P3- Biochemical Processes

1. P3- Biochemical Processes Processes within cells

2. Key Knowledge The nature of biochemical processes within cells • Catabolic and anabolic reactions – reactions releasing or requiring energy • Role of enzymes as protein catalysts • The role of ATP and ADP in energy transformations • Requirements for photosynthesis • Requirements for aerobic and anaerobic cellular respiration

3. Chemical reactions in cells In the cell reactions happen in steps- A biochemical pathway. • This allows for management of energy requirements. • Each step is controlled and facilitated by protein catalysts and coenzymes.

4. Cellular Metabolism • This refers to the thousands of chemical reactions that occur constantly in each living cell. • Heat is generated by the activity of cells as they break down and build molecules.

5. All metabolic reactions that occur in cells are controlled and regulated to maintain cell functions and to meet the energy needs of a cell. • A biochemical pathway. • Each step is controlled by an enzyme. • Key metabolic pathways include: • Photosynthesis • Cellular Respiration http://highered.mcgraw-hill.com/olc/dl/120070/bio09.swf

6. It is important the products don’t build up in a cell as it can inhibit the cells function: • In plantsglucose from photosynthesis is converted to starch which is stored by the plant. • In animals the products of cellular respiration diffuse from cells and release into the atmosphere.

7. Types of reactions: • Anabolic: a reaction that builds up complex molecules from more simple ones. • Catabolic: reactions, such as cellular respiration, that involve the breakdown of complex molecules to simpler products. • Aerobic: a reaction that requires oxygen. • Anaerobic: a reaction that doesn’t require oxygen. • Endergonic: an energy requiring chemical reaction. • Exergonic: a reaction that releases energy.

8. In endergonic reactions (reactions that absorb energy) – total net amount of energy is absorbed and locked up in the bonds of the products, which have more stored energy than the reactants. • In exergonic reactions (reactions that release energy) – total net amount of energy is released from the bonds of the reactants and the products have less energy than the reactants.

9. Types of reactions: The amount of energy needed for the reaction to occur is known as activation energy.

10. The energy shuttle • Cells capture the chemical energy released from exergonic reactions to fuel endergonic reactions. • These two reactions occur simultaneously in cells. • In this process some energy is lost as heat, which escapes from the cells into the atmosphere. • Reactions don’t always occur in the same place within the cell, energy needs to be transferred between reactions.

12. ATP is the universal primary source of free energy for all living organisms. ATP contains adenosine attached to a sugar group (ribose), which is bound to a chain of three phosphate groups. ATP: Adenosine triphosphate ATP is a well designed renewable energy source. When a cell requires energy to drive an endergonic reaction, the high energy chemical bonds attaching to the last phosphate group is broken, thus releasing stored energy

13. The energy that was held in that bond (now broken) is able to fuel a cellular reaction. The remaining molecule now has only two phosphate groups and is called ADP (adenosine diphosphate). This reaction is sped up by the enzyme ATPase. ATP  ADP

14. Free energy obtained from an exergonic reaction can also be used to add a phosphate group to ADP, converting it to ATP. The ATP-ADP cycle is the cells way of shuttling energy between reactions. The addition of a phosphate group to an organic molecule of any sort is called phosphorylation. ... and in reverse

15. ATP: a molecule that released energy for cellular reactions when its terminal phosphate group is removed. ADP: a compound composed of adenine and ribose with two phosphate groups attached; it is converted to ATP for energy storage when it gains a phosphate group (phosphorylation). Definitions

16. Characteristics of enzymes • Only a small amount of enzyme is needed to do a big job. They are not used up in the reaction.Can be re-used over and over. • An enzyme doesn’t change the direction of the reaction, but does speed up the reaction. • Make the reaction occur more easily by reducing activation energy. • An enzyme won’t change the final amount of product formed. • Are proteins • Are substrate specific

17. Enzymes Are Proteins The enzyme binds to the substrates by its active site The active site is a pocket formed by the folding of the protein where the substrates bind.

18. How enzymes bind their substrates • The active site of an enzymehas a shapethat complements the shape of the binding site of the substrate; that is, they ‘fit together’ like pieces of a jigsaw puzzle. • Two models exist to describe the mechanism of an enzyme binding with it’s substrate. • These are: • Lock and key model • Induced fit model has been refer red

20. Induced fit hypothesis http://scholar.hw.ac.uk/site/biology/activity6.asp

21. Enzyme specificity is at the heart of how enzymes control each step in a biological pathway. What allows proteins to be so specific in their function?

