The protein is one of the essential elements in our body. The word protein is coined by Jons J. Berzelius the Swedish chemist in 1883 (Trehan, 1987). It is the polymer of many chains of amino acids. There are many proteins in and outside the cell of our body performing great task. Protein is classified under two major groups based on their nature: 1. Fibrous protein and 2. Globular protein. Probably the protein is made into different there dimensional structure by its monomers, amino acid sequence. Therefore proteins are different from one another in structure as well their functions.( Lodish, et al,2008)
There are 20 different amino acids in animals and plants which makes the protein. These 20 different amino acids are arranged in different sequence in polypeptide chain and are folded. So determines different functions in our body.
This assignments share the information on how does each amino acid sequence in a polypeptide determines the three dimensional structure of protein and basically it has explanation on how the precise three dimensional structure of each protein determines its function in a cell. ( Albert, et al, 2008).
How does the sequence of amino acids in polypeptide determine the final 3-D structure of the Protein?
Shape of protein is specified by amino acid sequence.
Irrespective of an animals or plants there are 20 types of amino acids in proteins, each having their unique chemical properties. So protein consists of long amino acid chains, having linked to one another by covalent peptide bonds. Hence proteins are referred to as polypeptides. There are countless proteins in existence in nature with their unique amino acid sequence ( Albert , et al, 2008). Usually a protein has a polypeptide backbone formed by repeating sequence of atoms along the polypeptide chain. The portions of amino acids not involved in forming peptide bonds are side chain of amino acid. This gives every amino acid different properties. Because some of the side chains are non polar i.e., hydrophobic and others are polar , hydrophilic (negatively or positively charged).
Although atoms never overlap each other in polypeptide chain, even then long flexible polypeptide chain of protein can get folded in many different ways. However protein folding is constrained by many weak non covalent bonds that exist between the chains of amino acid atoms and polypeptide backbones ( Albert, et al, 2008). Basically weak bonds are Hydrogen bonds, electrostatic attractions and Vander Waals attractions. Although the non covalent bonds are weaker than other bonds still then, when many weak bonds coming together on a same plane in parallel manner, this can hold two regions of a polypeptide chain together. So the combined strength of non covalent bonds as will help to maintain the stable folded shape.
In this folding the non polar side chains of amino acids like phenylalanine, leucine , valine, etc… are arranged in the interior of molecule as to avoid from water. As well side chains of polar amino acids are arranged in outside (surrounding of non polar amino acids) due to hydrophilic in nature. Thus forming hydrogen bonds with water and other polar molecules. So, these interaction results in giving the 3- dimensional structure of proteins, which is also determined by sequence of different amino acids in polypeptide chain. (Albert ,et al, 2008)
The folding of polypeptide chain into a structure of protein is maintained by hydrogen bonds( (Lodish, et al, 2008) represents the secondary structure, like alpha -helix and beta â€"sheet (Fig1 ). These two folds are common secondary structure of protein. The single folded polypeptide back bone form alpha helix, i.e., spiral structure as given below
Fig 1 Alpha helix structure (Albert, etal, 2008)
But left handed alpha helix is less stable than right handed alpha helix according to Bhagvan, 2002. This is due to the carboxyl oxygen atom of peptide bond being bonded to amide hydrogen atom through hydrogen bonding which is parallel to the axis of the helix formed between every 4th peptide bond (the N-H and C=O). Here the side chains of amino acids are not involved. Inside the alpha -helix amino and carboxyl group are all hydrogen bonded respectively. In a complete one turn of alpha -helix 3.6 residues is present. The stable helix holds its backbone in straight and helical shape, with its side chains pointing outwards the hydrophilic or hydrophobic quality of particular helix depends on side chain. As polar amino group the carboxyl group are involved in Hydrogen bonding in helix. The proteins that are soluble in water are hydrophilic on outside surfaces and opposite for hydrophobic helix. Examples of such proteins compounds are hair, skin, nails, etc… these structure are insoluble in nature, because alpha -keratin has hydrophobic amino acid residues and disulfide cross links. (Lodish, et al, 2008).
In alpha -sheet the hydrogen bonds are formed between adjacent polypeptide chains, regardless of their direction (Nelson & Cox, 2008). But parallel polypeptide chain form parallel beta sheet and antiparallel forms antiparallel alpha sheet as given below:
Fig 2 showing antiparallel beta formed by hydrogen bondin( Albert, et al, 2008)
These two sheets differ in same or opposite N-terminal and C-terminal orients respectively. Hence the structure of proteins restricts or limits the kinds of amino acids to occur in alpha sheet. As when two beta sheets are layered together inside the protein, the side chain or R group of amino acid residues on surfaces is comparatively small. So the sandwich formed by alpha helix and beta sheet in protein ,etc in protein gives the three dimensional structure of protein. For example like Silk fibroin / fibroin of spider webs. So this determines the different conformation of sheets (Nelson & Cox, 2008).
