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Enzymes

Enzymes. Introduction to enzyme structure and function, and factors involving their actions and pathways. What is an enzyme?.

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Enzymes

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  1. Enzymes Introduction to enzyme structure and function, and factors involving their actions and pathways.

  2. What is an enzyme? • Almost all enzymes are proteins that act as biological catalysts. (Lehninger, Nelson, & Cox, 1993, p. 198) A catalyst speeds up chemical reactions. Enzymes speed up biological chemical reactions. (Campbell & Reece, 2002, p. 96) • Enzymes are highly specific to a type of reaction. (Lehninger et al., 1993, p. 198) • Enzymes must maintain their specific shape in order to function. Any alteration in the primary, secondary, tertiary, or quaternary forms of the enzyme are detrimental. (Lehninger et al., 1993 p. 199)

  3. Function of enzymes Enzymes have many jobs. They: • Break down nutrients into useable molecules. (Lehninger et al., 1993, p. 198) • Store and release energy (ATP). (Lehninger et al., 1993, p. 198; Campbell & Reece, 2002, pp. 162-163) • Create larger molecules from smaller ones. (Lehninger et al., 1993, p. 198; Campbell & Reece, 2002, pp. 295, 316-317) • Coordinate biological reactions between different systems in an organism. (Lehninger et al., 1993, p. 198; Campbell & Reece, 2002, pp. 101-102)

  4. Enzyme action overview • Enzymes are large molecules that have a small section dedicated to a specific reaction. This section is called the activesite. (Lehninger et al., 1993, p. 201) • The active site reacts with the desired substance, called the substrate. (Lehninger et al., 1993, p. 201) • The substrate may need an environment different from the mostly neutral environment of the cell in order to react. Thus, the active site can be more acidic or basic, or provide opportunities for different types of bonding to occur, depending on what type of side chains are present on the amino acids of the active site. (Campbell & Reece, 2002, p. 99)

  5. Enzyme action theories • Lock and Key: This theory, postulated by Emil Fischer in 1894, proposed that an enzyme is “structurally complementary to their substrates” and thus fit together perfectly like a lock and key. This theory formed the basis of most of the ideas of how enzymes work, but is not completely correct.(Lehninger et al., 1993, p. 205)

  6. Enzyme action theories • Induced Fit: An enzyme that is perfectly complementary to its substrate would actually not make a good enzyme because the reaction has no room to proceed to the transition state of the reaction. To go to completion, a reaction must go through the transition state. In the lock and key theory, the substrate or the enzyme cannot change conformations to the transition state. Therefore, enzymes must actually be complementary to the transition state so the reaction may proceed. This idea was researched by Haldane in 1930, and Linus Pauling in 1946. This idea led the Induced Fit theory, postulated by Daniel Koshland in 1958, where the enzyme itself can change conformations to facilitate the transition state of the substrate. This change in conformation of the enzyme allows the necessary functional groups at the active site to move closer to the substrate, enhancing the efficiency of the reaction.(Lehninger et al., 1993, pp. 206-208; Campbell & Reece, 2002, p. 98)

  7. Enzyme activity and inhibition • The “normal” way an enzyme functions is when the specific substrate binds to the active site and creates the products. • A similar substrate can also bond to the active site covalently and irreversibly. This prevents the enzyme from functioning. (Campbell & Reece, 2002, pp. 100-101) • A similar substrate can bind to the active site, not permanently, and prevents the desired substrate from entering the active site. This changes the products and functioning of the enzyme. This is called competitive inhibition. (Campbell & Reece, 2002, pp. 100-101) • A molecule can bond to another part of the enzyme and cause a change in conformation. This change causes the active site to change shape as well. This change in shape prevents the desired substrate from entering the active site. This is called non-competitive inhibition.(Campbell & Reece, 2002, pp. 100-101)

  8. Enzyme cofactors • A cofactor is a substance that is not a protein that must bind to the enzyme in order for the enzyme to work. (Thain & Hickman, 2000, p. 146) • A cofactor can be of organic origin. An organic cofactor is called a coenzyme. (Thain & Hickman, 2000, p. 144) • Cofactors are not permanently bonded. Permanently bonded cofactors are called prosthetic groups. (Thain & Hickman, 2000, p. 529)

  9. Enzyme cofactors cont. • An enzyme that is bonded to its cofactor is called a holoenzyme.(Thain & Hickman, 2000, p. 146) • An enzyme that requires a cofactor, but is not bonded to the cofactor is called an apoenzyme. Apoenzymes are not active until they are complexed with the appropriate cofactor. (Thain & Hickman, 2000, p. 38)

  10. Common coenzymes Many coenzymes are derived from vitamins: • NAD+ (nicotinamide adenine dinucleotide); derived from niacin (B3). (Ophardt, 2003, para. 1; Cofactor (biochemistry), n.d., Wikipedia, para. Organic) • Coenzyme A (CoA); derived from pantothenic acid (B5). (Ophardt, 2003, para. 1; Cofactor (biochemistry), n.d., Wikipedia, para. Organic) • FAD (flavin adenine dinucleotide); derived from riboflavin (B2). (Ophardt, 2003, para. 1; Cofactor (biochemistry), n.d., Wikipedia, para. Organic)

  11. Common coenzymes Coenzymes can be derived from sources other than vitamins: • ATP (adenosine triphosphate); derived from NADH from carbohydrates consumed. (Ophardt, 2003, para. 1; Unit 3: Demos, n.d., Cornell University) • CTP (Cytidine triphosphate); derived from glutamate and carbamoylphosphate. (Cofactor (biochemistry), n.d., Wikipedia, para. Organic; Cytidine Triphosphate, n.d., Wikipedia; Paustian, 1999, Figure 6) • PAPS (3'-Phosphoadenosine-5'-phosphosulfate); derived from adenosine 5'-phosphosulfate (APS) and sulfate ion. (Cofactor (biochemistry), n.d., Wikipedia, para. Organic; 3'-Phosphoadenosine-5'-phosphosulfate, n.d., Wikipedia,.)

