Molecular Biophysics PDF

MOLECULAR BIOPHYSICS BASIC COMPONENTS OF LIFE  complex biological structures or systems starts from the atomic level.  atom → smallest unit of living and non- living systems  molecule → bonded atoms.  macromolecule → more complex (large...

MOLECULAR BIOPHYSICS BASIC COMPONENTS OF LIFE  complex biological structures or systems starts from the atomic level.  atom → smallest unit of living and non- living systems  molecule → bonded atoms.  macromolecule → more complex (large) molecules  organelle → parts of the cell  cell → the basic units of life  tissue → cells that work together for similar function  organ → groups of tissue that work together for a specific purpose  organ system → several organs working together  organism → any living creature Living things are highly organized molecular structures. Interactions between atoms, Intramolecular organizations, Intermolecular interactions, directly determine the characteristics of living things. The properties of all compounds, including chemical elements and compounds necessary for living things, depend on their atomic structures.  Each element contains a certain type of atom.  When two or more atoms chemically bond together, they form a molecule. intramolecular and intermolecular interactions source ATOM  ATOMIC AND MOLECULAR CONTENT OF LIVINGS Despite the extraordinary diversity of biological species and individuals, biological molecules and biochemical reactions are not so diverse. Essential Elements in Other elements 0,7% the Body (99,3%) Calcium Ca Hydrogen H (61%) Phosphorus P Oxygen O (26%) Potassium K Sulfur S Carbon C (10%) Sodium Na Nitrogen N (2%) Chlorine Cl Magnesium Mg  TRACE ELEMENTS (0,01%) Iron Fe Trace elements are elements Iodine I present in the organism in very small amounts. Copper Cu Zinc Zn Iron is an essential element for Selenium Se almost all living organisms as it Cobalt Co participates in a wide variety of Chrome Cr metabolic processes, including Fluorine F oxygen transport, deoxyribonucleic acid (DNA) synthesis, and electron transport.  When two or more atoms chemically bond together, they form a molecule.  bond: the forces of attraction that tie atoms together.  Chemical bonds are formed when the electrons in the outermost electronic “shell” of an atom (valence electrons) interact. The nature of the interaction between the atoms depends on their relative electronegativity.  Compounds have less energy (more stable) than the substances from which they form. Ex: water has less energy than the hydrogen and oxygen.  The type of energy stored in a bond is potential. Neutral atoms Ions Molecules  TYPES OF BONDS Metallic Bond  force that holds atoms together in a metallic substance. a metallic bond arises from the electrostatic attractive force between conduction electrons and positively charged metal ions (cations).  ions held together in a crystalline lattice in a “sea of mobile electrons” valence electrons move freely among all metal atoms (mobile). Such bonds are characterized by the following features.  Atoms in metals are closely packed in crystalline structures.  Electrons spread out among the atoms to form electron clouds. These free electrons promote thermal and electrical conductivity.  Metallic bonds are nondirectional because the outer electrons are shared by many atoms.  The overall energy of individual atoms is lowered by metallic bonds. Metallic bonds are relatively strong bonds. Within the metal crystal lattice, electrons belong to the whole crystal rather than individual ions. The mobility of electrons distinguishes metallic bonds from all others. Metals with strong metallic bonds have moderately high melting point and boiling point. Ionic Bond  Ions are formed when atoms gain or lose electrons.  An ionic bond is formed when valence electrons are transferred from one atom to the other to complete the outer electron shell.  Transfer of electrons is energetically unfavorable (ionization energy is larger than electron affinity energy), but energy of the resulting attraction between the ions is larger than the energy cost to transfer electrons.  Reactive metals such as alkali metals can react directly with the highly electronegative halogen gases to form an ionic compound “salts”.  Disrupting the arrangement of ions in a crystalline ionic compound requires a large amount of energy. So, ionic compounds have high melting, boiling points, and heats of vaporization. For the same reasons, they are hard - a strong force is needed to break up the crystal lattice of them. Covalent Bond  Involves sharing electrons because both elements have high electronegativities.  Usually is between two non-metals (ex. H, C, O, N…)  Sharing of electrons can be equal (non-polar) or unequal (polar)  Covalent bonding like ionic bonding results in a more stable compound, because the atoms involved meet the “octet rule”.  Covalent bonds are very strong bonds. o The bond formed by the sharing of one or more double valence electrons between atoms of the same type or different is called a covalent bond (as a result of the fusion of electron clouds in the outer orbitals of atoms). strong interaction In molecules or crystals such as N2, CO2, H2O, CH4 etc., atoms are bonded by covalent bonds.  A “shared” pair of electrons makes a SINGLE BOND (2 total e-).  2 “shared” pairs makes a DOUBLE BOND (4 total e-).  3 “shared” pairs makes a TRIPLE BOND (6 total e-). Bond Polarity Polar Covalent Bonds (between two atoms)  A covalent bond in which electrons are not shared equally between two atoms.  Because electrons spend more time around the more electronegative atom, it causes one atom to become slightly negative and the other slightly positive.  This type of molecule has a dipole (two poles), due to a pair of opposite charges separated from each other. Ex: HCl In HCl, chlorine has a higher electronegativity than hydrogen, but, the attraction of Cl atom towards electrons is not sufficient to remove an electron from H. Consequently, the bonding electrons in HCl are shared unequally in a polar covalent bond. The unequal sharing of the bonding pair results in a partial negative charge on Cl atom and a partial positive charge on H atom. Non-polar Covalent Bond (between two atoms)  If both of the atoms have the same electronegativity, then the electrons are shared equally.  Since the atoms are the same, they will have the same electronegativity and share the electron(s) equally.  When electrons are shared equally, their bonds will never have a dipole moment and the bond will be non-polar. There is no charge separation. Molecule Polarity Polar Molecule  A polar (also known as a dipole) molecule is asymmetrical which results in an uneven distribution of charge throughout the entire molecule.  Ex: H2O which has a bent shape and is assymetrical Non-Polar Molecule  A non-polar molecule is symmetrical in shape which results in an even distribution of charge.  Ex: CH4 which is tetrahedral symmetrical in shape INTERMOLECULAR INTERACTIONS  The attractive forces between molecules are not as strong as the intramolecular forces that hold the compounds together.  But, strong enough to control physical properties such as boiling and melting point, vapor pressures and viscosity.  WEAK INTERACTIONS Intermolecular forces are weaker than intramolecular forces (e.g. ionic, metallic, or covalent bonds).  Van der Waals interactions  Dipole-dipole  Ion-dipole  Induced dipole  Ion-induced dipole  Dipole-induced dipole interactions  London dispersion forces  Hydrogen bonding VAN DER WAALS INTERACTIONS  Intermolecular forces were named Van der Waals forces in memory of Johannes van der Waals (1837- 1923), who studied intermolecular interactions in gases.  Van der Waals forces are responsible for the behavior of liquids and solids and are electrostatic in nature.  Weak but everywhere.  The forces responsible for the liquefaction of gases and the freezing of liquids are the Van der Waals forces.  Structures that form double molecular bonds such as (H2)2, (O2)2, Ar-HF, Ar-HCl, H2-Ne, H2-Ar, H2-Kr and H2-Xe can be mentioned.  van der Waals is a distance-dependent interaction between atoms or molecules. At a certain r0 value, interaction begins and a stable bonding occurs. Dipole-dipole interactions Polar molecules that have permanent dipoles are attracted to each other via electrostatic attractions.  The partial positive, δ+, end of one is attracted to the partial negative, δ−, end of the other and vice-versa.  