Biochemians unite!

Posts tagged “ATP

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:


Youtube Video Review 2- ATP & Respiration – Hank Green

Hey everyone, Richie here! As I was browsing about the Internet, I came across this interesting video on respiration, and I thought I would share my thoughts on it. 🙂 The topic being discussed is cellular respiration, which is essentially the process by which organisms obtain energy from their diet. The glucose gained from the food we eat combines with oxygen to form carbon dioxide, water and energy. This energy now needs to be converted to ATP so that the body can use it. Now, there are three steps in converting glucose to the desired product of ATP, which are glycolysis, the Krebs cycle, and the electron transport chain (ETC). In glycolysis, glucose, a 6-carbon compound, is eventually broken down to two 3-carbon compounds called pyruvate molecules. Two ATP molecules are invested into this step so that a net gain of two ATP can be made, as well as two pyruvates and two NADH. This process occurs without the presence of oxygen in the cytoplasm of cells. The Krebs cycle, named after Hans Krebs, occurs in the inner membrane of the mitochondria. The two pyruvates made in glycolysis are used up to form Acetyl CoA, which combines with oxaloacetic acid to produce citric acid. A series of oxidation reactions occur for citric acid to be converted to oxaloacetic acid, and the cycle is repeated to use up both pyruvate molecules. The last step is the ETC, where the electron carriers NADH and FADH2 use the electrons that they are carrying to provide energy for the movement of protons across the inner membrane of mitochondria. At the end of the three steps, it takes one glucose molecule to generate about 38 molecules of ATP.

The cell respiration process!!! All in one Diagram!

The cell respiration process!!! All in one Diagram!

After listening to this video, I can say that I definitely understood the points that the presenter had made. He was able to take complicated processes, such as glycolysis and the Krebs cycle, and break them down into simplistic concepts which were easy to grasp. It was also interesting how the presenter didn’t just dive straight into the topic, but instead, he chose to show the viewers the relevance of ATP production in the body by using the example of exercise. However, the level of detail that we are required to know on this topic was not covered in this video. He gave a brief overview of the processes that go on in cellular metabolism, but did not go into much detail about the actual steps of each process. An improvement that can be made to this video is to go through the technical aspects of this topic in a little more detail to ensure that the viewers appreciate all the steps of cellular respiration. Therefore, I think that this is a good video to help persons to understand the basic concepts entailed in cellular respiration, but not a good video to study from.

So guys, it’s been a pleasure science-blogging you guys… this is it for me… it has been a really fun and edifying experience, personally! I speak for myself but my amazing colleagues will be singing the same tune when their turn arrives, I hope you follow our blog and attempt our activities (even check out and ‘thumb’s up’ the video we made on enzymes lol) my bones still aching… just kidding lol take a look at the video and you will see why :).

Rock star Richie OVER AND OUT!!!

http://www.youtube.com/watch?v=00jbG_cfGuQ

Picture Reference:

Cell Respiration Process – http://upload.wikimedia.org/wikipedia/commons/7/74/CellRespiration.svg


Reflection 7- TCA and ETC…… what are these strange abbreviations o_O

Hello again my Biochemistry enthusiasts! 🙂 This is Reshi here, and boy has it been a stressful semester so far. To add to the stress, I wasn’t sure what I was supposed to write for this topic of TCA and ETC. Well, I remember the ETC part from high school, but when I saw TCA, I got a mental block. I don’t remember ever hearing about that cycle! I probably must have fallen asleep in my Biology class again. So on doing some research, I saw that the TCA cycle is the same thing as the citric acid cycle, or the Krebs cycle. Now that I remember lol.

Cellular respiration process!

Cellular respiration process!

Since we are on topic of the TCA (tricarboxylic acid) cycle, or Krebs cycle as I remember it, I would like to share a few thoughts on it, as well as on the ETC (electron transport chain). So we are all familiar with the fact that cellular respiration is essential for us to produce energy. The site of energy formation is the mitochondria and thus, these structures are plentiful in our body cells. As Richie had discussed in last week’s post, glycolysis is the first step in this energy formation process. The whole point of glycolysis, well at least in my opinion, is to produce two molecules of pyruvate, as well as two molecules each of adenosine triphosphate (ATP) and NADH. A link reaction then occurs in the mitochondrial matrix, which links the glycolysis and Krebs cycle together. Here, the pyruvate molecules become oxidized to form Acetyl CoA. 2 pyruvate + CoA + 2NAD+ —> 2 Acetyl CoA + 2CO2 + 2NADH

The Link Reaction in action!

The Link Reaction in action!

