Lecture 8 Enzyme Energetics

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1 Lecture 8 Enzyme Energetics 1

2 Last Lecture We talked about protein conformational change, signal cascades, phosphorylation, and ATP. We shall review these things even more in depth today 2

3 In this lecture Physics!! Energy The laws of thermodynamics Free energy Metabolism The role of ATP Enzymes Enzyme inhibitors and regulators 3

4 What is energy? The ability to do work Comes in two main forms Potential energy Example: Chemical Energy Example: Gravitational Energy Kinetic energy Example: Thermal energy (heat) 4

5 A diver has more potential energy on the platform than in the water. Diving converts potential energy to kinetic energy. Climbing up converts the kinetic energy of muscle movement to potential energy. A diver has less potential energy in the water than on the platform. 5

6 The behavior of energy is governed by the laws of thermodynamics 1 st law of thermodynamics: energy cannot be created or destroyed 2 nd law of thermodynamics: energy transfer or transformation is never 100% efficient. Part of the energy is lost Energy transfer increases the entropy (disorder) of the universe 3 rd law of thermodynamics: the entropy of a perfect crystal at a temperature of absolute zero is zero 6

7 Entropy The universe s tendency towards disorder A system (such as an organism) requires energy input in order to not succumb to entropy What happens when entropy is at maximum for the entire universe? Heat death of the universe 7

8 What does entropy have to do with life? Living cells unavoidably convert organized forms of energy to heat. We increase the entropy of the universe. Energy flows into an ecosystem in the form of light and exits in the form of heat 8

9 Does life violate the second law of thermodynamics? Life is highly organized, which seems the opposite of what entropy says should happen Single organisms are open systems Energy and mass freely flow in and out Earth is a (mostly) closed system Massive amounts of energy flows in from the sun; relatively little energy leaves That surplus of energy is used to build up complexity In the long-term (billions of years) life and the Earth will eventually succumb to entropy. But for now, we re okay 9

10 10 27 x energy difference Earth s energy budget About 3, 850,000 exajoules of sunlight energy is absorbed the Earth yearly Plants capture about 3,000 exajoules/year Total energy use in the U.S. is ~94 exajoules Energy released in the 2011 Japanese earthquake and tsunami is ~1.1 exajoules The kinetic energy of a flying mosquito is about 1/160 th of a nanojoule 10

11 Measuring energy If we have a way to measure change in energy, we have a way to measure how likely a chemical reaction will spontaneously take place A living system s free energy ( G) is energy that can do work when temperature and pressure are uniform, as in a living cell 11

12 Free energy as an indication of stability Only processes with a negative G are spontaneous Spontaneous processes can be harnessed to perform work A more stable system has the lowest amount of free energy Less probability of a spontaneous chemical reaction coming around and changing things Equilibrium is a state of maximum stability 12

13 Figure 8.5 More free energy (higher G) Less stable Greater work capacity In a spontaneous change The free energy of the system decreases ( G 0) The system becomes more stable The released free energy can be harnessed to do work Less free energy (lower G) More stable Less work capacity (a) Gravitational motion (b) Diffusion (c) Chemical reaction 13

14 Entropy and biochemical reactions Entropy determines if biochemical reactions will spontaneously take place Entropy favors a reaction that increases disorder Diffusion is a spontaneous process because it increases entropy 14

15 Entropy and chemical reactions An exergonic reaction proceeds with a net release of free energy and is spontaneous An endergonic reaction absorbs free energy from its surroundings and is not spontaneous 15

16 Thermodynamics and biology research Energetics of the HIV gp120-cd4 binding reaction The binding thermodynamics were of unexpected magnitude; changes in enthalpy, entropy, and heat capacity greatly exceeded those described for typical protein-protein interactions. These unusual thermodynamic properties were observed with both intact gp120 and a deglycosylated and truncated form of gp120 protein that lacked hypervariable loops V1, V2, and V3 and segments of its N and C termini. Together with previous crystallographic studies, the large changes in heat capacity and entropy reveal that extensive structural rearrangements occur within the core of gp120 upon CD4 binding. CD spectral studies and slow kinetics of binding support this conclusion. These results indicate considerable conformational flexibility within gp120, which may relate to viral mechanisms for triggering infection and disguising conserved receptor-binding sites from the immune system. 16

