also common amongst affected individuals. The majority of affected individuals will show progressive deterioration with interfused with stages where they may show improvement which can last up to ten years in some cases. However it is more likely that the person will die around age 2 to three years. Also associated with Leigh syndrome are high levels of lactate in urine, blood or  cerebrospinal fluid of patients.

Brain lesions  (detected via Magnetic resonance imaging) are found in the  basal ganglia (movement associated region) the cerebellum (region associated with balance,coordination and movement) as well as the the brainstem. Demyelination  (loss of myelin coating around nerves) in conjuction with these brain lesions reduces the ability of muscle activation as well as the relay of sensory impulses back to the brain.

About 30% of Leigh syndrome is mitochondria DNA related. Most of the genes associated with Leigh syndrome are involved in energy generation in the mitochondria. This disease can be inherited by X linked transmission, autosomal linked transmission, maternal transmission or it may be sporadic. Many of the gene mutations associated with this disease affect proteins of protein complexes that are involved in oxidative phosphorylation (the process whereby the mitochondria uses oxygen to break down food into energy for use by the cell). There are other nuclear DNA mutations characteristic of Leigh’s syndrome which also affect steps concerning energy production and oxidative phosphorylation. Researchers link impaired oxidative phosphorylation to cell death  and tissues that require large amounts of energy including the brain, heart and muscles are especially affected.

There is unfortunately no cure for Leigh’s syndrome and the treatment is limited and not entirely effective.

reference:

http://www.ncbi.nlm.nih.gov/books/NBK1173/

Youtube video review…numero dos!

For my second Youtube video review I decided to pick a video using the opposite reasoning that was used to select my video for the first review. This time, rather than choose a topic that challenged me, i opted to go with a topic that I was well versed in and that it carbohydrates. The logic behind my choice of topic was that I would be able to access whether or not the information was useful and accurate.

Video title: Carbohydrates.

Youtube channel: Bozeman Biology.

Main points of the video:

Carbohydrates provide energy as well as structure (example cellulose in plants or chitin in the exoskeleton of an insect which is also the building block of fungi.)

1 sugar molecule= a monosaccharide

2 sugar molecules= a disaccharide

3-10 sugar molecules= an oligosaccharide.

Many sugar molecules linked together= a polysaccharide.

Empirical formula of all carbohydrates are the same: CH20 (ratio 1:2:1)

Glucose is the simplest sugar (6 Carbon) A lot of hydroxyl groups which makes it soluble in water. This is why it is utilized in the following:

a.cellular respiration.

b. produced by plants in photosynthesis.

Fructose: 5 sided sugar, sweeter than glucose. Found in fruit and corn syrup.

Galactose: A little less sweet than glucose.

Glucose, fructose and Galactose are the 3 basic monosaccharides. They all can be moved through our blood.

Sucrose/ table sugar(a disaccharide) =  Glucose + Fructose (both monosaccharides)

Sucrose must be broken down to it’s monosaccharides by sucrose before it can be used by the body.

Lactose= Glucose + Galactose.

Lactose broken down by lactase.

Lactose intolerance: Condition whereby a person lacks the enzyme lactase which leads to an irritation in the gut due to the fact that lactose cannot be broken down into its respective monosaccharides.

Lactose intolerance/tolerance is naturally selected.

Oligosaccharides

Biological Importance:

Important in the production of glycoproteins.

Fun fact: carrots have to be cooked for an hour for the body to be able to obtain the sugar from it.

Polysaccharides

Eg: starch (hundreds of glucose molecules linked together)

can be found in potatoes.

Is the storage molecule of plants.

Glycogen

A macromolecule with thousands of glucose molecules.

The storage molecule of animals.

Stored in the liver.

Cellulose

Structural  purpose.

Hydrogen cross bonds make it very durable.

Humans won’t have the enzymes to break it down in the gut. Bacteria in the gut of cows will help to break them down into sugars.

Hydrolysis

The breaking of sugars with the addition of water.

Dehydration

Losing a water molecule and forming a covalent bond between two monosaccharides.

Evolutionary Importance of sugar:

Sugar is an indicator of fruit and fruits contain other important nutrients needed by the human body. This is why humans are “programmed” to love sugar. However, too much sugar in the diet is now leading to an increase in heart disease and diabetes

My thoughts on this video: Once again I have randomly chosen a video that exceeds my expectations in a positive way.

Pros of this video:

1. The Youtube uploader Paul Andersen teaches science at Bozeman High School in Bozeman, MT. He is also the 2011 Montana Teacher of the Year. These credential speak volumes to me. They assure me that the information I am receiving  is very much accurate, reliable and specifically targeted towards students like myself.

2. The format of the video was very professional and well edited. I enjoyed that I could see the teacher in a smaller screen while he spoke and explained the concepts on the slides. This creates a classroom experience with out being in a classroom and made me feel like I was having a one on one class with the teacher.

3. Mr. Anderson spoke with simple language that was easy to understand and was able to break down complex terms in a way in which they could be easily comprehended.

