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Posts tagged “hydrogen bonds

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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Reflection 4- Amino Acids and Proteins Part 2

Hello everyone!! Rakeeru here to talk to you more about the structures of PROTEINS yes! PROTEINS again Oops. Don’t be sad this part is pretty much interesting. I’ll try my best to concise the knowledge that I gained from reading and watching our lecturer‘s YouTube video! Well let’s get started, yup, yup, yup!!!

Okay so the first level of proteins is the primary structure that consists of the sequence of amino acids in the polypeptides chain that was transcribe from genetic material.  ALL proteins contain a primary structure. It is essential that we know about the primary structures of the protein since it helps us in determining genetic diseases and abnormalities.

Primary Structure!

Primary Structure!

The secondary structure consists of two types, the alpha helix and beta pleated sheets. Let’s start with the alpha helix. Alpha helix is the most common helix. They appear to be in spiral form.  The helix is made up of a polypeptide chain; R groups are on the outer part of the peptide backbone. This arrangement allows for reduced steric interference that can destabilize the structure. Each turn holds 3.6 amino acids. The diagram below illustrates the structure of the alpha helix…see, it is not that difficult :). Notice that the hydrogen bonds from the amide are attached to the oxygen from the carbonyl group. With this bonding arrangement, the hydrogen bonds is in abundance as they stabilize the structure.

Alpha helix and beta pleated chains

Alpha helix and beta pleated chains

All amino acids are capable of bonds within the chain however there are some amino acids that disrupt the chains.  Let’s take proline for instance. When it bonds to the helix it does not have a hydrogen on the alpha amino group to donate, therefore it leaves residue which forms a “kink” and creates InStaBiLitY (destabilizes the structure). Some other amino acids that destabilize the helix are Aspartate, Histidine, Lysine, or Arginine as these are relatively too large  and obviously cannot make the 3.6 turn. They form ionic bonds or electrostatic repulsions or attractions between amino acid residues with charged R groups. With respect to bulky side chains such as Isoleucine, the branch from the β-carbon in the R group can impede the formation of the α-helix if they are plentiful.

Beta pleated sheet… have you ever wondered why that name was given? Well it’s obvious the structure appears to be pleated 😛  Like the alpha helix, the beta pleated sheet is made up of covalent peptide bonds and inter-molecular hydrogen bonds. The chains that make up this structure can either be parallel (where all the carbon and nitrogen terminals are on the same side) or antiparallel, where they are alternating in nature.

Interestingly, Alpha helices always have a right handed curl… just a fun fact I guess. lol. The thing about secondary structures is that they maximize the amount of hydrogen bonds in there structure hence stability is high!!!

Tertiary Structures are quite complex. When we talk about the tertiary structure, we are speaking about the folding of the secondary structure of the polypeptide. NOTE that tertiary structure is not as stable as primary and secondary, but tertiary structures can be stabilized by FOUR TYPES OF INTERACTIONS!!! They are the Disulfide bonds (that are the strongest since they are covalent in nature!), hydrophobic interactions which are the most important intermolecular bond, Hydrogen bonds and Ionic interactions.

First up the disulfide bonds… okay here goes…. This is formed when two cysteine residues containing sulfhydryl groups come together. An oxidation reaction occurs and a cystine molecule is formed where the amino acids are connected via a disulphide bridge. As Trav mentioned before lol.

 

The Four Types of Bonds!

The Four Types of Bonds!

Hydrogen bonding always the helpful guy ya know.  Easily gives away its one electron, what a helpful little guy. Okay a good example is glutamate and serine. The serine from Hydrogen  willingly donates its electron to oxygen from the carbonyl group in glutamate.

Serine Hydrogen bonding!

Serine Hydrogen bonding!

Hydrophobic interactions basically are the water hating bonds that are in the interior part of the tertiary structure.  With this being said, if a globular protein is placed in water, folding occur independently where the hydrophilic regions reaches outwards and the hydrophobic remains inwards.

Last but not least the Ionic interactions which are the bonding between a negatively charged atom of an R group and a positively charged atom of another. Example: Asparate and lysine. 

So we talked about how the tertiary structure have four interactions which encourages folding to occur. What about if I wanted to unfold the protein? Unfolding a protein can be accomplished by heating or using reagents(organic) such as strong acids or bases, detergents, etc .

The behavior of the protein after unfolding…..BAD NEWS!!!  The protein begins to fold in stages during its synthesis, rather than waiting for synthesis of the entire chain to be totally completed. But it gets better there this little guy Chaperones he does the magic ie. He ensures that there is proper folding.

Unfolded Protein!

Unfolded Protein!

