Metabolomics Extra Credit Assignment

In the field of biochemistry metabolomics it is often described as a “chemical fingerprint”. It involves understanding and generating a chemical profile of the extracellular and intracellular small molecules that are used at microscopic level in metabolism that occurs in cells, tissues, organs and even body fluids. Metabolomics is an extremely powerful field of study that can change the area of medicine, pharmacology and disease treatment. Understanding metabolites chemically and how they interact with the human body can be the foundation toward examining the underlying chemical activity occurring with a cell. This is helpful because having disease usually results in a disruption in a particular biochemical pathway. In this respect not only can treatment be direct but precision and accuracy in area of diagnostics can be transformed.

Metabolomics has so far changed the areas of Biomarker discovery and drug safety screens. It has empowered professionals in the fields of medicine, health and disease treatment, allowing them to make better and more informed decisions and in effect change the time and effectiveness of treatment for persons desperately in need of it.

One of the most interesting and promising results from metabolomics is involving personalized metabolomics. This area of study allows for an in-depth understanding and analysis of the metabolome of an individual which can eventually result in the production of personalized drugs and treatments. A personalized approach to treating an individual’s health will not only be more effective but will transform lives and the way in which health and treatment is approached.

 Reference

Ebi.ac.uk, (2014). The importance of metabolomics | Train online. [online] Available at: http://www.ebi.ac.uk/training/online/course/introduction-metabolomics/importance-metabolomics [Accessed 30 Nov. 2014].

Nielsen, J. and Jewett, M. (2007). The role of metabolomics in systems biology. Topics in Current Genetics, pp.1-10.

L-Carnitine Supplement Extra Credit Assignment

KEESHA MAHABIR

812001621

Supplement Extra Credit Assignment

The analysis of this supplement was done in a skit format to properly understand the mechanism of the L-Carnitine Supplement using biochemical knowledge learned in order to support claims made by the manufacturer.

Skit

Characters:

John-John works as an Accountant at a popular bank, he has an average body type. For the first time in his life John has enrolled at his local gym. Sports and athletics isn’t really his thing but like most guys, in their early 20’s, he wants to impress the girls and is interested in getting lean, muscular and fit.

Stacy- Stacy is a close friend of John and wants the best for him. She is currently perusing he degree in biology and has enrolled in their level 2, biochemistry course.

It’s a Saturday evening

Stacy: Hey, How’s gym life? Your probably really tired!

John: Yeh! Tell me about it, I have no clue what I’m doing.

Stacy: Dosen’t the gym have trainers? You should get some tips on diet and stuff, im sure that’s really important.

John: Since you mentioned it, I did get some information on what I should be taking, eating, you know all those supplement stuff.

*sound of typing computer keys*

Stacy: what are you doing?

John: Searching this supplement I was recommended… L-Carnitine.. yeh that’s it

Name of Supplement:L-Carnitine

Picture 1: L-Carnitine, supplement choosen

He pauses then continues

John: okay so lets see. Claim of manufacturer: *he reads to stacy* “L-Carnitine is a non-essential amino acid found primarily in red meat and other animal sources. In the body, carnitine facilitates the transfer of fatty acids into the mitochondria for cellular energy production. Carnitine supplementation may help promote fat loss by converting fat into fuel. Carnitine provides muscular energy by burning fat, which may also promote a positive environment for muscle growth.*” ….sounds convincing enough… I think!

Stacy: Hey hold on…*she remembers the beta oxidation rap* I know exactly what you’re talking about. Just had a quiz the other day!

She continues

Stacy: Beta oxidation occurs in the mitochondria and yields large amounts of ATP through the process by which long chain fatty acids are broken down into high energy generating compounds, FADH₂, NADH and acetyl CoA.

John; that’s nice, but what does beta oxidation have to do with L-Carnitine?

Stacy: I’m getting to that. You see… when long chain fatty acids enter the cytosol, they are immediately converted to fatty acyl CoA via the compound thiokinase

John: I distinctly remember you saying that beta oxidation occurs in the mitochondria?

Stacy: It does, and because beta oxidation occurs in the mitochondria, the fatty acid must be transported from the cytosol to the inner mitochondrial matrix.

There’s catch though!

The inner mitochondrial matrix is impermeable to CoA.