4. I admire the use of pictures as well as chemical structures of what ever he was speaking about. Its easier to learn something by seeing it. These figure will also play a role in remembering material since the brain is likely to associate facts with specific pictures.

5. The duration of the video was perfect, not too long, not too short. I was very impressed at the amount of material covered in the space of time and how he was able to explain things a such a manageable pace.

6. I loved that I actually learnt something new in this video despite covering the topic in school already. I learnt that latose intolerance was naturally selected. He explains that  if our ancestors raised cattle they were more likely to continue drinking milk through out their life  and on the other hand if they didn’t that it would be unlikely for them to drink milk regularly in their adulthood and as such lactase would not function the same. I also enjoyed learning about the evolutionary importance of carbohydrates.

Cons: As with my previous video review, I honestly have no negative reviews or improvements for this video. I think it is fantastic just the way it is and I am really glad that I found this channel, I’m sure it will come in handy during my study sessions.

Conclusion: Paul Andersen presented information on carbohydrates with the flair of an experienced educator. Any one will be able to understand these biochemistry related concepts with his explanations. I recommend these videos to any student who wants a clear and concise breakdown on carbohydrates. If I were to rate this video I would give it 5 out of 5 stars 🙂

Youtube video review…numero uno!

Hello biochemians! For my first youtube video review I decided to go with one based on glycolysis since that was a topic that gave me a bit of trouble. I thought this would be a great way of determining the quality of the information content and presentation of the video since if after watching it if I felt as though I understood glycolysis it would mean the video was of a high standard. I’m so relieved to say that the video I’m about to review is amazing! I am really impressed and have a much improved grasp on the topic of glycolysis.

Name of the video: Glycolysis made easy.

Claim of the video: To make glycolysis as easy as possible to understand.

Basic over view of the video:

The 1st molecule to enter the glycolysis pathway is glucose (6C molecule, hexagon shape) the reaction is facilitated by hexokinase which utilizes ATP which is Adenosine with 3 phosphates and in these phosphate bonds energy is stored. Kinase suggests that a phosphate group is either added or removed.ATP donates a phosphate group thus becoming ADP in donating a phosphate group it is donating energy as well. So a phosphate group is added at the sixth Carbon on glucose. This structure is therefore called Glucose-6-phosphate. This first reaction is rate limiting and requires energy (ATP).

The next step utilizes glucose-6-phosphate and the enzyme phosphoglucose isomerase (isomerase meaning the enzyme creates an isomer) which just changes the configuration of glucose-6-phosphate (not adding or subtracting any molecule). Glucose-6-phosphate gets transformed a pentagon structure, there are still 6 Carbon atoms which is called fructose-6-phosphate

Next important step goes from Fructose-6-phosphate to another energy required step. The enzyme phosphofructokinase.ATP comes in and donates a phosphate group to give ADP (as well as energy) and this phosphate group is added to the first Carbon. So the next structure has a phosphate group at the first carbon and at the 6th carbon and is called fructose-1,6-bisphosphate.

Fructose-1,6-bisphosphate is broken down into 2  3carbon structures by the enzyme Aldolase. IT can become either dihydroxyacetone phosphate or by the action of Triphosphate Isomerase it can become glyceraldehyde-3-phosphate. ( these two structures are isomers of one another). Utilizing this step the body regulates how much glycolysis occurs. If too much glycolysis occurs, this reversible reaction favors DHAP which acts like a “brake” on glycolysis. On the other hand if the body requires energy it will promote the formation of glyceraldehyde-3-phosphate.

Next step removes hydrogen ions using the enzyme glyceraldehyde dehydrogenase phosphate. NAD a hydrogen carrier and an inorganic phosphate group come into the reaction and the NAD picks up hydrogen while the phosphate is donated. 1, 3-bisphosphoglycerate (1, 3-bpg) is formed. (1, 3 BPG is a precursor to 2,3-BPG and 2,3-BPG regalutes haemoglobin’s affinity for oxygen in our red blood cells.)

1, 3-BPG is then acted on by phosphoglycerate kinase. This enzyme removes a phosphate from carbon1 so that ADP goes to ATP (bear in mind at this step 2 ATP s being produced since we are dealing with 2 3carbon structures, all these reactions are duplicated.) 3-phosphoglycerate is produced.

Phosphoglyceromutase changes around / mutates the molecule thereby changing 3-phosphoglycerate to 2-phosphoglycerate (takes the phosphate group from the 3rd carbon and attaches it to the 2nd carbon).

Next, Enolase converts 2-phosphoglycerate to phosphoenolpyruvate. In this step, water is released and the oxygen and the hydrogen come from the second and third carbon.

Pyruvate kinase acts on phosphoenolpyruvate, a phosphate group is removed so ADP turns into ATP (an energy producing step).Phosphoenolpyruvate is converted into pyruvate. Pyruvate then goes on to the Kreb’s cycle but if there is no oxygen present it goes on to form lactic acid.

Main points:

Glycolysis:

1.Occurs in the cytosol

2.Starts with glucose

3. Ends with 2 pyruvate

4. functions in anerobic and aerobic conditions.

