Last Post???? D:…Thoughts on the course overall.

Last Biochem post? O_o

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I know right, unbelievable xD *sigh* I never expected it to be so work intensive. I literally felt like this
->

cartoon-man-begging-mercy >.>…

All in all, it was…an experience. I enjoyed our lecturer’s mode of teaching, most times… lol The tutorials still creeped me out though >.> But it was good doing something different for a change. These past few weeks went by realllyyyy fast and yes procrastination became a friend of mine :s

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*hangs head in shame >.>* Anyways, so, I just want to say thanks to our amazing lecturer Mr JM without whom these topics in biochemistry would have elude our minds. I bet he expects us to be like this now ->

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O_o….LOL…Yeahhhh…Biochemistry 1 was indeed a challenge, but we put up a valiant effort till the end. Thumbs up for our Hokage of Biochemistry! ^_^ Thank you for being patient with us 🙂

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Cyanide Poisoning X_x

Cyanide contains a cyano group which consists of a carbon triply bonded to nitrogen. It has the ability to bind to metals thus giving it and inhibitory quality. Cyanide, when ingested, inhibits cytochrome oxidase which is an enzyme from the terminal mitochondrial respiratory chain. Cyanide has a ‘weak spot’ or ‘craving’ rightfully known as a ‘special affinity’ for the heme ion which the enzyme cytochrome oxidase happens to have two of along with two copper ions.

Cyanide binds to the protein crevices on first penetration then it binds to the iron enzyme complex rendering it incapable of using O2 for cellular respiration. This O2 which is not being used in turn saturates the blood imparting a cheery red colour which is the diagnoses or confirmation of cyanide poisoning. This formed cyanide-heme cytochrome oxidase complex results in a disruption of the electron transport chain as well as oxidation phosphorylation due to the enzyme, cytochrome oxidase, being inhibited.

An anaerobic condition results from the decrease in O2 and severely decreased ATP production which results in the increase of lactic acid build up. Cyanide is a poison which is an irreversible enzyme inhibitor. It acts as a non-competitive inhibitor for the cytochrome oxidase complex. It does not compete for the active sites of the enzyme as it has no similarity whatsoever to the substrate cytochrome. Rather, cyanide attaches itself to another site on the enzyme thus disrupting the enzyme’s shape. This brings the electron transport chain to a halt and therefore the cell can get no energy out of respiration. No energy means no life.Image

My MCQ

EXAM QUESTIONS

AMINO ACIDS

(1)    Two cysteine molecules will undergo a reduction reaction where the two ________   groups will lose their H via oxidation process to form a disulphide linkage.

(a)    Nitrogen hydryl

(b)   Sulphur hydryl

(c)    Sulphur oxide

(d)   Methyl

(e)   Carboxyl

(2)    Select the correct multiple answer using ONE of the keys A, B, C, D or E as follows:

A. 1, 2 and 3 are correct

B. 1 and 3 are correct

C. 2 and 4 are correct

D. only 4 is correct

E. all are correct

List amino acids with positively charged R groups:-

  1. Lysine
  2.  Arginine
  3. Histidine
  4. Aspartate

ENZYMES

(3)    Oxidoreductases are a class of enzymes which:-

(a)    Catalyse the transfer of C,N or P containing groups

(b)   Catalyse oxidation-reduction reactions

(c)    Catalyse cleavage of bonds by addition of water

(d)   Catalyse cleavage of C-C, C-s and certain C-N bonds

(e)   Catalyse racemization of optical or geometric isomers

(4)    Select the correct multiple answer using ONE of the keys A, B, C, D or E as follows:

A. 1, 2 and 3 are correct

B. 1 and 3 are correct

C. 2 and 4 are correct

D. only 4 is correct

E. all are correct

Enzymes-

(1)    Are biological catalysts

(2)    Speed up a chemical reaction

(3)    Provide an alternative pathway with lower activation energy

(4)    Provide an alternative pathway with higher activation energy

Published Paper Review 1 & 2

PUBLISHED PAPER 1

“Evolution: Revisiting the Root of the Eukaryote Tree”

Roger, Andrew J. Simpson, Alastair G.B.  2009. “Evolution: Revisiting the Root of the Eukaryote Tree” Accessed April 11, 2013.

http://www.sciencedirect.com/science/article/pii/S0960982208016886

Eukaryotes are organisms which have cell types containing specialized organelles in their cytoplasm. They also contain a membrane-bound nucleus which encloses their DNA or genetic material. This published paper goes into the evolution of the eukaryotes.

