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Posts tagged “phosphate group

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.

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REFLECTION 9- LOVELY LIPIDS PART 2

 

Butter

Hey there folks!! Rakeeru here and it’s finally my turn again to share some thoughts on this blog. This week was pretty much wacky because there was so much to do and so little time to do it. I kid, I kid! I ‘m a master procrastinator but nothing can stop me from sharing some cool stuff about lipids. My love for lipids will never die… lol. My mission is to help you understand lipids in a fun and enjoyable way. So we are going to be looking at three types of structural membranes of lipids, phosphodiate, Sphingosine and cholesterol.

Procrastination

Let’s talk GLYCEROLPHOSPHOLIPIDS! So you guys should be familiar with the structure of glycerol, but if you aren’t, then let’s recap a bit. Glycerol is an alcohol that has three carbon atoms, each bonded to an alcohol group.  Okay let’s go back to the glycerol phospholipids now. A Glycerol phospholipid, also known as a phosphodiate, has a glycerol as his backbone, where on carbon 1 only a saturated fatty acid chain is attached. On carbon 2 an unsaturated fatty acid chain is bonded and last but not least on carbon 3 a phosphate group is directly bonded to it. Note that when an alcohol is attached to an acid group it forms an ester bond.  Look at the lovely diagram below.

Glycerolphospholipid

A Glycerolphospholipid!

Now this entire molecule is said to be amphipathic, meaning it has a polar end and a non-polar end. (See picture below). The polar end is hydrophilic or “water loving” while the non-polar end is hydrophobic or “water hating”. The polar end is the made up of a phosphate group and a hydroxyl group.

Apolar, Polar

An amphipathic compund

(R1 and R2 represent the fatty acid chain , the X represents the hydroxyl group) So Trav told you about the ability of unsaturated fatty acids to form a kink, and I just want to add a few things to that… Not all unsaturated fatty acids show a kink (changes direction of the chain). Unsaturated fatty acids can either be in cis configuration or trans configuration.  ONLY CIS fatty acid chains display that appearance due to the fact that the C-3 and C-6 are on the same side of the double bond. (see the diagram below). In a trans fatty acid chain, the structure does not show any kinks. Instead, it follows the pattern of the fatty acid. It resembles the saturated fatty acid so  I call it “the sly one”, since I cannot tell which one is the unsaturated fat and which in the saturated. O Boy, knowing that all the good-tasting stuff (junk food) is high in trans-fat which is terrible for health is a little scary, since the transfatty acid is packed tightly which increases the LDL( Low Density lipoprotein) and decreases HDL (High Density lipoprotein).

cis, tran fatty acids

Showing off the kink

Okay moving on.. moving on… Another amazing lipid is… SPHINGOLIPID!!!  😀  This structure has a sphingosine backbone; sphingosine is an alcohol that has 18 CARBONS. There are many different functional groups attached to it. On carbon 1 and 3 there are hydroxyl groups present, an amino group attached to carbon 2 and a trans double bond is present in the middle of carbon 4 and 5. (See drawing below)

Sphingosine

  Remember I mentioned sphingosine is the backbone of the sphingolipid. What makes it a sphingolipid? It’s the presence of a saturated fatty acid chain. This fatty acid attaches to the carbon 2 that is bonded to an amino group to form an amide bond.

Sphingosine and Fatty Acid

A Sphingolipid!

On carbon 1, there is an R group; this is simply any other group that is attached to the carbon, for example if hydrogen is R group then the name of the entire structure is ceramide.  Ceramide is an oily substance that is found on the outer layer of the skin. It basically adds moisture to skin, which helps to prevent skin from drying and flaking. (Curel, 2014).  Another example is sphingo myelin, which is created when the R group is phospocholine. The sphingo myelin is found in red blood cells and myelin sheaths. What captured my attention is that sphingo myelin increases the speed at which nervous impulses conduct themselves by insulating the nerve fibers. (Voet, Voet and Pratt, 2008). Pretty kool stuff. 😀 Last but not the least, Cholesterol!!!  I’m sure you heard of this word before. But what exactly is cholesterol?  Well here goes, cholesterol is a molecule that has 27 carbons. This molecule has 3 rings that have 6 carbon atoms and 1 ring that only has 5. These rings are referred to as steroids and are stuck together.  Looking at ring B there is a double bond between carbon 5 and 6. There is a hydroxyl group on the carbon 3 atom and there is an alkyl group on the carbon 17. There are 2 methyl groups, one on carbon 19 and the other on carbon 18. By the way, in case you forgot what an alkyl group is, it’s a fragment of a molecule that has a general formula (CnH2n+1,). (Senese, 2010).

 Cholesterol

  Well what’s so important about cholesterol?  Believe it or not, without cholesterol we wouldn’t even exist. You know what’s amazing? The body is able to produce cholesterol on its own without consumption of food rich in cholesterol. (Mason W. Freeman, 2014). It plays an important role in the body:

  • it forms bile acids to make digestion a lot easier in the intestine,
  • Having cholesterol allows the body to produce vitamin D or hormones like testosterone. Testosterone is a steroid hormone that is produced in large amounts in males. It is responsible for the defining characteristics in men, and also for overall health and wellbeing.
  • Cholesterol, together with phospholipids, makes up the membrane of cells in animals.  Each cholesterol molecule attaches itself to a phospholipid group. The hydrophilic end of the cholesterol (where the hydroxyl group is located) is close to the hydrophilic end of the phospholipid. The hydrophobic portion of the cholesterol interacts with the hydrophobic portion of the phospholipid.

Just to spice things up a bit, have you ever wondered how cholesterol affects the fluidity of the membrane? Well it all depends on the temperature. In high temperature the cholesterol controls the movement of the phospholipid and lessens the fluidity. Heat energy encourages the phospholipids to move a lot which will destabilize the membrane. In low temperature the cholesterol controls the phospholipid by avoiding compaction. In cold conditions the phospholipid moves less and will become rigid.

Fluidity of membrane

Well that’s it for now! I hope my reflection was very informative and you guys learnt from this… Biochemistry is fun! BEST OF LUCK IN YOUR STUDIES!!!   😦 Unfortunately this is my last reflection… but my best buddy Shiv Shiv will do a tremendous job! Next up is nucleotides.. soo stay tuned… Until next time Rakeeru out!

Lipids can be good

 

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