LECTURE - 5 Biological Thermodynamics

Outline  Proteins Continued  Amino Acid Chemistry  Tertiary & Quaternary Structure  Biological Thermodynamics  Metabolic/Anabolic/Catabolic  Energy & Thermodynamics 1 st & 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 5.20f Hydrogen bond Disulfide bridge Polypeptide backbone Ionic bond Hydrophobic interactions

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

Figure 5.20f Disulfide bridge Polypeptide backbone Proteins – Tertiary Structure  Disulfide bridge Covalent bond between sulfhydryl groups on two neighboring cysteine residues

Figure 5.20f Hydrogen bond Polypeptide backbone Ionic bond Proteins – Tertiary Structure  Hydrophobic interactions  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

Proteins – Tertiary Structure  Other factors influencing folding  pH  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

Metabolic Pathway Figure 8.UN01 Enzyme 1 Enzyme 2 Enzyme 3 Reaction 1 Reaction 2Reaction 3 ProductStarting molecule A B C D

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 Kinetic Energy Heat Energy Chemical 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 (CH4) burns in O2 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 8.5a 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 8.6a (a) Exergonic reaction: energy released, spontaneous Reactants Energy Products Progress of the reaction Amount of energy released (  G  0) Free energy

Figure 8.6b (b) Endergonic reaction: energy required, nonspontaneous Reactants Energy Products Amount of energy required (  G  0) Progress of the reaction Free energy

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 8.7a (a) An isolated hydroelectric system  G  0  G  0

Figure 8.7b (b) An open hydroelectric system  G  0

Figure 8.7c (c) A multistep open hydroelectric system  G  0

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

Phosphate groups Adenine Ribose ATP (adenosine triphosphate)  The cell’s energy shuttle  Composed of:  ribose (a sugar)  adenine (a nitrogenous base)  three phosphate groups Figure 8.8a

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 8.8b 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 ATPADP PO 4 3- H2OH2O

Figure 8.9 Glutamic acid Ammonia Glutamine (b) Conversion reaction coupled with ATP hydrolysis Glutamic acid conversion to glutamine (a) (c) Free-energy change for coupled reaction Glutamic acid Glutamine Phosphorylated intermediate Glu NH 3 NH 2 Glu  G Glu = +3.4 kcal/mol ATP ADP NH 3 Glu P P i ADP Glu NH 2  G Glu = +3.4 kcal/mol Glu NH 3 NH 2 ATP  G ATP =  7.3 kcal/mol  G Glu = +3.4 kcal/mol +  G ATP =  7.3 kcal/mol Net  G =  3.9 kcal/mol 1 2 Chemical Work

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

Energy from catabolism (exergonic, energy-releasing processes) Energy for cellular work (endergonic, energy-consuming processes) ATP ADPP i H2OH2O Regeneration of ATP  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. Figure 8.11

ENZYMES  Enzymes speed up metabolic reactions by lowering energy barriers