CONCEPT 3: ANALYZING CELL METABOLISM AND ENZYME FUNCTION (CH 8, AP Inv 13) Holtzclaw: “Metabolism” pg 58-62; 324-325 Campbell: Read pg 142-145, 155-156 Look at figures on pg 147, 157-159 Online Activities

Fig. 8-1 Figure 8.1 What causes the bioluminescence in these fungi?

Concept 3: Learning Intentions An Introduction to Energy Metabolism Examples of endergonic and exergonic reactions. The key role of ATP in energy coupling. That enzymes work by lowering the energy of activation. The catalytic cycle of an enzyme that results in the production of a final product. The factors that influence the efficiency of enzymes. Investigation: Enzyme Activity The factors that affect the rate of an enzyme reaction such as temperature, pH, enzyme concentration. How the structure of an enzyme can be altered, and how pH and temperature affect enzyme function.

BUT FIRST… Basic Metabolism Forms of Energy Laws of Thermodynamics Order vs Disorder Free Energy

Metabolism Metabolism is the totality of an organism’s chemical reactions Catabolic pathways release energy by breaking down complex molecules into simpler compounds Ex: Cellular respiration Anabolic pathways consume energy to build complex molecules from simpler ones Ex: The synthesis of protein from amino acids

Metabolism A metabolic pathway begins with a specific molecule and ends with a product Each step is catalyzed by a specific enzyme In order to have these reactions occur, what do you need? Enzyme 1 Enzyme 2 Enzyme 3 D C B A Reaction 1 Reaction 3 Reaction 2 Starting molecule Product

Energy is the capacity to cause change! For example… hold up your pen… What is energy? Energy is the capacity to cause change! For example… hold up your pen…

Fig. 8-2 A diver has more potential energy on the platform than in the water. Diving converts potential energy to kinetic energy. Figure 8.2 Transformations between potential and 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.

Forms of Energy Energy exists in various forms, some of which can perform work Kinetic energy is energy associated with motion Heat (thermal energy) is kinetic energy associated with random movement of atoms or molecules Potential energy is energy that matter possesses because of its location or structure Chemical energy is potential energy available for release in a chemical reaction Energy can be converted from one form to another

The Laws of Energy Transformation Thermodynamics is the study of energy transformations Organisms are energy transformers When you climb a cliff and then dive off… what are the energy transformations? How did you get the energy to climb the hill in the first place?

The Laws of Energy Transformation Think: Describe the forms of energy found in an apple as it grows on a tree, then falls and is digested by someone who eats it.

The First Law of Thermodynamics According to the first law of thermodynamics, the energy of the universe is constant: – Energy can be transferred and transformed, but it cannot be created or destroyed For example, BC Hydro does NOT create energy… they transform it to a form that we use in our homes.

The Second Law of Thermodynamics During every energy transfer or transformation, some energy is unusable, and is often lost as heat According to the second law of thermodynamics: – Every energy transfer or transformation increases the entropy (disorder/randomness) of the universe Think: What are some examples (biological or non-biological) of the second law?

(a) First law of thermodynamics (b) Second law of thermodynamics Fig. 8-3 Heat CO2 + Chemical energy H2O Figure 8.3 The two laws of thermodynamics (a) First law of thermodynamics (b) Second law of thermodynamics

The Second Law of Thermodynamics Chew on this one: Every energy transfer increases the entropy of the universe Therefore, the universe is unstoppable in its increasing randomness!!! What is the impact on Biological systems?*** Free Write, Learning Walk, No hands Discuss

Biological Order and Disorder Cells create ordered structures from less ordered materials

Biological Order and Disorder Cells create ordered structures from less ordered materials Organisms also replace ordered forms of matter and energy with less ordered forms

Biological Order and Disorder Cells create ordered structures from less ordered materials Organisms also replace ordered forms of matter and energy with less ordered forms Energy flows into an ecosystem in the form of light and exits in the form of heat

Biological Order and Disorder The evolution of more complex organisms does not violate the second law of thermodynamics Entropy (disorder) may decrease in an organism, but the universe’s total entropy increases “Organisms are islands of low entropy in an increasingly random universe.” (Campbell, p145)

FREE-ENERGY CHANGE, G A living system’s free energy is energy that can do work when temperature and pressure are uniform, as in a living cell It can be thought of as a measure of instability. For example… on which platform would you have the greatest ability to do work? Which one would you feel most stable?

