Archive for the ‘Biochemistry’ Category

Beta Oxidation

Hey guys,
So the project for Biochemistry this semester was a video project. My group decided to based our video on Beta oxidation, giving the necessary steps and explaining them in detail. Please give us your support by looking at the video and commenting if you so desire.

Many Thanks.


The following is a review on a published article, “The Effect of Enzymes on Digestion.”, by Michael R. Bedford. Please note that his writings dealt with digestion in Birds.

Contrary to popular belief, that nutrients are always fully digested and absorbed in the blood stream, it is very unlikely that they ever do. Nutrients digestibilities vary between different dietary substances, however there are fours processes that help aid with digestibility. These four mechanisms are:

  • Deteriorating the cell wall 
  • Destroying ANF’s (supplements)
  • Supplying the Host’s Enzymes
  • Using intestinal bacteria

Destroying the cell wall.

Taken from www,newscenter.lbl,gov.

In this mechanism, Beta-glucanase, an enzymes, was used to break down the complex cell wall, rapidily allowing amylases and proteases to break down the cell’s content.

Getting rid of the ANF’s.

ANFs’ are supplements such as, non-starch polysaccharides, proteins, and amino acids.

It was observed that Beta-glucanase turned out to be soluble in barley. This was due to the Beta-glucan component being dissolved completely by the endosperm of the cell wall. ANF’s create viscosity, which reduces the effect of enzymes. Enzymes used to reduce intestinal viscosity are believed to improve digestion in the intestinal tract.

Viscosity. Taken from

Supplying the Host’s Enzymes.

Latest investigations has lead researchers to believe that the digestive tract may not have adequate enzymatic and absorption capacity to deal with all kinds of diets. However, work done by Bedford and Classen, proves that by adding the host enzymes, through means of supplements do in fact increase the rate at which these substances are digested.


Microbial presence?

The are millions of microbes present in your digestive tract. These microbes aid in digestion by breaking down the digestive substances to feed their own needs and produce, in some cases, helpful by products. Evidence to support the presence of microbes in our digestive tract is due to the presences of their by products in faeces.

Bacteria on the walls of the intestines


Bedford. Michael. R. 1996. ” The Effects of Enzymes on Digestion.” The Journal of Applied Poultry Research. Applied Poultry Inc, 1996. Accessed on April 11 2013.

Classen, H.L, T.A. Scotl, G.C. Irish, P. Hucl, M, and M.R Bedford, 1995.”The relationship of chemical and physical measurements to the apparent metabolize energy (AME) of wheat when fed to broiler chickens with and without and enzyme source”.Proc. of 2nd European Symp. on Feed Enzymes, Pages 65-77 Noordwijkerhout, NL. Accessed on April 11 2013.


What is an Inhibitor?

An inhibitor is any substance that diminishes the velocity of an enzyme catalysed reaction.

There are two main categories of inhibition- Reversible and Non-reversible. This entry deals with reversible inhibitors only. There are four types of reversible enzymes.

These are:

  • Competitive Inhibtors
  • Non-competitive Inhibitors
  • Uncompetitive Inhibitors
  • Mixed Inhibitors


Competitive inhibitors.

These inhibitors compete with the substrate molecules for the active site of the enzyme. Competitive inhibitors only bind to the active site of the free enzyme, note that it never binds to the enzyme-substrate complex. Competitive inhibitors do not change the Vmax, maximum velocity, of the reaction, however the substrate affinity binding to the active site of the enzyme, decreases. This means Km increases. (Remember high affinity = low Km and vice versa) .

In the case of allosteric enzymes. Both substrate and inhibitor cannot bind to the enzyme at the same time. When the Inhibitor binds to one active site, it temporarily changes the shape of the other active site, preventing the substrate from binding.

Taken from "Describe an Induced fit model" ,

Taken from “Describe an Induced fit model” ,


Non-Competitive Inhibitors.

Unlike competitive inhibitors,which only bind to the active site of the enzyme, non-competitive inhibitors can bind to the free enzyme as well as the enzyme substrate complex. Since the substrate can still bind to the enzyme, this tells us that Km is unchanged, however Vmax is reduced as the enzyme does not function with the inhibitor.


Uncompetitive Inhibitors.

These inhibitors only bind to the enzyme substrate complex. This means that the substrate can bind to enzyme although the inhibitor is already bound to it. This also tells us that both Vmax and Km are reduced.


Mixed Inhibitors.

Mixed inhibitors get the term “mixed” because they can act as competitive inhibitors, and only bind to the active site, or act and uncompetitive inhibitors and bind to the enzyme substrate complex. As a result of this, substrate affinity to the enzyme can either increase or decrease,(i.e. low or high Km values). From uncompetitive inhibitors, Vmax will always be reduced as the presence of the inhibitor decreases the velocity.