These forces are only important when the molecules are close to each other. As the difference between the electronegativities of atoms in a diatomic molecule increases, molecule polarity and the strength of dipole-dipole force also increases. So, the melting and boiling point of the substance will be higher. Ion-dipole interactions An ion-dipole interaction is the result of an electrostatic interaction between a charged ion and a molecule that has a dipole. It is an attractive force commonly found in ionic compounds (NaCl, KCl, etc.) dissolved in solutions, especially polar liquids. A cation can attract the partially negative end of a polar molecule (b), while an anion attracts the positive end of a polar molecule (a). Na+ only attracts the negatively charged end of water molecules and Cl- attracts the positively charged end of water molecules, leading to the orientation shown. Dipole-induced dipole interactions These quite weak forces are created when the polar molecules get close enough to the nonpolar molecules to distort the electron clouds of the nonpolar molecules and create temporarily induced dipoles. The strength of these forces depends on the number of valence electrons and on the polarity of polar molecule. Nonpolar compounds do not dissolve in water. The attractive forces between the nonpolar molecules are weak dispersion forces. Oil is non-polar, water is polar, they do not dissolve in each other. The oil with lower density remains on top.  LONDON DISPERSION FORCES London dispersion forces (Fritz London, 1930) occur between all atoms and molecules due to random motion of electrons. E.g, electron cloud of He atom contains 2e- and when averaged over time, these electrons will distribute themselves evenly around nucleus. However, at any given moment, electron distribution may be uneven, resulting in an instantaneous dipole. This weak, temporary dipole can subsequently influence neighboring He atoms through electrostatic attraction and repulsion. Random fluctuations in electron density within the electron cloud of a He atom results in a short-lived ("instantaneous") dipole. The attractive force between instantaneous dipoles and the resulting induced dipoles in neighboring molecules is called the London dispersion force. ***London forces cause nonpolar substances to condense to liquids and to freeze into solids. HYDROGEN BONDING  A H-bond is a primarily electrostatic force of attraction between a hydrogen atom which is covalently bound to a more electronegative atom (F, O, N, S etc.) or group, and another electronegative atom having a lone pair of electrons.  H bonds can be intermolecular or intramolecular. X and Y: C, N, O, F etc. Normal linear hydrogen bond  The hydrogen bond is responsible for many of the physical and chemical properties of compounds, including water.  between an alcohol and a water molecule  In a pure carboxylic acid, H bonding can occur between two molecules of acid to produce a dimer.  The hydrogen bond is common in solid sugars (eg., glucose and sucrose).  A molecule of water has two hydrogen atoms. Both of these atoms can form a hydrogen bond with oxygen atoms of different water molecules. SUMMARY OF INTERMOLECULAR INTERACTIONS I →? II →? III →? IV →? V →?  PHYSICAL PROPERTIES OF WATER AND ITS IMPORTANCE FOR LIVING THINGS WATER  Water is of major importance to all living things; in some organisms, 70-90% of their body weight comes from water.  Up to 70% of the human adult body is water.  The only common compound that can be found in natural environment in 3 states (solid-liquid-gas) is water.  A polar molecule (a dipole) is asymmetrical which results in an uneven distribution of charge throughout the entire molecule.  THE BOND BETWEEN WATER MOLECULES IS A H-BOND  Each water molecule can form hydrogen bonds with up to four neighbors.  Individual hydrogen bonds are weak and easily broken or formed.  But!-Many unique and important properties of water, including  its high surface tension,  high specific heat capacity,  high heat of vaporization,  high boiling point, are due to H-bonding. Four emergent properties of water that contribute to Earth's suitability as an environment for life: 1- Cohesive behavior 2- Ability to moderate temperature 3- The expansion of water upon freezing 4- Being an excellent solvent 1. COHESIVE BEHAVIOR  Cohesion refers to the attraction between molecules of same substance. Water molecules have strong cohesive forces because of their ability to form H-bonds with one another.  Cohesive forces are responsible for surface tension which results in the tendency of a liquid’s surface to resist rupture when placed under tension or stress. Surface Tension  Surface tension is the tendency of the surface of a liquid to behave like a stretched elastic membrane. Liquids naturally tend to minimize their surface area.  Water molecules at the surface will form H bonds with their neighbors, just like water molecules deeper within the liquid. Any molecule in the liquid is under the influence of attractive forces from all directions (balanced attraction). Water molecules on the surface of liquid experience an unbalanced attraction (tend to be pulled inward).  The surface tension of a liquid can be defined as the work required to create a new unit area by moving a sufficient number of molecules to the surface.  For a small droplet, surface tension causes increase in the internal pressure of the droplet to balance the force acting on the surface. water leaking from tap dripping into a spherical shape, when we fill a glass with water so much that it slightly overflows, the water does not overflow and forms a curve at the top of the glass, some creatures can walk on water without sinking, sliding stones on the lake, the surface tension is also very important for vital activities such as the transmission of water from the roots to the leaves in plants and trees. Capillary action To better understand surface tension, it is necessary to mention two forces: cohesive force and adhesion force.  Adhesion is the attraction between different kind of molecules, and it can be quite strong for water.  Cohesion refers to the attraction between the same kind of molecules. surface tension adhesion cohesion Cohesion > Adhesion Since the cohesion between water molecules accumulated on the leaves is greater than the adhesion force between water and leaf, water does not spread over the leaf, but closes on itself and takes a spherical shape. Adhesion > Cohesion If the adhesion force is greater than the cohesion, water drop spreads completely over leaf and wets the leaf.  Adhesion enables water to “climb” upwards through thin glass tubes (capillary tubes) placed in a beaker of water. This upward motion against gravity, known as capillary action, depends on the attraction between water molecules and the glass walls of the tube (adhesion), as well as on interactions between water molecules (cohesion).  adhesion > cohesion cohesion > adhesion water molecules tend to crowd fall of liquid in the towards the glass surface and capillary tube form a concave surface with a small angle of contact.  Why are cohesive and adhesive forces important for life?  They play a role in many water-based processes in biology, including the movement of water to the tops of trees and the tears drainage from tear ducts in the corners of eyes. Cohesion-tension combines the process of capillary action with transpiration or evaporation of water from plant stomata. As transpiration occurs, evaporation of water deepens the meniscus of water in the leaf, creating negative pressure (tension). The tension pulls water in the plant xylem. Cohesion causes more water molecules to fill the gap in the xylem. ABILITY TO MODERATE TEMPERATURE  high specific heat capacity and  high heat of vaporization of water helps maintaining a moderate temperature of organisms and environments. Heat capacity is defined as the amount of heat needed to raise the temperature of 1 g of a substance by 1 oC. Heat of vaporization is the amount of heat 1 g of a liquid must absorb for it to be converted to the gaseous state.  Water has one of the highest heat capacities because it has hydrogen bonds between molecules. The higher the heat capacity, the more thermal energy the substance is capable of storing in its chemical bonds. Due to hydrogen bonding, water has a very high heat of vaporisation. A great deal of energy is required to completely break these bonds and create a gaseous phase.  Because of high heat of vaporisation makes water a very good coolant. This is the reason why we sweat in order to cool ourselves.  When the heat is raised, the higher kinetic energy of water molecules causes H bonds to break completely and allows water molecules to escape into the air as gas.  Water molecules on the surface of skin absorb a relatively large amount of heat energy from skin to disrupt H bonds and vaporise. This tends to cool the surface of skin.  As water molecules evaporate, the surface they evaporate from gets cooler, this process called as evaporative cooling.  In humans and other organisms, the evaporation of sweat, which is about 99% water, cools the body to maintain a steady temperature.  In addition, its high heat capacity helps keeping the temperature fluctuations within limits that allow living things to survive.  