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)

Ten-Step Program?


The Embden- Meyerhof pathway or as we all call it, glycolysis, is the pathway for acquiring energy from carbohydrates. It is a ten step process and each step is enzyme catalyzed resulting in the production of energy in the form of ATP and NADH (Pratt, 2012).

  • It begins with glucose, a carbohydrate consisting of mainly six carbons.
  • The carb is  oxidized and two (3-carbon) pyruvate.
  • Each metabolized molecule produces two ATP and two NADH molecules.
  • Glycolysis interacts with other pathways of metabolic reactions.
  • During the pathway, other molecules (like glucose-6-phosphate) come in at the 2nd step.(Stoker, 2010)

prof troll

Three parts, ten steps, and no this isn’t a dance move :|.  Glycolysis is as complicated as it is tear-inducing (well… for those who’ll have to memorize it, anyway).

13_01Glycolysis-Steps_1-5 13_01Glycolysis-Steps_6-10

A few facts:

  • Glycolysis can occur in anaerobic and aerobic conditions.
  • It’s the oldest metabolic pathway known to man.
  • Abnormally high rates may lead to tumor cell formation (the Warburg effect).
  •  Glycolysis is occurs everywhere in the body.
  • It’s responsible for the process of fermentation where yeast is converted into alcohol.

( 2012)


With finals right around the corner…  the truth is…

bad time


Christ, Ethan J. “Columbia University Academic Commons.” 2009. (accessed March 8, 2014). February 15, 2012. (accessed March 8, 2014).

Pratt, Charlotte W. Essential Biochemistry. December 20, 2012. (accessed March 8, 2014).

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


Contributors: Christine, Roi (Editor)

Lights! Camera! Enzymes?


majestic cat

Think of activation energy as an evil majestic… cat (huh?) …keeping princess, umm (let’s call her derpina) prisoner


…and the substrate as our handsome, brave knight in shining armour… the valiant knight, with the help of his friend the wizard’s magic, has to slay (or pet) the fearsome beast in order to save Princess Derpina from his evil clutches.

The same goes for our buddy the substrate, to form a given product, substrates must overcome activation energy in order to react. Enzymes (wizards) facilitate this by lowering the “energy barrier”, speeding up the reaction (, n.d.)



The lock & key hypothesis states that on an enzyme reactants may only function when bound to a specific point, or active site on an enzyme (, 2014) . Enzymes are pretty great at distinguishing between molecules and even between isomers of the same molecule and with all the binding going on it’s just the active site and substrates involved.



Unlike a jigsaw puzzle, it’s not actually a perfect fit. Within the binding process the R-groups at the active site actually change its shape slightly, in order to fit to the substrate (induced fit), forming what’s known as an enzyme-substrate complex (, n.d.). The complex, is usually held together by hydrogen/ ionic bonds.

Enzymes undergo inhibition where molecules may interact with the enzyme, hindering its usual functionality.These may include: non-specific, reversible & irreversible- competitive/non-competitive inhibitors.


References: 2013. Ninja Cat Riding Majestic Unicorn. [image online] Available at: [Accessed: 4 Mar 2014]. n.d. Energy, ATP, Enzymes.. [online] Available at: [Accessed: 4 Mar 2014]. 2013. Funny Easter Quotes. [image online] Available at: [Accessed: 4 Mar 2014]. 2014. What are enzymes? | Novozymes. [online] Available at: [Accessed: 3 Mar 2014]. n.d. IB Biology Notes – 7.6 Enzymes. [online] Available at: [Accessed: 3 Mar 2014].

Contributor: Roi

Let’s Play The Name Game…



Enzymes have a protein backbone but there are also carbohydrate groups which are covalently bonded as well as metal ions which add to their stability (Chaplin, 2004)

Holoenzymes are special. 😉


They consist of  apoenzymes which are inactive in their original conformations  (proenzymes) and they are the polypeptide/protein part of the holoenzyme. For the formation of the apoenzymes’s final (tertiary) structure, extra amino acids on the proenzyme are removed.

Cofactors are another constituent of holoenzymes. They are usually derived from vitamins, i.e. non-protein substances which may be organic, and called a co-enzyme. Co-enzymes activate the protein by either altering its conformation or by participating in the chemical reaction (Ophardt, 2003).

(whew! mouthful there)

Together, apoenzymes and cofactors form biologically active enzymes containing active sites, which allow them to catalyze chemical reactions by acting upon a specific substrate.

Organic and Inorganic Catalysts face off…

Once  the active site binds to the substrate enzymes will begin to start catalyzing reactions.

Our buddies the enzymes have some… *ahem* interesting names… 😐 ?.

enzymes-classification (1)


Ophardt, C. E. 2003. Enzymes. [online] Available at: [Accessed: 6 Mar 2014]

Chaplin, M. 2004. Enzyme nomenclature. [online] Available at: [Accessed: 4 Mar 2014].

Tutorvista. 2014. Classification of Enzymes. [image online] Available at: [Accessed: 5 Mar 2014].

Photo Credits:

Contributors: India, Roi (Editor)