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Pap Pap Papain….

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This post is just to share a recent experiment I did but before we get to that lets just take a minute and look at this logo.

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To my knowledge this logo is misleading firstly the mixture they have is not 100% pure protein as the side of the box says it contains 15mg sodium in addition to 6g of proteins but I’m not here to argue that look at the back of the box.

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It says , “Indulge gelatine contains important proteins for healthier skin, hair and nails.”  This is misleading since we all know that gelatine is a hydrolysed form of the protein collagen and even though collagen does make up our skin and connective tissue we know that it is keratin that makes up our hair and nails and karetain and collagen are 2 completely different proteins.

  1. Collagen is made of 3 peptide chains which are left handed helix. These 3 helices are then coiled into a right handed coil (triple helix) forming the collagen structure. The peptide chains are predominantly made of glycine and proline and they both serve special roles within the molecule. Glycine works to stabilize since it is the smallest amino acid it fits on every third position of the chains which end up in the interior of the collogen structure or the center of the triple helix. Proline because of its cyclic structure aids in the formation of the coils in the triple helix structure of the collagen, since proline changes the direction of the chain due to is lack of maximum h bonds that can be formed.
  2. Keratin is a fibrous structural protein of hair, nails, horn, hoofs, wool, feathers, and of the epithelial cells in the outermost layers of the skin. The polypeptide chains of keratin are arranged in parallel sheets held together by hydrogen bonding.Of the amino acids in keratin, cystine may account for as much as 24 percent. The numerous disulfide bonds formed by cystine are responsible for the great stability of keratin: it is completely insoluble in hot or cold water and is not attacked by proteolytic enzymes (the enzymes that cleave protein molecules).

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Gelatine is made from collagen thus according to the research it is rich in Proline and glycine both of which are non essential amino acids meaning our body makes them we do not get them from our diet….. thus the box is misleading, Further more it says that the gelatine is important for hair and nails and since we know that keratin is responsible for hair and nails and keratin is mainly made of  cystine molecules the box is again wrong. (If it was made of cystine and keratin the following experiment would not have work as stated proteolytic enzymes such as papain doesn’t work in it)


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Now the video which i made based on the enzyme papain and how it works (its my first video so please feel free to give any tips)…..


Enzymes

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“So enzymes are biological catalysis that speeds up chemical reaction via providing an alternate pathway with lower activation energy.”JM

Remember from my protein post we can see that enzymes are proteins but are all enzymes proteins?

Nope…. some are RNA molecules called ribozymes and then we can also use some antibodies called abzymes (but also proteins).

Do we need a faster reaction why not just wait for it to happen naturally?

Well the answer to that is because you will die  :/ see some reaction within our bodies may take up to a trillion years if enzymes were not involved , according to Dr. Richard Wolfenden a distinguished professor of biochemistry, biophysics and chemistry at the University of North Carolina without a particular enzyme, a biological transformation he deemed “absolutely essential” in creating the building blocks of DNA and RNA would take 78 million years.

Can you believe that? Obviously we would be a cluster of carbon in the ground by that time however because of enzymes this reaction and many more can take place in a matter of milliseconds. Wolfenden also said “Without catalysts, there would be no life at all, from microbes to humans,” and this is certainly true.

We can show how enzymes work on a simple graph like the one below where we see how enzymes physically lowers the activation energy and as you should know the activation energy is the energy need to start the chemical reaction and a lower activation energy allows the reaction to take place faster.

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So how exactly do enzymes work??

Enzymes attach to substrate via there active site and a molecule called an enzyme substrate complex is formed, this complex then quickly breaks down to form the product as well as the original enzyme. During this reaction bond or formed and broken and it is important to note that the enzyme substrate complex or intermediate has the highest energy since this is where the chemical reactions take place. We should also appreciate that there is no change to the enzyme, the enzyme remains the same after the reaction as it was before and when the product releases the enzyme moves on to another substrate molecule.

NOTE:

The active site is a cleft in the enzyme’s protein structure formed by the folding of amino acid residues, each active site is different this is because each enzyme contains a different protein structure and the properties of the active site that facilitate the combination of the substrate is due to the R groups of the proteins within the active site cleft, creating a complementary shape to the substrate that they bind to. Enzymes DO NOT make permanent bonds to substrate instead they bond via weak temporary bonds.

 

There are main theories about how enzymes and substrates react and bond:

1) Fischer’s lock and key hypothesis

This was developed by a scientist named Hermann Emil Fischer and he basically said that each enzyme it’s substrate fits perfectly together and complement each other forming the enzyme substrate complex and then the products which is a different shape from the substrate. The enzyme therefore acts as a lock and the substrate the key and only the key (substrate) for that lock (enzyme) would work or react to form a product. Once the products are formed they are released from the active site.


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Although from this theory we can see that enzymes are highly specific and can only react with a certain substrate which must be perfectly complementary it is too strict as we know that this may not be the case in nature as most molecules are not perfect copies of each other thus another theory explains how enzymes react in this situation.

2) Koshland’s Induced fit hypothesis

 This theory states that contrary to fischer’s theory all the enzyme’s active site and substrate are not perfectly complementary, they vary slightly however as the substrate approaches the enzyme changes the shape of its active site to fit the substrate and so the enzyme substrate complex is formed and the products are formed and released. This theory shows that enzymes are flexible and conformationaly dynamic molecules.