17 The role of ATP ATP powers cellular work by coupling exergonic reactions to endergonic reactions 17

18 What ATP powers A cell does three main kinds of work Chemical Transport Mechanical To do work, cells manage energy resources by energy coupling, the use of an exergonic process to drive an endergonic one Most energy coupling in cells is mediated by ATP 18

19 Figure 8.10 Transport protein Solute ATP ADP P i P P i Solute transported (a) Transport work: ATP phosphorylates transport proteins. Vesicle Cytoskeletal track ATP ATP ADP P i Motor protein Protein and vesicle moved (b) Mechanical work: ATP binds noncovalently to motor proteins and then is hydrolyzed. 19

20 Coupling spontaneous processes to nonspontaneous ones A cotransport protein can couple downhill passive diffusion to a second uphill active transport of a different substance 20

21 ADP to ATP regeneration ATP is hydrolyzed into ADP in biochemical reactions, but then what happens? The cell recycles, turning ADP back into ATP ATP H 2 O Energy from catabolism (exergonic, energy-releasing processes) ADP P i Energy for cellular work (endergonic, energy-consuming processes) 21

22 Metabolic Reactions Metabolism is the totality of an organism s chemical reactions A metabolic pathway begins with a specific molecule and ends with a product Each step is catalyzed by a specific enzyme Enzyme 1 Enzyme 2 Enzyme 3 A B C D Reaction 1 Reaction 2 Reaction 3 Product Starting molecule Similar to a signal transduction pathway 22

23 Types of metabolic reactions Catabolic pathways release energy by breaking down complex molecules into simpler compounds Anabolic pathways consume energy to build complex molecules from simpler ones The synthesis of a polypeptide from amino acid monomers is an anabolic pathway 23

24 The activation energy barrier Every chemical reaction between molecules involves bond breaking and bond forming The initial energy needed to start a chemical reaction is called the free energy of activation, or activation energy (E A ) Thermal energy from the surroundings often supplies the activation energy 24

25 Free energy Figure 8.12 A B C D Transition state A B E A C D Reactants A B G O C D Products Progress of the reaction 25

26 How enzymes lower E A Enzymes catalyze reactions by providing another lower-energy way for the reaction to take place Enzymes do not affect the change in free energy ( G); instead, they hasten reactions that would occur eventually Biology definition: Enzymes lower Ea Chemistry definition: Enzymes provide another lower-energy pathway 26

27 Free energy Figure 8.13 Course of reaction without enzyme Reactants E A without enzyme E A with enzyme is lower Course of reaction with enzyme G is unaffected by enzyme Progress of the reaction Products 27

28 Enzyme vocabulary The reactant that an enzyme acts on is called the enzyme s substrate The enzyme binds to its substrate, forming an enzyme-substrate complex The active site is the region on the enzyme where the substrate binds Induced fit of a substrate brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction The suffix -ase denotes an enzyme 28

29 Figure Substrates enter active site. 2 Substrates are held in active site by weak interactions. Substrates Enzyme-substrate complex Active site Enzyme 29

30 Figure Substrates enter active site. 2 Substrates are held in active site by weak interactions. Substrates Enzyme-substrate complex 3 Active site can lower E A and speed up a reaction. Active site Enzyme 4 Substrates are converted to products. 30

31 Figure Substrates enter active site. 2 Substrates are held in active site by weak interactions. Substrates Enzyme-substrate complex 3 Active site can lower E A and speed up a reaction. 6 Active site is available for two new substrate molecules. Enzyme 5 Products are released. Products 4 Substrates are converted to products. 31

32 The enzymatic process The enzyme binds its substrate on the active site An enzyme-substrate complex forms Induced fit brings reactive functional groups of the enzyme into contact with the substrate The enzyme breaks and reforms the chemical bonds of its substrate The enzyme releases the products 32

33 Enzyme reactions: looking closer Enzymes work similarly to proteins in their binding specificities Only certain types of enzymes will bind certain substrates lock and key 33

34 Figure 8.14 Substrate Active site (a) Enzyme (b) Enzyme-substrate complex 34

35 Some examples of enzymatic reactions The enzyme sucrase breaks down the sucrose disaccharide into its monomers glucose and fructose through hydrolysis Sucrase Sucrose (C 12 H 22 O 11 ) Glucose (C 6 H 12 O 6 ) Fructose (C 6 H 12 O 6 ) 35

36 Enzymes in biochemical pathways 3, phosphoglycerate is a product of the phosphoglycerate kinase reaction, but a reactant for the phosphoglycerate mutase reaction Blue = enzyme Black = reactant/product Green = energy used 36

