Biochemians unite!

Author Archive

Metabolomics

Extra credit assignment- Metabolomics

BIOL 2360

Travis Peayarlal

813117868

Metabolomics is under the field of the “omics”. It involves the characterization of very small molecules known as metabolites found in biological samples. In epidemiology or disease mechanisms, it is considered a new and emerging form of technology which have gained a lot of attention. This outburst of advancement in disease diagnostics and analysis will encourage more growth in future projects under the field of metabolomics. A prime example where it will be useful is for cancer where there is urgent need for precise and cost efficient diagnostic tools and a dire urge to produce working therapies along with valid biomarkers to help with predicting accurate response to the therapy.

It is interesting to note that metabolomics have been known for decades but never drew scientist’s attention as compared to the omics such as genomics, transcriptiomics and proteomics. In the past metabolomics have only been used to help decipher inborn genetic errors of metabolism and congenital disorders. But now with the advancement of technology, new instruments have been developed which sparked the insurgence of attention metabolomics is now receiving. These include: nuclear magnetic resonance (NMR), gas chromatography, liquid chromatography and mass spectrometry (MS), along with software such as informatics and chemometrics.

 

Diagram showing the metabolomic process

Diagram showing the metabolomic process

As compared to all the other omics metabolomics is the most promising due to:

  • Since the physical changes (phenotype) are cases of adaptations in metabolome (organism), distresses are increased when translated to the metabolome which makes metabolomics a higly sensitive method as compared to genomics and tanscriptomics.
  • It is a lot more cost effective than other omics
  • It is easier when comparing information over certain conditions and biochemical derangements.
  • It is easier when transferring data analysis from organism to organism.

For diseases, metabolomics has several advantages than other omics for example in diabetes research where it:

  1. It can use a lot less smaller molecule metabolites and,
  2. Provide a method for measuring integrated phenotype’s changes in the genome as well as for transcriptome and proteome.

For a particular experiment where the aim was to create ways of transplanting pancreatic islet cells, NMR mass isotopomer have been used to research glucose metabolism in the cells that secretes insulin and also mitochondrial pathways that are capable of controlling glucose responsiveness. The cells are cultured [U-13C] glucose (D.Nagrath et al. 2011). Then the NMR-based isotopomer analyses the secretion of glutamate. This gives the opportunity of determining glucose to pyruvate along with its entry into the Krebs cycle via enzymatic conversions to Pyruvate dehydrogenase then into acetyl CoA. The isotopomer’s analysis encourages and results in the relative rates of each flux due to observing the components secreted during each cycle.

There are many more uses of metabolomics and it seems to have a lot of development in the future mainly in the areas of advanced metabolite detection mechanisms and data analysis which would provide impetus for clinical medicine in a wide scale.

References:

http://www.sciencedirect.com/science/article/pii/S0005272811000570

http://www.ncbi.nlm.nih.gov/pubmed/24966222


Supplements- Nature’s way Ginkgold

NWY-15268-2

                                                 Travis Peayarlal     813117868    Biochemistry IIA    BIOL2360 Extra Credit : Supplements

 

 

 

Nature’s way Ginkgold is a dietary supplement which claims to enhance all areas of the brain. Nature’s way stresses the fact that the Standardized Ginkgo Biloba (Ginkgold) extract has unique properties (20 active and coactive constituents). These enrich and benefit us by:

  • Supporting memory, concentration and mental activity of the brain.
  • Antioxidant protection against free radicals- oxidative stress affects ones brain health and blood vessel tissues.
  • Helps maintain blood vessel tone
  • Supports healthy circulation to the brain and the body’s extremities.

Basically it provides Mental Sharpness.

 

Recommendation: Take 1 tablet twice daily with water at meal times. For intensive use: Take 2 tablets twice daily with water at mealtimes.

