How Amino Acids Determine Three Dimensional Structure Biology Essay

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Proteins are the polymers of amino acids. They are made up of a large number of monomer units amino acids. The amino acids are linked together by the peptide bonds in a protein.

The linear arrangement of amino acids forms the primary structure of a protein. This linear sequences of amino acids sometimes folds at certain points in the polypeptide by the formation of disulfide bonds and hydrogen bonds. The structure formed is called as secondary structure of proteins.

When the secondary structure further folds due to the hydrophobic interactions and some other forces like hydrogen bonds, it results in the formation of complex structure which is now referred to as tertiary structure. The tertiary structure is also known as a three dimensional structures of proteins. We can see that the sequence of amino acids in the primary structure is responsible its final three dimensional structure.

The proteins perform different functions. Some act as carrier proteins (eg. hemoglobin), some as storage proteins (caesin) and some as signaling proteins. The function of proteins also depends on its structure. "The protein do not function if they are denatured from its native structure" (Lehninger , 1995).

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So the amino acid sequences of the polypeptide plays a vital role in determining the protein structure and finally its functions.

Protein

A protein is a polymer that is made up of many polypeptide linked monomers called the amino acids. This chain is often referred to as polypeptide chain. The proteins are the complex structures that under goes four levels of organizations; the primary structures , secondary, tertiary and quaternary structures. The monomers or the amino acids in a polypeptide are responsible for the structure of proteins. (Griffiths, 2008)

Different proteins have different structures which determine their various functions in the living system. For example the structure of hemoglobin is different from the keratin whereby they also perform different functions. As mentioned earlier, the protein or the polypeptide chain is formed of many monomers known as amino acids. These amino acids are arranged in a linear sequence linked each other by the peptide bonds. The linear sequence of amino acids joined together by the peptides, forms the Primary structure of the proteins. (David and Nigel, 2004).

For example, the first ten amino acids of human adrinocorticotrophin out of 39 is given below:

Ser - Tyr - Ser - Met - Glu - His - Phe - Arg - Trp - Gly ……….(Lehninger 1995)

When the backbone of polypeptide starts folding at some point, it forms a helical structure which is usually called as the secondary structure of the proteins. There are two most common form of secondary structures ; the α helix and the β pleated sheets.

• The α helix.

Fig. 1 (Source: Ophardt, 2003)

In this structure the polypeptide containing sequence of amino acids is wound in a helical manner around the imaginary axis drawn through the helical. In this structure the side chains or the R groups of amino acids are all positioned along the outside of the cylindrical helix. It has been found that there are 3.6 amino acids per turn of the helix and is 5.4 Š(Freifelder, 1986) long along the axis. Naturally occurring L-amino acids can form either right or left handed α helices.

In a polypeptide of amino acid sequence, the carbonyl oxygen of one amino acid forms the hydrogen bond with the hydrogen atom attached to the electronegative nitrogen atom of the fourth amino acid. Each successive turn of the helix is held to the adjacent turn by 3-4 hydrogen bonds (Freifelder, 1986) which stabilize the structure.

• The β pleated sheet.

The second type of secondary structure is the β conformation. Unlike the helical structure the polypeptide chain is formed into zigzag conformation. The zigzag polypeptide chain can arrange side by side in the form of series of pleats and hence it is known as β pleated sheet which are cross linked by interchain hydrogen bonds." The peptide linkage of the amino acid sequence also participate in this cross linking and provide greater stability" (Lehninger,1995).

The hydrogen bond are formed between the adjacent amino acid of a polypeptide. The side chains of the adjacent amino acid comes out from the zigzag structure in the opposite directions. The two segments of the polypeptide chain can form two types of β structure depending on the relative orientation of the segments.

• Parallel β pleated sheet.

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Fig. 2

If both the segments are aligned in the same direction, either from N-C terminal or from C-N terminal direction, it is said to be in parallel condition.

• Anti parallel β pleated sheet.

Fig. 3

(Source: Chodges, 2006)

If the two segments move in the opposite direction, that is if one segment is directed from N-C terminal and the other from C-N terminal, it is said to be in anti parallel form. (David Freidler,1986).

Tertiary structure.

Fig 4.

The third level of structure of protein is the tertiary structure. The extensive folding of backbone of polypeptide, where the amino acid that are far apart in the linear sequence and as well as those that are adjacent are connected to form a structure known as the three dimensional structures. The tertiary structure of protein is determined by its amino acid sequence. This was proved by the experiment, that the denaturation of some proteins are reversible through the process called renaturation.

