Thinking About Energy and Enzymes Thinking About Energy and Enzymes

Case Study: Frank Frank’s aldehyde dehydrogenase (ALDH) enzyme has a substitution at position 487. He has the amino acid lysine at this position instead of glutamic acid. Frank’s aldehyde dehydrogenase (ALDH) enzyme has a substitution at position 487. He has the amino acid lysine at this position instead of glutamic acid. You Try: Question 1 You Try: Question 1

Metabolism Metabolism = all an organism’s chemical reactions An emergent property!

Metabolism Overview Notice that this is an open system!

What is Energy?

Energy: Capacity to Do Work 1. Kinetic Energy- energy of movement 2. Potential Energy- energy due to location/structure 3. Chemical Energy- result of arrangement of atoms in molecules (potential energy in disguise!!)

First Law of Thermodynamics ?

Energy can be transferred and transformed, but not created or destroyed. What has Escher done??

Second Law of Thermodynamics ?

Every energy transfer increases the ENTROPY of the universe

Thermodynamics The quantity of energy in the universe is constant, but the quality is not!

Life is Ordered… Does this violate the second law of thermodynamics?

Life is Ordered… No! Life exists at the expense of free energy.

Free Energy (G) Ordered states (at left) have high free energy, or energy available to do work Ordered states (at left) have high free energy, or energy available to do work Disordered states (high entropy) have low free energy. Disordered states (high entropy) have low free energy.

Free Energy (G) Total Energy = usable energy + unusable energy Enthalpy (H)Free Energy (G)Entropy (S) or H = G + T S G = H – T S

More on Free Energy delta G = G final state – G starting state For a process to occur spontaneously, the system must either lose energy (decrease H) or lose order (increase S) This results in a negative value for

Free Energy (G) in Metabolism Metabolic reactions can be classified as either: EXERGONIC “Energy Outward” Negative delta G Spontaneous ENDERGONIC “Energy inward” Positive delta G Not Spontaneous! OR

You Try : Question 2

Closed Systems Reach Equilibrium: What happens if we reach equilibrium?!?

Organisms are Open Systems! = “Metabolic Disequilibrium”

Revisiting ATP

ATP does work by phosphorylating intermediates. Phosphorylation usually makes a molecule less stable/more reactive.

Example:

Enzymes The Chemistry of Life is driven by more than Thermodynamics! This is a spontaneous (negative delta G) reaction! So… 1. Why doesn’t table sugar break down into glucose and fructose in our kitchens? 2. Why does sucrose break down so easily in organisms?

Activation Energy

Enzymes Lower Activation Energy Barrier

Enzymes: Key Features Biological Catalysts- Enzymes can increase the rate of a reaction, but does not change the delta G! Biological Catalysts- Enzymes can increase the rate of a reaction, but does not change the delta G! Enzymes are specific, and typically only recognize one particular substrate Enzymes are specific, and typically only recognize one particular substrate Substrates interact with active sites on the enzyme as described by the induced fit model Substrates interact with active sites on the enzyme as described by the induced fit model Enzymes are affected by their environment Enzymes are affected by their environment

Enzyme Function

Enzymes: Induced Fit

Enzymes can orient substrates Enzymes can orient substrates Enzymes can induce strain in the substrate Enzymes can induce strain in the substrate Enzymes can temporarily add chemical groups to substrates Enzymes can temporarily add chemical groups to substrates Acid-base catalysis Acid-base catalysis Covalent catalysis Covalent catalysis Metal ion catalysis Metal ion catalysis Mechanisms for Enzyme Function

An Enzyme’s ACTIVITY is generally OPTIMIZED for its Environment How does this arise??

Thinking About Simple Enzyme Kinetics You try: Question 3

Many Enzymes Require COFACTORS or COENZYMES: Vitamin C (ascorbate) is a Coenzyme The hydroxylation of proline residues in collagen requires ascorbate. The hydroxylation of proline residues in collagen requires ascorbate. Vitamin C is, therefore, required for the maintenance of normal connective tissue as well as for wound healing. Vitamin C is, therefore, required for the maintenance of normal connective tissue as well as for wound healing. Vitamin C also is necessary for bone remodeling due to the presence of collagen in the organic matrix of bones. Vitamin C also is necessary for bone remodeling due to the presence of collagen in the organic matrix of bones.

Enzymes: Regulation Enzymes: Regulation Enzyme Inhibitors- Molecules that selectively inhibit the activity of specific enzymes Competitive Inhibitors Block substrates from entering active site Noncompetitive Inhibitors Bind to another region of the enzyme, changing the shape of the enzyme and limiting or preventing its activity

Enzyme Inhibitors Normal Function Noncompetitive Inhibition Competitive Inhibition

Cool Things To Do With Enzyme Inhibitors: Design Drugs Figure: COX 1 and 2 : The cyclo-oxygenase systems by drdoc on-line ©

Other Mechanisms: Allosteric Regulation Regulatory molecules may bind weakly to an allosteric enzyme, changing its shape and function

Other Mechanisms: Allosteric Regulation

Allosteric Regulation Often Explains Feedback Inhibition:

One Last Mechanism: Cooperativity The binding of one molecule of substrate to an allosteric enzyme may trigger a favorable conformational change in the other subunits

Thinking Ahead to Lab

Oxidation of Catechol (catalyzed by Catecholase) Our Model System: Factors that might affect the rate of this reaction?

How will we know if our enzyme is working and/or affected by its environment?

Introducing Your Reagents: “Potato Juice” = Enzyme Solution!

Thinking About Good Experimental Design What is a ‘control’? What does it tell me about my experiment? What is a ‘control’? What does it tell me about my experiment? What would a good control be for this experiment? What would a good control be for this experiment? With your lab group, complete the Prelab Sheet: 1)Identify factors that might affect enzyme function (generate hypotheses!) 2)Decide which factor you would like to test 3)Design your experiment!