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Michealis –Menten Curve

 

The reaction between enzymes and substrates can be expressed on a curve call a michealis –menten curve and this curve plots the velocity of the reaction against the substrate concentration (velocity is the amount of product formed per unit time or the amount of substrate being consumed).  As the enzymes start to bind to the active sites the velocity increases and when all the active sites are occupied the graph remains constant, this point is called vmax and the enzymes are said to be saturated. This graph keeps all variables constant except the concentration of substrate. This graph forms a hyperbolic shape.

NOTE: This graph only shows the reaction for michealis menten enzymes of enzymes with one actives site present.

If an Allosteric enzyme were to be observed and plotted on the graph it would give a sigmoidal shape. Allosteric enzymes are those with more than one active site.

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The black line shows the curve for an enzyme with one active site or a michealis –menten enzyme while the red show the curve for an allosteric enzyme.

This was the end of part one and honestly I never knew this much about enzymes who knew right… during cape (Alevels) we didn’t do much on enzymes unlike that of previous topics so this was all new to me but I coped well and I hope these notes help you . My next post will be a direct continuation from this and after that I will post 2 experiments I conducted recently …. Stay tuned hope you like 🙂

http://learning.covcollege.ac.uk/content/Jorum/MET_Enzyme-control_LM-1.2-05FEB08/page25.htm

http://www.med.unc.edu/biochem/news/without-enzyme-biological-reaction-essential-to-life-takes-2-3-billion-years-unc-study

http://www.activemotif.com/

Proteins

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Proteins
In the last post we established that proteins are made of a polypeptide chain/s and each protein is different due to the sequencing of the amino acids within the polypeptide chain. We also learned that in order to be called a protein the chain/s must have a molecular weight of over 5000g/mol. So let’s just get to it 😀
Importance of protein
Proteins are VERY important we are primarily made of proteins and they can be found in every aspect of our body, they can be used for :
Defence:

Antibodies are made of proteins and are used to protect our bodies from antigens by immobilizing them so they can be dealt with bywhite blood cells.Antibody

Movement:
Our muscles are made of proteins which can be easily contracted and relaxed which allows us to move.

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Enzymes:
Very importantly enzymes are proteins that regulate and catalyse chemical reactions within our bodies and are very specific and efficient some speed up reactions by almost 100% .

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Hormones:
Most hormones are made of proteins and act as messengers to help induce bodily activity example insulin for blood glucose concentration maintenance.


Structural support:
Fibrous proteins such as keratin and collagen act as support for connective tissues in ligaments as well as in structure such as hairs, feathers, quills etc.
The hard exoskeleton of insects is made of a glycoprotein called chitin.

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Storage:
Such as the “yolk” of eggs which is made of the protein Ovalbumin which acts as a food store for that developing foetus.

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Transport Proteins:
That help transport molecules around the body the most famous being haemoglobin and mayoglobin. As well as Cytochromes that act as a carrier protein in the electron transport chain.


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In other words Proteins are very important and can be found everywhere!!


Levels of Protein Structure:
Proteins can generally have 4 structures:
1) Primary structure:
The actual sequence of the proteins along the chain eg.
[-Serine-Alanine- Leucine-Leucine-Tryrocine-]
Or [-S-A-L-L-Y-]

(see what I did there )

2) Secondary Structure:
This is where the interesting stuff happens; here folding starts to take place and the alpha helix or beta sheet are formed.

Alpha helix – a rod like shape, the primary structure coils and this folding occurs due to hydrogen bonds being formed between the carbonyl oxygen on the pepide bond and the Hydrogen on the amino group. Hydrogen bonds are formed nearly parallel and the side chains or R groups of each amino acid are on the outside of the spiral.
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NOTE: the alpha helix is mostly dominant due to the maximum use of hydrogen bonding since every peptide linkage (except those on the ends) takes place in H bonding. This enormous amount of bonding gives the helix structure stability.
Proline is not welcomed because it is cyclic and so one of its hydrogen is not available for bonding thus it forms and uneven number of bonds and the structure bends or leans in that direction.
Glycine is also not welcomed because it has a high “conformational flexibility” simply meaning it destabilizes the alpha helix and this is due to the fact that glycine’s R group is H.
Bulky or large R groups destabilise the alpha helix.

Beta pleated sheet- hydrogen bonds form between peptide bond on the same chain or different chain on a horizontal plane. There are parallel and anti parallel sheets.
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3)Tertiary Structure
Here it gets more interesting as all the different types of bonding start to take place as side chains interact. The protein folds in on its self and forms: hydrogen bonding, salt bridges, disulfide bonds, and non-polar hydrophobic interactions.

Just so you understand how the bonding works:

Disulfide bonds

Oxidation of the sulfhydryl groups on cysteine. Different protein chains or are held together by the strong covalent disulfide bonds.

Hydrogen Bonding:

Where bonding occurs between two alcohols, an alcohol and an acid, two acids, or an alcohol and an amine or amide side groups.

Salt Bridges:
Salt bridges result from the neutralization o

f an acid and amine on side chains. Interaction is ionic between the positive ammonium group and the negative acid group. Any combination of the various acidic or amine amino acid side chains will have this effect.

Non-Polar Hydrophobic Interactions:
The hydrophobic interactions of non-polar side chains are believed to contribute significantly to the stabilizing of the tertiary structures in proteins. The non-polar groups mutually repel water and other polar groups and results in a net attraction of the non-polar groups for each other. This results in the non-polar side chains of amino acids being on the inside of a globular protein, while the outside of the proteins contains mainly polar groups.
(http://www.elmhurst.edu/~chm/vchembook/567tertprotein.html)

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4)Quaternary Structures

Here 2 or more polypeptide chains interact to form large structures one such is haemoglobin. However not all proteins consist of a quaternary structure.

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