THE EXPANSION UPON FREEZING  Expansion upon freezing comes from the fact that water crystallizes into an open hexagonal form. As this hexagonal lattice contains more gaps than in the liquid state, ice contains fewer molecules than the same volume of liquid water. Therefore, its density is less.  Because it is less dense, ice floats on the surface of liquid water (iceberg in the Arctic Ocean or the ice cubes in a glass).  The maximum density of water at around 4°C causes the water bodies to freeze first at the top.  In lakes, a layer of ice forms on top of liquid water, creating an insulating barrier that protects the animals and plant life in lake below from freezing. EXCELLENT SOLVENT  The dielectric constant (ε) of a solvent is a measure of its polarity. The higher the dielectric constant of a solvent, the more polar it is.  Because of its polarity and ability to form hydrogen bonds, water is an excellent solvent.  Hence, water can form electrostatic interactions with other polar molecules and ions.  When there are many water molecules relative to solutes (an aqueous solution), these interactions lead to the formation of hydration shell around the solute.  Hydration shells allow particles to be dispersed equally in water. Na+ only attracts the negatively charged end of water molecules and Cl- attracts the positively charged end of water molecules.  Water also disperses amphipathic molecules such as soaps to form micelles (the hydrophobic groups are hidden from exposure to water and the hydrophilic (polar) groups are on the external surface exposed to water). AQUEOUS SOLUTIONS Aqueous Solutions The solvent is water. A solution → A homogeneous mixture formed by two or more chemical substances coming together in any proportion. Solvent → the dissolving medium. Solute → the substance that is being dissolved. Dissolution → dispersion of a substance in another substance into particles too small to be seen with the naked eye, forming a homogeneous mixture. Solutions can be formed with many different types and forms of solute and solvent, as there are many solvents in nature and many substances that dissolve in these solvents. The best known solvent is water (excellent solvent). An aqueous solution → water containing one or more dissolved substance. In our body, reactions occur in the aqueous solution.  Water typically dissolves most ionic compounds and polar molecules.  Nonpolar molecules such as oil do not dissolve in water. Hydration is the process of solute particles being surrounded by water molecules arranged in a specific manner. the individual ions are then surrounded by solvent particles in a process called dissolution Hydration helps to stabilize aqueous solutions by preventing the (+) and (-) ions from coming back together and forming a precipitate. ions hydrated by H2O the substance solubility → the maximum amount of a substance that can dissolve in a certain amount of solvent at a certain temperature. Most substances have a limit to their solubility in a given amount of solvent. concentration → the amount of substance dissolved in a certain amount of solvent or solution. dilute solutions concentrated solutions solutions with low solutions with high concentration. concentration. saturated solutions → stable solutions that have dissolved the maximum amount of substance they can dissolve. unsaturated solutions → solutions that contain less amount of substance than that of a saturated solution. supersaturated solutions → solutions that have dissolved a greater amount of substance than the saturated solution concentration. no more solute will be dissolved. If the solute dissociates into ions while dissolving, such solutions are called ionic solutions (electrolyte solutions). Ionic solutions conduct electric current. Example; acid, base solutions, salt solutions. Covalently bonded compounds, on the other hand, disperse as molecules while dissolving in the solvent. They do not conduct electric current. Example; dissolution of alcohol and sugar in water. Sugar dissolves in water in molecular form without dissociating into ions. Dissolution is based on the attractive forces between molecules. The attractive forces between the solvent and solute molecules must be greater than the attractive force between the solvent and solute's own molecules to dissolve that solute. Generally, a dissolution occurs only if the solvent and the solute are of similar structure (like dissolves like). Polar solvents dissolve polar substances better, and nonpolar solvents dissolve nonpolar substances better. Eg., chloroform (less polar than water), or carbon tetrachloride (nonpolar), do not dissolve in water. Water-water molecules and chloroform-chloroform molecules attract each other more than water- chloroform molecules. Additionally, there is H bonding between water-water molecules, which further strengthens the attraction. The attractive force between water- chloroform molecules is not strong enough to break the hydrogen bond. a nonpolar liquid oil does not dissolve in water (two separate layers form -immiscible), However, ethanol, a polar compound, dissolves in water by being attracted to water molecules. Ethanol is mixed with water, they completely blend and dissolve into one another (miscible). Ionic Compounds When ionic compounds dissolve in water, the ions in the solid separate and disperse uniformly throughout the solution because water molecules surround and dissolve the ions, reducing the strong electrostatic forces between them (dissociation). Under most conditions, ionic compounds will dissociate nearly completely when dissolved, and so they are classified as strong electrolytes. Soluble solid: it completely dissolves in water (ions are formed). Slightly soluble solid: it partially dissolves in water. Insoluble solid: it does not dissociate in water (almost) (calcium carbonate (CaCO3) and silver chloride (AgCl)). Electrolytes Dissociation is the separation of ions that occurs when a solid ionic compound dissolves. Eg. sucrose Three different types of reactions with aqueous solutions are as follows: 1. Precipitation reactions 2. Acid-base reactions 3. Oxidation-reduction reactions 1. Precipitation reactions Aqueous solutions of soluble salts react to form an insoluble ionic compound (precipitate). The reaction occurs when oppositely charged ions in solution overcome their attraction to water and bond with each other, forming a precipitate that separates from solution. Eg.: when lead nitrate mixes with potassium iodide Pb(NO3)2 (aq)+ 2KI (aq) → PbI2 (s)+ 2KNO3 (aq) Lead iodide is not soluble product (the precipitate). 2. Acid-base reactions Due to acid and base reaction, a neutralization reaction occurs. Acid combines with base to produce water and a salt. Eg., HCl + NaOH → H2O + NaCl acids → substances that dissolve in water to produce H+ ions they taste sour. (HCl) inorganic acid, (CH3- CHOH – COOH) lactic acid organic acid bases → substances that dissolve in water to produce OH− ions. they taste bitter. (NaOH) inorganic base, (CH3NH2) methylamine organic base Acid-base theories Arrhenius proposed that acids are compounds that ionize to give hydrogen ions (H+), and bases are compounds that ionize to give hydroxide ions (OH–) in aqueous solution. Brønsted-Lowry theory defines an acid as a hydrogen-ion donor, and a base as a hydrogen-ion acceptor. Lewis proposed that an acid accepts a pair of electrons during a reaction, while a base donates a pair of electrons. Conjugate Acids and Bases A conjugate acid is the particle formed when a base gains a H+. A conjugate base is the particle that remains when an acid has donated a H+. Generalized acid-base reaction: HA + B  A + HB A is the conjugate base of HA, and HB is the conjugate acid of B. More simply, HA  A- + H+ HA is the conjugate acid, A- is the conjugate base Eg: H2CO3  HCO3- + H+ Strong Acids/ Bases Strong acids more readily release H+ into water, they more fully dissociate. H2SO4  2 H+ + SO42- Strong bases more readily release OH- into water, they more fully dissociate. NaOH  Na+ + OH- Acid-base dissociation For any acid, describe it’s reaction in water: HxA + H2O  x H+ + A- + H2O Equilibrium constant, K [ A][ H  ]x often denotes KA or KB for acids or bases…) K [ H x A] (changes with temperature) Strength of an acid or base is then related to the dissociation constant  Big K, strong acid/base! pK = -log K  lower pK=stronger acid/base! pH scale The pH scale is a concise way of describing the H+ concentration and hence the acidity or basicity of a solution. pH and the H+ concentration are related as pH = - log [H+] pH of a neutral solution is 7.00 ([H+]=1.0×10−7M), whereas acidic solutions have pH < 7.00 and basic solutions have pH > 7.00 Most biological fluids have a pH between 6 and 8. Human gastric juice is very acidic and has a pH of around 2. Henderson-Hasselbach Equation  [A ] pH  pK  log [ HA]  When acid or base added to buffered system with a pH near pK (when pH=pK, HA and A- are equal), the pH will not change much.  