The three dimensional arrangements of atoms in protein constitutes tertiary structure (Albert, et al, 2008). This structure is maintained by ionic bonds, hydrogen bonds (Fig 3 ), Vander Waals forces and hydrophobic interaction as mentioned in Bhagavan,2002). This structure includes longer range of amino acid sequences. For amino acids in polypeptide sequence residing in several secondary structures perhaps comes together with completely folded structure of protein. The bonds in polypeptide chain are determined then direction and angle of bonds of different residues amino acids. What i mean to say is that different angle of amino acid structure and their direction in polypeptide chain gives different form of folded protein structure. Thereby leading to the different three dimensional structure of protein.
Fig3 showing the hydrogen bonding in peptide linkage.( Albert, et al, 2008)
The interaction of polypeptide segments are assembled in tertiary position by weak bonding interactions as stated above. Finally result in the formation of rigid tertiary structure (fig4). Which is the three dimensional structures of protein like globular protein and fibrous protein.
Fig4 showing secondary ,tertiary and quaternary structures.(Albert, et al, 2008)
The diversity of protein structure and how structure determines functions for protein
As we have seen in the earlier different protein consists of exact amino acid sequence which allows it to fold up into a particular three dimensional structures or shape to give different functions. Generally proteins are grouped into two major groups according to function: Fibrous and Globular ( Trehan, 1987). The fibrous protein has polypeptide chain arranged in strands or sheets and it consists of large number of secondary structures which constitutes alpha helix and beta sheet. All fibrous proteins are formed by many hydrophobic amino acids resides, outer as well as inside the protein. So they are insoluble in nature. By nature they are flexible and strong since the constituents of the protein are due to repeating secondary structure so this gives the rigid structure to the fibrous protein. There are many types of fibrous protein as alpha keratin, collagen, silk, etc are the structural protein which gives mechanical support to cells and tissues.
Collagen; The collagen helix constitutes unique secondary structure. It is left handed alpha helix having three amino acids resides per turn. This structure usually have repeating tripeptide unit, Gly-X-Pro or Gly-X-His,Pro, X can be any amino acid residue usually glycine is found due to the close junction between individual alpha chain. Thereby amino acid sequence and twisted quaternary structure of collagen gives close package of three polypeptides. Thereby tight wrapping of alpha chain in collagen provide great strength for mechanical support as shown in Fig5. (Nelson & Cox, 2000)
Fig5 The structure of Collagen and Elastin fiber (Albert,e tal,2008)
Elastin is also on of the fibrous proteins which gives the mechanical support.
Silk: this structure have antiparallel beta pleated sheet where, polypeptide chains are running parallel to fiber axis with close chain that runs in the opposite direction. This arrangement gives hydrogen bonding by peptide residues of one chain with neighboring chains forming the rigid structure. Thus giving support to the cell.
In globular protein the different segment polypeptide chains folds to form the globular structure of protein. In globular conformation polar amino acids chain tend be outside interacting with water and non polar amino acid side chains are buried inside since it being hydrophobic and never interact with water.(Albert, et al, 2008).As shown in the fig6.
Fig 6 Folded and unfolded polypeptide chains ( Albert, et al, 2008)
Example, blood protein has almost 60 proteins present in blood plasma they are like;
Serum albumin; this is globular protein having less alpha helical configuration and some more amount of tertiary structure. So this has high attraction for fatty acids and anions, where they bind to it and serve as transport or carrier protein. ( Conn & Stumpf, 1976)
Hemoglobin; carries oxygen in the blood to reach various cells. In hemoglobin the ring structure of protophyrin has iron atom bound within it. This also has perpendicular bond coordination that is bound to nitrogen atom of histidine residue. Other open serves as a site for absorbing oxygen molecules. Therefore Hemoglobin carries oxygen to various cells for respiration. Since it having open site of histidine where oxygen can bind (Conn & Stumpf, 1976)
Enzymes like ribonuclease is one type of globular protein which help to catalyze the hydrolysis of certain bonds in RNA present in the ingested food by animal. The 124 amino acids in polypeptide chain are arranged in alpha helical conformation and many segments contain beta conformation. It also has the four disulfide bonds between the polypeptide chains which provide the stability to protein structure. The side chains of amino acids in polypeptide chains come together to form active sites and rest are involved in protein folding. So the globular protein like enzymes have free active sites on the protein surface which helps binds with other molecules. (Nelson & Cox, 2000). Thereby enzyme bringing the catalytic reaction by enzyme by binding its free active sites with other substrate molecules.
Conclusion
Therefore the protein is one of the essential components in the body of animals as well as plants. Protein usually consists of 20 amino acids regardless of plants or animals.All the protein has their definite structure that has been made by the sequence of amino acids. In so doing different protein play various functions in the body of organisms. Without protein the functions of cells in the body would not be working. Hence protein is necessary for cells in the body to function. For instance the haemoglobin which is one of the globular proteins doesn’t reach the oxygen to the cell then cell would die, eventually the organism. Even protein is used as the source for the detection of diseases in the organism at molecular level. Thus protein function in the body is the vast knowledge.