Now this is where my part comes in. The formation of the product Acetyl CoA is a vital step because it is used in the initial step of the TCA cycle. Before I go further, it is important to note that while glycolysis occurs in the cytoplasm of cells, the TCA cycle takes place in the matrix of mitochondria. This is where things can get pretty technical, so just bear with me as I try to simplify this process. So we have our two molecules of Acetyl CoA that have been formed essentially from one glucose molecule. However, only one of these 2-carbon structures can undergo the TCA cycle at a time, and thus, the cycle must be repeated so that both Acetyl CoA molecules are utilized.

The TCA/ Krebs Cycle

The TCA/ Krebs Cycle

  • At the beginning of the cycle, Acetyl CoA interacts with a 4-carbon structure known as oxaloacetate to form citrate, which is a 6-carbon compound. This reaction is catalyzed by citrate synthase. It is important that side reactions be kept to a minimum, since this initial step is very crucial to the entire cycle.
  • Since the position of one of the hydroxyl groups on the citrate molecule is not conducive to the process of oxidative decarboxylation (an oxidation reaction whereby a Carbon atom is lost), the structure needs to be slightly rearranged (Berg, Stryer, and Tymoczko 2002). Hence, the isomerization of citrate to isocitrate occurs. Isocitrate is also a 6-carbon molecule.
  • The next step is the conversion of isocitrate to α-ketoglutarate. We are moving from a 6-carbon to a 5-carbon structure, which indicates that oxidative decarboxylation is taking place. This redox reaction is catalyzed by isocitrate dehydrogenase. NAD+, an electron carrier, becomes reduced to NADH by utilizing the energy released from converting isocitrate to α-ketoglutarate.
  • Another oxidative decarboxylation reaction occurs in order for α-ketoglutarate to be converted to succinyl CoA, which is a 4-carbon molecule. Again, NAD+ is reduced to NADH and H+.
  • Succinyl CoA then goes on to form succinate, and is catalyzed by succinyl CoA synthetase. Guanosine Diphosphate (GDP) uses the energy given off from this reaction to combine with an inorganic phosphate and forms Guanosine Triphosphate (GTP). In the presence of nucleoside diphosphate kinase, GTP can be easily converted to ATP.  (GDP—>GTP—>ATP) 🙂
  • The last set of reactions is the conversion of succinate to the product oxaloacetate. However, this conversion has a few steps in between. Firstly, the succinate undergoes an oxidation reaction catalyzed by succinate dehydrogenase to produce fumarate. Another electron carrier, FAD, is involved in this particular reaction instead of NAD. This is because FAD is capable of removing two hydrogen atoms from a given molecule.  The FAD undergoes a reduction reaction to form FADH2. Then, a hydrolysis reaction occurs in the presence of fumarase catalyst, whereby fumarate is converted to malate. Lastly, malate undergoes oxidation with the catalyst malate dehydrogenase to form oxaloacetate. This time, NAD is used as the electron carrier and becomes reduced to NADH+ and H+.

So basically, after that long, complicated process, the whole point of the Krebs cycle is to generate reduced NAD and Reduced FAD so that they can be used in the next step of cellular respiration, which is the Electron Transport Chain (ETC).   In the ETC, a series of redox reactions occur as the electrons pass along the electron carriers. These carriers (large protein complexes) release energy, and this energy is used to make ATP. This process can be summed up in the Chemiosmostic Theory. I think I should expand a little more on this very interesting hypothesis.

The reduced NAD molecules go into the ETC and loses their Hydrogen. Each Hydrogen atom that has been given up splits into its constituent protons and electrons.

H —>H+ + e

The Electron Transport Chain!

The Electron Transport Chain!

The protons that arise from the split Hydrogen atoms are pumped into the intermembranal space in the mitochondria to increase the proton concentration. Since there is a high concentration of positive protons in the intermembranal space, these protons will move from a higher concentration to a lower concentration in the mitochondrial matrix down its electrochemical gradient. As protons leak from the intermembranal space through special protein complexes back into the matrix, the energy dissipated is used by ATP synthase to convert one ADP (adenosine diphosphate) to one ATP (adenosine triphosphate) for each pair of protons. Thus, each reduced NAD pumped three pairs of protons to produce three ATP molecules. Likewise, each reduced FAD pumps two pairs of proton which produces two ATP. At the end of the ETC, the electrons combine with a Hydrogen ion and an Oxygen atom to form water.