When the pH is further from the pK, additions of acid or base will change the pH a lot. Organisms are Sensitive to pH Changes. 3. Oxidation-reduction reactions An oxidation-reduction reaction takes place between a metal and a non- metal. A widely encountered class of oxidation–reduction reactions is the reaction of aqueous solutions of acids or metal salts with solid metals (e.g. the corrosion of metal objects). Oxidation-reduction reactions involve the transfer of electrons between molecules. Oxidation and reduction always occur together. The combustion of fuels, the corrosion of metals, and even the processes of photosynthesis and cellular respiration also involve reduction and oxidation reactions. photosynthesis Eg., reactions in which nicotinamide adenine dinucleotide NAD+ and flavin adenine dinucleotide FAD+, which are important in cellular respiration, gain or lose electrons (oxidation-reduction reactions).  MEDICAL SCHOOL GRADE I MODULE II MOLECULE TO CELL I 21st November 2024 Biophysics – Thermodynamic Concepts and Bioenergetic Processes Dr. Şerife CANKURTARAN SAYAR [email protected]  TERMS OF THERMODYNAMICS and BIOENERGETICS https://www.api.simply.science/images/content/biology/animal_form_and_function/basic_principles/conceptmap/Bioenergetics_basics.htm l  TERMS of THERMODYNAMICS and BIOENERGETIC PROCESSES 1 – REVERSIBLE AND IRREVERSIBLE PROCESSES 2 – ENTROPY and II. LAW of THERMODYNAMICS  Terms of Thermodynamics and Bioenergenics Did you know that? Why NaCl cristal dissolve in water? Can direction of the biochemical reactions be predicted before they happen? What is entropy? And what does it govern in biochemistry / physicalchemistry? What is the relationship between entropy and Bill Nye the Science Guy information?  Terms of Thermodynamics and Bioenergenics 1 – REVERSIBLE AND IRREVERSIBLE PROCESSES  Terms of Thermodynamics and Bioenergenics To maintain life in biological systems, some processes must be operated. The operation of processes depends on the use of energy and the occurrence of a series of chemical reactions. It can be explained by the laws of thermodynamics how chemical reactions take place, and their "directions“. It can be predicted in terms of the laws of thermodynamics.  Terms of Thermodynamics and Bioenergenics Why do we need to learn consepts and “laws” of thermodynamics? Biochemical reactions are based on and “must obey” the “Laws” of Thermodynamics There is no exception to Laws of Thermodynamics We can explain: direction of a biochemical reaction (CO2 + O2 → C6H12O6 or C6H12O6 → CO2 + O2) whether a biochemical reaction can spontanously exist or not (formation of a compound, coupling, binding, )  Terms of Thermodynamics and Bioenergenics If we don’t know consepts and “laws” of thermodynamics…. we try to expain all biochemical reactions individualy, one by one we think the biochemical elements (factors) have minds and ideas, and they choice what they do We attribute mind and ability to the biochemical factors direction of a biochemical reaction (CO2 + O2 → C6H12O6 or C6H12O6 → CO2 + O2) whether a biochemical reaction can spontanously exist or not (formation of a compound, coupling, binding, recognition of the hormones by the receptors)  Terms of Thermodynamics and Bioenergenics *** WHY SHOULD WE LEARN THE LAWS OF THERMODYNAMICS, THERMODYNAMIC CONCEPTS AND THE THERMODYNAMIC FUNDAMENTALS OF BIOCHEMICAL REACTIONS OR PROCESSES? *** If we do not know the laws of thermodynamics, we will have to attribute "mind - idea - ability" to each chemical element (recognition, etc.). For example: How can the bases (Adenine, Guanine, Cytosine and Thymine) which form DNA helix “recognize” each other? How does cytosine “recognise guanine and decide” to bind it?  Terms of Thermodynamics and Bioenergenics *** WHY SHOULD WE LEARN THE LAWS OF THERMODYNAMICS, THERMODYNAMIC CONCEPTS AND THE THERMODYNAMIC FUNDAMENTALS OF BIOCHEMICAL REACTIONS OR PROCESSES? *** If we do not know the laws of thermodynamics, we will have to attribute "mind - idea - ability" to each chemical element (recognition, etc.). For example: How does the acetylcholine (Ach) receptor “understand and recognize” the chemical trying to bind is Ach? How does it "know" that the ion trying to pass through is K+?  Terms of Thermodynamics and Bioenergenics *** WHY SHOULD WE LEARN THE LAWS OF THERMODYNAMICS, THERMODYNAMIC CONCEPTS AND THE THERMODYNAMIC FUNDAMENTALS OF BIOCHEMICAL REACTIONS OR PROCESSES? *** If we do not know the laws of thermodynamics, we will have to attribute "mind - idea - ability" to each chemical element (recognition, etc.). For example: How does hemoglobin “know and recognize” whether the gas which should bind or apart is O2 or CO2? How does it “decide” to bind or apart?  Terms of Thermodynamics and Bioenergenics *** WHY SHOULD WE LEARN THE LAWS OF THERMODYNAMICS, THERMODYNAMIC CONCEPTS AND THE THERMODYNAMIC FUNDAMENTALS OF BIOCHEMICAL REACTIONS OR PROCESSES? *** If we do not know the laws of thermodynamics, we will have to attribute "mind - idea - ability" to each chemical element (recognition, etc.). For example: How do the Enzyme and Substrate “recognise” each other? How do they “decide” to bind? Enzym ve substrate Enzym + substrate complex  Terms of Thermodynamics and Bioenergenics *** WHY SHOULD WE LEARN THE LAWS OF THERMODYNAMICS, THERMODYNAMIC CONCEPTS AND THE THERMODYNAMIC FUNDAMENTALS OF BIOCHEMICAL REACTIONS OR PROCESSES? *** If we do not know the laws of thermodynamics, we will have to attribute "mind - idea - ability" to each chemical element (recognition, etc.). Instead of explanations that require “intelligence and ideas such as recognition, decision-making, etc.,” THE LAWS OF THERMODYNAMICS!!!  Terms of Thermodynamics and Bioenergenics 1 – REVERSIBLE AND IRREVERSIBLE PROCESSES NaCl crystal dissolves in water. Why?  Terms of Thermodynamics and Bioenergenics 1 – REVERSIBLE AND IRREVERSIBLE PROCESSES NaCl crystal dissolves in water. Why? When phospholipids are randomly placed into water, they form bilayers, micelles, or liposomes. Why?  Terms of Thermodynamics and Bioenergenics 1 – REVERSIBLE AND IRREVERSIBLE PROCESSES NaCl crystal dissolves in water. Why? When phospholipids are randomly placed into water, they form a bilayer, micelle, or liposome. Why? A drop of water dropped on a floor tends to become a sphere. Why?  Terms of Thermodynamics and Bioenergenics 1 – REVERSIBLE AND IRREVERSIBLE PROCESSES NaCl crystal dissolves in water. Why? When phospholipids are randomly placed into water, they form a bilayer, micelle, or liposome. Why? A drop of water dropped on a floor tends to become a sphere. Why? Particles in a container spread all over the container when the container volume is enlarged. But they don’t collect at the edge of the container. Why?  Terms of Thermodynamics and Bioenergenics 1 – REVERSIBLE AND IRREVERSIBLE PROCESSES NaCl crystal dissolves in water. Why? When phospholipids are randomly placed into water, they form a bilayer, micelle, or liposome. Why? A drop of water dropped on a floor tends to become a sphere. Why? Particles in a container spread all over the container when the container volume is enlarged. But they don’t collect at the edge of the container. Why? An ice cube placed in water at room temperature melts, but the water does not freeze and turn into ice. Why?  Terms of Thermodynamics and Bioenergenics 1 – REVERSIBLE AND IRREVERSIBLE PROCESSES NaCl crystal dissolves in water. Na+ and Cl- interact with individual H2O molecules. Why? When phospholipids are randomly placed into water, they form a bilayer, micelle, or liposome. Why? A drop of water dropped on a floor tends to become a sphere. Why? Particles in a container spread all over the container when the container volume is enlarged, but do not collect at the corners of the container. Why? An ice cube placed in water at room temperature melts, but the water does not freeze and turn into ice. Why? The common feature of these processes (given conditions) is that they are "irreversible"  Terms of Thermodynamics and Bioenergenics 1 – REVERSIBLE AND IRREVERSIBLE PROCESSES When ice is put into water at room temperature  Terms of Thermodynamics and Bioenergenics 1 – REVERSIBLE AND IRREVERSIBLE PROCESSES When ice is put into water at room temperature the ice turns into water (irreversible) Ice at 0⁰C’ Water at around Water at room temperature room temperature  Terms of Thermodynamics and Bioenergenics 1 – REVERSIBLE AND IRREVERSIBLE PROCESSES When ice is put into water at room temperature the water does not freeze and turn the ice turns into water (irreversible) into an ice cube Ice at 0⁰C’ Water at around Water at 0⁰C’ Water at room temperature room temperature  Terms of Thermodynamics and Bioenergenics 1 – REVERSIBLE AND IRREVERSIBLE PROCESSES When ice is put into water at room temperature the water does not freeze and turn the ice turns into water (irreversible) into an ice cube Ice at 0⁰C’ Water at around Water at 0⁰C’ Water at room temperature room