Exergonic and Endergonic Reactions in Metabolism 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 nonspontaneous Spontaneous change Spontaneous change

Progress of the reaction Fig. 8-6 Reactants Amount of energy released (∆G < 0) Energy Free energy Products Progress of the reaction (a) Exergonic reaction: energy released Products Figure 8.6 Free energy changes (ΔG) in exergonic and endergonic reactions Amount of energy required (∆G > 0) Energy Free energy Reactants Progress of the reaction (b) Endergonic reaction: energy required

NOW… ATP in energy coupling Energy of Activation Catalytic Cycle efficiency of enzymes

How does a Cell do Work? A cell does three main kinds of work: Chemical ex) Building glycogen Transport ex) active transport across a cell membrane Mechanical ex) beating cilia in the trachea 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 – a molecule with a very high free energy

Energy is released from ATP when the terminal phosphate bond is broken The bonds between the phosphate groups of ATP’s tail can be broken by hydrolysis Energy is released from ATP when the terminal phosphate bond is broken This release of energy comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves Phosphate groups Ribose Adenine For the Cell Biology Video Stick Model of ATP (Adenosine Triphosphate), go to Animation and Video Files.

H2O P P P Adenosine triphosphate (ATP) P + P P + Energy Fig. 8-9 P P P Adenosine triphosphate (ATP) H2O Figure 8.9 The hydrolysis of ATP P + P P + Energy i Inorganic phosphate Adenosine diphosphate (ADP)

FYI: ATP drives endergonic reactions by phosphorylation, transferring a phosphate group to some other molecule, such as a reactant Phosphate groups Ribose Adenine

The Regeneration of ATP ATP is a renewable resource that is regenerated by addition of a phosphate group to ADP The rate of renewal is VERY fast! 10 millions ATP molecules are turned over every second in every one of your cells… if this didn’t happen you would use up your body weight in molecules in one day. P i ADP + Energy from catabolism (exergonic, energy-releasing processes) Energy for cellular work (endergonic, energy-consuming ATP H2O

Enzymes A catalyst is a chemical agent that speeds up a reaction without being consumed by the reaction An enzyme is a catalytic protein Hydrolysis of sucrose by the enzyme sucrase is an example of an enzyme-catalyzed reaction Even though the reaction is “spontaneous”/exergonic/ releases free energy, it would happen WAY to slow (years) without help from the enzyme due to its very high energy of activation. With the enzyme, the reaction takes seconds.

Sucrose (C12H22O11) Sucrase Glucose (C6H12O6) Fructose (C6H12O6) Fig. 8-13 Sucrose (C12H22O11) Sucrase Figure 8.13 Example of an enzyme-catalyzed reaction: hydrolysis of sucrose by sucrase Glucose (C6H12O6) Fructose (C6H12O6)

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 (EA) (to contort the bonds) Activation energy is often supplied in the form of heat from the surroundings

Progress of the reaction Fig. 8-14 A B C D Transition state A B EA C D Free energy Reactants A B Figure 8.14 Energy profile of an exergonic reaction ∆G < O C D Products Progress of the reaction

How Enzymes Lower the EA Barrier Enzymes catalyze reactions by lowering the EA barrier; they do not affect the change in free energy (∆G) Animation: How Enzymes Work

Progress of the reaction Fig. 8-15 Course of reaction without enzyme EA without enzyme EA with enzyme is lower Reactants Free energy Course of reaction with enzyme ∆G is unaffected by enzyme Figure 8.15 The effect of an enzyme on activation energy Products Progress of the reaction

Substrate Specificity of Enzymes 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 Most enzymes are capable of 1000 substrate actions per second! For the Cell Biology Video Closure of Hexokinase via Induced Fit, go to Animation and Video Files.

Substrate Active site Enzyme Enzyme-substrate complex (a) (b) Fig. 8-16 Substrate Active site Figure 8.16 Induced fit between an enzyme and its substrate Enzyme Enzyme-substrate complex (a) (b)

Catalysis in the Enzyme’s Active Site In an enzymatic reaction, the substrate binds to the active site of the enzyme. Think of four mechanisms which allow the active site to lower an EA barrier…

Catalysis in the Enzyme’s Active Site Four mechanisms which allow the active site to lower an EA barrier: Orienting substrates correctly – providing a place for reactants to find each other Straining substrate bonds – contorting reactants towards transition state through weak H and ionic interactions from the R groups in the protein Providing a favorable microenvironment – ex) acidic conditions via acidic R-groups Covalently bonding to the substrate – this covalent bonding is temporary… it is released in subsequent reactions

