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Cell Biology And Biochemistry Assignment
Introduction to enzyme
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Enzymes can be termed as the biological catalyst, which is a protein that helps in speeding up any chemical reaction without layering the characteristics of itself. Enzymes in biochemistry are protein substances that reduce activation energy of a reaction to improve reaction rate. Enzymes are made of amino acids that are linked with each other via an amide such as a peptide bond in a linear chain system. However, different structures include linear acid, coiling order due to hydrogen bonding, 3D shape and multiple polypeptide chain structure. Different enzymes contain non-protein parts along with protein parts that are known as co-factor. The function of enzymes is intrinsically linked to the 3D structure that helps in determining binding strategy, catalysis rate and regulation in a reaction. This study will provide the detailed action of enzyme along with factors that can influence their function during reaction.
Biological molecules
Structure of carbohydrates, proteins and lipids
Carbohydrates are the important micro molecules that are composed of carbon, oxygen and hydrogen with the formation formula of Cx(H2O)y. Diversity in the structure of carbohydrates has maintained a great interest in structural glycol biology (Scherbinina and Toukach, 2020). An example of such carbohydrates is glucose and fructose that are made with carbon, hydrogen and the molecule of oxygen.
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Figure 1: Glucose
(Source: Bbc.co.uk, 2022a)
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Figure 2: Fructose
(Source: Bbc.co.uk, 2022a)
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Protein structure is generally a 3D structure of respective atoms that are bound through an amino acid chain. The general formula of any protein indicates RCH(NH2)COOH where R is any group that can vary based on the type of a 3D protein molecule. However, protein molecules are not entirely populated with a large number of diverse oligomeric components (Laniado and Yeates, 2020).
3D structure of a protein molecule
(Source: Sbg.bio.ic.ac.uk, 2022)
Proteins are polymers that are especially polypeptide bonds present in a sequence with presence of more than one amino acid. The alpha centred carbon is directly linked to the amino group, carboxyl group along with hydrogen atoms that make the structure of protein strong.
Lipids can be termed as an important component of cell membrane as the structure is made of glycerol backbone along with presence of two fatty acids in addition to the phosphate group (Ncbi.nlm.nih.gov, 2021). General chemical formula of a lipid molecule is CH3(CH2)nCOOH where -COOH is the carboxylic group using which reaction takes place and n ranges from 2 to 28. As mentioned in the below image, the above part is the glycerol section where acidic groups are present whereas the below section is fatty acid section. Three important structures are present in lipids such as triglycerides, sterols and receptive phospholipids.
Structure of lipid
(Source: Bbc.co.uk, 2022b)
Relation of structure to function
The ratio of carbon, hydrogen and oxygen in carbohydrates is 1:2:1 provides a vital source of energy for cells as well as provides strong support of structure for plant cells. Carbohydrates are three types such as monosaccharaides, disaccharides and polysaccharides based on the presence of functional groups. However, carbohydrates have a completely unparalleled complex structure compared to other biological molecules such as lipids or proteins (Grayet al. 2019). An example of such carbohydrates is Glucopyranose and Glucofuranose that are presented in the image below. Other functions as per the structure of carbohydrates include storage of energy, building macromolecules, sparing proteins and helping in metabolism of lipids.
Different carbohydrates
(Source: Grayet al. 2019)
The 3D structure of a protein is the determining factor of its function for reaction as it can easily react with other proteins or macromolecules to form a complex assembly. Based on the structure, protein is termed as an important building block in the body that acts as a good source of energy. Protein is beneficial in creating hormones, enzymes as well as transporting different molecules within cells.
Lipids include fats, oils, different hormones, and membranes that can act as chemical messenger based on their structure. Based on the structure, lipids are used for strong energy production of signalling along with acts as the structural components of different cell membranes. Different groups in hydrophilic heads and arrangement of side chains are essential in maintaining structure as well as a pattern for reaction in lipids (Storcket al. 2018).
