LECTURE 5 Biological Thermodynamics Outline Proteins Continued Amino

LECTURE - 5 Biological Thermodynamics

Outline Proteins Continued � Amino Acid Chemistry � Tertiary & Quaternary Structure Biological Thermodynamics � Metabolic/Anabolic/Catabolic � Energy 1 st & Thermodynamics & 2 nd Laws applied to biological processes Free Energy ATP

Proteins – Tertiary Structure Interactions amongst side (R) groups Interactions include: � � hydrogen bonds ionic bonds hydrophobic interactions van der Waals interactions Strong covalent bonds called disulfide bridges may reinforce the protein’s structure

Figure 5. 20 f Hydrogen bond Hydrophobic interactions Disulfide bridge Ionic bond Polypeptide backbone

Proteins – Tertiary Structure Hydrogen bond Polypeptide backbone Usually form between COOH and HO on different residues Can form between N and H on different residues

Proteins – Tertiary Structure Figure 5. 20 f Disulfide bridge Polypeptide backbone Covalent bond between sulfhydryl groups on two neighboring cysteine residues

Proteins – Tertiary Structure Figure 5. 20 f Hydrophobic interactions � � Hydrogen bond side-chains aggregate create pockets within proteins that effectively exclude water ionic bond � � interactions between positively and negatively charged residues occur deep in the protein, away from water Ionic bond Polypeptide backbone

Proteins – Tertiary Structure Other factors influencing folding � p. H � Location of secondary structures � The chemical make-up of the solution it’s in � Temperature

Proteins Quaternary Structure Multiple polypeptide subunits Subunits may be loosely or tightly bound together Many enzymes

Proteins Structure Shape of the protein is critical for it’s function � Location of the active site � Orientation/interaction with other molecules Loss of the proper shape can destroy function � DNA mutations � Temperature � Denaturation

Proteins - Review Made out of 20 amino acids Form follows function � Four structural levels Important Functions Enzymes � Structural Support (collagen/keratin) � Storage ( � Hormones � Transport � Cellular communications � Movement � Defense against foreign substances �

Metabolism The totality of an organism’s chemical reactions Metabolic Pathway begins with a specific molecule and ends with a product � Each step is catalyzed by a specific enzyme

Figure 8. UN 01 Metabolic Pathway Enzyme 2 Enzyme 1 A Reaction 1 Starting molecule B Reaction 2 Enzyme 3 C Reaction 3 D Product

Catabolic pathways Release energy � Complex Simple � Example: Cellular respiration, the breakdown of glucose in the presence of oxygen

Anabolic pathways Consume energy � Simple Complex � Example: Synthesis of a protein from amino acids

Energy The capacity to cause change Forms of Energy: � Kinetic energy: energy associated with motion � Heat (thermal energy): kinetic energy associated with random movement of atoms or molecules � Potential energy: energy that matter possesses because of its location or structure � Chemical energy: potential energy available for release in a chemical reaction Energy can be converted from one form to another

Energy Potential Energy Chemical Energy Kinetic Energy Heat Energy

Thermodynamics The study of energy transformations Isolated system: closed or isolated from surroundings. � Liquid in thermos Open system: energy and matter can be transferred between the system and its surroundings � Organisms are open systems

First Law of Thermodynamics The energy of the universe is constant � Energy can be transferred and transformed, but it cannot be created or destroyed Also called the principle of conservation of energy

Second Law of Thermodynamics During every energy transfer or transformation, some energy is unusable � Unusable energy is often lost as heat The Second law of thermodynamics � Every energy transfer or transformation increases the entropy (disorder) of the universe

1 st & 2 nd Laws Applied Chemical Energy (food) CO 2 & H 2 O Heat Cells unavoidably convert organized forms of energy to heat

Spontaneous Processes Occur without energy input; they can happen quickly or slowly � Examples: A drop of food coloring will spread in a glass of water. Methane (CH 4) burns in O 2 gas. Ice melts in your hand. Ammonium chloride dissolves in a test tube with water, making the test tube colder For a process to occur without energy input, it must increase the entropy of the universe

Spontanious Processes

Biological Order/Disorder Cells create ordered structures from less ordered materials Does the evolution of more complex organisms violate the second law of thermodynamics?