temperature When ice is put into water at 0⁰C  Terms of Thermodynamics and Bioenergenics 1 – REVERSIBLE AND IRREVERSIBLE PROCESSES When ice is put into water at room temperature the water does not freeze and turn the ice turns into water (irreversible) into an ice cube Ice at 0⁰C’ Water at around Water at 0⁰C’ Water at room temperature room temperature When ice is put into water at 0⁰C If a small amount of heat is given, the ice can turn into water at 0⁰C (reversible) Ice at 0⁰C’ Water at 0⁰C’ Water at 0⁰C’  Terms of Thermodynamics and Bioenergenics 1 – REVERSIBLE AND IRREVERSIBLE PROCESSES When ice is put into water at room temperature the water does not freeze and turn the ice turns into water (irreversible) into an ice cube Ice at 0⁰C’ Water at around Water at 0⁰C’ Water at room temperature room temperature When ice is put into water at 0⁰C If a small amount of heat is lost, If a small amount of heat is given, the the water can turn into ice at ice can turn into water at 0⁰C 0⁰C(reversible) (reversible) Ice at 0⁰C’ Ice at 0⁰C’ Water at 0⁰C’ Water at 0⁰C’  Terms of Thermodynamics and Bioenergenics 1 – REVERSIBLE AND IRREVERSIBLE PROCESSES Reversible process: if the process can be turned back such that both the system and the surroundings return to their original states. Irreversible process: the system and the surroundings do not return to their original condition once the process is initiated The "state" a system goes to when we leave it alone: spontaneous process or favorable state It is very important to know whether a reaction is reversible or preferable in bioenergetics Thermodynamics can predict the direction of reactions, not how fast!  Terms of Thermodynamics and Bioenergenics 1 – REVERSIBLE AND IRREVERSIBLE PROCESSES Reversible process: if the process can be turned back such that both the system and the surroundings return to their original states. Irreversible process: the system and the surroundings do not return to their original condition once the process is initiated The "state" a system goes to when we leave it alone: spontaneous process or favorable state It is very important to know whether a reaction is reversible or preferable in bioenergetics Thermodynamics can predict the direction of reactions, not how fast! How can we predict the direction (favorable or unfavorable, spontaneous or nonspontaneous) of a reaction? II. LAW of THERMODYNAMICS......  Terms of Thermodynamics and Bioenergenics 1 – REVERSIBLE AND IRREVERSIBLE PROCESSES Let’s remember the examples: NaCl crystal dissolves in water. Na+ and Cl- interact with individual H2O molecules. Why? When phospholipids are randomly placed into water, they form a bilayer, micelle, or liposome. Why? A drop of water dropped on a floor tends to become a sphere. Why? Particles in a container spread all over the container when the container volume is enlarged, but do not collect at the corners of the container. Why? An ice cube placed in water at room temperature melts, but the water does not freeze and turn into ice. Why? II. LAW of THERMODYNAMICS....  Terms of Thermodynamics and Bioenergenics 2 – ENTROPY and II. LAW of THERMODYNAMICS A correct concept and an accurate explanation: ENTROPY Sidney  Terms of Thermodynamics and Bioenergenics 2 – ENTROPY and II. LAW of THERMODYNAMICS h tt p s :/ / k i n t r o n i c s. c Sidney  Terms of Thermodynamics and Bioenergenics 2 – ENTROPY and II. LAW of THERMODYNAMICS II. Law of thermodynamics: "The total energy of the universe is constant, its total entropy (S) is constantly increasing.“  Terms of Thermodynamics and Bioenergenics 2 – ENTROPY and II. LAW of THERMODYNAMICS System: space region where reactants, products, solvents are located Universe: System and its surroundings Closed System: A system that exchanges energy, not matter, with its surroundings. Isolated System: A system that does not exchange matter or energy with its surroundings. Open system: A system that exchanges matter and energy with its surroundings. The surroundings The surroundings The surroundings En E n erg e r y g The The Mat The y system system ter system The Universe = system + surrounding  Terms of Thermodynamics and Bioenergenics 2 – ENTROPY and II. LAW of THERMODYNAMICS Entropy (S) The natural tendency of system to disorder and randomness Entropy is a physical value that describes the degree of order of a system It was first used by Rudolf CLAUSIUS in 1851  Terms of Thermodynamics and Bioenergenics 2 – ENTROPY and II. LAW of THERMODYNAMICS Entropy (S) The natural tendency of system to disorder and randomness Entropy is a physical value that describes the degree of order of a system It was first used by Rudolf CLAUSIUS in 1851 Number of possible states of the system. It is a measure of randomness  Terms of Thermodynamics and Bioenergenics 2 – ENTROPY and II. LAW of THERMODYNAMICS Entropy (S) The natural tendency of system to disorder and randomness Entropy is a physical value that describes the degree of order of a system It was first used by Rudolf CLAUSIUS in 1851 Number of possible states of the system. It is a measure of randomness The lower the degree of order, the larger the entropy. When a process leads to increase in disorder, ΔS (S final – S initial) will be positive for this process  Terms of Thermodynamics and Bioenergenics 2 – ENTROPY and II. LAW of THERMODYNAMICS Entropy (S) Number of possible states of the system. It is a measure of randomness. What does it mean?  Terms of Thermodynamics and Bioenergenics 2 – ENTROPY and II. LAW of THERMODYNAMICS Entropy (S) Number of possible states of the system. It is a measure of randomness. What does it mean? If we have 24 empty boxes and we want to put a ball in “a box”….. There are 24 possibilities (states, boxes) where we find the ball at any given time S24  Terms of Thermodynamics and Bioenergenics 2 – ENTROPY and II. LAW of THERMODYNAMICS Entropy (S) Number of possible states of the system. It is a measure of randomness. What does it mean? If we have 24 empty boxes and we want to put a ball in “a box”….. There are 24 possibilities There are 12 possibilities (states, boxes) (states, boxes) where we find the ball where we find the ball at any given time at any given time S24 S12 The number of possible states decreases, entropy decreases  Terms of Thermodynamics and Bioenergenics 2 – ENTROPY and II. LAW of THERMODYNAMICS Entropy (S) Number of possible states of the system. It is a measure of randomness. What does it mean? If we have 24 empty boxes and we want to put a ball in “a box”….. There are 24 possibilities There are 12 possibilities There are 3 possibilities (states, boxes) (states, boxes) (states, boxes) where we find the ball where we find the ball where we find the ball at any given time at any given time at any given time S24 S12 S3 The number of possible states decreases, entropy decreases The number of possible states decreases, entropy decreases  Terms of Thermodynamics and Bioenergenics 2 – ENTROPY and II. LAW of THERMODYNAMICS Entropy (S) Number of possible states of the system. It is a measure of randomness. What does it mean? If we have 24 empty boxes and we want to put a ball in “a box”….. There are 24 possibilities There are 12 possibilities There are 3 possibilities There is only 1 possibility (states, boxes) (states, boxes) (states, boxes) (state, box) where we find the where we find the ball where we find the ball where we find the ball ball at any given time. at any given time at any given time at any given time No disorder! S24 S12 S3 S1 The number of possible states The number of possible states decreases, entropy decreases decreases, entropy decreases The number of possible states decreases, entropy decreases  Terms of Thermodynamics and Bioenergenics 2 – ENTROPY and II. LAW of THERMODYNAMICS Entropy (S) The lower the degree of order, the larger the entropy. When a process leads to increase in disorder, ΔS (S final – S initial) will be positive for this process An increase in the order in a system ΔS (S final – S initial) is negative for a process always requires an input of energy Biological and biochemical examples!!!  Terms of Thermodynamics and Bioenergenics 2 – ENTROPY and II. LAW of THERMODYNAMICS Qualitative Explanation of Entropy: Teapot and Distribution of Heat. Water in a teapot (system) is boiled (S system, teapot increases) and then heating is stopped.  Terms of Thermodynamics and Bioenergenics 2 – ENTROPY and II. LAW of THERMODYNAMICS Qualitative Explanation of Entropy: Teapot and Distribution of Heat. Water in a teapot (system) is boiled (S system, teapot increases) and then heating is stopped.  