Monthly Archives: March 2014

Would You Like A Nucleoside With That?




Nucleosides are made of nitrogenous bases attached to a RNA or DNA sugar without any phosphate groups. (Probably could be reckoned to a bee without its sting)

Nucleoside- Sugar +Base

05_26NucleicAcidComponent nucleoside

Examples of Nucleosides- Cytidine, Uridine, Adenosine, Inosine, Thymidine.


– Are made up of just one nitrogenous base attached to a sugar with no phosphate groups

– Through hydrolysis of nucleotides the phosphate group is removed and the remaining structure is the nucleoside.

An example of a nucleoside is our very energy currency molecule ATP, you know, that energy currency we’ve mentioned?  ATP is composed of adenine, a ribose sugar and a triphosphate. So if it has three phosphates how does this qualify as a nucleoside? ATP is actually a nucleotide, however the portion of the molecule minus the phosphates (adenine+ribose sugar) is what’s considered a nucleoside.



·         DNA and RNA precursors.

·         Biosynthetic intermediates, which include glycogen, UDP-glucose, phosphoglycerides, CDP- and diacylglycerol(Suarez 2007)

·   Nucleotide triphosphates (yes we’re referring to good old ATP), energy coinage ;).

·        Adenine nucleotides are substituents of the coenzymes, NAD(P)+, FAD, and CoA.

· They function as metabolic regulators:  (a) hormonal actions are mediated by c-AMP; (b) The activation of phosphorylase and deactivation of glycogen synthase by ATP-dependent protein phosphorylation;

Allosteric regulators – the deactivation of glycogen synthase and activation of by AMP activated by ATP respectively (Joseph 2009)


In case you’ve been wondering, thus far, there are just two types of nucleic acids found in the cell:

In the nucleus- DNA (Deoxyribonucleic acid)

In the cytoplasm- RNA (Ribonucleic acid)


DNA has the genetic code to make RNA.

RNA converts the primary sequence of amino acid code to one for more complex proteins.
DNA and RNA structure, an extremely brief overview:



-double stranded, hence 2 polynucleotides along each other

-wound together to form double helix

-formed via Hydrogen bonding between bases, forming base-pairs.

-base pairs are specific where C binds to G,A binds to T known as complementary base pairs.


Main structure of RNA

-has ribose sugar

-has the base uracil

-single stranded

-shorter than DNA



References: “Nucleoside vs Nucleotide – Difference and Comparison | Diffen.” 2014. (accessed 30 Mar 2014). “DNA_Notes.” 2014. (accessed 30 Mar 2014). “BIOLOGICAL FUNCTIONS OF NUCLEOTIDES.” 2014. (accessed 30 Mar 2014).


Images taken from:


Contributors: Le Frenchie, India, Roi (editor)


Nucleotide Factoids?


Even though there’s a lot of genetic material floating around in our cells they only account for less than 6% of the weight of the cell, of which RNA makes up the majority 0.5% of the weight of a cell being RNA molecules while DNA only accounts for less than 1% of the mass. (Cooper 2000)

For storage purposes we know that the DNA in our body is heavily compressed and coiled in the cell but if we were to stretch out the length of all the DNA molecules in your body it could reach the moon and back 6000 times? (Talk about a long ladder… whoa).

The average human genome (all of an organism’s genetic material) has the equivalent storage capacity of a 4Gb flash drive.
Since each cell in body has a copy and its estimated thats there’s an average of 100 trillion cells in the human body,  (Matthews 2009) that means if humans were hard drives, we will would have 400 trillion GB of storage space!! Thats more than we’d know what to do with (With all of that memory, 😛 imagine the processing power of the human brain, my fellow computer fanatics).

What are nucleotides you ask? Well fear not, my biochemians, though I’m no hero  I’m coming to save the day anyway.

Nucleotides are the molecules which are the main components that composed RNA and DNA. They are imperative for survival since they are used in enzyme reactions, production of chemical energy and cell signalling (Wisegeek n.d.).


The nucleic acids DNA (deoxyribonucleic acid) and ribonucleic acid (RNA), made up of nucleotides joined by phosphodiester linkages between the Carbons 3 and 5 are the 2 major molecules of genetic information.

