Biochemians unite!


Reflection 4- Amino Acids and Proteins Part 2

Hello everyone!! Rakeeru here to talk to you more about the structures of PROTEINS yes! PROTEINS again Oops. Don’t be sad this part is pretty much interesting. I’ll try my best to concise the knowledge that I gained from reading and watching our lecturer‘s YouTube video! Well let’s get started, yup, yup, yup!!!

Okay so the first level of proteins is the primary structure that consists of the sequence of amino acids in the polypeptides chain that was transcribe from genetic material.  ALL proteins contain a primary structure. It is essential that we know about the primary structures of the protein since it helps us in determining genetic diseases and abnormalities.

Primary Structure!

Primary Structure!

The secondary structure consists of two types, the alpha helix and beta pleated sheets. Let’s start with the alpha helix. Alpha helix is the most common helix. They appear to be in spiral form.  The helix is made up of a polypeptide chain; R groups are on the outer part of the peptide backbone. This arrangement allows for reduced steric interference that can destabilize the structure. Each turn holds 3.6 amino acids. The diagram below illustrates the structure of the alpha helix…see, it is not that difficult :). Notice that the hydrogen bonds from the amide are attached to the oxygen from the carbonyl group. With this bonding arrangement, the hydrogen bonds is in abundance as they stabilize the structure.

Alpha helix and beta pleated chains

Alpha helix and beta pleated chains

All amino acids are capable of bonds within the chain however there are some amino acids that disrupt the chains.  Let’s take proline for instance. When it bonds to the helix it does not have a hydrogen on the alpha amino group to donate, therefore it leaves residue which forms a “kink” and creates InStaBiLitY (destabilizes the structure). Some other amino acids that destabilize the helix are Aspartate, Histidine, Lysine, or Arginine as these are relatively too large  and obviously cannot make the 3.6 turn. They form ionic bonds or electrostatic repulsions or attractions between amino acid residues with charged R groups. With respect to bulky side chains such as Isoleucine, the branch from the β-carbon in the R group can impede the formation of the α-helix if they are plentiful.

Beta pleated sheet… have you ever wondered why that name was given? Well it’s obvious the structure appears to be pleated 😛  Like the alpha helix, the beta pleated sheet is made up of covalent peptide bonds and inter-molecular hydrogen bonds. The chains that make up this structure can either be parallel (where all the carbon and nitrogen terminals are on the same side) or antiparallel, where they are alternating in nature.

Interestingly, Alpha helices always have a right handed curl… just a fun fact I guess. lol. The thing about secondary structures is that they maximize the amount of hydrogen bonds in there structure hence stability is high!!!

Tertiary Structures are quite complex. When we talk about the tertiary structure, we are speaking about the folding of the secondary structure of the polypeptide. NOTE that tertiary structure is not as stable as primary and secondary, but tertiary structures can be stabilized by FOUR TYPES OF INTERACTIONS!!! They are the Disulfide bonds (that are the strongest since they are covalent in nature!), hydrophobic interactions which are the most important intermolecular bond, Hydrogen bonds and Ionic interactions.

First up the disulfide bonds… okay here goes…. This is formed when two cysteine residues containing sulfhydryl groups come together. An oxidation reaction occurs and a cystine molecule is formed where the amino acids are connected via a disulphide bridge. As Trav mentioned before lol.


The Four Types of Bonds!

The Four Types of Bonds!

Hydrogen bonding always the helpful guy ya know.  Easily gives away its one electron, what a helpful little guy. Okay a good example is glutamate and serine. The serine from Hydrogen  willingly donates its electron to oxygen from the carbonyl group in glutamate.

Serine Hydrogen bonding!

Serine Hydrogen bonding!

Hydrophobic interactions basically are the water hating bonds that are in the interior part of the tertiary structure.  With this being said, if a globular protein is placed in water, folding occur independently where the hydrophilic regions reaches outwards and the hydrophobic remains inwards.

Last but not least the Ionic interactions which are the bonding between a negatively charged atom of an R group and a positively charged atom of another. Example: Asparate and lysine. 

So we talked about how the tertiary structure have four interactions which encourages folding to occur. What about if I wanted to unfold the protein? Unfolding a protein can be accomplished by heating or using reagents(organic) such as strong acids or bases, detergents, etc .

The behavior of the protein after unfolding…..BAD NEWS!!!  The protein begins to fold in stages during its synthesis, rather than waiting for synthesis of the entire chain to be totally completed. But it gets better there this little guy Chaperones he does the magic ie. He ensures that there is proper folding.

Unfolded Protein!

Unfolded Protein!

The quaternary structure of a protein occurs when the tertiary polypeptide chains link together via the same inter-molecular bonds as the tertiary structures.

One major issue that captured my attention was aging ( Yea, it’s an issue for me).  Men and women produce collagen daily. It provides us with structural support for our skin. As we age the collagen is lost and denatured. The appearance is not quite wanted as it disfigures the face in other words sagging, wrinkles occur. However, studies have shown that aging process can proceed at a slower rate. Doctors recommend supplement pills (contains collagen) that will help in the building up sufficient amount of collagen to prevent sagging. In conclusion we cannot prevent the process of aging but we can use supplements to help. Well I ‘m out for the day. Next up is Shiv shiv to talk about Enzymes! Rakeeru out!

