Cell Biology And Biochemistry Assignment Sample

Cell Biology And Biochemistry Assignment

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Introduction to enzymes

An enzyme is defined as a biological catalyst that accelerates the speed of chemical reactions inside the body. It is typically a protein that works on a highly specific substrate and breaks into a specific product or products. Nevertheless, ribozymes are considered to be enzymes due to their catalytic activities and they are made up of RNA molecules. Enzymes require a suitable temperature and pH for activation and remain as it is at the end of the reaction. Primarily two types of enzymes can be classified, which are simple enzymes and conjugated enzymes. Enzymes that are simple; primarily made up of only a chain of amino acids and do not contain any non-protein part (Jindal and Warshel, 2017). On the other hand, conjugated enzymes consist of apoenzyme, coenzyme or cofactor, prosthetic group as well as an active site. All these components together form the “Holoenzyme”. Apoenzyme is nothing but only the protein part of the enzyme, made up of amino acids, having 3D structure and is inactive in nature. Apoenzyme has specific bind sites for binding cofactors as well as coenzymes. Cofactors are simply non-protein substances or can be metal ions. Mn2+, Mg2+, Fe2+/Fe3+, Cu2+, etc. are some of the examples of cofactors. For example, Mg2+ is a cofactor for Hexokinase enzyme that converts glucose into glucose-6-phosphate which is the first step of carbohydrate metabolism (Glycolysis).

Similarly, coenzymes are also a non-protein part and are covalently bonded with the apoenzyme. These are complex organic compounds that can bind with more than one enzyme, cause enzyme activity and assist them in reacting with the substrate. B-complex vitamins are an integral part of coenzymes (Pochapsky and Pochapsky, 2019). “NAD (Nicotinamide adenine dinucleotide)”, and “NADP (Nicotinamide adenine dinucleotide phosphate)” etc. are some of the examples of coenzymes. For example, NAD+ is required in transformation of glyceraldehyde-3-phosphate to 1,3-bisphosphoglycerate which is one of important steps of glycolysis. Prosthetic groups are similar to coenzymes; however, it can be organic or inorganic that covalently binds to the enzyme, such as “FMN (Flavin mononucleotide)”, “biotin”and “FAD (Flavin adenine dinucleotide)” are examples of prosthetic groups (Chaudhry and Varacallo, 2018). The most important part of the enzyme is the active site where the substrate binds with the enzyme. This site consists of amino acid residues and forms bonds with a specific substrate only (Klinman, 2015). The tertiary structure of hexokinase enzyme is composed of three alpha helices and five beta sheets that binds ATP and provides energy for activation that helps conversion of glucose to glucose-6-phosphate.

Biological molecules

Carbohydrate is a polymer that is made up of monomers. Carbohydrates can be classified into monosaccharide, disaccharide, and polysaccharide. Monosaccharides are glucose, fructose, galactose and mannose and have 6 carbon, 12 hydrogen, and 6 oxygen molecules in their structure. Two monosaccharides join together and form disaccharides; for example two glucose molecules join by α-1,4 glycosidic linkage between 1st carbon and 4th carbon to form maltose, one glucose and one fructose join to form sucrose (Navarro et al. 2019). All the disaccharides have 12 carbon, 22 hydrogen and 11 oxygen in their structure. Polysaccharides such as starch and dextrin are formed by more than 10 molecules of monosaccharide (Bio.libretexts.org, 2022). Therefore, monosaccharides are the monomers and polysaccharides are the polymers in case of carbohydrates.

Maltose is a reducing sugar due to “aldehyde group” in its structure, which can reduce Fehling's reagent, making it a reducing sugar. One aldehyde group of 1st carbon and hydroxyl group of second carbon form a bond and leave an aldehyde group of the second glucose. However, for sucrose, aldehyde group of glucose and ketone of fructose make bonds and that is why it cannot reduce Fehling's reagent making it a non-reducing sugar. Ptyalin/pancreatic amylase enzyme acts on starch (polysaccharide), maltase acts on maltose and produces glucose molecules (monomers) (Lanecc.edu, 2018).

Protein is a polymer and consists of monomers of “amino acids (AA)”. Each amino acid has an “amino group (-NH2)”, as well as “carboxyl group (-COOH)”, a “hydrogen atom” and a “side group” attached to a centre carbon that is linked together to form a polypeptide chain. This side-chain sometimes has a sulphur atom such as in cysteine and methionine AA. The peptide bond refers to the joining of the “α-amino group” with the “carboxyl group” of two amino acids, and thus, all the amino acids join together to make a polypeptide chain or protein (Bio.libretexts.org, 2021). Pepsin enzyme secreted by peptic cells of the stomach is an endopeptidase and breaks the peptide bonds in the interior molecules of proteins and forms amino acids. There are many other peptidase enzymes such as chymotrypsin, carboxypeptidase that work on the peptide chain to produce amino acids.