22. Enzymes • Even though enzymes are manufactured inside cells, their site of function may be either within the cell (intracellular) or outside the cell (extracellular). • Intracellular enzymes speed up and control metabolic reactions inside the cell. • Extracellular enzymes are secreted from the cell and catalyse reactions outside the cell. For example, digestive enzymes are secreted from specialised cells in the lining of the gut but act on food in the gut.

23. Naming enzymes • It is usually easy to tell if a substance is an enzyme, they often have the suffix – ase eg: protease, lipase, amylase, nuclease, ATPase etc. • Unfortunately, there is always an exception to the rule eg: pepsin and trypsin, found in the mammalian gut and work on breaking down protein.

25. Enzymes lower activation energy

26. Adding ferric ions (Fe3+) to hydrogen peroxide increases rate of decomposition and therefore make it less toxic. • Catalase – a catalytic protein, one of the fastest, found in the liver. It contains a Fe ions which speed up decomposition of hydrogen peroxide to water and oxygen by 100million times, making it less toxic. • This ability to lower the activation energy needed is why enzymes are so important. Enzyme power

27. Enzyme power • Enzymes generally work rapidly. • Catalase: one of the fastest acting enzymes. It is found in several organs and tissues, including the liver, where its job is to speed up the decomposition of hydrogen peroxide (H2O2) into oxygen and water. 2 H2O2 2H2O + O2

28. Enzyme power • Hydrogen peroxide is a toxic by-product of metabolism so it is essential that the cell removes it quickly. • Hydrogen peroxide has a high activation energy, which means that the energy needed to decompose it to water and oxygen is high.

29. Enzymes are large globular proteins. Earlier we looked at the formation of proteins. At the tertiary structure the protein has its definitive shape. During this stage in an enzyme a pocket or groove is formed (usually made by a beta pleated sheet). This groove or pocket can accommodate one or more specific substrate molecules and is called the active site. Enzymes – fast workers The active site is highly specific for a particular substrate. This model of enzyme action is known as the lock and keymodel.

30. The bonds that form between an enzyme and the substrate can also modify the shape of the enzyme so that the substrate can be fully accommodated. This is knows as the induced fit model of enzyme action. It is important to note that enzymes are generally proteins, but not always eg: ribozymes http://www.youtube.com/watch?v=V4OPO6JQLOE Enzymes – fast workers

31. Coenzymes & cofactors Coenzymes assist catalysis by binding to enzymes or by functioning as carriers of electrons and protons. They may also carry specific atoms or groups of atoms, such as phosphate, that are required for or produced by chemical reactions The catalytic activity of many enzymes also depends upon the presence of metallic cations. Cations that bind to an enzyme, and increase the rate of catalysis are called cofactors

32. Cofactors: small inorganic substances (e.g. zinc ions and magnesium ions) that need to be present in addition to an enzyme to catalyse a certain reaction • Coenzymes: non-protein organic substances that are required for enzyme activity. • Small molecules compared to the enzyme • Major role in metabolic pathways • Can function as a carrier, donor or acceptor of a substance involved in the reaction and/or may bind with an enzyme to activate it.

33. Important Coenzymes

34. Cellular Metabolism: the thousands of cellular reactions that occur constantly in living cells. Biological Pathway: series of steps in a reaction where the product from one step becomes the reactant for the next, each step is regulated by an enzyme. Aerobic – in the presence of oxygen Anaerobic – in the absence of oxygen ATP: Endergonic = Catabolic : ADP ADP: Exergonic = Anabolic : ATP ATPase releases the third phosphate to turn ATP to ADP and the process of phosphorylation attaches a third phosphte to ADP to create ATP. Activation energy: the amount of energy needed for a reaction to occur (enzymes are so effective as they are able to lower this activation energy to get the reaction started quicker). Products need to be removed from the cell so that they do not build up and slow down vital metabolic reactions. Key Knowledge

35. Enzymes are organic catalysts (speed up reaction). Generallyproteins, however not always eg: ribozymes. Enzymes are recycled. Intracellular enzymes: work within the cell. Extracellular enzymes: created in a cell and then excreted to work outside of the cell. Enzymes generally end with the suffix ‘ase’ eg: lipase, amylase. Beta folded sheets created in secondary stage of protein production become the enzymes active site. The active site of the enzyme binds with the substrate of the reactant. Highly specific: lock and key model. When the active site and substrate binds the enzyme can change shape, this is knows as the induced fit model. Enzymes need help: cofactors (inorganic substances eg: zinc)and coenzymes (non protein organic substances). Key Knowledge

36. Factors that influence enzyme activity • Factors that influence enzyme activity include: • pH • Temperature • Inhibitors • Enzyme concentration • Substrate concentration • Cofactors and coenzymes