  12. Coenzyme reactions Coenzymes help transfer a functional group to a molecule.(Cofactor (biochemistry), n.d., Wikipedia, para. Organic) For example, coenzyme A (CoA) is converted to acetyl-CoA in the mitochondria using pyruvate and NAD+. (Lehninger et al., 1993, p. 544, Table 18-1) Acetyl-CoA can then be used to transfer an acetylgroup (CH3CO) to aid in fatty acid synthesis.(Diwan, 1998, Pyruvate Dehydrogenase & Krebs Cycle)

  13. Fatty acid synthesis I Coenzyme A is converted to acetyl-Coenzyme A Diagrams and equation modified from: http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/part2/krebs.htm

  14. Fatty acid synthesis II • Once acetyl-coenzyme A is created, eight acetyl groups are used to create palmitate, a 16 carbon saturated fatty acid. Palmitate can then be used to create other fatty acids. (Baggott, 1998, Overview: Reaction sum) • The process from acetyl-CoA to palmitate is seven steps and requires other enzymes and the addition and removal of several functional groups. (Baggott, 1998, Enzymes and Isolated Reactions: Activities of FA Synthase)

  15. Fatty acid synthesis III • Diagrams modified from: http://rpi.edu/dept/bcbp/molbiochem/MBWeb/mb2/part1/fasynthesis.htm • Equation from: http://library.med.utah.edu/NetBiochem/FattyAcids/5_1b.html

  16. Factors that affect enzyme action Enzymes are mostly affected by changes in temperature and pH. (Campbell & Reece, 2002, pp. 99-102) • Too high of a temperature will denature the protein components, rendering the enzyme useless. • pH ranges outside of the optimal range will protonate or deprotonate the side chains of the amino acids involved in the enzyme’s function which may make them incapable of catalyzing a reaction.

  17. Factors that affect enzyme action Enzymes are also affected by the concentration of substrate, cofactors and inhibitors, as well as allosteric regulation and feedback inhibition. (Campbell & Reece, 2002, pp. 99-102) • The concentration of substrate will dictate how many enzymes can react. Too much substrate will slow the process until more enzyme can be made. • The availability of cofactors also dictate enzyme action. Too little cofactors will slow enzyme action until more cofactors are added. • An influx of competitive or non-competitive inhibitors will not necessarily slow the enzyme process, but will slow the amount of desired product.

  18. Factors that affect enzyme action • Enzymes that can be activated will be affected by the amount of activator or inhibitor attached to its allosteric site. An abundance of an allosteric activator will convert more enzymes to the active form creating more product. • Enzymes that are part of a metabolic pathway may be inhibited by the very product they create. This is called feedback inhibition. The amount of product generated will dictate the number of enzymes used or activated in that specific process.

  19. Summary of enzymes • Enzymes are mostly proteins • They are highly specific to a reaction • They catalyze many reactions including breaking down nutrients, storing and releasing energy, creating new molecules, and coordinating biological reactions. • Enzymes use an active site, but can be affected by bonding at other areas of the enzyme. • Some enzymes need special molecules called cofactors to carry out their function. • Cofactors that are organic in nature are called coenzymes. • Coenzymes are usually derived from vitamins. • Coenzymes transfer functional groups for the enzyme they work with. • Enzymes are affected by changes in pH, temperature, the amount of substrate, cofactors and inhibitors, as well as the amount of allosteric inhibitors and activators and concentration of products that control feedback inhibition.

  20. References • 3'-Phosphoadenosine-5'-phosphosulfate. (n.d.). In Wikipedia. Retrieved from http://en.wikipedia.org/wiki/3%27-Phosphoadenosine-5%27-phosphosulfate • Campbell, N.A., & Reece, J.B. (2002). Biology. San Francisco, CA: Benjamin Cummings. • Cofactor (biochemistry). (n.d.). In Wikipedia. Retrieved from http://en.wikipedia.org/wiki/Cofactor_(biochemistry) • Cytidine triphosphate. (n.d.). In Wikipedia. Retrieved from http://en.wikipedia.org/wiki/Cytidine_triphosphate • Diwan, J.J. (1998-2007). Fatty Acid Synthesis. Retrieved from http://rpi.edu/dept/bcbp/molbiochem/MBWeb/mb2/part1/fasynthesis.htm • Diwan, J.J. (1998-2007). Pyruvate Dehydrogenase & Krebs Cycle. Retrieved from http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/part2/krebs.htm • Leninger, A.L., Nelson, D.L., & Cox, M.M. (1993). Principles of biochemistry. New York, NY: Worth Publishers. • Ophardt, C.E. (2003). Virtual chembook. Retrieved from http://www.elmhurst.edu/~chm/vchembook/571cofactor.html • Paustian, T. (1999-2006). Nucleotide Synthesis. Retrieved from http://eglobalmed.com/core/VirtualMicrobiology/www.bact.wisc.edu/Microtextbook/index4d4a.html?name=Sections&req=viewarticle&artid=68&page=1 • Thain, M., & Hickman, M. (2000). The penguin dictionary of biology. London, England: Penguin Books Ltd. • Unit 3: Demos. Where do all those ATP come from? (n.d.). Retrieved from http://www.biog1105-1106.org/demos/105/unit3/atpcomefrom.html

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