½ O2 + 2H+ + 2e —>H2O

The formation of water results from the electron carrier cytochrome c which contains the large transmembranal protein, cytochrome oxidase, to catalyze the above reaction while facilitating the pumping of protons from the matrix into the intermembranal space via energy released from the electron produced from the first equation. Okay, I know that was a lot of information to take in, but take it one step at a time. Just remember that respiration is not simply the intake and exhalation of air, but a series of biochemical reactions that result in the formation of energy. Sadly this is my last reflection 😦 and I must say, I really enjoyed doing these posts! So until we meet again in the future, this is Reshi closing off. Keep calm and study hard my Biocheminions!!!! 🙂

 

References:

http://www.ncbi.nlm.nih.gov/books/NBK22427/ http://chemistry.about.com/od/biochemistry/ss/citricacidcycle.html

 

Picture References:

Link reaction and Krebs- http://img.docstoccdn.com/thumb/orig/44745072.png.

Cellular respiration- http://www.uic.edu/classes/bios/bios100/lectures/09_08_cellular_respiratio-L.jpg

Link reaction- http://revisionworld.co.uk/files/LinkReaction.JPG.

Krebs Cycle- http://13morima.files.wordpress.com/2011/11/krebs_cycle.jpeg

ETC- http://cnx.org/content/m46451/latest/2508_The_Electron_Transport_Chain.jpg


MCQ Structured Question on Glycolysis!

                   Which of the following is true about glycolysis?

 I.            Glycolysis occurs in the mitochondria.

II.            The end products of glycolysis are two pyruvic acid molecules together with two packets of ATP.

III.            Enzyme that is used to convert glucose-6-phosphate into fructose 6 phosphate is hexose

IV.            Enzyme that converts fructose 1,6- bisphosphate into glyceraldehyde 3 phosphate is adolase

a)      I, II

b)      II,III

c)      II,IV

d)     None of the above


Glycolysis can be fun…?

Glycolysis

Hey everyone, it’s been 5 weeks since I discussed Cells with you. Now I am here to make Glycolysis your new best friend! Yes, you know I am kidding… Or am I… *evil laugh* lol. Besides, if there is one thing Richie likes to do it is to make you understand and I assure you, you won’t be clicking that little white x in that red box at the top of your screen any time soon!

glycolysis factory

 

Steps in Glycolysis

Steps in Glycolysis

 

Glycolysis is a group of 10 intracellular (cytoplasmic) chemical reactions that makes up the most ancient metabolic pathway to synthesize pyruvate and other chemicals that include the energy currency, ATP, for the cell’s existence… How interesting!  Glycolysis literally means the splitting of 6 carbon glucose into two 3 carbon pyruvates. It is important to understand that it occurs in the cytoplasm and NOT THE MITOCHONDRIA. Yes, I know a lot of people who didn’t grasp this concept from A-levels. 😛 Furthermore, very primitive bacteria that lived in the geological time period when the planet was an anaerobic environment employed this pathway. How cool is that! The first five of the 10 metabolic reactions (in sequence) can be described as vitally investing energy in the form of ATP. The other five reactions produce a surplus, in other words a profit is achieved which ensures that the process of glycolysis doesn’t defeat the purpose of respiration which is to supply an organism with energy as there is a net gain in ATP.

Unfortunately, this is the end of the unpretentious, bigger picture of the process 😦

Worried man

However I will try my best to make you grasp the concepts of each reaction! 🙂

relieved

I assure you, the names of the involved enzymes are the toughest aspect of glycolysis, and learning the stages will be much more fun if you keep that into consideration. Here is a little tip: try learning it without the intimidating names of the enzyme catalysts first! So…. HERE WE GO!

The first reaction is a phosphorylation reaction that involves adding a phosphate (from an ATP) to the 6th carbon atom of glucose to create the structures, glucose-6-phosphate and ADP. This irreversible stage is called the first priming reaction and the enzyme that catalyzes it is called Hexokinase. The biological significance is to trap glucose within the cell since there are no channel proteins capable of transporting this modified form of glucose across the plasma membrane.

'Glucose' trapped in a 'Cell' lol

‘Glucose’ trapped in a ‘Cell’ lol

In the second reaction (a reversible reaction), the enzyme Phosphohexose isomerase converts the aldose sugar glucose-6-phosphate into its ketose isomer, fructose-6-phosphate.

The third reaction is in fact the irreversible second priming reaction, where fructose-6-phosphate is converted into fructose-1,6-bisphosphate (Regina Bailey. 2014), when a phosphate from another molecule of ATP is added to its first carbon via the enzyme Phospho-fructokinease-1 (PFK 1). As seen in the product’s name (fructose-1,6-bisphosphate), ‘bis’ implies that both phosphates are attached to different carbon atoms. Indeed, as we have seen, in the first priming reaction, the phosphate was added to carbon 6, while in this reaction the second phosphate was added to carbon 1. (Don’t say diphosphate!!!)

