8.0 Introduction

1. Life Viewed as Constant Flow of Energy
1. Required for Each of the Significant Properties of Life fig 8.1
2. Bioenergetics: How Energy Behaves in Living Systems

1. The Flow of Energy in Living Things
1. Energy Is the Ability to Do Work
1. Exists in two states
1. Kinetic energy: Energy of motion
2. Potential energy: Stored energy that has the capacity of moving

2. Living organisms transform potential energy into kinetic energy

2. Thermodynamics Is the Study of Energy
1. Energy is readily measured by its conversion into heat
2. Unit of heat: 1000 calories = 1 kilocalorie (kcal)

3. Oxidation-Reduction
1. Life exists on earth because it is able to capture energy from the sun
2. Energy from the sun transformed into chemical energy
1. Process called photosynthesis
2. Done by plants, algae and certain bacteria
3. Combine water and carbon dioxide to make sugars
4. Energy stored in covalent bonds between sugar atoms

3. Certain reactions pass electrons from one molecule to another
4. Oxidation: Atom or molecule loses an electron, becomes oxidized
1. Oxygen strongly attracts electrons
2. Oxygen is most common electron acceptor in biological systems

5. Reduction: Atom or molecule gains an electron and is reduced
6. Redox reactions occur together, electron transfers from one atom to other fig 8.2
7. Reactions play key role in flow of energy through biological systems
8. Light adds energy and boosts electron to higher energy level

2. The Laws of Thermodynamics
1. First Law of Thermodynamics
1. Energy can be transformed but not created or destroyed
2. Total amount of energy in the universe remains constant
3. Animals transfer food potential energy into their own chemical bonds fig 8.1
4. Energy is not lost but may be changed into other forms
1. Converted to kinetic energy, light, electricity
2. Also dissipated as heat

5. Heat harnessed to do work only via heat gradient
1. Temperature difference between two areas
2. Cells too small to maintain substantial internal heat differences

2. Second Law of Thermodynamics
1. All objects tend to become less ordered, disorder is increasing
2. Spontaneous conversion from order/low stability to disorder/stability fig 8.3

3. Entropy
1. Measure of disorder of a system = S
2. Universe has progressively become disordered since beginning, increasing entropy

3. Free Energy
1. Bonds Between Atoms Hold Molecules Together
1. Free energy: Energy available to break and form chemical bonds = G
2. Enthalpy: Energy within a cell that is available to do work = H
3. Temperature = T

2. Free Energy = Ordering Influences - Disordering Influences
1. G = H – TS
2. Change in free energy: ”G =”H – T”S fig 8.4
3. Positive ”G: Endergonic reactions
1. Products contain more free energy than the reactants
2. Reactions do not occur spontaneously, requires input of energy

4. Negative ”G: Exergonic reactions
1. Products contain less free energy or more disorder than reactants
2. Reactions occur spontaneously, release excess usable free energy

4. Activation Energy
1. Reactions Require an Input of Energy to Get Started
1. Must break chemical bonds before new bonds can be created
2. Activation energy: Required to destabilize existing chemical bonds fig 8.5a
3. Rate of exergonic reaction depends on activation energy needed to start reaction
4. Large activation energy, reaction proceeds slowly

2. Catalysis
1. Stressing chemical bonds makes them easier to break fig 8.5b
2. Catalyst: Substance that carries out catalysis
3. Cannot violate basic laws of thermodynamics
4. Accelerates reaction in both forward and reverse directions
5. Direction of reaction dependent on free energy
6. Analogy of bowling ball rolling down hill

1. Enzymes
1. Enzymes Carry Out Catalysis in Living Organisms
1. Are generally proteins (or RNA) with specialized shapes
2. Permit temporary associations with the molecules that are reacting
3. Lower activation energy required for new bonds to form
1. Bring two substrates together in the correct orientation
2. Stress particular bonds of a substrate

4. Example: Formation of carbonic acid from carbon dioxide and water
1. Reaction proceeds in either direction
2. Reaction is slow because of a great activation energy
3. Carbonic anhydrase: Enzyme that speeds the reaction
4. Enzymes given the name of their substrate with the ending -ase

2. Thousands of Different Enzymes Exist
1. Each enzyme catalyzes a different reaction
2. Different cells contain different complements of enzymes

2. How Enzymes Work
1. Globular Protein Enzymes Possess Surface Clefts Called Active Sites fig 8.6
1. Enzymes are specific in their choice of substrate
2. Form enzyme-substrate complex
3. The substrate must fit precisely into the active site
1. Amino acid side groups of enzyme react with substrate
2. Bond stressed or distorted, activation energy decreased

4. Substrate binding causes enzyme to slightly change shape
1. Induced fit: Binding may induce shape adjustments in the protein fig 8.7
2. Substrate itself may act as activator

3. Factors Affecting Enzyme Activity
1. Temperature fig 8.8a
1. Increasing temperature increases random motion and rate of reaction
2. Beyond temperature optimum rate not increased
3. Below optimum
1. Hydrogen bonds and hydrophobic interactions not flexible
2. Does not permit induced fit necessary for catalysis

4. Above optimum
1. Forces too weak to maintain enzyme's shape
2. Enzymes denatures

5. Human enzyme temperature optima range from 35ºC to 40ºC
6. Hot spring bacteria proteins have more stable enzymes, optima to 70ºC

2. pH fig 8.8b
1. Hydrogen ion concentration disrupts bonds between oppositely charged amino acids
2. With more H+ ions fewer negative, more positive charges occur
3. Most enzymes have a pH optimum of 6 to 8
4. Enzymes that function in acids retain 3-D shape when many H⁺ present