The 1980s-1990s saw the prevailing view that eukaryotes were influenced by ribosomal RNA genes. Recently, however, a ‘six-super groups’ hypothesis and the unikont-bikont root hypothesis had emerged to classify the deep eukaryote phylogeny, however, there was some controversy.

A recent paper had reported the classification of the enigmatic protist Breviata anathema which lives in oxygen poor conditions, lacks classical mitochondria and its flagellar apparatus has at least one additional non-flagellated basal body. It was originally classed in one of the “six-super groups” as an Archamoebea (a group of mitochondrion-lacking amoebozoans). However, it was found that this group of eukaryotes contained mitochondrial marker proteins and mitochondrion-derived organelles which proved the hypothesis of this group originating before the endosymbiotic era of mitochondria to be false. Thus it was found that no eukaryotic linkages persisted from a pre-mitochondrial phase of evolution.  Analysis indicate that Breviatais closely related to Amoebozoa which is the super-group the Archamoebae also belong to. This relationship demonstrates that Breviata too descends from a mitochondrion-containing ancestor.

It is also suggested that Breviata be placed inside Amoebozoa as the sister group of Archamoebae, as they might share a common anaerobic ancestor. Cavalier-Smith had argued that ancestral eukaryotes had simple kinetid containing a basal body which anchored one flagellum. He suggested that unikonts retained ancestral organization and the bikonts came from an ancestor that had a posterior and anterior flagella.

However, recent studies showed that the bikonts characteristic occurs during cell division in the daughter cells. The problem of unikonts actually having more than one flagellum or basal body incorporated a problem with the hypothesis. These results were also based on a very narrowinf sampling of the available eukaryotes.

From this published paper, it was deduced that there are several important taxa whose phylogenetic affinities to the major super-groups have not really been delved into and as such there a lot unknown about them and how certain aspects of the eukaryote tree should be classified.

 

PUBLISHED PAPER 2

“pH affecting organelles of liver cells.”

Diwu, Zhenjun, Chii-Shiarng ChenCailan ZhangDieter H Klaubert and Richard P Haugland. 1999. “A novel acidotropic pH indicator and its potential application in labeling acidic organelles of live cells”. Accessed April 11,2013.

http://www.sciencedirect.com/science/article/pii/S1074552199800593

From the published paper it was understood that ‘ratio imaging’ is significantly limited due to the lack of appropriate fluorescent probes (mainly for acidic organelles). Fluorescent dyes are not appropriate for staining these acidic organelles (such as lysosomes) due to their fluorescence being decreased under neutral or acidic conditions thus limiting the labelling of the organelle. A compound 2-(4-pyridyl)-5-((4-(2-dimethylaminoethyl-aminocarbamoyl) methoxy)phenyl)oxazole (PDMPO) was prepared to combat this problem as it emits intense yellow fluorescence at low pH and gives an intense blue at higher pH.

Thus, with this new compound, it was possible to label the acidic lysosomes of liver cells. The two varying fluorescence colours given at low and high pH made the detection of pH fluctuation possible.

From this paper, it was deduced that the lysosomes of liver cells are extremely acidic and as such a compound had to be developed specifically to study these acidic organelles.

Glycolysis

This video contained a lot of useful information. It stated that glucose is broken down by the process of glycolysis. One glucose molecule is broken down into 2 three carbon molecules. This produces a net gain of energy which is captured by ATP and NADH.

Pyruvate which is the break down product in eukaryotes is imported into the mitochondria and is fed into the citric acid cycle and electron transport chain.

Glycolysis involves 10 steps. The first 3 steps invest ATP which is later recovered.In the 4th and 5th step, however, this allows glucose to be split while in the last 5 steps energy is released as ATP and NADH.