Formation and breakdown of polymers
Polymers are generally formed due to addition as well as condensation strategy of polymerisation by joining different molecules. Monomers come close together during formation using a chemical bonding supramolecular via polymerisation. A diverse range of polymers can easily be produced with specified polymerisation whereas specific polymers can exhibit a large range of properties (Zhou et al. 2020). Four steps are associated with polymer formation such as addition, initiation, propagation and termination. Initiation stage includes addition of free radicals within components of which polymers will be formed. Propagation step includes successive addition of the monomer units by forming a strong chain to make a polymer. The last step is termination that includes elimination of free radicals and reviving the polymers of those monomers. However, temperature, light, electricity, magnetism and ultrasound influence effective polymer formation from monomers. An example includes polymerisation of ethene molecules to form polyethylene as mentioned in the below image.
Polyethylene from ethene
(Source: Bbc.co.uk, 2022c)
Polymers can easily be broken into their monomers using hydrolysis reactions in which binds can be broken using water. The presence of heat, light, presence of air and water can break the chains of polymers into their corresponding monomers.
Concept of activation energy
Activation energy can be termed as the minimum amount of energy that is required for activation of an atom or any molecule to such a condition in which a chemical reaction can take place. Activation energy is necessary for chemical reactions to boost the reaction by controlling the surroundings of that reaction. A low amount of activation energy indicates faster reaction due to effective collision of particles within a reaction whereas high activation energy indicates a slow rate of reaction due to less collision among particles (Bbc.co.uk, 2022d). The below graph indicates T2 is a higher temperature than T1 that denotes higher kinetic energy of molecules than activation energy that increases the rate of reaction.
Activation energy
(Source: Bbc.co.uk, 2022d)
Enzyme action
A. Lock and key
Lock and key is a theoretical model of enzymatic activity that determines fittings of enzymes into a substrate. This study indicates that the activated site of enzyme is properly structured to fit into a substrate to facilitate a chemical reaction. This model indicates that catalytic site of an enzyme is pre-shaped and a receptive substrate fits there such as a key into the lock (Bhatia and Bhatia, 2018). Drawback of this model denotes implied rigidity of catalytic sites along with an inability to explain structure of enzymes.
Figure 8: Lock and key model
(Source: Bbc.co.uk, 2022e)
B. Induced fit
Induced fit model indicates an interaction of enzyme and substrate that denotes substrate is highly capable of inducing an accurate alignment with active site of enzymes. Flexibility of this model is an advantage that shows conformational changes in respective active sites of enzymes in which substrates can fit. This method suggests a competitive inhibition along with allosteric modulation and the inactivation of enzymes during denaturation (Bhatia and Bhatia, 2018). Enzymes change the shape as mentioned in this model for fitting substrates within that can enhance rate of reaction. The advantage of using this model is that it indicates flexibility of enzyme structure that can complement the structure of substrate to make effective bonds.
Factors that affect enzyme activity
Concentration of enzyme and substrate: Presence of a high rate of enzyme in any substrate increases the velocity of a chemical reaction that supports faster formation of equilibrium. Presence of substrate supports stochastically switching of enzymes between two equilibriums such as bound or free to substrate (Zhao et al. 2018). Increasing the concentration of a substrate helps in increasing the velocity of an enzymatic reaction that helps in achieving equilibrium at a faster rate.
Concentration of enzyme on rate
(Source: Alevelbiology.co.uk, 2022)
pH value: Amino acids in substrate helps in determining the activity of enzymes that is based on pH value of a reaction. Some enzymes are native towards high pH whereas most enzymes work accurately in slight pH conditions. Therefore, change in pH influence the ionisation process of enzymes that strongly affects the rate of enzyme activity. The below graph is an example that shows at optimal pH the rate of enzyme reaction is optimal such as at 8 compared to 2 and 13 pH.
pH influence in rate
(Source: Bbc.co.uk, 2022f)
Temperature: Velocity of reaction increases due to increase in activity of enzymes due to increase in temperature. A slight temperature change can strongly influence a decreasing rate of enzymatic activity. Therefore, enzymes are highly active at optimal temperatures only that show great reaction with substrate.
Temperature role in reaction rate
(Source: Alevelbiology.co.uk, 2022)
Inhibitor or activators: Inhibitors present in a reaction bind with the enzyme to create barriers for increasing its activity. However, activators help to make the reaction faster by increasing activity such as the use of Mg2+, Zn2+ and other ions.
