Cell Biology And Biochemistry Assignment Sample

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Cell Biology And Biochemistry Assignment 

Introduction to Enzyme

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Enzymes are referred to as “Biocatalysts” that accelerate the rate of reactions inside the living organism. Mostly these enzymes are protein in nature except the Ribozymes, which are composed of RNA, a nucleic acid. Enzymes are classified according to function in living cells; for example, oxidoreductase enzymes perform oxidation-reduction reactions. Enzymes are involved in certain biological processes such as digestion, excretion, metabolism, as well as respiration. An enzyme has very high specificity for its substrate and thus it produces a product at the end of the chemical reaction (Lewis and Stone, 2020). Several amino acids (AAs) starting from approximately 62 to as high as 1000 AAs make linear chains that later form a three-dimensional structure of the enzymes.

Every enzyme has a particular tertiary structure that determines its biological functions. The simple linear chain forms the primary structure of any protein; α-helix as well β-pleated sheet forms the secondary structure of the protein. This secondary structure is formed by the bond between a carbonyl bonds (keto bond) with the hydrogen of the amino group. The side chains of amino acids (R group) together form the tertiary or 3D structure by forming covalent bonds with each other. Hence, if looking at the structure of the enzymes (except ribozymes) a 3D structure of chains of amino acids can be visible (Sanvictores and Farci, 2020). All these enzymes have a specific structure that is unique to a particular substrate or similar substrates of the same class. There is an active site of every enzyme, which is also called the "substrate-binding site", which is highly specific to its substrate/substrates. Enzyme activity gets disrupted following application of high heat that denatures the three-dimensional structure and secondary structure of the enzyme (Hong et al. 2018). Hence, the denatured enzyme can no longer attach to its substrate to produce the products.

Enzyme Structure

Figure 1: Enzyme Structure

(Source: Cen.acs.org, 2021)

There are mainly two types of enzymes in all living cells and these are simple enzymes and conjugated enzymes. Some simple enzymes are “ptyalin, pepsin, chymotrypsin, and trypsin”, which are primarily digestive enzymes. It has only the protein part or “Apoenzyme” in its structure (Ianiro et al. 2016). There are no non-protein organic or inorganic parts present other than the protein part. However, conjugated proteins such as "pyruvate dehydrogenase", "hexokinase", "glyceraldehyde-3-phosphate dehydrogenase" enzymes have some non-protein parts in their structure. Those are some examples of metabolic enzymes that produce energy in the body. Other than the apo-enzyme, some enzymes have some organic non-protein portion, called coenzymes attached to them (Lewis and Stone, 2020). These co-enzymes accelerate the enzyme action and it frequently participates in chemical reactions. NAD+, NADP, TPP, are some coenzymes. NAD is a coenzyme formed from vitamin B3, niacin and is called “Nicotinamide Adenine Dinucleotide”. Coenzyme TPP is formed from Thiamine (B1) and is an important coenzyme in glucose metabolism (Glycolysis) (Chaudhry and Varacallo, 2018). Some metal factors also attach with the enzymes to enhance the rate of reaction, known as a cofactor. Some cofactors can be organic or inorganic and these are called prosthetic groups. "Biotin", "lipoic acid", "heme", "pyridoxal phosphate" (derived from vitamin B6), "FAD (Flavin adenine dinucleotide)", as well as "FMN (Flavin mononucleotide)" are some examples of prosthetic groups. All these are part of the "holo-enzyme" and are covalently bound with the enzyme to maximise the catalytic activity. K+ is an inorganic metal cofactor that participates in a chemical reaction with pyruvate kinase enzyme that synthesises pyruvic acid from phosphoenol pyruvic acid, which is the last step of glycolysis (Hausinger, 2019). Some other examples of cofactors are Mn2+, Mg2+, Zn2+, Fe2+, etc. Thus, the structure of the enzyme determines the function of the enzyme.