Supplement Facts
Serving Size 1 Tablet
Servings Per Container 50
Amount Per Serving % Daily Value
Ginkgold Ginkgo biloba extrat (leaf) standardized to 24% Ginkgo flavone glycosides and 6% terpene lactones 60mg **

** Daily Value not established

 

033674067352_2

Ginkgo biloba is a species of tree that is known for being the world’s oldest, living up to 1000 years. They can be found in south and east USA, south France, Korea and China. The leaves of this ancient tree is used for modern herbal medicines and supplementary. The reason the Ginkgo is famous for creating the effect of enhanced cognitive functions is because of the active ingredients. It can be split into two groups of active constituents which includes:

  • The ginkgo flavone glycosides and,
  • Terpene lactones.

The ginkgo flavone glycosides makes up 24% of the extract and is the main reason for the antioxidant properties that ginkgo has and also mild inhibition of platelet sticking together. The antioxidant action also affects the brain and retina of the eye. This is useful for those with diabetic retinopathy (diabetic eye disease that leads to blindness due to blood vessels in the eye changing) and macular degeneration (loss of vision).

The terpene lactones in ginkgo extracts are ginkgolides and bilobalide. This makes up around 6% of the extract. These two are important increasing blood circulation to the brain and also other areas of the body. It also provides a protection for nerve cells. Blood circulation is very effective by ginkgo as it regulates the elasticity and tone of the blood vessels.

References:

http://www.naturalproductsinfo.org/index.php?src=gendocs&ref=Sep08_Herbal&category=zHealthnotes_Newsletter


Biochemistry video on Ketone bodies!!!- Invasion of the Ketone Body Snatchers


Image

Word search!!!

Word search for Cell dev


Wordle

10723317_367741540046948_111044021_n

Worldle for Cell and Dev


Reflection 10- Nucleotides and Nucleic Acids

experiences-reflection

Hey y’all! It’s the one and only Shiv Shiv here again. Well it’s not been so long since I blogged for you guys but yet I’m still VERY ecstatic! Wanna know why? Cuz it’s the last reflection!!! And I have been given the honor to do the last blog… kinda sad at the same time… 😦 cuz I will be the one to reminisce on the past! Don’t get me wrong though! I’m not complaining! It’s my privilege to reflect on the journey throughout this blog. Learning about blogs, expressing myself and sharing information for the world to read for the first time, made me a little nervous yet excited. It helped me try my best knowing that there are anonymous people out there from all corners of the globe that may stumble upon my work! This semester was a lot more hectic than the first yet it seemed to just fly-by. I assume it was due to me settling in being a freshman and all. In terms of Biochemistry, this course I personally consider very interactive and fun. It indoctrinated me into this mind-set of doing work, work, and work. All the credit goes to my hardworking, extremely friendly and down-to-Earth lecturer, Mr. Jason Matthew, AKA JM. This guy has given us podcast videos on almost all the topics. How awesome is that? I must say they were really helpful in making me understand the course and I was not bamboozled by most of the information even after watching the videos after the first time! Oh damn! It seems I am getting carried away here and forgetting the real purpose of this reflection! So down to the heart of the matter… this reflection is all about Nucleotides and Nucleic Acids!

Nucleic acids are one of the four basic kinds of organic molecules made up of DNA and RNA they consist of all the CHNOPS elements excluding sulphur. This funny abbreviation (CHNOPS) stands for the elements: carbon, hydrogen, nitrogen, oxygen, phosphorus and as you could infer from above, the S stands for sulphur lol.

 chnops

    DNA stores genetic information and it is transferred from the nucleus to the ribosome via a type of RNA called messenger RNA (mRNA for short).  I must say… such a small structure has a lot of information, it’s amazing how interesting our life can be! Nucleic acids are polymeric nucleotides that also make up proteins and also ATP an energy transfer agent. ATP is a nucleotide that provides energy for most cellular functions, it undergoes hydrolysis when there is a chemical energy change in the molecule where it loses a phosphate converting ATP to ADP. Nucleotides are the building blocks of DNA, RNA and nucleic acids. They are made up of phosphate groups essential for nucleotide polymerization (with a strong negative charge), pentose sugars (that in polymer biochemical structures creates a sugar backbone) and a nitrogenous base that differs in each nucleotide. The base sequence in DNA (which has a double helix) contains the following nucleosides A, C, G, T while in RNA strands, (a single helix), T is replaced by U. Nucleosides can be classified into 2 categories based on their size Purines with 2 rings (larger) and Pyrimidines with one ring (smaller). Purines are Adenine and Guanine while the pyrimidines are thymine, cytosine and uracil… in you guessed it… RNA lol

