ENZYMES

1. ENZYMES

2. Biological Catalysts • Enzymes are complex proteins, usually having either tertiary or quarternary structure, and are responsible for mediating chemical reactions in organisms

3. Dissolving away • For example, think about hydrolysis reactions that use water to break apart major macromolecules • If hydrolysis reactions were that easy to initiate, that means you would dissolve every time you contacted water!

4. Catalysts • Most reactions in organisms cannot happen without the help of enzymes • These enzymes accelerate the rate of reactions and push them forward • Therefore, enzymes are known as catalysts –they lower the energy required to initiate a chemical reaction, increasing the likelihood that the reaction occurs

5. Lock and Key • Enzymes, structurally, are designed to fit specific SUBSTRATES – the reactants in the biochemical reactions • This is known as a “lock and key” mechanism where each enzyme is specialized

6. The substrate binds on the ACTIVE SITE of the enzyme where the chemical reaction will occur Other binding sites might be present on the enzyme that are secondary to the active site. These are known as ALLOSTERIC SITES and generally do not result in the formation of a new product via a chemical reaction Enzyme + substrate  enzyme substrate complex

7. Tertiary and Quarternary structure • Notice, therefore, that enzymes are complex proteins – often having at least tertiary structure and sometimes quarternary structure • The complex possibilities seen in protein folding produces a large number of structural shapes necessary to produce specialized enzymes for each possible chemical reaction

8. Specificity is key • Because they are so specific, each enzyme is designed to accelerate only one type of chemical reaction • http://highered.mcgraw-hill.com/sites/0072495855/student_view0/chapter2/animation__how_enzymes_work.html

9. Enzymes are custom made • On top of being specific to certain reactions, enzymes are also designed to function optimally under certain conditions • The following factors can affect enzyme function: • pH • Temperature • salinity

10. Why the sensitivity? • Enzymes are located everywhere in living organisms • Each living organism must survive in ecosystems that can affect their internal systems (for example, crustaceans living in high temperature sea vents) • Even organisms that have their internal systems well shielded from the external enviornment (like us)

11. Specialists in special systems • For example, within a human being, pH levels can vary within the digestive system • The stomach is a highly acidic area (pH = 1) whereas the duodenum is a more basic area thanks to the pancreas (pH = 5-6) • Therefore, enzymes that function in the stomach must be able to function in low pH vs. those that function in the duodenum that must function in higher pH

12. Why? • This comes back down to understanding the biochemistry of enzymes • Remember that functional groups in amino acids create enzymes that can be more basic, acidic, hydrophilic or hydrophobic • These characteristics help an enzyme to survive better in certain environments

13. Coming undone • Enzymes can “denature” - acidic/basic environments or increased temperatures can interfere with basic bonds (disulfide bridges, Vanderwaals interactions, etc.) that will cause the enzyme to unfold • Remember: a loss of structure = loss of function • An enzyme that cannot hold its 3D shape loses its ability to “fit” with a substrate • http://www.sumanasinc.com/webcontent/animations/content/proteinstructure.html • http://www.lew-port.com/10712041113402793/lib/10712041113402793/Animations/Enzyme_activity.html

14. Pepsin • http://www.biotopics.co.uk/JmolApplet/pepsin.html • Pepsin will denature at pH levels of more than 5.0 • This means that as food moves from your stomach to your duodenum pepsin is inactivated by the increase in pH – this allows other proteases in the duodenum to take over protein digestion

17. Temperature • In regard to temperature, the ideal temperature for most enzymes is dependent on the average internal temperature of the organism • Human enzymes function optimally at internal body temperature = 370 • However, as mentioned before, there are some enzymes that can function well at more extreme temperatures

18. Enzyme kinetics • Enzymes are used widely in the production of various chemical substances in manufacturing, or for laboratory tests because they are such efficient ways to speed up chemical reactions • Enzymes can be used over and over again to catalyze numerous reactions (they will degrade eventually though) • Therefore, the knowledge of optimal ranges of enzyme function are beneficial for this reason

19. Enzyme kinetics • Therefore, enzyme kinetics is the study of enzymatic function – how fast an enzyme can catalyze a reaction • The speed at which an enzyme can catalyze a reaction is best illustrated by how much product is produced in the chemical reaction over time • Substrate + enzyme  product + enzyme

21. Vmax and Km • Vmax = fastest rate at which substrate can be produced by the enzyme • Km is a rate constant - it describes how much the enzyme “wants” to binds to the substrate – it usually is related numerically to half of Vmax

22. Why does it plateau? • In general it makes sense that if you add more substrate to a given concentration of enzymes, you should get more product • However, you should notice that the curve plateaus eventually • Why?

23. Think about function • Remember that in order to carry out a reaction, the enzyme must bind to a substrate • If a small concentration of substrate is added to a group of enzymes, it makes sense that more product can be produced as the concentration increases – because you are engaging more and more enzymes in the reaction process

24. Think about function • But if the concentration of enzyme is not increased, and more and more substrate is added, the rate of product production starts to slow down • If each enzyme in the reaction is attached to a substrate, adding more substrate will not increase the rate of reaction since each enzyme is already occupied with a substrate

25. Think about function • Therefore it can be said that the enzyme concentration is the limiting factor • Increasing the amount of substrate will not cause the rate of the reaction to in increase unless enzyme concentration increases

26. Inhibition • Inhibition occurs when enzyme function is tampered with – this is sometimes necessary to control enzymatic function • This can occur two ways: • COMPETITIVE INHIBITION: another substance binds to the active site of the enzyme • NON-COMPETITIVE INHIBITION: another substance binds to a non-active site – an allosteric site that prevents the binding of the main substrate

28. The most common form of non-competitive (allosteric) inhibition occurs when the binding of an inhibitor to an allosteric site causes a conformational change in the enzyme making it unable to bind with the usual substrate

31. Why does Vmax and Km change? • Binding the active site will make the enzyme less “desirous” to bind the substrate – since it is already bound to something else – this affects Km • Binding an allosteric site might not change the enzyme’s desire to bind the substrate, but it will affect its ability to carry out chemical reactions, therefore affecting Vmax