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Posts tagged “Nucleus

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:

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Word Cloud 2- Nucleotides and Nucleic Acids

DNA- wordle 2

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


So let’s reflect on The Cell!

Hey guys, Richie’s here! Let’s get the ball rolling!

          Lectures, tutorials all greeted by hungry minds starved by the Christmas vacation,, proved to be nothing short of stimulating. It was a breath of relief when I learnt that the pass rate last year for this course was 90%! But then again, I am not aiming just to pass this course. 🙂  Blogging was a word I met browsing the internet, reading books, but never did I believe that I would have been given this task for a lovely percentage of my Biochemistry course! The fear of the unknown was my initial reaction. Now as I am reflecting on my progress thus far, I am grateful for this opportunity (and the fact that it is a group assignment!). It gives us, the Biochemistry3RST team, the perfect avenue to display our academic and creative skills for the entire global audience! (You can probably tell how excited I am based on the amount of exclamation marks I used hitherto.) Each week you can look forward to pieces from fresh, alternating minds and this continuous renewal of our human resource is what will keep this blog inundating your minds with pretty cool Biochem stuff. 🙂

BIOCHEM JPEG (2)

             The first science I learnt in high school was the cell. My first note began something like this: “The cell was discovered by an English inventor and scientist called Robert Hooke who described the cork from the bark of a tree as being made up of thousands of tiny boxes. He called these boxes cells.” It’s still embedded in my memory after about seven odd years of teenage woes, ups and overcoming academic barriers. I remember seeing the name Robert Hooke on the Wednesday of our second lecture and I became overwhelmed by memories of learning the descriptions of these fascinating cellular organelles that build my interest which led me onto this path to a Biochemistry major.

Robert Hooke

Robert Hooke, the first person to use the word “Cell”.

This blog is to foster a love for a subject which has a rep for being tough, and the producer of low GPA’s. Upon saying so, it’s time for me to get down to earth with some of the greatly underrated yet awesome organelles! We all heard about the nucleus. It is perhaps the first sub-cellular component that we all knew existed, even without formal knowledge of life science, it being the largest organelle and the cell’s brain… Also the mitochondrion being the intracellular power station as it synthesizes ATP the energy currency and its characteristic geographical structure… (Stalactites and stalagmites!) So what about the ribosomes and other protein processing organelles? These tiny yet essential structures (ribosomes) synthesize proteins which are the bases for enzyme activity, your hair and nails, and other intriguing aspects of life, I mean, even your DNA are nucleic proteins!

DNA wrapped around histones forming nucleosomes... How interesting!!

DNA wrapped around histones forming nucleosomes… How interesting!!

The might mitochondrion!! lol

The might mitochondrion!! lol

This organelle that has to be seen with an electron microscope consist of Ribosomal RNA (rRNA) and is made in the nucleolus (within the nucleus). A ribosome has a large and small subunit and it is the latter that receives messenger RNA (mRNA) that is transcribed from your DNA in your nucleus. This mRNA feeds data about how to make proteins into the ribosomes which assemble them from amino acids.

Assembly of proteins in a ribosome with mRNA in action!

Assembly of proteins in a ribosome with mRNA in action!

In eukaryotic cells (cells that contain membrane bound organelles and are between 10-100 µm) ribosomes can be found concentrated on a single membrane organelle called the rough endoplasmic reticulum (the last part of the name was quite funny to me when I was 12!). The RER is connected to the outer membrane of the nucleus and synthesized proteins are collected in the spaces between its membranes called the cisternae. Here, these spruce proteins are then modified into glycoproteins and lipoproteins by the attachment of other biomolecules.

The ER connected to the nucleus' outer membrane and studded with tiny ribosomes.

The ER connected to the nucleus’ outer membrane and studded with tiny ribosomes.

If a mutated gene is transcribed into mRNA, then the resulting protein assembled in RER will be an inaccurate, unacceptable variation of the protein. The implications of this is of great medical proportions as the protein will not be able to effectively carry out its purpose, or fail to do it entirely. Cystic fibrosis (CF) occurs when a particular cell membrane chloride channel protein (Cystic Fibrosis Transmembrane Regulator- CFTR) is not properly manufactured and is trapped in the Endoplasmic Reticulum and consequently degenerated. CF leads to an accumulation of mucus in bodily organs such as the pancreas and lungs. Furthermore, ‘stress’ of the Endoplasmic Reticulum due to accumulation of amino acids and fatty acids, lack of glucose and dwindling calcium ion supplies can ultimately trigger the cell’s destruction and it plays a role in infamous diseases such as Parkinson’s and Alzheimer’s.