Biological molecules

Activation Energy

Activation energy is referred to as the minimum amount of energy that is required to start a particular reaction. In case of biological reactions, the substrates undergo certain chemical reactions and produce some products. The role of the enzyme in this context is to lower this activation energy and ensure a faster rate of the reaction. Without the presence of enzymes, these chemical reactions would need much higher energy for completion. This activation energy is significantly lower in presence of enzymes because the substrates bind with enzymes in such a way that it influences the breaking of old bonds and the formation of new bonds at a faster rate (Bio.libretexts.org, 2021). Therefore, it can be said that the requirement of initial energy to start a reaction is significantly lower in presence of enzymes.

Activation Energy

Figure 2: Activation Energy

(Source: Ck12.org, 2016)

Carbohydrate

Carbohydrate is the major source of energy and is present in almost all food in little or larger amounts except in oils. It is called the "polyhydroxy aldehydes" or "polyhydroxy ketone" due to presence of aldehyde or ketone group in its structure. The monomeric form of carbohydrate is referred to as "monosaccharide" and it is called simple sugar of free sugar. "Glucose", "fructose", "galactose" are monosaccharides that are joined together with glycosidic bonds to produce polysaccharides, the polymeric form (Med.libretexts.org, 2020). The role of the enzyme is to break these glycosidic linkages in the monosaccharide chain. Simple enzymes like ptyalin, maltase, and lactase are digestive enzymes that break glycosidic bonds of starch, dextrin, maltose, and lactose respectively. Among these carbohydrates, starch and dextrin are polysaccharides and upon digestion, they first produce some disaccharides like maltose, sucrose, and lactose. "Maltase", "sucrase", and "lactase" then work on these disaccharides to produce two monomers each. These two carbohydrates are joined by α-glycosidic bonds that form maltose and are broken by maltase. Glucose has aldehyde in its first carbon as well as many hydroxyl and hydrogen in its structure. This aldehyde on glucose with the hydroxyl of glucose makes a α-glycosidic bond, releases one molecule of water and forms maltose, a disaccharide. Maltase reacts with maltose at its active site and produces two molecules of glucose at the end (Media.lanecc.edu, 2018). Thus polysaccharides are broken down by digestive enzymes and monosaccharides are released.

Protein

Proteins are the polymeric forms that are produced by chains of amino acids. Therefore, upon digestion by digestive enzymes, amino acid monomers are produced. Two amino acids are joined by carboxyl (-COOH) and amine (+NH2) groups and release one molecule of water in this process. These chains of amino acids are joined together by peptide bonds and the digestive enzymes break these peptide bonds to release amino acids (Sanvictores and Farci, 2020). Human body has different types of proteolytic enzymes such as "pepsin", "trypsin", "chymotrypsin", "carboxypeptidase", etc. All these enzymes have unique tertiary substrate binding sites that attach proteins like "albumin", "globulin", "collagen", and “elastin" and liberate products like "lysine", "leucine", "histidine", "tryptophan", "tyrosine" like amino acids following digestion. Pepsin of the stomach initiates this digestion process and finishes in the intestine where pancreatic proteases and intestinal proteases break the tertiary peptide bonds in the polypeptide chain (Med.libretexts.org, 2020). For example, trypsin hydrolyses peptide linkages containing arginine or lysine and chymotrypsin hydrolyses peptide linkages containing tyrosine and phenylalanine amino acids.

Fat

Chemically lipids are esters of fatty acids and glycerol and it is composed of mainly carbon, hydrogen, and oxygen. However, compound lipids do have some other elements in their structure. Glycerophospholipids are a type of compound lipid that has glycerol, fatty acids, phosphoric acid, as well as a nitrogen base in its structure. Therefore, in the case of simple lipids, which are the polymeric form, fatty acids, and glycerol, which is a type of alcohol, are the monomers. However, for compound lipids, other than fatty acid and alcohol, phosphate, nitrogen base is also the monomers (Ahmed et al. 2021). The digestion of fat is quite different from carbohydrate and protein, and here the role of bile salts is more significant than lipases. In the metabolism of fat or beta-oxidation, the roles of conjugated enzymes are most important. At the end of beta-oxidation ATP is produced, which provides energy to the body.