John: Go on things just got heated

Stacy: The fatty acyl CoA uses a specialized carrier, carnitine to transport the acly group from the cytosol to the mitochondrial matrix.

John: So carnitie is a carrier?

Stacy: Yes! But is a part of a larger process known as the carnitine shuttle system. It’s a highly organized cycle responsible for transporting the fatty acyl CoA in to the mitochondrial matrix.

 Stacy: Im sending you a picture right now!

Picture 2: Showing carnitine shuttle system

Stacy: The picture you see above might seem complex but is actually quite simple.

 The fatty acyl group is attached to the CoA group. When the energy of the cell is low,the fatty acyl CoA undergoes a transesterification reaction where the fatty acyl group is transferred to the OH group of the Carnitine. This reaction is catalyzed by the enzyme identified in the picture as Carnitine acyltransferase I. I should add that the compound formed is known as fatty acyl Carnitine and since there is no CoA can now enter the inner mitochondrial matrix via an anti-porter protein, seen in pink.

Once in the inner matrix, another enzyme Carnitine acyltransferase II detaches the carnirine carrier. CoA can now recombine with the fatty acyl group and the carnitine is free to exit the anti-porter protein and be used as a carrier once more.

John: Well that’s quite interesting!

Stacy: Yes! The claims made by the manufacturer is in essence very true. The fatty acylCoA , now in the mitochondrial matrix can undergo the process of beta oxidation and eventually produce large amounts of ATP via the citric acid cycle and electron transport chain.

The carnitine shuttle system is a necessary step for the breakdown of fatty acids into energy.

Let me introduce my self

2 a )As a palisade cell, i am located right beneath the surface of the cuticle and epidermal layer of the leaf, specifically in the mesophyll region. At first i might not seem as extravagant as other cells, but if you look closer you would see that I am essential and play a very important role in capturing light energy from the sun to fuel the very basic process of photosynthesis. 

You see, I am adapted to do this, specialized i like to call it. My cytoplasm is filled with a certain distinguishing organelle, the chloroplast, which has the ability to covert stored energy from sun light to chemical energy through photosynthesis.

Since cells like me contain higher amounts of chloroplast as compare to other cells, we produce higher amounts of carbohydrate necessary for complex metabolic process of the plant.

b)Everything about me is geared towards ensuring the capture of light for photosynthesis, from my shape, to the organelles present. My shape is cylindrical and elongated. This specific shape allows me to have maximum exposure towards sun light.It is for this reason that i am also located close to the surface of the leaf.

The organelle I mentioned earlier, that is the chloroplast. They give plants the ability to photosynthesis.It is the actual site for photosynthesis and contain a pigment called chlorophyll that give plants their green colour.  These oval shaped organelles are uniquely complex with a vast network or membranes occurring within a aqueous matrix called the stroma. This area is enclosed within a double membrane phospholipid bilayer. Vital substances such as proteins and enzymes are dissolved within the matrix, necessary for various processes. DNA, ribosomes and starch in the from of granules (produced from photosynthesis is stored here.

The vast network of membrane with in the initial envelope (double membrane) is known as the thylakoids. Contained within the thylakoids are molecules necessary for electron transport, and photosystems (carry out the photochemistry of photosynthesis.

Thylakoids appear as discs and stacked upon each-other this is known as the grana.

Click here for palisade cell animation

 

I choose you Arabidopsis thaliana

When it comes to scientific research in biology,applying concepts in to real world applications and a hands on approach to leaning in general, Model organisms have become our “go to guys”. Model organisms are specifically chosen to study and understand various biological concepts due to extensive studies that have been carried out then. Not only this but they are usually small, easy to grow, maintain and most importantly can be easily manipulated.

Model organisms are crucial to improving the learning experience of students, on a mental level and on a more hands on approach. This approach can grasp the attention of students,and provide a unique learning experience that allows students to explore various concepts for themselves.

Model Organisms such as E.coli , yeast and the fruit fly (Drosophila melanogaster) are constantly being drawn upon and made reference in the biological teaching environment.

Due to the wide variety of studies conducted and data gathered on model organism, they are used in studies that collect information on other species and even humans.

The model organism chosen to conduct research an develop my further understanding of cell development and biology is the Arabidopsis thaliana ( mustard plant). The organ chosen is the leaves, specifically focusing on the mesophyll   cells of the palisade tissue.

