What are Proteins Made of?
Proteins are nitrogenous compounds present in living organisms. The protein molecule is large and made of blockchains of amino acids. The structural function of the protein molecule correlates to the properties of the amino acids that compose it. Meaning, proteins of similar function possess the same amino acid structure and composition.
Protein is present in different body parts like bones, hair, muscles, and other tissues. There are about 20 amino acids needed to form all the proteins in the human body, each of which is unique. The amino acid molecules consist of an amino group linked to a carbon atom, a carboxyl group attached to a hydrogen atom, and a side chain. The long chains of amino acids are held together by peptide bonds.
The side chain present in an amino acid can either be positively charged or negatively charged. Some amino acids, however, can have uncharged side chains. The side chains are an essential variable in the amino acid as they can bond together to maintain the shape and sequence of a protein molecule. The charged side chains can form ionic bonds, while the uncharged can form hydrogen bonds.
The side chains can form other bonds by interacting with each other with the help of weak van der Waals bonds. The interactions between the side chains guide the conformation and location of a particular protein.
Apart from the body functions of proteins, they also play a crucial role in drug production, catalyzing food, textile, developing vaccines, and detergent industries.
What are the four levels of protein structure?
The protein structure is vital to its function; for instance, the egg whites contain albumin, which is protein. The albumin gives the egg whites a specific shape because the amino acids present are hydrophobic and are held together by bonds. That’s why when you crack an egg on the pan, it has a specific shape, and heat destroys the bonds, denaturing the protein, and you have breakfast.
The confirmation of the protein has four structural levels, namely, primary, secondary, tertiary, and quaternary structures.
The primary structure is the most superficial level and is a sequence of amino acids in a polypeptide chain. Amino acids contain a basic group and an acidic carboxyl group, allowing the amino acids to join together and form long chains via peptide bonds.
A sequence with less than 50 amino acids is a peptide, while longer sequences are protein and polypeptide. A protein can consist of one or more polypeptides. The conformation of amino acids making a protein is encoded in DNA. A change in DNA sequencing will cause a shift in the protein’s amino acid sequence, which will affect its structure, shape, and function.
Protein synthesis involves transcription and translation with other modifications like glycosylation or phosphorylation. The processes are necessary for the protein to function as intended. The primary structure of proteins is made up of amino acids, while the biological properties attribute to the other protein structures.
The secondary structure of proteins or peptides is dependent on hydrogen bonding. There are two common types of secondary structures, the α-helix, and the ß-sheet.
In the α-helix strand, amino acids side chains can be extended outside. Hydrogen bonds formed between oxygen creating C=O bond and the hydrogen of each N-H group, four amino acids below it. The helix is made stable by the hydrogen bonds and the side chains in between N-H groups.
In the β pleated sheet, the hydrogen bonding is between the strands rather than within them. The bonding is inter-strands, not intra-strands, between the carbonyl and amino groups. The R-groups extend above and below the sheet. The two strands N-terminus to C-terminus can lie parallel or anti-parallel depending on whether the terminus lies in the same or opposite directions. The anti-parallel are more stable and more potent because the hydrogen bonds are well aligned.
Most proteins contain both α helices and β pleated sheets, some, however, some have one type of structure, and others possess neither.
The tertiary structure is a three-dimensional shape of a protein. The three-dimensional protein may seem irregular as the protein twists and bends to achieve maximum stability on low energy. The protein has stable bonds between the side chains of the amino acids.
The R-group interaction plays a part in the tertiary structure. The side chains contain carbon atoms that can vary and range from zero to nine. Identical charged side chains tend to repel while oppositely charged side chains attract.
The side chains of hydrophobic non-polar amino acids are mostly buried in the interior of the protein molecule like in phenylalanine or isoleucine, which helps them retain their aqueous physiologic state. The side chains form hydrophobic interactions with the alkyl groups of alanine, valine, leucine, and isoleucine while the aromatic groups like phenylalanine and tyrosine merge.
Disulfide bonds are a particular type of covalent bond between Sulphur containing chains and stronger bonds forming the tertiary structure. Formation of the disulfide bridges is on cysteine is vital in stabilizing and holding the protein together. Salt bridges between oppositely charged side chains help stabilize the tertiary structure of the protein.
Most protein molecules are of the primary, secondary and tertiary structures; however, other proteins are made of many polypeptide chains called subunits that make up the quaternary structure. The quaternary structure is dependent on how the subunits interact with each other forming larger complex proteins.
The subunits can be similar, homodimer or different, heterodimer. The protein shape is determined by the hydrogen bonding, disulfide bridges, London dispersion forces, and salt bridges; an excellent example of a protein with a quaternary structure is hemoglobin. Hemoglobin consists of four subunits, two α types and two β types.
Proteins are sensitive molecules with weak forces that denature easily when exposed to factors like temperature, metal ions, pH, hydrophobic surfaces, and shear movement. A denatured protein loses its biological function due to random folding and bending.
The protein structure is analyzed using advanced analytical equipment and products like those from Modern Biology which determine the molar ratios of the amino acids present. The sequences involve peptide mapping, Edman degradation, and mass spectroscopy. The stability of the protein is analyzed by unfolding the protein with methods like fluorescence, UV, infrared, and CD. The X-ray crystallography method of protein analysis involves placing solid crystals of the protein on an X-ray beam and using the deflected pattern to predict the atoms present in the protein crystal. The structure and stability of a protein molecule depend on its complexity and structure.