Fig. 8-17 Substrates enter active site; enzyme changes shape such that its active site enfolds the substrates (induced fit). 1 Substrates held in active site by weak interactions, such as hydrogen bonds and ionic bonds. 2 Substrates Enzyme-substrate complex Active site can lower EA and speed up a reaction. 3 Active site is available for two new substrate molecules. 6 Figure 8.17 The active site and catalytic cycle of an enzyme Enzyme 5 Products are released. Substrates are converted to products. 4 Products

Effects of Local Conditions on Enzyme Activity An enzyme’s activity can be affected by: Substrate concentration: activity increases with increasing substrate concentration until the saturation point is reached (where all active sites are occupied) General environmental factors, such as temperature and pH Chemicals that specifically influence the enzyme

Effects of Temperature and pH Each enzyme has an optimal temperature in which it can function Each enzyme has an optimal pH in which it can function

Optimal temperature for typical human enzyme Optimal temperature for Fig. 8-18 Optimal temperature for typical human enzyme Optimal temperature for enzyme of thermophilic (heat-tolerant) bacteria Rate of reaction 20 40 60 80 100 Temperature (ºC) (a) Optimal temperature for two enzymes Optimal pH for pepsin (stomach enzyme) Optimal pH for trypsin (intestinal enzyme) Figure 8.18 Environmental factors affecting enzyme activity Rate of reaction 1 2 3 4 5 6 7 8 9 10 pH (b) Optimal pH for two enzymes

Cofactors Cofactors are nonprotein enzyme helpers Cofactors may be inorganic (such as a metal in ionic form) or organic An organic cofactor is called a coenzyme Coenzymes include vitamins

Enzyme Inhibitors 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 Examples of inhibitors include toxins, poisons, pesticides, and antibiotics

Noncompetitive inhibitor Fig. 8-19 Substrate Active site Competitive inhibitor Enzyme Figure 8.19 Inhibition of enzyme activity Noncompetitive inhibitor (a) Normal binding (b) Competitive inhibition (c) Noncompetitive inhibition

Regulation of enzyme activity helps control metabolism Chemical chaos would result if a cell’s metabolic pathways were not tightly regulated A cell does this by switching on or off the genes that encode specific enzymes or by regulating the activity of enzymes

Allosteric Regulation of Enzymes 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

Allosteric Activation and Inhibition Most allosterically regulated enzymes are made from polypeptide subunits Each enzyme has active and inactive forms The binding of an activator stabilizes the active form of the enzyme The binding of an inhibitor stabilizes the inactive form of the enzyme

Figure 8.20 Allosteric regulation of enzyme activity Allosteric enyzme with four subunits Active site (one of four) Regulatory site (one of four) Activator Active form Stabilized active form Oscillation Non- functional active site Inhibitor Inactive form Stabilized inactive form Figure 8.20 Allosteric regulation of enzyme activity (a) Allosteric activators and inhibitors Substrate Inactive form Stabilized active form (b) Cooperativity: another type of allosteric activation

Cooperativity is a form of allosteric regulation that can amplify enzyme activity In cooperativity, binding by a substrate to one active site stabilizes favorable conformational changes at all other subunits

(b) Cooperativity: another type of allosteric activation Fig. 8-20b Substrate Inactive form Stabilized active form Figure 8.20b Allosteric regulation of enzyme activity (b) Cooperativity: another type of allosteric activation

Identification of Allosteric Regulators Allosteric regulators are attractive drug candidates for enzyme regulation Inhibition of proteolytic enzymes called caspases may help management of inappropriate inflammatory responses

Feedback Inhibition In feedback inhibition, the end product of a metabolic pathway shuts down the pathway Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed

Fig. 8-22 Initial substrate (threonine) Active site available Threonine in active site Enzyme 1 (threonine deaminase) Isoleucine used up by cell Intermediate A Feedback inhibition Enzyme 2 Active site of enzyme 1 no longer binds threonine; pathway is switched off. Intermediate B Enzyme 3 Intermediate C Figure 8.22 Feedback inhibition in isoleucine synthesis Isoleucine binds to allosteric site Enzyme 4 Intermediate D Enzyme 5 End product (isoleucine)

SPECIFIC LOCALIZATION OF ENZYMES WITHIN THE CELL Structures within the cell help bring order to metabolic pathways Some enzymes act as structural components of membranes In eukaryotic cells, some enzymes reside in specific organelles; for example, enzymes for cellular respiration are located in mitochondria