I come to you as…. a cell

YES! i know its been a long time since I’ve shared any info on the world of biochem.

However here we are now, and  i come to you as a cell. A cell? yes, and not just any cell, a palisade cell. 

As part of my blogging assignment for  BIOL2061 – Cell and Developmental Biology course, I delve into the world of cells, with a purpose of conveying my learning experience throughout this course in hopes that my journey inspires you.  

I think for the most part, it’s vital that we understand that a cell is not just to be taken for granted. No matter what cell. Cells are complex and diverse. It’s almost as though the have their own personality.

As i have mentioned in this blog before, while writing for my biochem course, cells are our basics, a foundation of biology. You’re going to learn about cells on your first day of class, whether its at, primary school, high school or at a university studies.

Cells are integrated and tightly woven into every aspect of biology. It is for this reason that understanding this topic is vital. Usually i’m only obligated to study cells for one topic at a time, now i’m doing an entire course and I can’t wait.

Now put that thinking cap on.Let’s begin my journey into my new life as a cell. 

 

Video review # 2 :Carbohydrates

This video is a very quick summary of carbohydrates. I believe it is very concise and touches on a lot of key information especially when it comes to the glycosidic bond formation.

The video first gives a quick introduction. They then further explain the formula of sugars. ie. (CH2O)n

They outline carbohydrates into:
Monosaccharides —-> single monomer or sugar molecule
Disaccharides —–> 2monomers or sugar molecules
Oligosaccharides —–> 3-20 monomers or sugar molecules
Polysaccharides—–> many monomers or sugar molecule

A monomer is the building block for a polymer

Alpha and Beta glucose result from the different configuration of the (OH) groups on the ring structures

Sugars can be named according to the number of carbon groups present eg.hexose and pentose

Glycosidic bonds are formed through the loss of water i.e dehydration or condensation between sugar molecules.

The video although simple, allowed me to reinforce key areas to the topic carbohydrates.

You light up my life Luciferase

I love lights, whether is fireworks, icicle lights or just simple stars. Lights have a way of making me feel alive. It’s no surprise to me when I came across the enzyme luciferase and its effect on fireflies and other organisms, giving them ability to glow. I just had to make a blog post on this. With that said, lets get down to some beautiful science.

Fireflies “light up” for a few reasons including, to detract predators, attracting prey and most notably to find a mate. Each species of firefly is able to glow differently and in different patterns, thereby allowing them to be distinguishable among each other.

The lighting and chemical reaction which allows these fireflies to glow occurs in the abdomen of the insect.  The type of natural lighting which occurs is known as bioluminescence. 

Simply put, oxygen together with calcium, luciferin and ATP(our energy) combine in a chemical reaction (it’s too slow however) as such, our enzyme luciferase triggers the reaction allowing the light to be produced.

“The structure of luciferase is heterodimeric; it consists of 2 subunits, alpha and beta.”

One thing to note, the light produced by the firefly is not as the light produced in our light bulbs. Our firefly produces what is call “cold light” where heat energy is not produced as in normal light sources. The reaction involving luciferase is very efficient in that 90% is pure light.

Another mechanism involving our friend luciferase occurs in  Omphalotus olearius, or what I really prefer calling them, jack-o’-lantern mushroom. Putting it simply, mushrooms that glow in the dark (we’re talking psychedelic here). The glowing mechanism actually works in the same way as fireflies involving luciferin and the enzyme luciferase. Unfortunately, these orange mushrooms aren’t edible, as they are (warning) toxic and can cause a range of unpleasant symptoms. So on that note, no! eating them won’t make yourself glow.

The enzyme itself is actually being genetically engineered into many other organisms and animals such as mice and silkworms. The technology has gone as far as bioluminescence imaging in the advances in biomedical research, most significantly in terms or cancer research.

This topic is incredibly interesting.  I definitely recommend you guys do some more reading.

links :

http://animals.about.com/od/insects/f/fireflies.htm

http://www.lifeslittlemysteries.com/654-what-makes-fireflies-light-up.html

http://www.scientificamerican.com/article.cfm?id=how-and-why-do-fireflies

http://learn.genetics.utah.edu/content/begin/dna/firefly/

Video review 1 :Glycolysis… where would we be without it !