Major Biological Molecules

Figure 3: Major Biological Molecules

(Source: Wou.edu, 2022)

Enzyme action

The lock and key model of enzyme action

This was the very first model of enzyme action, propagated by a German biochemist named "Emil Fisher". This model believes that the active site or the substrate-binding site of the enzyme is rigid and so, the substrate just fits perfectly at that site. This model states that the active site is nothing but a "pre-shaped template" which is complementary to the structure of the substrate. It is compared as just a key that is unique to a particular key and can unlock it; similarly, a single substrate can only bind to this active site and produces an enzyme-substrate complex (Tripathi and Bankaitis, 2017). However, this model has various limitations and cannot answer the reason for those enzymes that can bind more than one kind of substrate. Hexokinase can be a good example as it can bind all the monosaccharides such as glucose, fructose, and galactose and generate ATP.

Lock-and-key Model

Figure 4: Lock-and-key Model

(Source: Socratic.org, 2017)

The induced-fit model of enzyme action

Due to various limitations of the lock and key model, another model was proposed in 1958 by "Koshland" known as the "induced fit model". It is a more realistic approach than the previous one and it claims that the active site of the enzyme is not at all rigid or pre-shaped. It rather believes this active site is flexible and can mould into shape according to the substrate. The nascent active site has all the essential features of substrate binding and following interaction with the substrate, a conformational change is induced (Michel, 2016). This ensures the perfect fit of the substrate at the enzyme active site and initiation of chemical reactions. Following binding the substrate with the enzyme, an "enzyme-substrate complex" is formed and at the end of the reaction, the "enzyme-product complex" is produced. Only after formation of the enzyme-product complex, a product released from the enzyme.

Induced fit model

Figure 5: Induced fit model

(Source: Thesciencehive.co.uk, 2022)

Factors affecting enzyme activity

Several factors determine the enzyme activities and these are substrate concentration, enzyme concentration, temperature, pH, presence of coenzymes, etc. However, in this section, the role of temperature and pH will be discussed for enzyme activity.

Effect of pH

The optimum pH is considered that pH where the enzyme velocity is highest or in simpler words, the rate of conversion of substrates into products is highest. pH below or above this optimum pH can significantly disrupt this chemical reaction and can even completely destroy the enzyme. Some enzymes are intolerant to extreme acidic pH or extreme alkaline pH and prefer neutral pH for maximum velocity (Olukunle et al. 2015). This can be explained by the presence of hydrogen ions that interact with the active site of the enzyme and alter the ionic charges and bonds of the amino acids leading to denaturation. A higher concentration of hydrogen ions means higher acidity or pH less than 6. On the other hand, higher hydroxyl ions mean higher alkalinity or pH of more than 8. In both extreme cases, enzyme activity can be altered depending on the type of enzyme. The optimum pH of pepsin is 1-2 which is extremely acidic; however, the optimum pH of alkaline phosphatase is around 10-11, which is extreme alkaline (Herlet et al. 2017). Both these enzymes have the highest velocity in these extreme ranges of pH only.

Effect of pH

Figure 6: Effect of pH

(Source: Alevelbiology.co.uk, 2022)

Effect of Temperature

Optimum temperature is that temperature, where the velocity of enzyme is highest and below or above this temperature can alter enzyme activities. Temperature coefficient (Q10) is defined as enzyme activity that significantly rises with the increase of every 10°C and it is seen that Q10 is 2 between 0°C to 40°C in most of the enzymes. However, 35°C-45°C temperature is considered to be optimum and the velocity is maximum (Decaneto et al. 2015). The chances of denaturation are high in extremely hot temperatures (if higher than 50°C) except for Taq polymerase enzymes. Normal human temperature is 37°C and enzymes of the body show maximum velocity at this temperature. The chances of enzyme denaturation significantly rise in severe fever and the person can die instantly.

