Proteins: Differences In The Structures Of Primary, Secondary, Tertiary & Quaternary Proteins
What are Proteins? How does the Structure of Primary, Secondary, Tertiary & Quarternary Differ?
The series of monomers used to assemble proteins from peptide bonds are amino acids, which consist of an alpha carbon atom, carboxyl group, and hydrogen atom (Mrgscience, n.d.). In contrast, given there are four different levels of structure in a protein, structures differ depending on the protein’s function. The sequence of the molecules in simple proteins, e.g. albumins, (alpha-amino acids, an amino group, a carbon atom, a hydrogen atom, a carboxyl group, and a variable group), is an example of a primary structure (Bailey. R, 2019). The interaction of the protein with other proteins here is contingent on the folding of the polypeptide chain which provides the protein with its original 3D shape.
The secondary structure refers to the interactions between neighbouring amino acids when the protein begins to fold. Common elements found in these secondary structures are alpha-helix and beta-pleated sheets (Courses Lumenlearning, 2013). Hydrogen bonds mechanically stabilize the α-helices which form when an oxygen atom bonds with a carboxyl group and a hydrogen atom in the polypeptide backbone in an amino group (BYJUS, n.d.). Consequently, the amino acids fold into a helical structure that resembles a curled ribbon. β-pleated sheets arise when an amino group and a carboxyl group from intermittent planes of amino acids align in the opposite direction which is covalently linked by hydrogen bonds (Sarkar. D, 2019). DNA possesses a secondary structure because not only is its double helix a 3D composition, but the nucleotides concurrently additionally employ hydrogen bonding.
The 3D shapes the polypeptide chain evolves into is the tertiary structure, which is influenced by the hydrophobic interactions, hydrogen bonds, salt bridges, and disulfide bonds in a protein (Lubrizol Life Science, 2019) (Zoology Notes, 2017, Figure 8.70. Bonds that sustain the tertiary structure of proteins). In applying the solubility rule, given polar amino acids are hydrophilic, they are often found on the surface of proteins as they make proteins soluble in aqueous solutions. Whereas, nonpolar hydrophobic amino acids, which repel water tend to lie in the interior of the protein. Salt bridges refer to the adjacent positioning of oppositely charged side chains which form when an amino acid and amine acid neutralize (Lodish. H, Berk. A, Zipursky. S. L, et al, 2000). Throughout the electrostatic interaction of oppositely charged side chains, ionic bonds constitute between the negative acid group and the positive ammonium group. Oxidation of the sulfhydryl groups on cysteine form disulfide bridges covalent bonds, which acts as molecular “safety pins” to keep the parts of the polypeptide firmly attached to stabilize the folding of a single polypeptide chain.
A protein that owns two or more tertiary polypeptide chains (subunits) are termed an oligomers because they contain more than one subunit, e.g. dimers (two subunits), tetramers (four subunits), hexamers (6 subunits). Haemoglobin is an α2β2 tetramer and therefore a quaternary structure because it contains two alpha subunits and two beta subunits (Denyer. R, 2012). All subunits carry a heme prosthetic group that is attached to an iron molecule, which enables haemoglobin to bind itself to and transport four oxygen molecules at once from the lungs, in the blood to the rest of the body (Casiday. R and Frey. R, 2013).
What is Protein Synthesis? What are the Roles of mRNA, tRNA and rRNA in Protein Synthesis?
Protein synthesis concerns the process where ribosomes integrate the polypeptide chains from DNA into proteins, which is a crucial process in cell growth and repair. The process initially occurs in the cell’s nucleus through transcription which consecutively moves to the cytoplasm for translation.
Once mRNA generates the genetic code, a shorter RNA molecule called tRNA which decodes the genetic code synthesised by mRNA and transferring the correct amino acid to the ribosomes. In contrast, while tRNA is also a single-stranded polynucleotide, disparate to mRNA, tRNA molecules may twist into a distinctive folded structure which forms a three-leafed clover shape (CliffsNotes, 2015, Figure 2a. Secondary structure of tRNA molecule). Furthermore, due to the strong hydrogen bonds between their nucleotides, tRNA is also more stable than mRNA molecules, which support the bonding between every codon, amino acid, and anticodon. In tRNA, there are two regions, the amino acid binding site, where tRNA transfers and attaches a specific amino acid to its corresponding codon, and the anticodon region, which is on the opposite end of the tRNA and is accountable for decoding mRNA codons. Figure 2a states the D-loop contains the pyrimidine dihydrouridine base, which is the recognition site for aminoacyl-tRNA synthetase, that forms when adenosine triphosphate (ATP) hydrolyses, which acts as an enzymic catalyst for aminoacylation. Aminoacylation refers to the process of activating amino acids by attaching them to their corresponding tRNA; which is essential for producing proteins, and cell growth. In this reaction, aminoacyl transferase binds ATP to the amino acid which releases pyrophosphate (BioNinja, n.d., Figure 7.4.1. Amino acid activation), and aminoacyl tRNA synthetase binds to AMP-amino acid and tRNA. The T-loop acts as a recognition site for ribosomes to form a tRNA-ribosome complex in translation. Lastly, the A-loop holds the anticodons, e.g. UAA, UAG or UGA, and adds these stop codons to the polypeptide chain, to control the termination of translation; e.g. the anticodon for codon GCA is CGU (CliffsNotes, 2015, Figure 2b. Tertiary structure of tRNA).
rRNA assists with translating the sequences encoded in mRNA into a protein, combining with proteins to form ribosomes, monitoring the alignment of mRNA, tRNA and ribosomes, and catalysing the peptide bonds which form between two amino acids during protein synthesis with the use of the enzyme peptidyl transferase.