Nucleotide diagram

Purine and pyrimidines

Purines contain two rings while Pyrimidines contain one ring

Two nucleotides are bonded by a phosphodiester linkage and a covalent bond is formed between the OH on the 3’ (read as 3 prime) nucleotide and the phosphate of the other.

Formation of the phosphodiester linkage between two nucleotides

Formation of the phosphodiester linkage between two nucleotides

 

As mentioned before, DNA is a double helix. Its strands are antiparallel forming hydrogen bonds A to T and C to G while A to U and C to G in RNA. Antiparallel infers that one strand runs from the 3’ to 5’ end while the other is opposite. An illustration of this is provided bellow that would help you to visualize the principle:

Behold Anti-parallel strands!!!

Behold Anti-parallel strands!!!

Nucleotides bond in the 3’ and 5’ areas of their structures and this allows for the helical structure with the purine and pyrimidines bases on its inside and the sugars and phosphate on the outside of the DNA helix. There is antiparallel complementary base pairing where the hydrogen bonds hold the structures together.

A-T has two (2) hydrogen bonds, while C-G has three (3)...

A-T has two (2) hydrogen bonds, while C-G has three (3)…

Nucleic acids have been said to be the major compounds of all life as Polynucleotides in the form of DNA and RNA are the basic structure that make up and synthesize everything alive. The nitrogenous bases attach to the C-1’ of the ribose or deoxyribose, while the pyrimidines bond at the N-1 on the pentose and Purines through the N-9 position. Nucleic acids are in three forms they are B form which is seen in DNA, A form which is familiar to RNA structures and Z form, a seldom observed structure seen in some DNA sequences. These structures are part of what allows for the stability of nucleic acids, the stacking interaction or hydrophobic interaction of the bases allows for the expulsion of water in the structure to aid in stability when they stack on each other. Nucleic acid can be affected by strong acids and high temperature since it hydrolyzes phosphate riboses and deoxyroboses. High pH may have little effect on DNA structure but may cause changes in the isomeric forms of bases affecting their connectivity; this tautomeric change results in DNA denaturation.

A and B forms of polynucleotides

A and B forms of polynucleotides

So! Back to my philosophy from the beginning of this blog! Now what was I talking about… oh right! I was talking about our insightful lecturer Mr. JM and his awesome vids! Well apart from enjoying my time at tutorials and lectures, I also enjoyed the conversations and ideas contemplated with my teammates during meetings for our blog! My time with my colleagues were really fun and productive. We all chipped in and helped each other in times of need when someone was stuck or in dire straits. There were areas where some of us were stronger and at times weaker. This is what helped each of us pull our weight and ensure that the blog was a success! 🙂 On behalf of the Biochemistry3rst team, Shiv Shiv (me lol), Rakeeru, Trav, Reshi and the Group Leader, Richie, an eleven week journey is never easy to conclude. Never starve your mind of knowledge because you afraid of an academic adventure. Biochemistry may buzz in your head, this may be painful at times, but the harder the battle, the sweeter the victory.

Biochemistry3rst over and out!

good-bye

Reference:

Nelson, David, Michael Cox. 2005. “Nucleotides”. Lehninger Principles of Biochemistry, ed. Sara Tenney. New York: Freeman and Company.

Picture Reference:


Image

Word Cloud 2- Nucleotides and Nucleic Acids

DNA- wordle 2

DNA may be considered Genetics but its underlying Biochemistry is awesome!!!