Were you expecting a GORY image?! ;)

Were you expecting a GORY image?! 😛

Proteins continue their intracellular journey when they ‘pinch of’ from the RER as a membrane bounded vesicle which embeds itself into the cis/convex face of the Golgi apparatus. Like a postal delivery service, the proteins and modified biomolecules are given an address and depending on the type of protein/enzymes they are, they can remain in the cell (after leaving the Golgi apparatus) as a lysosome which destroys pathogens or it may leave the cell entirely. Lysosomes may also break down proteins in the form of dying organelles. They accomplish these combats by fusing their single membrane with that of a vesicle containing the pathogen or retired organelle, consequently secreting their enzymes (proteases and lipases) which does the exterminating. Proteasomes sole function is to degrade intracellular proteins; they have no business with the proteins in your digestive system that you ate. These help out the lysosomes in recycling amino acids.

Now... Linking all the protein synthesizing and processing organelles

Now… Linking all the protein synthesizing and processing organelles

Medical horrors such as the Tay-Sachs disease and Pompe’s disease are lipid storage maladies caused by the absence of one highly essential lysosomal enzyme. Both of the diseases are unfortunately hereditary but in the case of the latter, this rear ailment affects the heart and skeletal muscles. A mutated gene codes for an alternate, dissimilar form of the enzyme- acid, alpha-glucosidase (GAA) that usually breaks down glycogen to glucose and is found in lysosomes. The absence of GAA would starve muscles for glucose and lead to an accumulation of lysosomal glycogen throughout the body especially in the heart and skeletal muscles. In both cases despite treatment death can occur at early childhood. 😦 Such a sad thing to write before concluding my first post on this blog…

Symptoms of this monster of a disease in tiny kids :(

Symptoms of this monster  disease in tiny kids  😦

In retrospect, the chemistry of sub-cellular components being highly interesting is also quite relevant to modern science and medicine. Even though I focused my attention on the protein related organelles and diseases, the cell is a vast universe waiting for you to explore 🙂 and at this very moment research is being conducted in institutes worldwide research that can save lives as far as organelles and human diseases are concerned…. So my fellow Biocheminions, read, Read, READ, explore, Explore, EXPLORE to become the next generation of scientific heroes!!!

The cell is a vast universe waiting for you to explore!!!

The cell is a vast universe waiting for you to explore!!!

          Until I blog again, ACCENTUATE THE POSITIVE,

           Richie, over and out!

References:

http://teachers.sduhsd.k12.ca.us/mrall/ap%20bio/ap%20bio%20homework%20and%20ppts/extra%20credit/Organellesdiseases.pdf

http://www.ninds.nih.gov/disorders/pompe/pompe.htm

http://www.mhhe.com/biosci/ap/foxhumphys/student/olc/h-reading10.html

D.J Taylor, N.P.O Green, G.W. Stout, 1984 Biological Science 1. Cambridge University Press.

Images and Animation references :

http://bi0l0gy.wikispaces.com/file/view/rough_endoplasmic_reticulum.jpg/275154994/rough_endoplasmic_reticulum.jpg- Rough Endoplasmic Reticulum

http://en.wikipedia.org/wiki/File:Protein_translation.gif – Ribosome animation

http://www.cancer.gov/PublishedContent/Images/images/targetedtherapies/mm/clip_image006_0002.jpg – Histones wrapped in histones

http://media-cache-ak0.pinimg.com/236x/f8/30/57/f830573809212927254614f2277a779e.jpg – Robert Hooke

http://www.nature.com/scitable/content/ne0000/ne0000/ne0000/ne0000/14713129/U3CP3-3_MembraneTransport_k.jpg – Linkage of Organelles

http://www.pompe.com/~/media/Pompe/Images/Unused/pc_symptoms_baby_hcp_03.jpg- Pompe’s Disease

http://dishingitdaily.files.wordpress.com/2013/02/brain-cell-the-universe-birth-of-a-cell-death-of-a-star-eye-nebula.jpg – Cell and the Universe