3. Inhibitors and Activators
1. Activity dependent on presence of specific substances
1. Substances bind to enzyme and change its shape
2. When shape changes activity is altered

2. Inhibitors bind to enzyme and decrease its activity
1. Feedback inhibition: End product inhibits reaction early in pathway
2. Competitive inhibitors bind at same site as substrate
3. Noncompetitive inhibitors bind at different site fig 8.9

3. Allosteric site: Region where non-competitive inhibitor binds
4. Allosteric inhibitor binds to allosteric site to reduce enzyme activity fig 8.9b
5. Activators bind to allosteric sites
1. Keep enzymes in active configuration
2. Increase enzyme activity

4. Enzyme Cofactors
1. Cofactors Are Additional Components that Aid Enzyme Action
1. Many metallic trace elements are cofactors
2. Coenzymes are nonprotein organic molecules like vitamins
3. Serve as acceptors for electron pairs in redox reactions, shuttle energy
4. Example: Nicotinamide adenine dinucleotide (NAD⁺) fig 8.10
5. Structure of NAD⁺
1. Composed of nucleotides NMP and AMP
2. AMP acts as core, provides for enzyme shape recognition
3. NMP is active part, contributes site that readily accepts electrons

6. Important biological hydrogen acceptor
1. NAD⁺ acquires an electron and hydrogen to become reduced NADH
2. NADH carries energy of electron and hydrogen around in cells

5. Enzymes Take Many Forms
1. Multienzyme Complexes
1. Groups of several enzymes that catalyze successive steps of a reaction
2. Assembly is non-covalently bonded
3. Example: Bacterial pyruvate dehydrogenase multienzyme complex fig 8.11
1. Enzymes carry out three sequential reactions in oxidative metabolism
2. Each complex has multiple copies of each enzyme, 60 subunits total
3. Subunits work together

4. Increases catalytic efficiency
1. Product of one reaction delivered to next, if released would diffuse away
2. Eliminates possibility of unwanted side reactions
3. All reactions controlled as one unit

5. Example: Fatty acid synthetase complex
1. Catalyzes synthesis of fatty acids from two-carbon precursors
2. Includes seven enzymes and reaction intermediates

2. Not All Biological Catalysts Are Proteins
1. RNA catalyzes certain reactions involving RNA molecules
1. RNA catalysts called ribozymes
2. Accelerate reactions, show specificity to substrates

2. Two kinds of ribozymes
1. Intramolecular catalysts have folded structures, act upon selves
2. Intermolecular catalysts act on other molecules

3. Catalyzed reactions involve small RNA molecules
1. Chip out unnecessary sections from RNA copies of genes
2. Prepare ribosomes for protein synthesis
3. Facilitate replication of DNA in mitochondria

4. RNA may have evolved before proteins and catalyzed their formation

1. What Is ATP?
1. Adenosine Triphosphate (ATP) Is the Chief Energy Currency of All Cells
1. Bulk of photosynthesis channeled into ATP production
2. Energy stores in fat and starch

2. Structure of the ATP Molecule
1. Composed of three subunits fig 8.12
2. Five-carbon ribose sugar serves as the backbone
3. Adenine composed of two C–N rings attaches to the ribose
1. Nitrogen has unshared electrons
2. Weakly attracts hydrogen atoms
3. Called a nitrogenous base (one of four in DNA)

4. Triphosphate group attaches to the ribose

3. How ATP Stores Energy
1. Key lies in triphosphate group
1. Highly negatively charged, repel one another
2. Covalent bonds linking phosphates are unstable
3. Bonds are readily broken and energy transferred

2. Usually only outer-most bond is broken
1. ATP _ ADP + Pi + 7.3 kcal/mole
2. Adenosine diphosphate = ADP
3. Pi is inorganic phosphate group

4. How ATP Powers Energy-Requiring Reactions
1. Cells use ATP in exergonic reactions
2. Not spontaneous reactions, products possess more energy than the reactants
3. Can power cell activities
1. Terminal high-energy bond is more exergonic than others
2. Activation energy is usually less than 7 kcal/mole

4. Instability of phosphate bond makes ATP poor long-term storage molecule
5. Cells do not stockpile ATP but create it as needed
6. Cells contain a pool of ATP, ADP and phosphate

1. Biochemical Pathways: The Organizational Units of Metabolism
1. Metabolism
1. Sum of all chemical reactions carried out by an organism
2. Anabolism: Expend energy to make or transform bonds
3. Catabolism: Harvest energy when bonds broken

2. Reactions in Biological Systems Occur in Sequence
1. Product of one reaction becomes substrate for another fig 8.13
2. Organized units of metabolism
3. Location of enzymes helps map out model of pathway

3. How Biochemical Pathways Evolved
1. First primitive biochemical processes
1. Energy-rich molecules scavenged from the environment
2. Molecules existed in the existing organic soup

2. Catalyzed reactions were simple one-step processes
3. Without energy-rich molecules only cells that synthesized own energy survived
4. Energy utilizing reaction became coupled to energy-producing reaction
5. Evolution of pathways works backwards
1. Occur one step at a time
2. Final reactions generally evolve first, initial reaction evolves last

4. How Biochemical Pathways Are Regulated
1. Output of pathways must be controlled
2. Primitive organisms evolved feedback mechanisms
3. End product binds to allosteric site on enzyme that catalyzes first reaction
1. Binding to enzyme shuts down first reaction
2. Effectively shuts down whole pathway
3. Increase of cell products inhibits production of more product

4. Called feedback inhibition fig 8.14