Nucleotide characteristics:

They consist of 3 parts:

-a negatively charged phosphate group

-a pentose sugar (5 C ring)… Seen as ribose in RNA and deoxyribose in DNA.

-& a nitrogenous base. There are 5 bases, namely Uracil (U)Thymine (T), Adenine (A), Guanine (G) and Cytosine (C).

but be duly warned… thymine is found on only in DNA, whereas uracil is only found in RNA.



Cooper, Geoffrey M. The cell. Washington, D.C.: ASM Press, 2000. “DNA and the Molecular Basis of Heredity.” n.d.. (accessed 30 March 2014).

wiseGEEK. “What Are Nucleotides?.” n.d.. (accessed 30 March 2014).

Images from:


Contributors: Le Frenchie, India, Roi (editor)

Lipids and Alzheimers Disease D:



Seeing the word “Lipids”, may make you think “fats.”


But that’s just the tip of the iceberg.
Ice Cube

Yeah I know.


Lipids are actually a large group of molecules such as fats, phospholipids, glycerides and sterols and function mainly as a structural component in the cell membrane aiding in the normal functioning of the cell and in energy storage. (Lütjohannand Meichsner et al. 2012, 65–78).

Also you (might not) know that any change in lipid levels in the central nervous system in the brain can cause neuro-degeneration which is linked to Alzheimer’s disease.

When talking about Alzheimer’s we focus mainly on phospholipids which are found in the lipid bilayer of the cell membrane.


Amyloid-beta (Aβ or Abeta) are protein pieces found in the fatty membranes of nerve cells in the brain. They clump together to form plaques and it is a major contributor to Alzheimer’s disease (  n.d.) Aβ tends to bind to the phospholipids resulting in a change to the biophysical properties of the bilayer and this disrupts the membrane.

When Alzheimer’s patients are studied, they are found to have decreased levels of phospholipids in their brain tissue mainly in the frontal and parietal cortex. This reduction within the brain impacts the cell viability and the stability and permeability of the cell membrane leading to cell death or dysfunction.
For Alzeimer’s facts, check out this cool infographic from


Oh wait, there’s more…

Lipids & Obesity?
heh… Who would’ve thought -_-‘

A diet that is overly rich in saturated fatty acids is quite unhealthy for the individual consuming such substances.
This is due to the fact that the energy content of the food being consumed (due to the strong C-C single bonds existing between these fatty acids that make up the lipids contained in the food), is much greater than the energy that is actually required by the body. And so, because it would take a high amount of energy in order to break these bonds (that cannot be supplied by the body), the lipids are stored as excess fat deposits and overtime the individual becomes overweight (obese).




Dangers of Obesity

-Coronary heart disease- fatty deposits or plaque deposits coagulate in the arteries of the heart and cause blockage thereby limiting the amount of oxygen-rich blood supplied to the heart muscles which can lead to angina (chest pain) and eventually the individual suffers from a heart attack or stroke if the arteries supplying blood to the heart is completely blocked off.

– High Blood pressure- when there is a constant rise in pressure of the blood pushing against the walls of blood vessels which eventually damages the body.

-Type 2 diabetes- the blood glucose level becomes higher than the normal level (> 90mg/100cm3 of blood) and remains this way due to either the absence of insulin (which would usually act on regulating this glucose level back to normal) or due to the failure to respond properly to insulin itself. Diabetes type 2 has several issues and body malfunctioning conditions that are associated with the disease.

-Abnormal blood fats

-Metabolic Syndrome



-Obesity hypoventilation Syndrome

-Reproductive problems



( n.d.)

References: “What Is Alzheimer’s?.” n.d.. (accessed 23 March 2014).

Lütjohann, Dieter, Sabrina Meichsner and Hanna Pettersson. “Lipids in Alzheimer’s disease and their potential for therapy.” Clinical Lipidology 7, no. 1 (2012): 65–78. “What Are the Health Risks of Overweight and Obesity? – NHLBI, NIH.” n.d.. (accessed 20 March 2014).


Contributors: Thalia, Chris, Roi (editor)













Lipids are a pretty diverse family, generally classified as water-insoluble, organic substances … Like carbs, they’re made up of hydrogen and carbon, but their oxygen is present in significantly smaller amounts, usually tagging along …on the outside looking in *plays world’s smallest violin*. Since they’re mainly made up of non-polar hydrocarbons, it’s not surprising that lipids are hydrophobic. This insolubility in water means that lipids don’t form solutions, however, they do form emulsions (, n.d.)

basic lipid

Now about that diversity…


Lipids exist as triglycerides- fats (solid at room temp.) & oils (liquid at room temp.)- Phospholipids, steroids and waxes.