Terms of Thermodynamics and Bioenergenics 2 – ENTROPY and II. LAW of THERMODYNAMICS Qualitative Explanation of Entropy: Teapot and Distribution of Heat. Teapot (system) temperature decreases (S system, teapot decreases). Kitchen (environment) temperature rises slightly (S system + enviroment increases). favorabl e  Terms of Thermodynamics and Bioenergenics 2 – ENTROPY and II. LAW of THERMODYNAMICS Qualitative Explanation of Entropy: Teapot and Distribution of Heat.The process in the kitchen (environment) is irreversible. Heat cannot spontaneously enter the kettle. unfavorable  Terms of Thermodynamics and Bioenergenics 2 – ENTROPY and II. LAW of THERMODYNAMICS Let’s remember the examples: NaCl crystal dissolves in water. Why? When phospholipids are randomly placed into water, they form a bilayer, micelle, or liposome. Why? A drop of water dropped on a floor tends to become a sphere. Why? Particles in a container spread all over the container when the container volume is enlarged, but do not collect at the corners of the container. Why? An ice cube placed in water at room temperature melts, but the water does not freeze and turn into ice. Why? How can we predict direction of the process by change in entropy?  Terms of Thermodynamics and Bioenergenics 2 – ENTROPY and II. LAW of THERMODYNAMICS NaCl crystal dissolves in water. Na+ and Cl- interact with individual H2O molecules. Why? Na+ ve Cl- ions interact with each other by ionic bond.  Terms of Thermodynamics and Bioenergenics 2 – ENTROPY and II. LAW of THERMODYNAMICS NaCl crystal dissolves in water. Na+ and Cl- interact with individual H2O molecules. Why? Every single Na+ ve Cl- ions interact with lots of H2O molecules. These interactions which are not covalent are disrupted and created. One ion – millions of H20 molecules, Degree of disorders (entropy) increases.  Terms of Thermodynamics and Bioenergenics 2 – ENTROPY and II. LAW of THERMODYNAMICS Let’s remember the examples: NaCl crystal dissolves in water. Na+ and Cl- interact with individual H2O molecules. Why? When phospholipids are randomly placed into water, they form a bilayer, micelle, or liposome. Why? A drop of water dropped on a floor tends to become a sphere. Why? Particles in a container spread all over the container when the container volume is enlarged, but do not collect at the corners of the container. Why? An ice cube placed in water at room temperature melts, but the water does not freeze and turn into ice. Why? How can we predict direction of the process by change in entropy?  Terms of Thermodynamics and Bioenergenics 2 – ENTROPY and II. LAW of THERMODYNAMICS When phospholipids are randomly thrown into water, they form a bilayer, micelle, or liposome. ΔS (S final – S initial) is positive ΔS (S final – S initial) > 0 Only borderline phospholipid molecules will come face to H2O molecules force phospholipids to line face with H2O. Fewer H2O molecules will stay steady. up properly. High degree of H20 molecules (low entropy) (high entropy)  Terms of Thermodynamics and Bioenergenics 2 – ENTROPY and II. LAW of THERMODYNAMICS When phospholipids are randomly thrown into water, they form a bilayer, micelle, or liposome. ΔS (S final – S initial) >0 Only borderline phospholipid molecules will come H2O molecules force phospholipids to face to face with H2O. Fewer H2O molecules will st line up properly steady. Entropy will increase  Terms of Thermodynamics and Bioenergenics 2 – ENTROPY and II. LAW of THERMODYNAMICS Oil droplets tend to coalesce when thrown into water. ΔS (S final – S initial) is positive ΔS (S final – S initial) > 0  Terms of Thermodynamics and Bioenergenics 2 – ENTROPY and II. LAW of THERMODYNAMICS Let’s remember the examples: NaCl crystal dissolves in water. Na+ and Cl- interact with individual H2O molecules. Why? When phospholipids are randomly placed into water, they form a bilayer, micelle, or liposome. Why? A drop of water dropped on a floor tends to become a sphere. Why? Particles in a container spread all over the container when the container volume is enlarged, but do not collect at the corners of the container. Why? An ice cube placed in water at room temperature melts, but the water does not freeze and turn into ice. Why? How can we predict direction of the process by change in entropy?  Terms of Thermodynamics and Bioenergenics 2 – ENTROPY and II. LAW of THERMODYNAMICS When the volume of the container is enlarged, the particles in a container spread all over the container, but do not collect at the edge of the container. The number of places where any particle can be found is greater in final than in initial If the seperator is removed Diffusion ΔS (S final – S initial) is positive ΔS (S final – S initial) > 0  Terms of Thermodynamics and Bioenergenics EXTRA  Terms of Thermodynamics and Bioenergenics 2 – ENTROPY and II. LAW of THERMODYNAMICS Qualitative Explanation of Entropy: Information and Entropy. A passage from Julius Caesar, act IV, scene 3 There is a tide in the affairs of men, Which, taken at the flood, leads on to fortune; EXTRA Omitted, all the voyage of their life Is bound in shallows and in miseries. Meaningful, carries information, is organized, Not meaningful, carries little/no information, low entropy disorganized, high entropy ΔS (S final – S initial) is positive ΔS (S final – S initial) > 0  Terms of Thermodynamics and Bioenergenics 2 – ENTROPY and II. LAW of THERMODYNAMICS Qualitative Explanation of Entropy: Information and Entropy. Primary, secondary, tertiary and quaternary structures of proteins EXTRA Primary structure: Only aminoacid chain is known. The chain can turn into any type of protein. The highest number of folding possibilities and combinations. The least information  Terms of Thermodynamics and Bioenergenics 2 – ENTROPY and II. LAW of THERMODYNAMICS Qualitative Explanation of Entropy: Information and Entropy. Primary, secondary, tertiary and quaternary structures of proteins EXTRA Secondary structure: Aminoacid chain and alpha helixes – beta sheets are known Less number of folding possibilities and combinations. More information  Terms of Thermodynamics and Bioenergenics 2 – ENTROPY and II. LAW of THERMODYNAMICS Qualitative Explanation of Entropy: Information and Entropy. Primary, secondary, tertiary and quaternary structures of proteins EXTRA Tertiary structure: Aminoacid chain, alpha helixes – beta sheets and folding pattern/arragment are known. It can’t be any other type of unit. But some units can form different “units”. Less number of folding possibilities and combinations. More information  Terms of Thermodynamics and Bioenergenics 2 – ENTROPY and II. LAW of THERMODYNAMICS Qualitative Explanation of Entropy: Information and Entropy. Primary, secondary, tertiary and quaternary structures of proteins EXTRA Quaternary structure: Aminoacid chain, alpha helixes – beta sheets, folding pattern and the number of units are known. It can’t be any other type of protein. The least number of folding possibilities and combinations. The most information  Terms of Thermodynamics and Bioenergenics Did you know that? Why NaCl cristal dissolve in water? Can direction of the biochemical reactions be predicted before they happen? What is entropy? And what does it govern in biochemistry / physicalchemistry? What is the relationship between entropy and information? Bill Nye the Science Guy  Terms of Thermodynamics and Bioenergenics Well, now you know NaCl cristal dissolve in water, because…. Direction of the biochemical reactions can be predicted before they happen by using term of….. Entropy is… It governs in biochemistry / physicalchemistry to ….. The relationship between entropy and information is….. Bill Nye the Science Guy  Terms of Thermodynamics and Bioenergenics Living systems are not "isolated" but "open systems". Living systems exchange energy and matter with their environment. Both their entropies and energies are changing. A concept is needed that is a function of energy and entropy: Gibbs Free Energy.... Next “episode”: GIBBS FREE ENERGY  Thanks… [email protected]  Terms of Thermodynamics and Bioenergenics Previously on… Entropy (S) The natural tendency of system to disorder and randomness Entropy is a physical value that describes the degree of order of a system Number of possible states of the system. It is a measure of randomness The lower the degree of order, the larger the entropy. When a process leads to increase in disorder, ΔS (S final – S initial) will be positive for this process An increase in the order in a system ΔS (S final – S initial) is negative for a process always requires an input of energy Biological and biochemical examples!!!  Terms of Thermodynamics and Bioenergenics Previously on… Let’s remember the examples: NaCl crystal dissolves in water. Why? When phospholipids are randomly placed into water, they form a bilayer, micelle, or liposome. Why? A drop of water dropped on a floor tends to become a sphere. Why? Particles in a container spread all over the container when the container volume is enlarged, but do not collect at the corners of the container. Why? An ice cube placed in water at room temperature melts, but the water does not freeze and turn into ice. Why? How can we predict direction of the process by change in entropy?  