Effect of Temperature

Figure 7: Effect of Temperature

 (Source: Alevelbiology.co.uk, 2022)

Conclusion

The primary focus of this essay was to discuss the structure and function of enzymes. In this regard, the activation energy, carbohydrate, protein, fat structure, and functions were aligned with enzymes. Lock and key model and induced fit model were discussed to understand enzyme action and in the end, discussion was done on external factors affecting enzyme activity.

References

Ahmed, S., Shah, P. and Ahmed, O., 2021. Biochemistry, lipids. StatPearls [Internet]. Available at: https://www.ncbi.nlm.nih.gov/books/NBK525952/ [Accessed on 5 March 2022]

Alevelbiology.co.uk, 2022. Factors Affecting Enzyme Activity.Available at: https://alevelbiology.co.uk/notes/factors-affecting-enzyme-activity/ [Accessed on 5 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 5 March 2022]

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Hausinger, R.P., 2019. New metal cofactors and recent metallocofactor insights. Current opinion in structural biology59, pp.1-8. Available at: https://www.sciencedirect.com/science/article/am/pii/S0959440X18301404 [Accessed on 5 March 2022]

Herlet, J., Kornberger, P., Roessler, B., Glanz, J., Schwarz, W.H., Liebl, W. and Zverlov, V.V., 2017. A new method to evaluate temperature vs. pH activity profiles for biotechnological relevant enzymes. Biotechnology for biofuels10(1), pp.1-12.Available at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5637330/pdf/13068_2017_Article_923.pdf[Accessed on 5 March 2022]

Hong, N.S., Petrovi?, D., Lee, R., Gryn’ova, G., Purg, M., Saunders, J., Bauer, P., Carr, P.D., Lin, C.Y., Mabbitt, P.D. and Zhang, W., 2018. The evolution of multiple active site configurations in a designed enzyme. Nature communications9(1), pp.1-10.Available at: https://www.nature.com/articles/s41467-018-06305-y.pdf[Accessed on 5 March 2022]

Ianiro, G., Pecere, S., Giorgio, V., Gasbarrini, A. and Cammarota, G., 2016. Digestive enzyme supplementation in gastrointestinal diseases. Current Drug Metabolism17(2), pp.187-193. Available at: https://www.ingentaconnect.com/contentone/ben/cdm/2016/00000017/00000002/art00011?crawler=true [Accessed on 5 March 2022]

Lewis, T. and Stone, W.L., 2020. Biochemistry, Proteins Enzymes. StatPearls [Internet]. Available at: https://www.ncbi.nlm.nih.gov/books/NBK554481/ [Accessed on 5 March 2022]

Med.libretexts.org, 2020. Carbohydrates. Available at: https://med.libretexts.org/Bookshelves/Anatomy_and_Physiology/Book%3A_Human_Anatomy_and_Physiology_Preparatory_Course_(Liachovitzky)/03%3A_Molecular_Level-_Biomolecules_the_Organic_Compounds_Associated_With_Living_Organisms/3.03%3A_Carbohydrates[Accessed on 5 March 2022]

Med.libretexts.org, 2020. Protein Digestion, Absorption and Metabolism.Available at: https://med.libretexts.org/Courses/American_Public_University/APUS%3A_An_Introduction_to_Nutrition_(Byerley)/APUS%3A_An_Introduction_to_Nutrition_1st_Edition/05%3A_Proteins/5.04%3A_Protein_Digestion_Absorption_and_Metabolism[Accessed on 5 March 2022]

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Olukunle, O.F., Babajide, O. and Boboye, B., 2015. Effects of temperature and pH on the activities of catechol 2, 3-dioxygenase obtained from crude oil contaminated soil in Ilaje, Ondo State, Nigeria. The Open Microbiology Journal9, p.84.Available at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4598378/pdf/TOMICROJ-9-84.pdf[Accessed on 5 March 2022]

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