Factors affecting the velocity of the reaction are:

  • Substrate concentration [S]
  • Enzyme concentration [E]
  • Temperature
  • pH

Velocity is measures by : Amount of substrate ÷ time taken

How does temperature affect velocity?

All enzymes work at a optimum temperature, meaning that a slight raise above or decline, will cause the enzyme to stop working.


Denaturation- Denaturation is a co-operative process, if one bond breaks it causes a chain reaction, leading to all bonds breaking. In this event, the bonds broken are hydrophobic bonds, disulphide bonds and ionic bonds. ( Please refer to older post on amino acids and proteins to see how these bonds are formed).


pH affects the ionization of the enzyme. Functional groups such as the amine group can be dissociated into a anion or cation. Ionic baonds are mostly affected by pH.


The descending slope after the optimum pH shows enzymes being denatured. So we can also so as pH increase or decrease, of the optimum temperate, enzymes activity decreases.

Michaelis-Menton Curve


This curve shows how velocity varies with substrate concentration.

Assumptions to M-M curve.

  1. Relative concentration of enzymes and substrates ( [E] and [S]), all active sites are saturated
  2. Steady state assumption: The rate of formation is equal to the rate of substrate breakdown.
  3. Initial velocity, Vo, will measure rate at the start of the reaction. (i.e To = Vo)

Km, is a michaelis-menton constant. It is equivalent to [S]= Vmax ÷ 2. It reflects the affinity of the enzyme for that substrate. ( Higher the Km, lower the substrate affinity and vice versa.

Vmax, is the maximum velocity or rate at which happens when all actives sites are saturated.


Lineweaver- Burke plot.


A Lineweaver- Burke Plot is a double reciprocal plot. It is always in straight lines. The point of the line where y intercepts is know as Vmax. Notice how all labels are the reciprocal of their’ nomal state.


The lock and Key hypothesis was brought about Emil Fisher in 1894.  According to the video, enzymes are specifically shaped to match their preferred substrate. This hypothesis greatly shows the specificity of enzymes, however it does not explain the transition state that enzymes achieve.

Most substrates do not fit perfectly in the active site of enzymes. Daniel Koshland, 1958, proposed a new model, called the induced fit model. Enzymes being globular, flexible proteins, reshape their active site to better support the substrate they bind to. Bear in mind that, reshaping to fit the shape of the substrate does not permanently change the structure of the enzyme. The enzyme remains unchanged and ready to bind to more substrate.

There are six classes of enzymes and they should be learnt in this specific order:

  1. Oxidoreductases
  2. Transferases
  3. Hydrolases
  4. Lyases
  5. Isomerases
  6. Ligases

This is the order in which we assign an enzyme commission number (EC), which is a numerical number, based on the reactions they catalyse. For example, Adenosinekinase (E.C. is used to transfer a phosphate group from ATP. The two in the E.C number means that it belongs to the group transferases.


These enzymes catalyses all redox reactions in which oxygen or hydrogen are gained or lost.  Examples of these are peroxides, lactate dehydrogenase.


These enzymes are responsible for the transportation of functional groups of molecules such as amino groups, acetyl groups or phosphate groups. Examples of these are alanine kinase. (Kinase’s transfers phosphate groups)


These enzymes , affect substrates via hydrolysis. (i.e Adding water.) Eg. Lipase or sucrase.

Lyases break down molecules by removing groups of atoms without going throught the process of hydrolysis. For example, Oxalate dehydrogenase.


Enzymes of this class re-arrange the atoms of the substrate they bind to. Example, Glucose phosphate isomerase.


These enzymes combine two molecules together using energy received through the break down of ATP to ADP. Most common example, DNA ligase.

Time for enzymes.

Posted: April 2, 2013 in Biochemistry, Enzymes

Enzymes are large globular proteins that catalyse many biochemical reactions to sustain life. Most enzymes are proteins, while some are made up of RNA. Like all catalyst, enzymes work by lowering the activation energy for a reaction, this therefore increases the rate at which the reaction takes place.

Enzymes have three distinct features:

  • Catalytic power
  • Specificity
  • Regulation

Catalytic power.

Enzymes bind to molecules, known as substrate, and break them down or synthesis them into product. The number of substrate converted into product per enzyme, is called the turnover point or Kcat.


Enzymes are usually very specific proteins. This enables them to work extremely proficient.


Enzymes are not altered by the reactions they take part in. This allows them to continuously break down more and more substrates.