Step 1: The Hexokinase enzyme uses ATP to phosphorylate glucose and primes it for later energy releasing reactions. The glucose is converted into glucose-6-phosphate and ADP is released. (Irriversible reaction)

Step 2: Phosphohexose isomerase opens the ring form of glucose-6-phosphate to the open chain form and performs a reversible reaction in which the carbonyl group of glucose-6- phosphate changes its position from the 1st C to the 2nd C. A new water molecule is created along with fructose-6-phosphate which is then converted to its ring form.

Step 3: Phosphofructokinase 1 converts fructose-6-phosphate to fructose 1,6-biphosphate.

Step 4: Aldolase splits fructose 1,6-biphosphate into glyceraldehyde 3-phosphate and dihydroxyacetone phosphate.

Step 5: Triose phosphate isomerase converts dihydroxyacetone to glyceraldehyde 3-phosphate, (There are 2 molecules of glyceraldehyde 3-phosphate.

Step 6: Glyceraldehyde 3-phosphate dehydrogenase converts glyceraldehyde 3-phosphate to 1,3-bisphosphoglycerate (oxidation reduction reaction adds the energy necessary to convert).

Step 7: Phosphoglycerate kinase converts 1,3 bisphosphoglycerate to 3-phpsphoglycerate. ATP accepts phosphate.

Step 8: Phosphoglycerate mutase converts 3-phpsphoglycerate to 2-phosphoglycerate.

Step 9: Enolase converts 2-phosphoglycerate to phosphoenolpyruvate via the loss of 2 water molecules.

Step 10: Pyruvate kinase converts phosphoenolpyruvate to Pyruvate.

Overall, the net energy that is produced in glycolysis is 2 ATP + 2 NADH from a molecule of glucose.

This video gave a very well done  in-depth analysis of the ten steps in glycolysis. Everything was well done except for the fact that they forgot to mention that the first 3 steps in glycolysis were the Preparatory phase and the rest was the the pay-off phase.

I give this video 4/5 stars.

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Oh Enzyme…Video Review

From the video, there were a lot of important points.

Three remarkable scientists namely Louis Pasteur, Edward Buckner and James Sonar were able to formulate theories about enzymes based on their observations and experiments they conducted.

Essentially, it was noted that enzymes can be defined as biological catalysts which speed up the rate of a chemical reaction by providing an alternate pathway with lower activation energy. They themselves remain unchanged after the reaction is completed. Most enzymes are proteins and some are RNA molecules.

In the transition state, the structure of the substrate changes into the structure of the product. During this, some bonds are broken while others are partly formed.

The activation energy is the minimum amount of energy required for a reaction to occur, thus, this means that if the energy requirement is lowered, more substrate can be converted into product.

Enzymes have 3 distinctive features:-

– catalytic power

– specificity and

– regulation

Kcat is the number of molecules of substrate that can be converted to product per enzyme molecule per second and it is also known as the turnover number.

It was noted that there were a lot of confusion in naming enzymes and so a system (namely the 6 major classes of enzymes) was implemented to diminish the confusion.

The 6 major classes of enzymes include:-

(1) Oxidoreductases – which catalyze the transferring of an electron or oxidation reactions.

(2) Transferases – which catalyze the transfer of C,N or P containing groups.

(3) Hydrolases – which catalyze cleavage of bonds by the addition of water.

(4) Lyases – which catalyze cleavage of C-C, C-S and certain C-N bonds.

(5) Isomerases – which catalyze racemization of optical isomers.

(6) Ligases – which catalyze the formation of bonds between C and O, S, N coupled to hydrolysis of high-energy phosphates.

Thus from this the EC of enzymes can be read, For example, glucokinase has an EC of 2.7.1.2. From the first number of the EC it can be concluded that this enzyme is a transferase enzyme.

On to co-factors. These are the nonprotein component of enzymes. They can be inorganic or organic. A holoenzyme results from the combination of an apoenzyme which is an inactive protein part, and a co-factor which is a nonprotein part. This gives rise to an active enzyme.

Amino acids, cysteine reaction

Amino acids, cysteine reaction

Two cysteine molecules undergo a reduction reaction in which the two SH groups lose their H. This occurs via an oxidation process which forms a disulhpide linkage. Upon combination, these two cysteine molecules form one cystine molecule. This is a reversible reaction. Reducing the disulphide linkage of the cystine molecule will cause it to undergo a reduction reaction which converts this molecule back into two cysteine molecules.