Time: Time includes longer incubation of enzymes in substrates indicating heated reaction and formation of ore products.
Conclusion
Complete details on properties of enzymes are presented in this study along with their effective structure. Different structures of carbohydrates, proteins and fats are presented along with their functions. Formation strategy of polymers includes a combination of monomers in presence of free radicals. Temperature, air and other factors, concept of activation energy, lock and key theory and induced fit theory indicate reactivity of enzymes with substrates. Factors that affect enzyme activity indicate temperature, pH, substrate and enzyme concentration and others.
Reference list
Journals
Bhatia, S. and Bhatia, S., 2018.Introduction to enzymes and their applications. Introduction to pharmaceutical biotechnology, 2, pp.1-29.
Gray, C.J., Migas, L.G., Barran, P.E., Pagel, K., Seeberger, P.H., Eyers, C.E., Boons, G.J., Pohl, N.L., Compagnon, I., Widmalm, G. and Flitsch, S.L., 2019. Advancing solutions to the carbohydrate sequencing challenge. Journal of the American Chemical Society, 141(37), pp.14463-14479.
Laniado, J. and Yeates, T.O., 2020. A complete rule set for designing symmetry combination materials from protein molecules. Proceedings of the National Academy of Sciences, 117(50), pp.31817-31823.
Scherbinina, S.I. and Toukach, P.V., 2020. Three-dimensional structures of carbohydrates and where to find them. International journal of molecular sciences, 21(20), p.7702.
Storck, E.M., Özbalci, C. and Eggert, U.S., 2018. Lipid cell biology: a focus on lipids in cell division. Annual review of biochemistry, 87, pp.839-869.
Zhao, X., Gentile, K., Mohajerani, F. and Sen, A., 2018.Powering motion with enzymes. Accounts of chemical research, 51(10), pp.2373-2381.
Zhou, Y.N., Li, J.J., Wu, Y.Y. and Luo, Z.H., 2020. Role of external field in polymerization: mechanism and kinetics. Chemical Reviews, 120(5), pp.2950-3048.
Websites
Alevelbiology.co.uk, 2022.Factors Affecting Enzyme Activity, Available at: https://alevelbiology.co.uk/notes/factors-affecting-enzyme-activity/ [Accessed on: 3/3/2022]
Bbc.co.uk, 2022a.Biological molecules, Available at: https://www.bbc.co.uk/bitesize/guides/z8wsgk7/revision/2 [Accessed on: 3/3/2022]
Bbc.co.uk, 2022b.Biological molecules, Available at: https://www.bbc.co.uk/bitesize/guides/z8wsgk7/revision/3 [Accessed on: 3/3/2022]
Bbc.co.uk, 2022c.More organic chemistry, Available at: https://www.bbc.co.uk/bitesize/guides/z3v4xfr/revision/6 [Accessed on: 3/3/2022]
Bbc.co.uk, 2022d.Controlling the rate, Available at: https://www.bbc.co.uk/bitesize/guides/z2gccdm/revision/4 [Accessed on: 3/3/2022]
Bbc.co.uk, 2022e.Biological molecules, Available at: https://www.bbc.co.uk/bitesize/guides/z8wsgk7/revision/5 [Accessed on: 3/3/2022]
Bbc.co.uk, 2022f.Enzymes, Available at: https://www.bbc.co.uk/bitesize/guides/z88hcj6/revision/2 [Accessed on: 3/3/2022]
Ncbi.nlm.nih.gov, 2021.Biochemistry, Lipids, Available at: https://www.ncbi.nlm.nih.gov/books/NBK525952/#:~:text=Lipids%20are%20an%20essential%20component%20of%20the%20cell%20membrane.,As%20such%2C%20phospholipids%20are%20amphipathic. [Accessed on: 3/3/2022]
Sbg.bio.ic.ac.uk, 2022.Introduction to proteins and protein structure, Available at: http://www.sbg.bio.ic.ac.uk/ezmol/EzMol_Data/images/student/pdf/protein-structure.pdf [Accessed on: 3/3/2022]