Biological Order/Disorder Entropy (disorder) may decrease in an organism, but the universe’s total entropy increases 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

Free-energy The free-energy change of a reaction tells us whether or not the reaction occurs spontaneously. Free-energy - The energy that can do work when temperature and pressure are uniform � The energy that cells can use to do work G

Change in free energy (∆G) The change in free energy (∆G) during a process is related to the change in enthalpy, or change in total energy (∆H), change in entropy (∆S), and temperature in Kelvin (T) ∆G = ∆H – T∆S Only processes with a negative ∆G are spontaneous Spontaneous processes can be harnessed to perform work

Free Energy, Stability & Equilibrium Free energy is a measure of a system’s instability, its tendency to change to a more stable state During a spontaneous change, free energy decreases and the stability of a system increases Equilibrium is a state of maximum stability A process is spontaneous and can perform work only when it is moving toward equilibrium

Figure 8. 5 a • 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

Free Energy and Metabolism The concept of free energy can be applied to the chemistry of life’s processes

Exergonic reaction Proceeds with a net release of free energy and is spontaneous ( G is less than 0)

Endergonic Reaction Absorbs free energy from its surroundings and is nonspontaneous ( G is greater than 0).

Figure 8. 6 a (a) Exergonic reaction: energy released, spontaneous Free energy Reactants Amount of energy released ( G 0) Energy Products Progress of the reaction

Figure 8. 6 b (b) Endergonic reaction: energy required, nonspontaneous Free energy Products Energy Reactants Progress of the reaction Amount of energy required ( G 0)

Metabolism and Equilibrium Reactions in a closed system eventually reach equilibrium and then do no work Cells are not in equilibrium; they are open systems experiencing a constant flow of materials A defining feature of life is that metabolism is never at equilibrium A catabolic pathway in a cell releases free energy in a series of reactions

Figure 8. 7 a G 0 (a) An isolated hydroelectric system G 0

Figure 8. 7 b (b) An open hydroelectric system G 0

Figure 8. 7 c G 0 (c) A multistep open hydroelectric system

Exergonic & Endergonic reactions in the cell – ATP 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

Figure 8. 8 a ATP (adenosine triphosphate) The cell’s energy shuttle Composed of: ribose (a sugar) � adenine (a nitrogenous base) � three phosphate groups � Phosphate groups Adenine Ribose

Hydrolysis of ATP = ADP + Energy 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

Figure 8. 8 b Adenosine triphosphate (ATP) Energy Inorganic phosphate Adenosine diphosphate (ADP) The hydrolysis of ATP

Hydrolysis of ATP Mechanical, transport, and chemical work are powered by the hydrolysis of ATP The energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction Overall, the coupled reactions are exergonic

ATP phosphorylated intermediates ATP drives endergonic reactions by phosphorylation � ATP can transfer a phosphate group to some other molecule, such as a reactant � Called a phosphorylated intermediate ATP ADP PO 43 - H 2 O

Figure 8. 9 (a) Glutamic acid conversion to glutamine Glutamic acid (b) Conversion reaction coupled with ATP hydrolysis NH 3 Glu NH 2 GGlu = +3. 4 kcal/mol Glutamine Ammonia NH 3 P 1 Glu ATP Glu 2 ADP Glu Phosphorylated intermediate Glutamic acid NH 2 Glutamine GGlu = +3. 4 kcal/mol (c) Free-energy change for coupled reaction Glu NH 3 GGlu = +3. 4 kcal/mol + GATP = 7. 3 kcal/mol ATP NH 2 Glu ADP GATP = 7. 3 kcal/mol Net G = 3. 9 kcal/mol Chemical Work Pi ADP Pi

Figure 8. 10 Transport protein Solute ATP ADP P Pi Pi Solute transported (a) Transport work: ATP phosphorylates transport proteins. Cytoskeletal track Vesicle ATP ADP ATP Motor protein Protein and vesicle moved (b) Mechanical work: ATP binds noncovalently to motor proteins and then is hydrolyzed. Pi

Figure 8. 11 Regeneration of ATP is renewable � regenerated by adding a phosphate group to adenosine diphosphate (ADP). The energy to phosphorylate ADP comes from catabolic reactions in the cell. ATP Energy from catabolism (exergonic, energy-releasing processes) ADP H 2 O Pi Energy for cellular work (endergonic, energy-consuming processes)

ENZYMES Enzymes speed up metabolic reactions by lowering energy barriers