More on Lipids…

(We swear there are pictures in there…)


Lipid metab..

-They are formed by condensation reactions between fatty acids and an alcohol.


-A condensation type of reaction occurs when two molecules or functional groups combine to form one single molecule together with the elimination of a small molecule such as water (H2O).


-Lipids contain fatty acids with the acidic group (-COOH-) AKA, the carboxyl group and an alcohol such as glycerol which contains 3 hydroxyl (-OH-) groups.


-A glycerol molecule can condense with 3 fatty acid molecules to form a triglyceride molecule

-Triglycerides can be further classified as fats or oils depending on whether they are solids (fats) or liquid (oils) at room temperature therefore, how saturated or unsaturated the fatty acids that make up the triglyceride are:


-Fatty acids that contain one or more double bonds (C=C) are said to be unsaturated whilst those that contain single (C-C) bonds are said to be saturated

-Unsaturated fatty acids have much weaker bonds than that of saturated fatty acids; therefore at room temperature the bonds of unsaturated fatty acids are easily broken. This explains why Compounds containing unsaturated fatty acids tend to exist in the form of oils at room temperature whilst those that contain saturated fatty acids tend to exist as solids.


(Champe and Harvey et al. 2005)


There’s always a rebel…


Phospholipids aren’t that unlike their siblings the triglycerides. Phospholipids are formed by a bond between the glycerol of a lipid and a phosphorous molecule (K). However, unlike triglycerides they have two fatty acid chains, (diglyceride). So what about the place where the 3rd triglyceride would’ve been? That’s actually occupied by a phosphate group, attached to a polar region of the molecule. Hold up… Something’s a bit fishy about that?

basic structure of a few membrane lipids


Well, I’m sure you remember that lipids are generally classified as non-polar, hydrophobic molecules.While that’s still true for the fatty acid region, the phosphate group at the head of the compound is polar *gasp*….and hydrophilic.

That’s why phospholipids are great emulsifiers, they can interact with oil at their non-polar hydrophobic end, and with water at their hydrophilic head. Furthermore, these characteristics (and the tendency of phospholipids to clump together, exposing their polar heads), are precisely why cells utilize phospholipids in their membranes; they get the best of both worlds: functionality, by having their membranes interact with their water rich interior and exterior, and  exclusivity, as phospholipids form a continuous barrier around the cell. Think of the Phospholipids as that ever so indifferent bouncer at your favourite club?
(Connexions 2013).




Champe, Pamela C, Richard A Harvey and Denise R Ferrier. Biochemistry. Philadelphia: Lippincott/Williams & Wilkins, 2005.

Connexions. “Organic Compounds Essential to Human Functioning.” 2013. (accessed 20 March 2014) “The Chemistry of Biology: Lipids |” n.d.. (accessed 14 March 2014).


Contributors: Thalia, Chris, Roi (editor)

The ETC! Rap Up..



From the TCA cycle we know:

1. Each molecule of pyruvate yields 3 NADHs and 1 FADH2 (coenzymes) for every cycle

2. …Because glucose is split into two pyruvates, one molecule of glucose gives: 6 NADHs+2 FADH2s.

The link reaction, which precedes the TCA cycle

The link reaction, which precedes the TCA cycle. Pyruvate is oxidized to Acetyl CoA, which enters the TCA cycle.

Glycolysis, and the link reaction give us 2 ATPs, 2 NADHs & 2 NADHs repectively. The TCA Cycle doesn’t produce much energy (Net ATP= 2) so it’s safe to say that the TCA cycle produces these coenzymes to produce energy in the ultimate, energy mother lode… the Electron Transport Chain!!!.
On average, the ETC produces *drumroll please* 34 molecules of ATP…

Where do the NADHs and FADH2s from the TCA Cycle fit in?