Rose Dawson... Old and Young Comparison from Titanic (1997)

Rose Dawson… Old and Young Comparison from Titanic (1997)

Picture References:

Rose Dawson-

Unfolded Protein-

Hydrogen Bonding with Serine-

Four bonding types-

Alpha helix and Beta pleated chains-

Primary Structure-

Publish Paper Review 1-Exercising and Synthesis in Muscles (Workout under the skin) by Shiv Shiv


The purpose of the review is to relay to one how muscle protein turnover is regulated in humans during strenuous physical activities and how it is affected by environmental factors, such as nature of nutrients, the natural differences between males and females, the rate of production of proteins and getting older. Strenuous activity can be classified as exercise. Furthermore, exercise can then be subdivided into resistance and non-resistance types. Exercise alters the state of your muscles which are built from proteins, so during exercise, “muscle protein synthesis” (MPS) and “muscle protein breakdown” (MPB) occur. MPS is the process by which damaged or exhausted proteins from muscles are replaced by that which is regenerated or synthesized from our biological units (cells). This is depressed by both resistance and non-resistance exercise, that temporarily inhibits protein synthesis. MPB is the degradation of proteins into polypeptides or amino acids by the process of hydrolysis or the activity of the proteases enzymes on peptide bonds. This natural process of breakdown remains constant during exercise. After physical activity, a stage synonymous with the term ‘fasted state’, MPS & MPB are elevated and there is a negative balance in the net muscle protein. A reverse in this trend, where a positive net balance can occur once more, is if there is increased amino acid availability which would inevitably cause a rise in MPS. The postexercise period is when there is improved amino acid availability which allows the net muscle mass to increase, but only if there is a high quality protein intake of 15 to 20 grams. This would allow full absorption for accretion of muscle mass. The natural responses of the body to feeding, exercising and protein synthesis are reduced to such an extent with age that little impact is made on our anatomies with respect to muscle gain. Young women and men have been proven to possess few differences pertaining to muscle building and exercise. Conversely, reports suggests that a difference clearly exist in the muscle protein turnover when concerning elderly women who have underwent menopause.


  Many aspects of this topic grasped my attention, even the strong science which at some time proved to be a puzzle without a solution lol. I am certain I wouldn’t retain everything I’ve encountered when doing the review of this paper but I will remember general concepts that is now one with my thinking…. My time spent exercising now is appreciated much more as I understand what is behind the reasons I may feel sore and get bigger lol yea rite, but now I have grasped the theory behind muscle building and what occurs beneath the skin where all the real hard work is being done. I know now I’m going to have a higher protein diet after gym. 😀 It really is something to think about… I even have the urge to dig deeper to satisfy my newly awaken curiosity… I am going to do just that! 🙂

Shiv Shiv over and out!!!

I want you to exercise


Kumar.V, Philip.A, Kenneth.S, and Michael.J.R, 2009. “Human muscle protein synthesis and breakdown during and after exercise.” Division of Clinical Physiology, School of Graduate Entry Medicine and Health, Uttoxeter Rd., Derby. Accepted in final form17 January 2009.

Picture references:


Sexy Lady exercising pic-

I want you to get some exercise-×300.jpg

Reflection 3- The Powerful Proteins!!!


Hello everybody!!! This is your boy Trav here! Just stopping by to reflect on the past week of what went down. Well this week was all about proteins, proteins, proteins… oh and can’t forget those amino acids… the building blocks that make up these proteins! So I was so glad to hear that I was given the privilege to reflect on this wonderful topic of proteins. In fact I am very intrigued by proteins at the moment, especially since I recently joined the gym and stuff… and well you know a lot of protein is required in my diet! So the word protein may have special meaning to some; for me it is for Biochemistry and for my muscle building!

gym, bodybuilding pic

So I have been rambling on about this word protein, but what is a protein you may ask? Well a protein is a folded substance that is made up of many amino acids that are linked together by peptide bonds. A peptide bond is simply a condensation reaction where there is a loss of that chemically equivalent to a water molecule and a linkage is formed.

A Peptide bond!

A Peptide bond!

Proteins comes in different levels. These levels include: primary, secondary, tertiary and quaternary structures. Not all proteins make it to the tertiary and quaternary structures though. The primary structure of proteins are basically the sequence that the amino acids are bonded. The secondary structure involves the arrangement of the polypeptide chain to form the alpha helix or beta pleated sheets via Hydrogen bonds ONLY. The tertiary level occurs when these polypeptide chains bond to one another and start to fold. Tertiary structures are held together by four types of bonds. These include: hydrogen bonds, ionic bonds, disulphide bridges and hydrophobic interactions. A great example of these are globular proteins and most enzymes are globular! And finally quaternary, this occurs when tertiary proteins are combined. A great example is haemoglobin in blood which has four globular proteins that surrounds an iron ion (lol) within a haem group.

A haemoglobin molecule and the haem groups!

A haemoglobin molecule and the haem groups!