37 What affects enzymatic activity? Protein activity is affected by: Temperature ph Salt concentrations Enzymes are proteins, and are affected by the same things! All proteins have an optimal temperature and ph under which they operate 37

38 Humans and bacteria have different sets of proteins that operate at difference optimal temperatures Same with ph 38

39 What else affects enzyme activity? Cofactors/coenzymes Competitive/noncompetitive inhibitors Allosteric regulators 39

40 What else affects enzyme activity? Cofactors and coenzymes can also enhance or inhibit enzyme activity Cofactors are nonprotein enzyme helpers Cofactors may be inorganic (such as a metal in ionic form) or organic An organic cofactor is often called a coenzyme Coenzymes include vitamins 40

41 Cofactors and coenzymes Metal ion cofactors The trace elements required in our diet are often metal ion cofactors Zinc in alcohol dehydrogenase Magnesium in glucose-6-phosphatase Vitamins Folic acid Vitamin C 41

42 Enzyme inhibitors Inhibitors are special molecules that slow down or halt enzymes Competitive inhibitors bind to the active site of an enzyme, competing with the substrate Noncompetitive inhibitors bind to another part of an enzyme, causing the enzyme to change shape and making the active site less effective 42

43 Figure 8.17 (a) Normal binding (b) Competitive inhibition (c) Noncompetitive inhibition Substrate Active site Competitive inhibitor Enzyme Noncompetitive inhibitor 43

44 Reversible vs. irreversible inhibitors Reversible inhibitors can detach themselves from the enzyme, allowing it to become active again Irreversible inhibitors either covalently modify or bind to the enzyme and permanently disable it 44

45 Examples of inhibitors Protease inhibitor a competitive reversible inhibitor of the HIV protein protease Ritonavir, an HIV protease inhibitor Ritonavir bound to HIV protease in the active site 45

46 Examples of inhibitors II DFP diisopropyl fluorophosphate is a potent neurotoxin Inhibits acetylcholinesterase, which breaks down the neurotransmitter acetylcholine If acetylcholine is not broken down, it accumulates and nerve impulses cannot be stopped Prolonged muscle contraction Irreversible noncompetitive inhibitor 46

47 Allosteric Regulators Allosteric regulation may either inhibit or stimulate an enzyme s activity Allosteric regulation occurs when a regulatory molecule binds to a protein at one site and affects the protein s function at another site Allo = at a distance Noncompetitive inhibitors and allosteric regulators can have the same mechanism of action 47

48 48

49 The whole picture Human glyoxalase I Two zinc ion cofactors are shown in purple A competitive inhibitor called S-hexylglutathione is shown as a space-filling model in green, blue and red. It is in the active site. 49

50 Inhibitors and Allosteric Regulators in Drugs How a drug, protein or enzyme works is called its mechanism of action Starting with a specific biological target then creating a molecule designed to affect it is called rational drug design 50

51 SSRIs Selective serotonin reuptake inhibitors Zoloft, Celexa, Prozac Serotonin is used as a neurotransmitter, a chemical signal used in cell communication Low levels of serotonin is believed to cause depression Used to treat depression The first class of drugs to use rational drug design 51

52 The normal nerve cell A nerve cell releases serotonin as a local signal Serotonin binds to serotonin receptors on an adjacent nerve cell and the signal is sent The serotonin is then released from the adjacent nerve cell The original nerve cell reuptakes the leftover serotonin back into the cell through a transporter protein 52

53 SSRI mechanism of action SSRIs slow the reuptake of serotonin by the original nerve cell An SSRI is a competitive inhibitor of the serotonin reuptake transporter. Serotonin is the normal ligand Serotonin repeatedly binds the receiving cell, causing the same chemical signal to be sent repeatedly Most serotonin receptors are GPCRs 53

54 54

55 Serotonin Celexa/Citalopram Zoloft/Sertraline tureid=3gwu&bionumber=1 55

56 Useful Links ic_entropy - a simple explanation of entropy chp06/ html - interactive animation of allosteric regulation 56

57 Vocabulary 1 st law of thermodynamics 2 nd law of thermodynamics Entropy Energy of activation Energy coupling Endergonic, exergonic reactions Metabolism Catabolic, anabolic reactions Substrate Active site Competitive, noncompetitive inhibitors Allosteric Regulators Mechanism of action Rational drug design 57

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