……………………..Drumroll please!

drumroll please

They’re electron donors, basically they give these electrons to electron carriers, such as cytochromes, FMN, and coenzyme Q which make up the electron transport chain. This all happens in the inner membrane of the mitochondria and involves reducing O2 to H20 with the last cytochrome in the ETC, cytochrome.
Proton and electron transport are a dream-team, together they pump electrons along a chain of channel proteins which swap these electrons to send protons to the outer compartment of the mitochondria.

However, this buildup of protons (forming an electrical, and pH gradient) doesn’t last very long. The restless, energetic protons re-enter the matrix of mitochondria through the inner mitochondrial membrane via the enzyme ATP synthase resulting in ATP synthesis. For every NADH apprx. 3 ATPs are produced along with 2 ATP’s per FADH2…

That’s how we get those 34 ATP’s folks! (Harvey and Ferrier 2011).

If that didn’t sink in… well…  there’s these pieces of awesomeness right here. Pretty sure this “Thrift Shop”   parody and  “Oxidate It Or Love It / Electron to the Next One” were made to be my geeky Biochem survival guide.




Harvey, Richard A and Denise R Ferrier. Lippincott’s illustrated reviews, biochemistry. Philadelphia: Wolters Kluwer Health, 2011.
Lam, Wilson. “TCA (Kreb’s) Cycle Rap – Wilson Lam (Macklemore – Thrift Shop Parody).” Digital video, 2013. (accessed 22 March 2014).
Mcfadden, Tom. “Oxidate It Or Love It / Electron to the Next One.” Digital video, 2013. (accessed 22 March 2014).

Contributor: Roi

When Krebs Goes Wrong.




Due to its metabolic significance in energy and the production of substances needed as building blocks for other functions and reactions, disorders of the TCA cycle usually affect the entire body, with severe effects on organs and systems. These may include:
–          Pyruvate Carboxylase Deficiency

–          Phosphoenolpyruvate carboxykinase deficiency

–          Pyruvate Dehydrogenase Complex Deficiency

–          Dihydrolipoamide Dehydrogenase Deficiency

–          2-Ketoglutarate Dehydrogenase Complex Deficiency

–          Fumerase Deficiency

–          Succinate Dehydrogenase Deficiency

–          Pyruvate Transporter Defect


Pyruvate Dehydrogenase (E) deficiency

–          This is a rare neurodegenerative disorder (affecting both males and females) in which pyruvate is not converted to acetyl coA (needed for the TCA cycle) due to the absence or not functioning enzyme, Pyruvate Dehydrogenase. Instead the enzyme lactate dehydrogenase converts it to lactic acid.

–          Pyruvate Dehydrogenase enzyme deficiency, thus causes several complications such as the condition lactic acidosis which severely affects the brain in particularly. Symptoms of the disease include developmental defects, decreased muscle tone (spasticity) and even death.

There is currently no proven treatment for this disease ( 2014).

Oh… okay

sad face

References: 2012. Pyruvate dehydrogenase deficiency – Genetics Home Reference. [online] Available at: [Accessed: 14 Mar 2014].

KILL BILL ANIMATED GIF. n.d. [image online] Available at: [Accessed: 16 Mar 2014].

Contributors: Thalia, Roi (editor)



Details, Details…  


The TCA/Krebs/Citric Acid Cycle occurs in the mitochondrial matrix. It’s the final pathway whereby oxidative type of metabolism of amino acids, fatty acids and carbohydrates converge; i.e. their carbon skeletons are converted to carbon dioxide and water, also in turn generating a form of usable energy in the form of ATP (Adenosine-Triphosphate).


The Krebs cycle is the third of four metabolic pathways including: Glycolysis Pyruvate Processing and oxidative phosphorylation which are all interlinked.All of the individual steps that are involved in the TCA cycle amount to one great purpose. Basically, citric acid (citrate), a substance high in energy, is formed from oxaloacetate and acetyl CoA. Step-by-step, citrate loses little energy pockets, partly in the form of carbon dioxide and water also as GTP, NaOH and FADH2 (which provides electrons to complete the respiratory chain following the TCA cycle).

Finally, as a result of all these shenanigans, ATP (the mighty energy storing molecule) is produced and aids in most of the bio-chemical processes that occur within the body.In the TCA cycle, the remaining substances (not used for ATP production) are used to reconstruct the oxaloacetate molecule which would join to an acetyl CoA molecule thereby repeating the entire cycle once more (Encyclopedia Britannica 2013).