The quaternary structure of a protein occurs when the tertiary polypeptide chains link together via the same inter-molecular bonds as the tertiary structures.

One major issue that captured my attention was aging ( Yea, it’s an issue for me).  Men and women produce collagen daily. It provides us with structural support for our skin. As we age the collagen is lost and denatured. The appearance is not quite wanted as it disfigures the face in other words sagging, wrinkles occur. However, studies have shown that aging process can proceed at a slower rate. Doctors recommend supplement pills (contains collagen) that will help in the building up sufficient amount of collagen to prevent sagging. In conclusion we cannot prevent the process of aging but we can use supplements to help. Well I ‘m out for the day. Next up is Shiv shiv to talk about Enzymes! Rakeeru out!

Rose Dawson... Old and Young Comparison from Titanic (1997)

Rose Dawson… Old and Young Comparison from Titanic (1997)

Picture References:

Rose Dawson- http://images4.fanpop.com/image/photos/20800000/Titanic-Rose-titanic-20855390-2560-1557.jpg

Unfolded Protein- http://www.nononsensestrength.com/proteinfolding.jpg

Hydrogen Bonding with Serine- http://www.chemguide.co.uk/organicprops/aminoacids/serinehbond.gif

Four bonding types- http://cnx.org/content/m47925/latest/Figure_03_04_08.jpg

Alpha helix and Beta pleated chains- http://www-3.unipv.it/webbio/anatcomp/freitas/2008-2009/elica_foglietto.jpg

Primary Structure- http://www.aboutthemcat.org/images/organic-chemistry/primary-structure.png


Reflection 3- The Powerful Proteins!!!

ps2

Hello everybody!!! This is your boy Trav here! Just stopping by to reflect on the past week of what went down. Well this week was all about proteins, proteins, proteins… oh and can’t forget those amino acids… the building blocks that make up these proteins! So I was so glad to hear that I was given the privilege to reflect on this wonderful topic of proteins. In fact I am very intrigued by proteins at the moment, especially since I recently joined the gym and stuff… and well you know a lot of protein is required in my diet! So the word protein may have special meaning to some; for me it is for Biochemistry and for my muscle building!

gym, bodybuilding pic

So I have been rambling on about this word protein, but what is a protein you may ask? Well a protein is a folded substance that is made up of many amino acids that are linked together by peptide bonds. A peptide bond is simply a condensation reaction where there is a loss of that chemically equivalent to a water molecule and a linkage is formed.

A Peptide bond!

A Peptide bond!

Proteins comes in different levels. These levels include: primary, secondary, tertiary and quaternary structures. Not all proteins make it to the tertiary and quaternary structures though. The primary structure of proteins are basically the sequence that the amino acids are bonded. The secondary structure involves the arrangement of the polypeptide chain to form the alpha helix or beta pleated sheets via Hydrogen bonds ONLY. The tertiary level occurs when these polypeptide chains bond to one another and start to fold. Tertiary structures are held together by four types of bonds. These include: hydrogen bonds, ionic bonds, disulphide bridges and hydrophobic interactions. A great example of these are globular proteins and most enzymes are globular! And finally quaternary, this occurs when tertiary proteins are combined. A great example is haemoglobin in blood which has four globular proteins that surrounds an iron ion (lol) within a haem group.

A haemoglobin molecule and the haem groups!

A haemoglobin molecule and the haem groups!

Now, I am sure you are wondering what amino acids are and what they are made off. Well amino acids are the building blocks of proteins as stated previously and they are made up of an amino group, carboxylate anion, a hydrogen and an R-group, all bonded to a central alpha carbon. To make things easier to comprehend I have put a diagram showing this below.

Can you guess which is the alpha carbon?

Can you guess which is the alpha carbon?

Now you may be thinking how do amino acids differ from one another? Well basically the R-groups on each amino acid are different, for example for glycine; it only has a Hydrogen atom as its R-group and it is the smallest while the second is Alanine, with its CH3 R-group. There are 20 different amino acids, so essentially 20 different R-groups.

I remember in one of my lectures, our lecturer was pronouncing cysteine sort of funny. He told us that we would understand the reason why in a few minutes and surely I understood why when he started to explain the bonding of two cysteine to form cystine. I think u can see why now too o_O lol!