37. Enzymes are sensitive: The optimum temperature for an enzyme is that in which they naturally occur in. For most of the enzymes associated with plants and animal metabolism, there is little activity at low temperatures – it slows down the number of collisions, but doesn’t denature the enzyme. As the temperature increases, so does the enzyme activity. This is because as the temperature increases molecules become more excited and collide more often. This increase in collisions increases the opportunity for a substrate to bump into its enzymes active site. However, if the point is reached where the temperature is too high and the enzyme structure is damaged, the enzyme ceases to function; this is called enzyme or protein denaturation. Factors effecting enzyme capabilities

38. Poisons often work by denaturing enzymes or occupying the enzyme’s active site so that it does not function. Some enzymes will not function without cofactors, such as vitamins or trace elements. A change in pH affects the amino acid chain of a protein. As a solution becomes more basic, proteins tend to lose hydrogen ions. In acidic solutions, proteins gain hydrogen ions. Buffered solution: weak acid, are better solutions for chemical reactions that water (neutral) due to the H being released from the acidic solution, creates a buffer for H or OH being released. If the charges on the amino acids in a protein are changed, then the bonds that maintain the three-dimensional structure of a protein can be changed. Factors effecting enzyme capabilities

39. Pepsin in the stomach (pH1.5). Catalase works in a neutral environment of cells in the liver (pH 7). Alkaline Phosphatase in bone (pH 9.5). For example...

40. Effect of having more substrate... • The amount of substrate present in a reaction can limit the amount of product produced. • More substrate will result in more product until all enzymes are working at their maximum capacity (enzyme saturation)

41. Effect of having more enzyme... • When the amount of enzyme in a system is increased, then the amount of product increases until: the product starts to inhibit enzyme action the substrate is depleted. • The rate of reaction is proportional to the enzyme concentration provided there is enough substrate present.

42. pH affects enzyme activity • The pH scale is 1–14, where 1 is very acidic, 14 is very basic, 7 is neutral. • The optimum pH for an enzyme is that at which the enzyme shows maximal activity. • Each enzyme has an optimum pH (enzymes are very sensitive to pH). • Changing pH affects enzyme function because hydrogen bonds break, and therefore the 3D shape of the enzyme changes.

43. pH affects enzyme activity • Different enzymes have different optimum pH values. • For example, in the stomach the enzyme pepsin has a low optimum pH, so the stomach produces acid to maintain this low pH. The enzymes of the pancreas need a higher pH to work.

44. Temperature affects enzyme activity • Warming increases the rate of most chemical reactions, including enzyme catalysed reactions. • Extra heat energy is taken up by molecules so they move faster. This increases the rate of interaction between substrate and enzyme. • Lower temperatures meant that molecules move more slowly. This decreases the rate of interaction between substrate and enzyme. • Although temperatures either side of the optimum temperature will decrease enzyme activity, extremes of heat and cold have different effects.

45. Temperature affects enzyme activity • Most enzymes have an optimum temperaturerange, which is the temperature at which the enzyme’s catalytic activity is greatest. • Temperatures outside the optimum temperature range will decrease enzyme activity.

46. Temperature affects enzyme activity • The rate of enzyme activity increases with increasing temperature until the enzyme begins to denatureor break down. • The temperature at which denaturation begins is referred to as the critical temperatureof an enzyme. • Denaturation means that the tertiary structure of the protein is permanently changed and cooling it back down again won’t restore the enzyme’s function. • In contrast, enzymes are not denatured when it is too cold. • Enzymes that are inactivated because of low temperatures become active againwhen the temperature is returned to normal.

47. Different types of inhibitors • Competitive inhibitors • Inhibitory molecule competes with the substrate for the active site. • Slow down enzyme activity by blocking substrate binding to active site. • Non-competitive inhibitors • Allow the substrate to bind to the active site. • Slow down enzyme activity by binding elsewhere to enzyme.

48. Inhibitors • An inhibitor is any chemical that changes the shape of the active site of the enzymeso that it has alower affinity for substrate. • Inhibitors may be reversible or irreversible. • Reversible inhibitorsare used to control enzyme activity as they only temporarily deactivate enzymes. • Heavy metals such as lead, mercury and arsenic are toxic because they are irreversible inhibitors of enzymes. • Inhibition may be competitive,non-competitive or allosteric.

49. Regulating enzyme affinity • Affinity refers to the ease with which the enzyme binds with a substrate. • Cells do this by attaching other molecules to the enzyme to change the shape of its active site. • This allows cells to increase or decrease the rate of reaction in particular circumstances.