Terms of Thermodynamics and Bioenergenics Previously on… NaCl crystal dissolves in water. Na+ and Cl- interact with individual H2O molecules. Why? Na+ ve Cl- ions interact with each other by ionic bond.  Terms of Thermodynamics and Bioenergenics Previously on… NaCl crystal dissolves in water. Na+ and Cl- interact with individual H2O molecules. Why? Every single Na+ ve Cl- ions interact with lots of H2O molecules. These interactions which are not covalent are disrupted and created. One ion – millions of H20 molecules, Degree of disorders (entropy) increases.  Terms of Thermodynamics and Bioenergenics Previously on… Let’s remember the examples: NaCl crystal dissolves in water. Na+ and Cl- interact with individual H2O molecules. Why? When phospholipids are randomly placed into water, they form a bilayer, micelle, or liposome. Why? A drop of water dropped on a floor tends to become a sphere. Why? Particles in a container spread all over the container when the container volume is enlarged, but do not collect at the corners of the container. Why? An ice cube placed in water at room temperature melts, but the water does not freeze and turn into ice. Why? How can we predict direction of the process by change in entropy?  Terms of Thermodynamics and Bioenergenics Previously on… When phospholipids are randomly thrown into water, they form a bilayer, micelle, or liposome. ΔS (S final – S initial) is positive ΔS (S final – S initial) > 0 Only borderline phospholipid molecules will come face to H2O molecules force phospholipids to line face with H2O. Fewer H2O molecules will stay steady. up properly. High degree of H20 molecules (low entropy) (high entropy)  Terms of Thermodynamics and Bioenergenics Previously on… When phospholipids are randomly thrown into water, they form a bilayer, micelle, or liposome. ΔS (S final – S initial) >0 Only borderline phospholipid molecules will come H2O molecules force phospholipids to face to face with H2O. Fewer H2O molecules will st line up properly steady. Entropy will increase  Terms of Thermodynamics and Bioenergenics Previously on… Oil droplets tend to coalesce when thrown into water. ΔS (S final – S initial) is positive ΔS (S final – S initial) > 0  Terms of Thermodynamics and Bioenergenics Previously on… Let’s remember the examples: NaCl crystal dissolves in water. Na+ and Cl- interact with individual H2O molecules. Why? When phospholipids are randomly placed into water, they form a bilayer, micelle, or liposome. Why? A drop of water dropped on a floor tends to become a sphere. Why? Particles in a container spread all over the container when the container volume is enlarged, but do not collect at the corners of the container. Why? An ice cube placed in water at room temperature melts, but the water does not freeze and turn into ice. Why? How can we predict direction of the process by change in entropy?  Terms of Thermodynamics and Bioenergenics Previously on… When the volume of the container is enlarged, the particles in a container spread all over the container, but do not collect at the edge of the container. The number of places where any particle can be found is greater in final than in initial If the seperator is removed Diffusion ΔS (S final – S initial) is positive ΔS (S final – S initial) > 0  MEDICAL SCHOOL GRADE I MODULE II MOLECULES TO CELLS I 21st November 2024 Biophysics – Gibss Free Energy and Energy Exchanges in Biological Systems Dr. Şerife CANKURTARAN SAYAR [email protected]  Gibbs Free Energy and Kinetics of Biochemical Reactions Distribution of Energy Did you know that? Can the direction of a reaction be explained with only change in entropy? What is Gibbs free energy? What are equilibrium and nonequilibrium reactions? What is energy coupling? What are energetically coupled reactions in living system? Bill Nye the Science Guy  GIBBS FREE ENERGY AND KINETICS OF BIOCHEMICAL REACTIONS 1 – GIBBS FREE ENERGY 2 – KINETICS OF BIOCHEMICAL REACTIONS 3 – ENERGY DISTRIBUTION and COUPLING IN BIOLOGICAL WORLD  Gibbs Free Energy and Kinetics of Biochemical Reactions - Distribution of Energy 1 – GIBBS FREE ENERGY  Gibbs Free Energy and Kinetics of Biochemical Reactions - Distribution of Energy 1 – GIBBS FREE ENERGY Entropy: A natural tendency of system molecules to disorder and randomness, the degree and measure of disorder, a measure of the system's enterable states (disorder, randomness).  Gibbs Free Energy and Kinetics of Biochemical Reactions - Distribution of Energy 1 – GIBBS FREE ENERGY Entropy: A natural tendency of system molecules to disorder and randomness, the degree and measure of disorder, a measure of the system's enterable states (disorder, randomness). Enthalpy (H) is the sum of all kinds of energy that matter collects in its structure. In reaction kinetics, it is a function of the energies of the chemical bonds formed and broken in the reaction under constant pressure. Absolute value (H) cannot be measured, change (ΔH) can be measured  Gibbs Free Energy and Kinetics of Biochemical Reactions - Distribution of Energy 1 – GIBBS FREE ENERGY Entropy: A natural tendency of system molecules to disorder and randomness, the degree and measure of disorder, a measure of the system's enterable states (disorder, randomness). Enthalpy (H) is the sum of all kinds of energy that matter collects in its structure. In reaction kinetics, it is a function of the energies of the chemical bonds formed and broken in the reaction under constant pressure. Absolute value (H) cannot be measured, change (ΔH) can be measured For heat-releasing reactions (exothermic) ΔH (H final – H initial) < 0 For heat-absorbing reactions (endothermic) ΔH (H final – H initial) > 0  Gibbs Free Energy and Kinetics of Biochemical Reactions - Distribution of Energy 1 – GIBBS FREE ENERGY Entropy: A natural tendency of system molecules to disorder and randomness, the degree and measure of disorder, a measure of the system's enterable states (disorder, randomness). Enthalpy (H) is the sum of all kinds of energy that matter collects in its structure. In reaction kinetics, it is a function of the energies of the chemical bonds formed and broken in the reaction under constant pressure. Absolute value (H) cannot be measured, change (ΔH) can be measured For heat-releasing reactions (exothermic) ΔH (H final – H initial) < 0 For heat-absorbing reactions (endothermic) ΔH (H final – H initial) > 0 T: Temperature (⁰K), always positive!  Gibbs Free Energy and Kinetics of Biochemical Reactions - Distribution of Energy 1 – GIBBS FREE ENERGY Gibbs free energy (G), ΔG = ΔH – TΔS G: Gibbs free energy H: Enthalpy T: Temperature (⁰K), always positive! S:Entropy  Gibbs Free Energy and Kinetics of Biochemical Reactions Distribution of Energy 1 – GIBBS FREE ENERGY Gibbs Free Energy and Its Analogs Change in Gibbs free energy describes the direction of the reaction (whether a reaction can occur spontaneously or not)  Gibbs Free Energy and Kinetics of Biochemical Reactions Distribution of Energy 1 – GIBBS FREE ENERGY Gibbs Free Energy and Its Analogs Change in Gibbs free energy describes the direction of the reaction (whether a reaction can occur spontaneously or not)  Gibbs Free Energy and Kinetics of Biochemical Reactions Distribution of Energy 1 – GIBBS FREE ENERGY Gibbs Free Energy and Its Analogs Change in Gibbs free energy describes the direction of the reaction (whether a reaction can occur spontaneously or not)  Gibbs Free Energy and Kinetics of Biochemical Reactions Distribution of Energy 1 – GIBBS FREE ENERGY Gibbs Free Energy (G), ΔG = ΔH – TΔS  Gibbs Free Energy and Kinetics of Biochemical Reactions Distribution of Energy 1 – GIBBS FREE ENERGY Gibbs Free Energy (G), ΔG = ΔH – TΔS ΔH (H final – H initial) < 0 Heat releasing reaction (exothermic) ΔH (H final – H initial) > 0 Heat absorbing reaction (endothermic)  Gibbs Free Energy and Kinetics of Biochemical Reactions Distribution of Energy 1 – GIBBS FREE ENERGY Gibbs Free Energy (G), ΔG = ΔH – TΔS ΔH (H final – H initial) < 0 Heat releasing reaction (exothermic) ΔH (H final – H initial) > 0 Heat absorbing reaction (endothermic) ΔS (S final – S initial) > 0 Increase in entropy of the system ΔS (S final – S initial) < 0 Decrease in entropy of the system  Gibbs Free Energy and Kinetics of Biochemical Reactions Distribution of Energy 1 – GIBBS FREE ENERGY Gibbs Free Energy (G), ΔG = ΔH – TΔS ΔH (H final – H initial) < 0 Heat releasing reaction (exothermic) ΔH (H final – H initial) > 0 Heat absorbing reaction (endothermic) ΔS (S final – S initial) > 0 Increase in entropy of the system ΔS (S final – S initial) < 0 Decrease in entropy of the system ΔG (G final – G initial) < 0 The reaction can occur spontaneously. Downhill ΔG (G final – G initial) > 0 The reaction can not occur spontaneously. Uphill  Gibbs Free Energy and Kinetics of Biochemical Reactions Distribution of Energy 1 – GIBBS FREE ENERGY Gibbs Free Energy (G), ΔG = ΔH – TΔS ΔH (H final – H initial) < 0 Heat releasing reaction (exothermic) ΔH (H final – H initial) > 0 Heat absorbing reaction (endothermic) ΔS (S final – S initial) > 0 Increase in entropy of the system ΔS (S final – S initial) < 0 Decrease in entropy of the system ΔG (G final – G initial) < 0 The reaction can occur spontaneously. Downhill ΔG (G final – G initial) > 0 The reaction can not occur spontaneously. Uphill The sign of ΔG (> 0 or < 0 ) describes the direction of the reaction (whether a reaction can occur spontaneously or not)  Gibbs Free Energy and Kinetics of Biochemical Reactions Distribution of Energy 1 – GIBBS FREE ENERGY Gibbs Free Energy (G), ΔG = ΔH – TΔS ΔH (H final – H initial) < 0 Heat releasing reaction (exothermic) ΔH (H final – H initial) > 0 Heat absorbing reaction (endothermic) ΔS (S final – S initial) > 0 Increase in entropy of the system ΔS (S final – S initial) < 0 Decrease in entropy of the system ΔG (G final – G initial) < 0 The reaction can occur spontaneously. Downhill ΔG (G final – G initial) > 0 The reaction can not occur spontaneously. Uphill The sign of ΔG (> 0 or < 0 ) describes the direction of the reaction (whether a reaction can occur spontaneously or not) The absolute value of ΔG describes how the reaction is far from equilibrium.  