The enzymes are known as biocatalysts as they enhance the rate of a chemical reaction (Russel & Gordey, 2014). The enzymes are proteinaceous in nature and function by binding to the substrate molecule at the binding site or the active site forming an enzyme-substrate complex. This complex is then converted into an enzyme-product complex following the release of the product molecule. The enzymes function as catalysts by lowering the activation energy of the biochemical reaction and thereby enhancing the reaction rate. This essay will explore the mode of enzyme action as validated through the lock and key hypothesis and also provide the details regarding the various levels of protein structure and causes of protein denaturation.
The protein is a complex three-dimensional structure that is formed after spatial arrangement and folding of the polypeptide chain produced through translation. The protein structure can be primary, secondary, tertiary, and quaternary based on the complexity and folding arrangement of the polypeptide chain.
The folding of this protein chain results in the development of highly specific pockets that provide the specificity to the enzyme and allow the action. The lock and key hypothesis of enzyme action were proposed by Emil Fischer in 1899 who explained that each enzyme possesses a highly specific substrate-binding pocket or the active site. The specificity has been contrasted analogous to the lock and key where for each lock, that is, an enzyme, there is only one key, a substrate. The binding of the enzyme to substrate in the lock and key fashion results in the formation of an enzyme-substrate complex which eventually leads to a product.
Enzymes, as catalysts are highly susceptible to the changes in temperature, pH, and substrate concentration for their mechanism of action. The rise in temperature breaks the intermolecular bonds of the protein structure resulting in protein denaturation affecting the reaction rate of a biochemical process. The three-dimensional conformation and protein modelling also makes it susceptible and highly specific to the working environment. For instance, enzyme salivary amylase has the optimum pH for activity at 6.8 and optimum temperature between 32 °C to 37 °C (Russel &Gordey, 2014). Diversions from these specificities affect the enzyme activity and function and can even cause denaturation. Denaturation of protein due to increase in temperate occurs because of the disruptions of the hydrogen and non-polar interactions (Woodget et al., 2019). Alteration in the pH levels can also cause protein denaturation by affecting the biochemistry of the amino acids and altering the charge on the ionizable groups disrupting the protein structure.
Therefore, it can be summarized that enzymes are highly efficient proteins that function with high specificity to facilitate the biochemical reactions of the body. This is possible only via the possession of the highly specific protein folding and structure.
The genetic code is degenerate (Agris et al., 2018). This statement implies that there is more than one codon that can code for one amino acid during the process of translation. This degeneracy in the genetic code has been explained through the wobble hypothesis. The Wobble hypothesis was first predicted by Francis Crick in 1966 as he has postulated that the 5’base at the anticodon loop of tRNA that binds to the 3’base of mRNA during the process of translation is not spatially confined and therefore can cause non-standard base pairing (Watson, 2014). As a consequence, there are about 61 amino acids that are coded through only 40 known tRNAs (Agris et al., 2018). This essay will summarize how the wobble hypothesis impacts the process of translation for protein formation.
The central dogma of the biology dictates that the DNA is replicated, transcribed, and translated into amino acids to form protein structures that provide the functionality to the genetic code. DNA is a polymer formed with nucleotides. Each nucleotide is constituent of a nucleoside (deoxyribose sugar + nitrogenous base) and a phosphate group (NIH, 2020). The structure of these nitrogenous bases differs and hence they have been classified into purines (Adenine and Guanine) and pyrimidines (Cytosine and Thymine). Another pyrimidine, Uracil, is found in the RNA molecules in the cells (NIH, 2020). This polynucleotide chain undergoes a process of transcription where the nitrogenous bases are on the DNA strand are transcribed into a messenger RNA (mRNA) through RNA polymerase and the transcription machinery. This mRNA is then latched to a tRNA which facilitates the process of translation through the ribosomes. The process of translation requires reading of the mRNA N-bases in the combination of 3 bases called as a “codon” (Watson, 2014). Each codon represents one amino acid that is translated into the polypeptide chain through the protein machinery.
The anticodon loop of the tRNA binds with the codon triplet on the mRNA in the process of translation. However, the binding of the first two bases is stringent and strictly as per the Watson-Crick binding. However, in the third position, a non-canonical binding may occur that can cause a “wobble” or mispairing of the bases in the process of translation. As a consequence to wobble, the amino acid that is being incorporated in the polypeptide chain can be altered based on the wobble at this position.
The four common wobble base pairs known are Guanine-Uracil, hypoxanthine-uracil, hypoxanthine-adenine, and hypoxanthine-cytosine (Shu, 2017). As the amino acid chain and the protein structure is dependent on the mRNA sequence read by the tRNA, wobble hypothesis results in variability. It is only because of this wobble that the multiple codons can code for a single amino acid. This wobble is also beneficial in cases of synonymous mutations that prevent aberrations due to nitrogenous base transitions and transversions (Shu, 2017). Therefore, it can be concluded that the wobble hypothesis plays a significant role in protein formation and is also the cause of degeneracy of the genetic code.
Agris, P. F., Eruysal, E. R., Narendran, A., Väre, V. Y., Vangaveti, S., & Ranganathan, S. V. (2018). Celebrating wobble decoding: Half a century and still much is new. RNA Biology, 15(4-5), 537-553.https://www.tandfonline.com/doi/full/10.1080/15476286.2017.1356562
Nannipieri, P., Trasar-Cepeda, C., & Dick, R. P. (2018). Soil enzyme activity: A brief history and biochemistry as a basis for appropriate interpretations and meta-analysis. Biology and Fertility of Soils, 54(1), 11-19 https://link.springer.com/article/10.1007/s00374-017-1245-6
NIH (2020). What is DNA?.https://ghr.nlm.nih.gov/primer/basics/dna
Ruiz, M. J. (2019). “All cats are gray in the dark” Parity between genetic and non-genetic factors in development.https://www.researchgate.net/publication/335505687_All_cats_are_gray_in_the_dark_Parity_between_genetic_and_non-genetic_factors_in_development
Russell, P. J., &Gordey, K. (2014). IGenetics (No. QH430 R87). Benjamin Cummings.
Shu, J. J. (2017). A new integrated symmetrical table for genetic codes. Biosystems, 151, 21-26.https://www.sciencedirect.com/science/article/abs/pii/S0303264716302854
Watson, J. D. (2014). Molecular biology of the gene (7th edition). Pearson.
Woodgett, J. R. (2019). How to continually make the case for fundamental science: From the perspective of a protein kinase. Biochemistry and Cell Biology, 97(6), 665-669. https://www.nrcresearchpress.com/doi/abs/10.1139/bcb-2019-0130
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