This video I chose on glycolysis I found to be easy to understand yet very detailed. I loved the use of diagrammatic representations of the molecules to explain each step.

Video link: http://www.youtube.com/watch?v=zvpbS-t5O1I

I created these tables as a summary of the video. I thought this method for me personally would make the process seem less overwhelming. I hope it helps you to.

During glycolysis, glucose, a six carbon compound is broken down to 2 units of pyruvate 3 carbon compound. The main focus of glycolysis is to break down glucose for energy. Usually the process is divided into two stages, 1 and 2.

STAGE 1 : Glucose is phosphorylated and broken down into two units of glyceraldehyde-3-phosphate

Summary- Glucose is phosphorylated and broken down into two units of glyceraldehyde-3-phosphate through enzyme catalysed reactions. Investment phase using ATP.

STAGE 2: Glyceraldehyde 3 phosphate further converted to pyruvate

Summary- Two units of glyceraldehydes-3-phosphate are further converted into two units of pyruvate. This occurs through enzyme catalysed reaction. Pay off phase, producing ATP. 

Overall reaction of glycolysis:

Glucose + 2NAD+ +2ADP + 2Pi  —->2pyruvate + 2NADH + 2H+ + 2ATP + 2H2O

Primordial Soup Theory…. it may not be that simple

From previous blog posts, it is very clear that I love getting back to the basics. It makes for a great foundation. With that in mind, nothing says basic biology like the Primordial Soup Theory. Believe it or not, it’s one of my favorite topics, mostly because there is a wide variation of contrasting opinions. Nothing gets your mind working like a good science debate on the origins of life.

So lets get down to it. The Primordial Soup Theory is one of many theories explaining the origins of life.

It explains that the warm temperatures of the earth and its water bodies, a mix of gases including Methane (CH4), hydrogen (H2), ammonia (NH3), and water vapor (H2O)  together with  some form of energy ( assuming lightning) were responsible for the formation of the first building blocks of life, the amino acid.

Stanley Miller and physicist Harold Urey devised an experiment in 1952 which simulated these conditions, and were successfully able to observe the formation of small amounts of amino acids.

Like many theories there were several criticisms including arguments which show that the some gases used in the experiment such as methane and ammonia we not present in early earth.

One of the most compelling arguments in my opinion suggest that life, that is our building blocks, the amino acid, came from meteorites which fell on earth. 1969, a meteorite fell over Murchison, Australia. This meteorite after being analysed was found to contain over 90 amino acids, 19 of those which are found on earth.

In addition to all of this, Jeffrey Bada a student of Stanley Miller inherited samples of an 1958 experiment in which Miller added hydrogen sulphide to the mix of gasses previously used in the 1952 experiment.

Analysis of the sample showed the abundance of 23 amino acids and four amines. The results as such suggest that hydrogen sulphide from volcanoes could have played a vital role in the formation of amino acids in early earth, enriching the original combination of gases of used in miller’s 1952 “soup” experiment.

Now while the evidence pertaining to the, meteorite and the experiment of 1958 is extremely impressive, we are left with somehow more questions than answers.

Don’t ‘panic however, to ease your mind , Scott Sandford, a research scientist at NASA’s Ames Research Centre in California says “In the end, if life was trying to get started, my guess is the process wasn’t very picky about where the molecules came from, “[Early life] didn’t care if that amino acid was formed in space or a lightning strike in Earth’s atmosphere or came out of a hydrothermal vent… So in the end, it is possible life got started from acquiring building blocks from a wide variety of sources.”

I think that is the best answer anyone has ever given. Let’s not get off tracked though, there are several other theories beside the  two I have present here today. This link gives some other theories http://www.livescience.com/13363-7-theories-origin-life.html . So give them a read and tell me your opinion. What do you think of our friend the amino acid. How did he really come about? Are we underestimating or overestimating the abilities of nature and our planet? or are our minds shifted in the wrong direction.

Link: http://www.livescience.com/13339-primordial-soup-chemistry-reaction-amino-acids-life.html

http://www.chem.duke.edu/~jds/cruise_chem/Exobiology/miller.html

http://leiwenwu.tripod.com/primordials.htm

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Amino acid and Protein