Now, I am sure you are wondering what amino acids are and what they are made off. Well amino acids are the building blocks of proteins as stated previously and they are made up of an amino group, carboxylate anion, a hydrogen and an R-group, all bonded to a central alpha carbon. To make things easier to comprehend I have put a diagram showing this below.

Can you guess which is the alpha carbon?

Can you guess which is the alpha carbon?

Now you may be thinking how do amino acids differ from one another? Well basically the R-groups on each amino acid are different, for example for glycine; it only has a Hydrogen atom as its R-group and it is the smallest while the second is Alanine, with its CH3 R-group. There are 20 different amino acids, so essentially 20 different R-groups.

I remember in one of my lectures, our lecturer was pronouncing cysteine sort of funny. He told us that we would understand the reason why in a few minutes and surely I understood why when he started to explain the bonding of two cysteine to form cystine. I think u can see why now too o_O lol!

The bond between the 2 cysteine to form cystine is a disulphide bridge or disulphide linkage and it is an oxidation reaction that takes place. An oxidation reaction is when there is a loss of electrons or in this case the loss of 2 hydrogens, one from each cysteine. It is a reversible reaction so that means that a reduction reaction can take place to reform 2 cysteine from cystine. A reduction reaction is basically gaining electrons/ hydrogen for this case… so the opposite of an oxidation reaction.( please don’t be mind-boggled, refer to the picture below lol)

cysteine and cystine

Then he went on to talk about the amino acids that are essential to us. I made a list of them below:

  • Arginine– our lecturer sparked my interest when he talked about the uses and importance of this amino acid and so I did some research that I would like to share with you a little later.
  • Isoleucine
  • Leucine
  • Histidine
  • Methionine
  • Threonine
  • Tryptophan
  • Valine
  • Lysine
  • Phenylalanine

Just to recap, there are 20 amino acids but these are the 10 essential amino acids that we have to get from our diet as adults (we cannot make them on our own!!!). Oh and to clarify, ALL 20 amino acids are important but the 10 above can only be gained from the diet and nutrition you eat while the non-essential can be synthesized by your body. My lecturer then talked about how it is possible to create non- essential amino acids in the lab that we will see next year! Can’t wait for that! So excited!

I have then learnt that there are two types of proteins, complete and incomplete. Complete proteins are those that contains all the essential amino acids. A good source of complete proteins are from animals (meat). Incomplete proteins are those that do not have all the essential amino acids and a common example are vegetables while an exception to this is beans which are considered a complete protein (Lucky for you vegetarians!).



So I am sure you are wondering how you test for the presence of proteins or amino acids in a food sample or substance? Sorry, it can’t be done in the kitchen! Must be done in the lab lol. Well I learnt that the Ninhydrin test is used to test for the presence of amino acids (usually colourless before). For a positive confirmation of amino acids present, a purple colour would be seen.  There is one amino acid that gives a yellow colour instead of purple and it is Proline. Proline is special in that it forms a ring structure due to the R-group bonding with the amino group and so the N is not free to react with the Ninhydrin. This means that no ammonia is formed and therefore the purple colour is not created. Oh and I would like you to note that this is a test for AMINO ACIDS not for proteins! My lecturer really stressed on that point and he explained it was because you cannot use Ninhydrin to find the presence of proteins. Some interesting facts I found on Ninhydrin… There is a Ninhydrin spray that is used on crime scenes to see and visualize fingerprints that contains trace amounts of amino acids.

Diagram of Proline showing the bonding of the R-group to the amino group to form a ring structure

Diagram of Proline showing the bonding of the R-group to the amino group to form a ring structure

Are you curious to know what the test for proteins are? Well, the Biuret test is common for testing the presence of proteins in a sample. For a positive Biuret test, the colour changes from a light blue due to the Cu2+ ions in solution to a purple colour. What happens is the Biuret reagent reacts with the polypeptide chain of the proteins which forms a complex that has a strong purple colour.

Before I leave your presence, remember that I said that I have some information to share with you about Arginine? Well Arginine seems to have some very interesting uses when it comes to body building and muscle growth! Arginine is considered a precursor to nitric oxide which is a vasodilator since it helps to relax and widen blood vessels. This helps with improving the circulation of blood flow to the muscles during workouts. This means that you would get a better supply of the much needed energy! It helps with muscle growth as it is needed for the production of most proteins. L-arginine promotes the release of hormones and fat metabolism. This results in well-toned muscle mass since it reduces the fat stores under the skin and therefore promotes muscle growth. Interestingly enough, Arginine also helps boost the immune system (way to put the icing on the cake). This is excellent as continuous physical activity can lead to overtraining which can cause minor illnesses. Well that’s it for Arginine and from me. Hope you find this interesting as I sure did! Lol. Look forward to part two on proteins from my good friend Rakeeru! Laterz and until next time! Trav out!


Picture References:

  • Proline diagram-
  • http://
  • Beans picture-
  • Haemoglobin molecule-
  • Peptide bond diagram-
  • Body building logo-
  • 2 Cysteine forming Cystine-
  • Amino Acid Structure-–U-fUdPOJEtDzVGgDY_/aminoacidstruc.jpg