Enymes, Krebzymes?- A little regulation goes a long way…

Just in case you may have wondered if this little party ever stops, it doesn’t.

giphy (5)

…but it does slow down

In the cell, its need for ATP determines the rate of the Krebs cycle.

How, you might ask?

Both the Krebs cycle and its predecessor glycolysis, are continuously regulated by enzyme stimulation and inhibition. The cell, a responsible little factory, always prefers efficiency, and products never are manufactured in excess. This allows both glycolysis, and the Krebs cycle to work like a well-oiled machines. Once there’s more than enough ATP present to cater to the cell’s demanding energy needs, glucose is stored as fat or glycogen, ‘til the cell needs more.

Since we’re on the subject of more, activators do exactly the opposite.  Their function is regulatory, and they ensure that energy requirements are met. Activators, namely Ca2+ and ADP increase the manufacturing of products when the cell states that there’s not enough to go around. They essentially tell the enzymes, a-ketoglutarate dehydrogenase and isocitrate dehydrogenase, to increase the rate of production (Lodish 2008).



Encyclopedia Britannica. 2013. tricarboxylic acid cycle (biochemistry). [online] Available at: [Accessed: 16 Mar 2014].

FAMILY GUY ANIMATED GIF. n.d. [image online] Available at: [Accessed: 16 Mar 2014].

Lodish, H. F. 2008. Molecular cell biology. New York: W.H. Freeman and Co.

wait, The Krebs cycle occurs IN the matrix?!. n.d. [image online] Available at: [Accessed: 16 Mar 2014].

Contributors: Thalia, Roi

A Cycle by Any Other Name…


The Krebs cycle was named after the German/British biochemist, Sir Hans Adolf Krebs who later received a Nobel Prize for his discovery. His research on metabolic processes led to his discovery of both the Krebs and urea cycles.


giphy (4)

The Krebs cycle is a set of reactions which living cells carry out in order to make energy. Most aerobic organisms gain energy through the Krebs cycle via the breakdown of glucose and other simple sugars in the presence of O2. However, this isn’t a one man show… the Krebs cycle is only the second of four stages in ATP (energy) formation, occurring between glycolysis and oxidative phosphorylation ( n.d.).

Fig 1: The Citric Acid Cycle

Fig 1: The Citric Acid Cycle

Also, the first product that is formed from the reactions of the cycle is citric acid, which is another name for the Krebs cycle. Incidentally, it’s also one of the final reactants in the cycle due to its being regenerated to actually complete the cycle. This doesn’t end there, actually citric acid is also called tricarboxylic acid because it contains 3 carboxylic groups (COOH) hence citric acid is also called tricarboxylic (TCA) cycle.

You Should Know…

  1. The Krebs cycle starts with the condensation reaction involving one oxaloacetic acid molecule and one acetyl COA (coenzyme A) molecule -(acetyl COA  is a coenzyme A derivative)
  2. Acetyl COA is actually formed from pyruvic acid.
  3. Citric acid is formed by a reaction between acetyl COA and oxaloacetic acid; in enzyme-catalyzed reactions citric acid acts as a substrate and 7 intermediate compounds are formed ( mainly succinic, fumaric and malic acid)
  4. Malic acid is converted to oxaloacetic acid which then combines with acetyl COA to produce citric acid.
  5. 2 molecules of CO2 and 8 atoms of Hydrogen are formed as byproducts with every reaction of the cycle. While it’s other products for every molecule of Acetyl CoA include: 3 NADH’s,1 FADH2, &1 ATP.
  6. CO2 is removed from the blood by the end product of the reaction
  7. H2 atoms are converted to hydride ions to the electron transport systems needed for oxidative phosphorylation process.

    Krebs cycle steps….

  • Condensation
  • Isomerisation
  • Dehydrogenation
  • Decarboxylation
  • Oxidative Decarboxylation
  • Substrate level ATP/GTP Synthesis
  • Dehydration (Oxidation) of succinic acid
  • Dehydration (Oxidation) of malic acid


You bet your life it’s important…

  • The intermediate compounds such as succinic acid, fumaric acid and malic acid are used to make nucleotides, amino acids, fats, chlorophyll and cytochromes.
    • succinyl COA, an intermediate, is involved chlorophyll formation
    • a-ketogluteric acid, oxaloacetric acid and pyruvic acid and form Amino  acids.