"For example the denaturation of ribonuclease by exposure to concentrated urea solution in presence of reducing agent loses its catalytic activity. The reducing agent break down the four disulfide bonds and the urea disrupts the stabilizing hydrophobic interactions thus unfolding the polypeptide. But it was found that when urea and reducing agent are removed, the ribonuclease refolds by forming disulfide bonds and in the same position as that of its nstive structure".(Nelson and Cox, 2003). This shows that the 3D structure of ribonuclease is due to the disulfides bonds formed by the cystein residues and hydrophobic interactions of the amino acid sequence in a polypeptide chain. It was also found out that the amino acid sequence in a polypeptide chain contains all the information required for protein folding into its native structure.(David and Michael, 2003).

Some protein lacking disulfide cross link can also refold into its native structure after denaturation. Afinsen and his colleagues found out that the nuclease from staphylococcus cells losses its biological activities at pH-3 but when restored to pH-7, it regains its activities. This shows that the amino acid sequence specifies the distinctive tertiary structure.(Lehninger,1995).

The most important interactions responsible for tertiary structures are:

• Ionic bonds between oppositely charged groups in acidic and basic amino acids.

• Hydrogen bonds.

• Hydrophobic interactions.

The disulfide bonds and hydrophobic interactions bring the distant amino acids together. Van der waals forces produce specific interactions between the clusters of amino acids in a polypeptide (Freifelder,1986). All these factors are responsible for stabilizing the 3D structure of proteins.

A human being produces over 50000-100000 different proteins(David and Michael, 2003). Each protein has a unique 3D structure and the structure gives it a unique function. Each protein has unique amino acid sequence and its plays a fundamental role in determining the 3D structure of protein and finally it's function.

It was clear from the above described experiment that when a protein is denatured by some denaturing agent, it loses its biological activity completely, but regains its function on removal of denaturing agents. This explains that the complex structures are responsible for the function of the proteins.

For example the shape of the enzymes is very specific to the shape of its substrates. The shape of the enzyme should fit completely into the substrates to catalyze the reactions or else the reaction is inhibited.

Also the hemoglobin and myoglobin both functions as a oxygen carrier in blood and muscles respectively. Both these proteins contain heme prosthetic group to which the oxygen binds." In myoglobin, the heme prosthetic group is non covalently bound to it and is essential for its activity. The four polypeptide chains in hemeglobin, two α and two β are bound together tetrahedrally to form spherical shape as shown in the figure below. The α helices can bind four molecules of oxygen "(Hames and Nigel, 2004).

Fig. 5 (Source: Diwan, 2008)

Lipoproteins transport water insoluble lipids and cholesterol in our body. It has the hydrophilic group facing outsite. Triglyceride fats and cholesterol ester are carried shielded from water by the phospholipid monolayer and the apoprotein as shown in the figure above. (Diwan, 2008)

There are two major groups of protein which are differentiated based on their structures.

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• A protein which is long and thin is the fibrous protein.

• The spherical protein in which the α helices and β structures are short and interspersed with randomly coiled region and compact structure forms the globular proteins.

Fibrous proteins.

The fibrous proteins are typically responsible for the structure of cells, tissues and organisms. Some of the fibrous proteins are collagen (protein of tendon, cartilage and bone), elastin, silk, and keratins (proteins of hairs and nails).

• Collagen

Fig. 6 (Source:Mcdarby, 2009)

It is the major protein component of tendon, cartilage, bone, skin and blood vessels. It provides tensile strength. It consist of three polypeptide chains. These three polypeptides come together to form a triple helical structure held together by hydrogen bonds. In tendons, it forms rope like fibres of high tensile strength and in skin it forms fibres that can expand in all directions providing strength (Hames and Nigel, 2004).

• The Keratins

Fig. 7

It is the protein of skin, hairs, wool, scales, feathers and nails which provide strength. The α keratins contain cysteine residues and hence contains many disulfide bonds.the α keratin is a helical structure. The two strands are wound about each other to form super twisted coil. This supertwisting provide the overall strength to the structures.

Globular protein

Fig. 8

In this type of proteins, the polypeptide chains are tightly folded into compact spherical or globular shapes. They usually functions for cell mobility. This includes transport proteins such as hemoglobin (transport oxygen in blood) and myoglobin (transport oxygen in muscles), the contractile proteins such as myosin (thick filament of myofibril) and actin (thin filament of myofibril) and the storage proteins such as ovalbumin (egg white protein) and casein (milk protein). (Lehninger, 1995).

Conclusion

We have by now found out that the final Three Dimensional structure of proteins is the result of its amino acid sequence in primary structure, because we found out that the forces responsible for stabilizing the 3D structure such as hydrophobic interactions and hydrogen bonds are as a result from the amino acids sequence in its polypeptide. So the sequence of amino acids is very important for determining the 3D structure.

Also found out that the structure determines the function of various proteins. Different amino acid sequence has different structure which in turn has different functions. For example the hemoglobin is different from casein. The former is a carrier protein and the later is a storage protein. They have different structures and hence they functions differently.

Therefore we conclude that the amino acid sequence determines the structure of the proteins and in turn structures determine the respective functions of the proteins.