In the fourth reaction (reversible), the enzyme Aldoses catalyzes a lysis reaction, where the fructose-1,6-bisphosphate is split into glyceraldehyde-3-phosphate and dihydroxyacetone-phosphate (DHAP) (Regina Bailey. 2014). The products that are synthesized are isomers of each other. They are both Triose sugars!

"Glucose" starring Van Damme doing the splits

“Glucose” starring Van Damme doing the splits

halfway there

Halfway through the process!

The fifth reaction, rapidly catalyzed by the enzyme Triose phosphate isomerase brings about the conversion of dihydroxyacetone-phosphate (DHAP) into a glyceraldehyde-3-phosphate. This reaction occurs very quickly because at the instant when the enzyme binds with the substrate, the intermediate formed is so highly unstable, that it is quickly converted into its product. Consequently, Triose phosphate isomerase is considered a kinetically perfect enzyme. You can now see that at the end of the ‘energy investing phase’ that 2 ATPs were used in phosphorylation reactions, while two glyceraldehyde-3-phosphate molecules were synthesized.

Fun fact!: All enzymes of glycolysis has induced fit structures!!!

redox is coming

The sixth step (or the first in the ATP generating phase) involves converting the two glyceraldehyde-3-phosphates into two 1,3-Bisphosphoglycerates. To achieve this, the enzyme Glyceraldehyde 3-phosphate dehydrogenase oxidizes the glyceraldehyde-3-phosphates (removes a hydrogen from each) and the co enzyme NAD+ collects the hydrogen and becomes reduced (NADH). The formation of NADH is essential for glycolysis to continue. The oxidation of the glyceraldehyde-3-phosphate fulfills the energy requirements for the same enzyme, Glyceraldehyde 3-phosphate dehydrogenase, to catalyze a phosphorylation reaction where an inorganic phosphate is added to the oxidized glyceraldehyde-3-phosphate to create the final product 1,3-Bisphosphoglycerate. Remember that in this stage, two 1,3-Bisphosphoglycerates are produced! In other words, a hydrogen is removed from each glyceraldehyde-3-phosphate and it forms NADH. A phosphate is then added to each modified glyceraldehyde-3-phosphate, to form the product 1,3-Bisphosphoglycerate.

In the seventh reaction, two molecules of ATP are being synthesized in a process known as Substrate Level Phosphorylation. The enzyme Phosphoglycerate Kinase removes a phosphate from the first carbon of each of the two 1,3-Bisphosphoglycerates and then these high energy phosphate groups are combined with ADP molecules to create two ATP. Once the phosphates have been removed, the molecules are now called 3-Phosphoglycerates.

The 3-Phosphoglycerates then undergo ‘change in structure’ when the enzyme Phosphoglycerate mutase converts them firstly to 2,3-bisphosphoglycerates (intermediates). Furthermore, the phosphate on carbon 3 is then removed hence two 2-Phosphoglycerates are formed.

changing shape

A 3-Phosphoglycerate undergoes a change in structure

In the ninth reaction, the two 2-Phosphoglycerates are converted into two Phosphoenolpyruvates (PEP) due to the loss of water (dehydration reaction) catalyzed by the enzyme, Enolase.

Finally, the last reaction!!!

yes-finally-pl-ffffff

You guessed it, here the two PEPs are converted into two pyruvates and two more ATP are being synthesized from ADPs. Pyruvate Kinase is the enzyme catalyzing this reaction. It removes the phosphates from the PEPs, and adds it to the ADPs.  This reaction releases a lot of energy in addition to what is stored in the ATPs. This energy is released as heat. It partly contributes to making you perspire during exercise. The two ATPs produced in this final step can be referred to as the energy/ATP profit gained from glycolysis.

Yay! Now we have two pyruvates. That’s pretty cool, but wouldn’t it be cooler if we knew what happens to each pyruvate after synthesis? It will be my pleasure to briefly discus three of these ‘fates’ with you.  🙂

Let us first observe the metabolic pathway in aerobic conditions. Once oxygen is present, the pyruvate is converted to Acetyl CoA. This pathway is called the Link Reaction since it connects Glycolysis to the Krebs cycle. Converting pyruvate into Acetyl CoA is a decarboxylation reaction. The removal of carbon dioxide would lead to a two carbon structure; simultaneously an NAD+ is reduced and the rest of the pyruvate is combined with Coenzyme-A to form Acetyl CoA.