Energy in the form of ATP is made during the Krebs cycle ( 2012).


References: “Krebs Cycle | Chemistry Learning.” 2014. (accessed 16 Mar 2014).

DISNEY ANIMATED GIF. 2014. [image online] Available at: [Accessed: 15 March 2014]. “Krebs cycle |” 2014. (accessed 16 Mar 2014).

Frey, R. 2007. A diagram of cellular respiration including glycolysis, Krebs cycle (AKA citric acid cycle), and the electron transport chain. [image online] Available at: [Accessed: 15 March 2014]. n.d. Glycolysis. [online] Available at: [Accessed: 16 March 2014].

Contributors:  Thalia, India, Roi (editor)

Glycolysis In Ancient Egypt?!


Glycolysis is involved in the process in which yeast ferments a starch sources (in beer barley or malt) in our very converted and sometimes fattening drink that we men love to enjoy during our football matches (I’ll drink to that).


Egyptians were the first peoples to perfect the process of fermenting beer by using yeast mixed with malt around 2200BC. In alcoholic fermentation the process that makes our beloved drink, the starches are first broken down to pyruvic acid (a ketone/ simple alpha-keto acid), via glycolysis, and then 2 enzymes (pyruvate decarboxylase and alcoholic dehydrogenase) then convert the pyruvic acid into CO2 and ethanol
and tada… beer!!!
(Berg and Tymoczko et al. 2007).


Factoid: During the construction of the pyramids labourers were paid in beer instead of gold so in essence:

no glycolysis= no beer= no pyramids of Giza.

So take a moment to thank glycolysis the next time you take a drink.


Berg, Jeremy M, John L Tymoczko and Lubert Stryer. Biochemistry. New York: W.H.Freeman & Co Ltd, 2007. “Ancient Egypt Society: Beer.” 2010. (accessed 08 Mar 2014).


Contributors: Christine, Le Frenchie, Roi (Editor)

The Dark Side of Glycolysis…


Glycolysis is a biochemical pathway used to obtain energy from carbohydrates. A very interesting fact about glycolysis is that it can occur in almost any living organism, usually under anaerobic conditions, and in mammals such as ourselves, glycolysis is occurring in every part of our bodies at any given moment.

However, like most things in this cruel, cold world… there’s a dark side to glycolysis…

giphy (3)

Circa 1924, Nobel laureate Otto Heinrich Warburg, discovered (by accident),  that most cells that became cancerous had an extremely high rate of glycolysis occurring up to 200 times the rate of a normal cells. This led to a hypothesis at the time that cancer was fundamentally caused by this factor of “runaway glycolysis”. A hallmark of the Warburg hypothesis is that is allows glycolysis to occur in the presence of oxygen which causes fermentation instead of oxidation.
This phenomenon deals with how glycolysis is used for energy production in tumor cells unlike other cells which use mitochondrial oxidative phosphorylation (Christ 2009).

dr evil 2

There has been a lot of research put into investigating this  and luckily enough, the world was rewarded with the cancer detection method known as the positron emission tomography (PET) scan which is used worldwide for detecting cancer cells in patients.

It has been suggested that the products of this fermentation interferes with apoptosis (the process by which body kills damaged cells) allowing the increase of the rate of glycolysis in these damaged cells. This mechanism of fermentation instead of oxidation of the sugars can lead to cancers in the liver, testicles and other parts of the human body.

sad face

The occurrence of this particular form of fermentation in the brain’s frontal, temporal and parietal lobes has been determined as one of the main causes for Alzheimer’s, it affects the nervous tissue in the brain resulting in memory loss. (, 2012).


Christ, Ethan J. “Columbia University Academic Commons.” 2009. (accessed March 8, 2014). “Graphics Gallery: An Antibody Molecule.” 2014. (accessed 8 Mar 2014). (accessed March 8, 2014). Pratt, Charlotte W. Essential Biochemistry. December 20, 2012.

Schwartz, L. Cancer. Berlin: Springer, 2004

Stoker, H. Stephen. General, Organic and Biological Chemistry. Belmont: Brooks/Cole, Cengage Learning, 2010.


Contributors: Christine, Le Frenchie, Roi (Editor)