The bond between the 2 cysteine to form cystine is a disulphide bridge or disulphide linkage and it is an oxidation reaction that takes place. An oxidation reaction is when there is a loss of electrons or in this case the loss of 2 hydrogens, one from each cysteine. It is a reversible reaction so that means that a reduction reaction can take place to reform 2 cysteine from cystine. A reduction reaction is basically gaining electrons/ hydrogen for this case… so the opposite of an oxidation reaction.( please don’t be mind-boggled, refer to the picture below lol)

cysteine and cystine

Then he went on to talk about the amino acids that are essential to us. I made a list of them below:

  • Arginine– our lecturer sparked my interest when he talked about the uses and importance of this amino acid and so I did some research that I would like to share with you a little later.
  • Isoleucine
  • Leucine
  • Histidine
  • Methionine
  • Threonine
  • Tryptophan
  • Valine
  • Lysine
  • Phenylalanine

Just to recap, there are 20 amino acids but these are the 10 essential amino acids that we have to get from our diet as adults (we cannot make them on our own!!!). Oh and to clarify, ALL 20 amino acids are important but the 10 above can only be gained from the diet and nutrition you eat while the non-essential can be synthesized by your body. My lecturer then talked about how it is possible to create non- essential amino acids in the lab that we will see next year! Can’t wait for that! So excited!

I have then learnt that there are two types of proteins, complete and incomplete. Complete proteins are those that contains all the essential amino acids. A good source of complete proteins are from animals (meat). Incomplete proteins are those that do not have all the essential amino acids and a common example are vegetables while an exception to this is beans which are considered a complete protein (Lucky for you vegetarians!).

Beans!!!

Beans!!!

So I am sure you are wondering how you test for the presence of proteins or amino acids in a food sample or substance? Sorry, it can’t be done in the kitchen! Must be done in the lab lol. Well I learnt that the Ninhydrin test is used to test for the presence of amino acids (usually colourless before). For a positive confirmation of amino acids present, a purple colour would be seen.  There is one amino acid that gives a yellow colour instead of purple and it is Proline. Proline is special in that it forms a ring structure due to the R-group bonding with the amino group and so the N is not free to react with the Ninhydrin. This means that no ammonia is formed and therefore the purple colour is not created. Oh and I would like you to note that this is a test for AMINO ACIDS not for proteins! My lecturer really stressed on that point and he explained it was because you cannot use Ninhydrin to find the presence of proteins. Some interesting facts I found on Ninhydrin… There is a Ninhydrin spray that is used on crime scenes to see and visualize fingerprints that contains trace amounts of amino acids.

Diagram of Proline showing the bonding of the R-group to the amino group to form a ring structure

Diagram of Proline showing the bonding of the R-group to the amino group to form a ring structure

Are you curious to know what the test for proteins are? Well, the Biuret test is common for testing the presence of proteins in a sample. For a positive Biuret test, the colour changes from a light blue due to the Cu2+ ions in solution to a purple colour. What happens is the Biuret reagent reacts with the polypeptide chain of the proteins which forms a complex that has a strong purple colour.

Before I leave your presence, remember that I said that I have some information to share with you about Arginine? Well Arginine seems to have some very interesting uses when it comes to body building and muscle growth! Arginine is considered a precursor to nitric oxide which is a vasodilator since it helps to relax and widen blood vessels. This helps with improving the circulation of blood flow to the muscles during workouts. This means that you would get a better supply of the much needed energy! It helps with muscle growth as it is needed for the production of most proteins. L-arginine promotes the release of hormones and fat metabolism. This results in well-toned muscle mass since it reduces the fat stores under the skin and therefore promotes muscle growth. Interestingly enough, Arginine also helps boost the immune system (way to put the icing on the cake). This is excellent as continuous physical activity can lead to overtraining which can cause minor illnesses. Well that’s it for Arginine and from me. Hope you find this interesting as I sure did! Lol. Look forward to part two on proteins from my good friend Rakeeru! Laterz and until next time! Trav out!

References:

Picture References:

  • Proline diagram-
  • http:// koofers-static.s3.amazonaws.com/flashcard_images/4ebfb0836c18115133cbbef6d2a7af43.jpg
  • Beans picture- http://atasteofbrazil.files.wordpress.com/2013/07/beans.jpg
  • Haemoglobin molecule- http://swift.cmbi.ru.nl/gv/students/mtom/quaternary_haemoglobin.gif
  • Peptide bond diagram- http://www.mun.ca/biology/scarr/iGen3_06-03_Figure-Lsmc.jpg
  • Body building logo- http://logos.co/1024/royalty-free-vector-logo-of-a-bodybuilder-over-a-red-circle-by-patrimonio-523.jpg
  • 2 Cysteine forming Cystine- http://mandysbiochemistrylair.files.wordpress.com/2013/04/350px-cysteine_vs_cystine10.jpg
  • Amino Acid Structure- http://api.ning.com/files/xO6ybWgUbfFlk7GUXm9d8dfR–U-fUdPOJEtDzVGgDY_/aminoacidstruc.jpg