5. 2 ATP used, 4 ATP produced so there is a net gain of 2 ATP per glucose molecule. Also 2 NADH+  and H produced per glucose molecule and 2 H20 per glucose molecule.

Important to memorise:

1.Remember the rate limiting steps, that is, the ones that require ATP.

2. Remember that ATP and ADP regulate glycolysis. When the body needs energy it will promote glycolysis and ATP production and when the body has too much ATP it will down regulate glycolysis.

3.Remember  where phosphates and hydrogen enters and leaves.

What I love about this video:

1. To begin the narrator of this video is actually a Doctor. This made me sure that the information was reliable. I felt comfortable knowing that I would be receiving accurate information from someone who is sure to understand glycolysis. The best teachers are those who are very knowledgeable in what they are teaching.

2. The video was very professional the use of already prepared slides of chemical structures and a voice over impressed me in comparison to many other glycolysis videos where by the information is presented using programs such as paint which can be at times difficult to understand the uploader’s hand writing.

3. The information was presented in steps and in order as how they would actually take place, this made it easier to understand.

4. I really love the way the names of the substances involved in glucose (example the enzymes) were broken down and translated so that it was possible to infer what its function was. This will really come in handy to someone like me who is not good at memorizing information and prefers to understand so in an exam . This way if I temporarily forget I can figure out the action of an enzyme for example just based on it’s name!

5. I like that he included a summary of the main points at the end. This could be useful when limited study time is available or If I just want a concise overview of the topic.

6.I especially like that he mentions what should be mentioned to earn extra marks in an exam question on glycolysis. This information is very useful to students because sometimes we are unsure of what or what not to include in our answers.

7. The duration of the video was perfect,not too short not too long. I am actually amazed at the amount of information he was able to provide in this amount of time while moving at a very manageable pace.

Imporvement suggestions: Sorry I have none! I am normally a very critical person and almost always have suggestions for improvement especially with educational youtube videos, but to be honest this video exceeded my expectations. It’s perfectly useful just the way it is, I don’t see any way in which it should be improved.

Conclusion: I was very skeptical about this video’s title and claim but honestly the claim was met. The doctor managed to make glycolysis as easy as possible to understand. If I were to rate this video I would honestly give it 5 out of 5 stars. I was so impressed that I not only liked the video but I also commented. Any student having trouble understanding glycolysis or any one who wants a simple refresher on the topic should check this video out 🙂

By tjchadee

Tales from the Front line…. I mean tutorials :P

front line

At times BIOL 1362 tutorial sessions can feel like a war zone. Bullets… I mean questions, flying everywhere!  Little did I know that today one of my good friends Kashiff would be a casualty in this biochem battle. So if you remembered at the end of the last session Mr. Matthew taught us the titration of glutamate. We were given a sample question to attempt at home and would be discussing it in today’s class. If you recall I was thrilled at how I grasped the concept all due to Mr. Matthew’s wonderful teaching style but being the forgetful soul I am after one week had passed I totally forget what to do :/

But have no fear BiochemJM is here!!! This blog post and video save my life 😀

http://biochemjm.wordpress.com/2013/03/04/titration-of-amino-acids-calculations/

What I LOVE about Matthew as a lecturer is that the man is so dedicated to helping us learn. Other lecturers settle at presenting an hour long slide show to us in class and move on with their life. But then there are true educators like this great man who go above and beyond for his students and provide so much additional reference material for us. As a student I feel obligated to get an amazing grade in this course because he has provided us with all the tools necessary and I would feel like all his hard work has gone to waste if I don’t try my very best. To sum it up I actually care about biochemistry (a subject that I previously despised) and all because of the efforts of Mr. Matthew. I honestly cannot say the same for any of my other courses.

Anyways sorry about going off on a tangent there, where were we? Ah yes the tutorial. So throughout the tutorial me and my friend Kashiff can’t help but feel like Mr. Matthews line of vision leads directly to us. I start to feel like an idiot for wearing my zebra print jacket to class because nothing makes you stand out like a zebra print jacket. Anyways when the time comes for Mr. Matthew to choose someone to put answer on the board he chooses Kashiff. Rather than feel relieved I start feeling nervous and sick to my stomach because I know that Kashiff has no clue what’s going on. So he gets up and stares blankly at the board. Seeing that he is struggling Mr. Matthew allows someone to give him the the equation for calculating the Isoelectric Point. Kashiff writes the word pH wrong and Mr. Matthew is stunned, I sink in my seat. Sensing that Kashiff needs help Mr. Matthew tells him to pick any one of his friends to give him assistance. Time freezes kashiff looks at me and I telepathically tell him “Do NOT choose me.” But Kashiff is not a telepath and so he calls my name. I don’t know why I was so hesitant before because I knew the answer and Mr. Matthew was pretty cool about it.

However I did make a mistake in the working in my assignment, I didn’t put the protonated form. So at the end of the class I did something unexpected and approached Mr. Matthew and asked him to explain it to me and he was so cool about it! I walk out of class feeling totally confident and it feels pretty great! 😀

By tjchadee