Gibbs Free Energy and Kinetics of Biochemical Reactions Distribution of Energy 1 – GIBBS FREE ENERGY Gibbs Free Energy (G), ΔG = ΔH – TΔS ΔH (H final – H initial) < 0 Heat releasing reaction (exothermic) ΔH (H final – H initial) > 0 Heat absorbing reaction (endothermic) ΔS (S final – S initial) > 0 Increase in entropy of the system ΔS (S final – S initial) < 0 Decrease in entropy of the system ΔG (G final – G initial) < 0 The reaction can occur spontaneously. Downhill ΔG (G final – G initial) > 0 The reaction can not occur spontaneously. Uphill The sign of ΔG (> 0 or < 0 ) describes the direction of the reaction (whether a reaction can occur spontaneously or not) The absolute value of ΔG describes how the reaction is far from equilibrium. (We’ ll remember this when we discuss equilibrium reactions)  Gibbs Free Energy and Kinetics of Biochemical Reactions Distribution of Energy 1 – GIBBS FREE ENERGY ΔG = ΔH – TΔS Ekzotermik Entropi azalır ∆G’ nin işareti T’ ye bağlı Düşük sıcaklıklarda spontan Ekzotermik Endotermik Entropi artar Entropi artar ∆G’ nin işareti ∆G her zaman < 0 T’ ye bağlı Reaksiyon spontan Yüksek sıcaklıklarda spontan  Gibbs Free Energy and Kinetics of Biochemical Reactions Distribution of Energy 1 – GIBBS FREE ENERGY ΔG = ΔH – TΔS Ekzotermik Entropi azalır ∆G’ nin işareti T’ ye bağlı Düşük sıcaklıklarda spontan Endotermik Entropi artar ∆G’ nin işareti T’ ye bağlı Yüksek sıcaklıklarda spontan  Gibbs Free Energy and Kinetics of Biochemical Reactions Distribution of Energy 1 – GIBBS FREE ENERGY ΔG = ΔH – TΔS Endotermik Entropi artar ∆G’ nin işareti T’ ye bağlı Yüksek sıcaklıklarda spontan  Gibbs Free Energy and Kinetics of Biochemical Reactions Distribution of Energy 1 – GIBBS FREE ENERGY ΔG = ΔH – TΔS  Gibbs Free Energy and Kinetics of Biochemical Reactions Distribution of Energy 1 – GIBBS FREE ENERGY ΔG = ΔH - TΔS  Gibbs Free Energy and Kinetics of Biochemical Reactions Distribution of Energy 1 – GIBBS FREE ENERGY ΔG = ΔH - TΔS  Gibbs Free Energy and Kinetics of Biochemical Reactions Distribution of Energy 1 – GIBBS FREE ENERGY ΔG = ΔH - TΔS  Gibbs Free Energy and Kinetics of Biochemical Reactions Distribution of Energy 1 – GIBBS FREE ENERGY ΔG = ΔH - TΔS  Gibbs Free Energy and Kinetics of Biochemical Reactions Distribution of Energy 1 – GIBBS FREE ENERGY ΔG = ΔH - TΔS  Gibbs Free Energy and Kinetics of Biochemical Reactions Distribution of Energy 1 – GIBBS FREE ENERGY ΔG = ΔH - TΔS  Gibbs Free Energy and Kinetics of Biochemical Reactions Distribution of Energy Did you know that? Can the direction of a reaction be explained with only change in entropy? What is Gibbs free energy? What are equilibrium and nonequilibrium reactions? What is energy coupling? What are energeticly Bill Nye the Science Guy coupled reactions in living system?  Gibbs Free Energy and Kinetics of Biochemical Reactions Distribution of Energy Well, now you know Can the direction of a reaction be explained with only change in entropy? What is Gibbs free energy? What are equilibrium and nonequilibrium reactions? What is energy coupling? What are energeticly coupled reactions in living system? Bill Nye the Science Guy  Thanks… [email protected]  MEDICAL SCHOOL GRADE I MODULE II MOLECULES TO CELLS I 22 nd November 2024 Biophysics – Gibbs Free Energy and Kinetics of Biochemical Reactions Dr. Şerife CANKURTARAN SAYAR [email protected]  Gibbs Free Energy and Kinetics of Biochemical Reactions Distribution of Energy Did you know that? Can the direction of a reaction be explained with only change in entropy? What is Gibbs free energy? What are equilibrium and nonequilibrium reactions? What is energy coupling? What are energetically coupled reactions in living system? Bill Nye the Science Guy  Gibbs Free Energy and Kinetics of Biochemical Reactions Distribution of Energy 1 – GIBBS FREE ENERGY Gibbs Free Energy (G), ΔG = ΔH – TΔS  Gibbs Free Energy and Kinetics of Biochemical Reactions Distribution of Energy Previously on… Gibbs Free Energy (G), ΔG = ΔH – TΔS ΔH (H final – H initial) < 0 Heat releasing reaction (exothermic) ΔH (H final – H initial) > 0 Heat absorbing reaction (endothermic)  Gibbs Free Energy and Kinetics of Biochemical Reactions Distribution of Energy Previously on… Gibbs Free Energy (G), ΔG = ΔH – TΔS ΔH (H final – H initial) < 0 Heat releasing reaction (exothermic) ΔH (H final – H initial) > 0 Heat absorbing reaction (endothermic) ΔS (S final – S initial) > 0 Increase in entropy of the system ΔS (S final – S initial) < 0 Decrease in entropy of the system  Gibbs Free Energy and Kinetics of Biochemical Reactions Distribution of Energy Previously on… Gibbs Free Energy (G), ΔG = ΔH – TΔS ΔH (H final – H initial) < 0 Heat releasing reaction (exothermic) ΔH (H final – H initial) > 0 Heat absorbing reaction (endothermic) ΔS (S final – S initial) > 0 Increase in entropy of the system ΔS (S final – S initial) < 0 Decrease in entropy of the system ΔG (G final – G initial) < 0 The reaction can occur spontaneously. Downhill ΔG (G final – G initial) > 0 The reaction can not occur spontaneously. Uphill  Gibbs Free Energy and Kinetics of Biochemical Reactions Distribution of Energy Previously on… Gibbs Free Energy (G), ΔG = ΔH – TΔS The sign of ΔG (> 0 or < 0 ) describes the direction of the reaction (whether a reaction can occur spontaneously or not)  Gibbs Free Energy and Kinetics of Biochemical Reactions Distribution of Energy Previously on… Gibbs Free Energy (G), ΔG = ΔH – TΔS The sign of ΔG (> 0 or < 0 ) describes the direction of the reaction (whether a reaction can occur spontaneously or not) A + B → AB G initial G final ΔG (G final – G inital) < 0 for this reaction The reaction is spontaneous, A and B can form AB complex, “spontaneously” A and B have natural tendency to bind each other ☺  Gibbs Free Energy and Kinetics of Biochemical Reactions Distribution of Energy Previously on… Gibbs Free Energy (G), ΔG = ΔH – TΔS The sign of ΔG (> 0 or < 0 ) describes the direction of the reaction (whether a reaction can occur spontaneously or not) A + C → AC G initial G final ΔG (G final – G inital) > 0 for this reaction The reaction is not spontaneous, A and C cannot form AC complex “spontaneously” A and C do not have a natural tendency to bind each other   Gibbs Free Energy and Kinetics of Biochemical Reactions Distribution of Energy Previously on… An example: Why does Guanine bind to Cytosine not another base? Guanine + Cytosine → GuanineCytosine G initial G final ΔG (G final – G inital) < 0 for this reaction The reaction is spontaneous, Guanine can bind to Cytosine to form GuanineCytosine base couple, “spontaneously” Guanine and Cytosine have natural tendency to bind each other ☺  Gibbs Free Energy and Kinetics of Biochemical Reactions Distribution of Energy Previously on… An example: Why does Guanine bind to Cytosine not another base? Guanine + Adenine → GuanineAdenine G initial G final ΔG (G final – G inital) > 0 for this reaction The reaction is not spontaneous, Guanine cannot bind to Adenine to form GuanineAdenine base couple, “spontaneously” Guanine and Adenine do not have a natural tendency to bind each other   Gibbs Free Energy and Kinetics of Biochemical Reactions Did you know that? What are equilibrium and nonequilibrium reactions? What is energy coupling? What are energeticly coupled reactions in living system? Bill Nye the Science Guy  GIBBS FREE ENERGY AND KINETICS OF BIOCHEMICAL REACTIONS 1 – GIBBS FREE ENERGY 2 – ENERGY DISTRIBUTION and COUPLING IN BIOLOGICAL WORLD 3 – KINETICS OF BIOCHEMICAL REACTIONS  Gibbs Free Energy and Kinetics of Biochemical Reactions 2 – ENERGY DISTRIBUTION and COUPLING IN BIOLOGICAL WORLD Living organisms are “open systems”. They get energy from the environment in two ways: 1) Sun lig