Fat (lipid) is a polymer that is made up of “carbon”, “hydrogen” and “oxygen” and simple lipids are formed by esters of fatty acid and glycerol (alcohol). However, phospholipid, a compound lipid, is formed by fatty acids, phosphoric acid, a nitrogenous base and an alcohol. Therefore, fatty acid digestive enzymes such as gastric lipase, intestinal lipase and bile work on lipids and form monoglycerides/diglycerides and glycerol (Med.libretexts.org, 2020). Figure shows the

Digestion of carbohydrates, protein and fat produce monomers like glucose, amino acid (lysine/leucine/isoleucine, etc.) and for lipid chylomicrons, fatty acids and glycerols are formed by the action of digestive enzymes which simple enzymes are having no cofactor or non-protein attached to it. However, for metabolism, these monomers act as the substrates and these are bound with active sites of conjugated enzymes for energy production. In both cases, activation energy is required. Activation energy is the minimum amount of energy required for conversion of substrate into its products. Any two molecules undergoing a chemical reaction need to break an energy barrier to start reacting. Enzymes lower this activation energy and accelerate the pace of reaction with less amount of energy (Bio.libretexts.org, 2021). Figure 1 shows the concept of activation energy.

Figure 1: Activation Energy

(Source: Bio.libretexts.org, 2021)

Enzyme action

a. Lock and Key model

Emil Fischer proposed this model and it claims that active site shape or substrate binding site is complementary to the shape of the substrate that ensures the binding of a particular substrate with the enzyme. Just like a key is unique to a single lock and fits properly, similarly the shape of the substrate is just like the key and enzyme is the lock. The substrate binds with the enzyme due to its perfect fit with the active site and makes enzyme-substrate complex. Following the chemical reaction, the product is released from the enzyme and the enzyme is reused for another reaction (Tripathi and Bankaitis, 2017).This model only represents the enzyme-substrate interaction.

Figure 2: Lock and Key model

(Source: Socratic.org, 2017)

b. Induced fit model

Due to some flaws in the lock and key concept, another theory that has been propagated for understanding the enzyme action on the substrate is the induced fit model. This model does not believe that the enzyme has complete specificity with the substrate. This is because some enzymes can react with similarly structured substrates and not only a particular substrate. It was first proposed by Daniel Koshland and he claimed that both the substrate and enzyme's active site change their structures until they both fit properly with each other. This model rejected the concept of rigid structure of enzyme active site and proposed a more flexible structure that changes until the substrate fits this active site. Therefore, at first, the substrate binds with the enzyme and forms an “enzyme-substrate complex”. After chemical reactions, the substrate changes into a product and at first forms an enzyme-product complex. Following that, the product gets released from the active site of the enzyme(Galburt and Tomko, 2017). The enzyme does not get used in the process; rather it catalyses the reaction and remains unchanged at the end for reuse.

Figure 3: Induced fit model

(Source: Biologydictionary.net, 2020)

Factors affecting enzyme activity

Two external factors that affect enzyme activity are temperature and pH.

Temperature

Temperature has a significant influence on the rate of enzyme activity and the temperature at which there is highest activity is referred to as "Optimum temperature". Temperature lowers than this, reduces enzyme activity and if the temperature continues to increase and crosses optimum temperature, enzyme activity slowly starts to decrease. Too much increase in temperature denatures the enzyme, making it completely lose its functionality. In the human body, 37.5°C is the normal temperature and enzyme activity is optimum at this temperature (Bbc.co.uk, 2022). A rise in temperature or hyperthermia causes the breakdown of intramolecular structure and intermolecular bonds, which denature enzymes.

Figure 4: Optimum temperature and enzyme activity

(Bbc.co.uk, 2022)

pH

Other than temperature pH plays a significant role as well in enzyme activity. The protein part of the enzyme can get denatured and lose its activity even if there is a slight change in pH. pH scale is ranging from 1-14 and here 7 is neutral, <7 is acidic as well as >7 is alkaline (basic) pH. The activity of enzymes presents in human cells for metabolism and very importantly in digestion is critically determined by pH and the pH at which they show their maximum activity is referred to as optimum pH. For example, ptyalin enzyme works best at mild acidic to neutral pH, which is 6.5. However, pepsin works best at pH≤2 and higher pH can decrease its functionality (Chem.libretexts.org, 2020). The figure shows the role of pH in enzyme activity.