Lactate Fermentation results  from  high physical activity

Lactate Fermentation results from high physical activity

In anaerobic conditions, Lactate fermentation (in animals) or ethanol production (in yeast and plants), are possible scenarios (Myda Ramersar 2011). Lactate fermentation mostly occurs in erythrocytes (red blood cells) and skeletal muscle. Red blood cells lack mitochondria therefore the Krebs cycle and Oxidative phosphorylation cannot occur (rendering the Link reaction useless). Consequently, glycolysis is the sole means for the cells to acquire their energy. Skeletal muscle cells, conversely, respire anaerobically only when oxygen availability is minimal. Since each cell contains a fixed amount of oxidized NAD+, once all of it is reduced by glycolysis, the process will come to a grinding halt. Imagine how bad that would be for your poor cells. 😦 Luckily the process of lactate fermentation (catalyzed by the lactate dehydrogenase enzyme) reconverts NADH into NAD+ by the following generalized equation:

pyruvate + NADH –> lactate + NAD+

Ethanol fermentation in a breadshell

Ethanol fermentation in a breadshell

You can see that the product of glycolysis (pyruvate) is involved in securing its continued synthesis!!!

In the production of ethanol for commercial wine/beer brewing, a fermentation pathway that involves the use of yeast’s ability to respire anaerobically, is utilized. This pathway incorporates the pyruvate first being converted into acetaldehyde by the enzyme pyruvate decarboxylase, and then to ethanol by the enzyme ethanol dehydrogenase. In the latter stage, NADH is oxidized hence glycolysis can continue! Oh and I am sure you guessed it, bread making also incorporates fermentation by yeast. 🙂 Did you realize the amount of science that is involved in making the dough rise? Mind boggling right!

I hope you follow my tip when studying glycolysis. It helps to get the general idea and then work on the details of the process. It helped me 🙂 I would like to take this time to thank you for reading our posts, attempting the MCQ and word search puzzle. Feel free to leave comments and for any post you wish, especially for the MCQ 🙂 The Biochemistry3RST team would love to know if we helped boost your understanding of any topic we blogged on! This might be my last reflection, but I am not abandoning you in your Biochem Jungle 😛 there is more to come. 🙂 Until next time guys! Time for me to rock and roll outa here! Richie, over and out!!!

my-job-here-is-done

References:

· Bailey, Regina. 2014. “10 Steps of Glycolysis”. Accessed March 9th, 2014.                                                                              http://biology.about.com/od/cellularprocesses/a/aa082704a.html

Ramersar, Myda, Mary Jones, Geoff Jones. 2011. Biology for CAPE Unit 1. Cambridge: Cambridge University Press.

Picture References:

Glycolysis Cycle- http://cnx.org/content/m44442/latest/Figure_07_07_02.jpg

Bad time-http://biochemicalminds.files.wordpress.com/2014/03/438e532c9e230ecc312a6c59d925469876c4d3b7b625269fe843155b755b3c55.jpg

Glycolysis Factory- http://dynamic.pixton.com/comic/t/a/6/q/ta6qxsk7epuocem8_v2_.png

Worried man- http://thumbs.dreamstime.com/z/worried-business-man-1741735.jpg

relieved- http://i.imgur.com/RkFZOm0.jpg

prison- http://img.naij.com/n/0b/3/prison-cube_1_.jpg

epic split- Van Damme http://static.squarespace.com/static/51b3dc8ee4b051b96ceb10de/t/52857605e4b0975b1b06bd27/1384478226902/jean-claude-van-dammes-epic-truck-splits-stunt.jpg

redox- http://cdn.memegenerator.net/instances/400x/37209536.jpg

halfway there- https://i.chzbgr.com/maxW500/7762225664/hB8C603B1/
changing shape- http://www.capstoneclassroom.com/product/covers_lg/9781432932763.jpg

FINALLY- http://www.chesnok.com/daily/wp-content/uploads/2013/10/yes-finally-pl-ffffff.jpeg

Link reaction- http://www.revisionworld.com/sites/revisionworld.com/files/rw_files/LinkReaction.JPG

running- http://www.dailyhiit.com/hiit-blog/wp-content/uploads/2013/10/running-wallpaper-41.jpg

breadshell- http://media.tumblr.com/bfa7ee6595e07c7553f6e3372f7ee1d8/tumblr_inline_mpd9c5Kekm1qz4rgp.jpg

My job is done- http://www.troll.me/images/the-chuck-norris/my-job-here-is-done.jpg


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