Figure 5: Optimum pH and enzyme activity

(Bbc.co.uk, 2022)

Conclusion

In this essay, a brief discussion was done on enzyme structure, function, formation and breakdown of biological molecules. In the end, a discussion was done on two different enzyme models and two external factors affecting enzyme activity.

References

Bbc.co.uk, 2022. Enzymes. Available at: https://www.bbc.co.uk/bitesize/guides/z88hcj6/revision/2 [Accessed on 4 March 2022]

Bio.libretexts.org, 2021. Activation Energy.Available at: https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/06%3A_Metabolism/6.2%3A_Potential_Kinetic_Free_and_Activation_Energy/6.2D%3A_Activation_Energy [Accessed on 4 March 2022]

Bio.libretexts.org, 2021. Structure & Function - Amino Acids. Available at: https://bio.libretexts.org/Bookshelves/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/02%3A_Structure_and_Function/202%3A_Structure__Function_-_Amino_Acids [Accessed on 4 March 2022]

Bio.libretexts.org, 2022. Carbohydrates. Available at: https://bio.libretexts.org/Bookshelves/Microbiology/Microbiology_(OpenStax)/07%3A_Microbial_Biochemistry/7.02%3A_Carbohydrates [Accessed on 3 March 2022]

Chaudhry, R. and Varacallo, M., 2018. Biochemistry, glycolysis. Available at: https://europepmc.org/books/nbk482303[Accessed on 3 March 2022]

Chem.libretexts.org, 2020. The Effect of pH on Enzyme Kinetics. Available at: https://chem.libretexts.org/Bookshelves/Physical_and_Theoretical_Chemistry_Textbook_Maps/Map%3A_Physical_Chemistry_for_the_Biosciences_(Chang)/10%3A_Enzyme_Kinetics/10.7%3A_The_Effect_of_pH_on_Enzyme_Kinetics [Accessed on 4 March 2022]

Galburt, E.A. and Tomko, E.J., 2017. Conformational selection and induced fit as a useful framework for molecular motor mechanisms. Biophysical chemistry, 223, pp.11-16.Available at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5357456/pdf/nihms851169.pdf [Accessed on 4 March 2022]

Jindal, G. and Warshel, A., 2017. Misunderstanding the preorganization concept can lead to confusions about the origin of enzyme catalysis. Proteins: Structure, Function, and Bioinformatics, 85(12), pp.2157-2161. Available at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5760166/pdf/nihms929869.pdf [Accessed on 3 March 2022]

Klinman, J.P., 2015. Dynamically achieved active site precision in enzyme catalysis. Accounts of Chemical Research, 48(2), pp.449-456. Available at: https://pubs.acs.org/doi/pdf/10.1021/ar5003347 [Accessed on 3 March 2022]

Lanecc.edu, 2018. Digestion and Absorption of Carbohydrates.Available at: https://media.lanecc.edu/users/powellt/FN225OER/Carbohydrates/FN225Carbohydrates4.html [Accessed on 4 March 2022]

Med.libretexts.org, 2020. Digestion and Absorption of Lipids. Available at: https://med.libretexts.org/Bookshelves/Nutrition/Book%3A_An_Introduction_to_Nutrition_(Zimmerman)/05%3A_Lipids/5.04%3A_Digestion_and_Absorption_of_Lipids [Accessed on 4 March 2022]

Navarro, D.M., Abelilla, J.J. and Stein, H.H., 2019. Structures and characteristics of carbohydrates in diets fed to pigs: a review. Journal of animal science and biotechnology, 10(1), pp.1-17. Available at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6480914/pdf/40104_2019_Article_345.pdf [Accessed on 4 March 2022]

Pochapsky, T.C. and Pochapsky, S.S., 2019. What your crystal structure will not tell you about enzyme function. Accounts of Chemical Research, 52(5), pp.1409-1418. Available at: https://pubs.acs.org/doi/pdf/10.1021/acs.accounts.9b00066 [Accessed on 3 March 2022]

Socratic.org, 2017. What does the lock and key hypothesis state?Available at: https://socratic.org/questions/58f64d5c11ef6b44e4d659b6 [Accessed on 4 March 2022]

Tripathi, A. and Bankaitis, V.A., 2017. Molecular docking: From lock and key to combination lock. Journal of molecular medicine and clinical applications, 2(1). Available at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5764188/pdf/nihms856098.pdf [Accessed on 4 March 2022]