Physical Chemistry 66 PDF

General Basis of Biochemistry By Prof. Dr. Abdellah Abusrie Ali Omar M.B.B.Ch, MS, M.D Professor of Medical Biochemistry 22/03/1446 BMC 1  Element is a Substance formed of Only One Type of Atoms May be Metal (iron) or Non-Metal...

General Basis of Biochemistry By Prof. Dr. Abdellah Abusrie Ali Omar M.B.B.Ch, MS, M.D Professor of Medical Biochemistry 22/03/1446 BMC 1  Element is a Substance formed of Only One Type of Atoms May be Metal (iron) or Non-Metal (chlorine)  Atom (Structural Unit) Contain 3 Types Of: Protons; Positively Charged Particles (Inside Nucleus) Neutrons; Neutral Charged Particles (Inside Nucleus) Electrons; Negatively Charged Particles (Outside the Nucleus Located in Certain Orbits Around Nucleus)  Atomic Weight (Atomic Mass) Number of Protons & Neutrons (All Contents of Nucleus) Determine Physical Properties of Element  Atomic Number Number of Protons Only Number of Electrons Only Determine Chemical Properties of Element  Ion is an Atom which can Carry Charge i.e. One or More Electrons are Removed (Positive ion = Cation) or One or More Electrons are Added (Negative ion = Anion) Proton is Hydrogen Atom which its Electron is Removed i.e. Remaining Proton of Hydrogen atom  Isotopes are Different Forms of Same Element have Same Atomic Number (Same Chemical Properties) Same Position in Periodic Table But Differ in Atomic Weight (Differ in Physical Properties)  Types of Isotopes Stable Isotopes i.e. Not Emit Radiation e.g. Oxygen 16, 17, 18. Radioactive Isotopes i.e. Emit Radiation from Nucleus in form of α particle; Positively Charged Particle (Nucleus of Helium i.e. 2 Protons & 2 Neutrons) Β particle; Negatively Charged Electrons Gamma Rays; Electromagnetic Radiation  Uses of Isotopes In Diagnosis: e.g. Thyroid Gland Diseases In Treatment: e.g. Many Cancers by radioactive Materials In Research through Introduction of Radioactive material into the body to know its fate  Acids (Proton Donors) are Substances that Give Protons (Hydrogen Ions) in Solution May be; Strong Acids which Dissociate (ionizes) Completely in solution i.e. Give Large Number of Protons Weak Acids which Dissociate (ionizes) Slightly in solution i.e. Give Small Number of Protons True Acidity = pH of Solution Concentration of Hydrogen Ions in Solution Titratable Acidity Concentration of Hydrogen Ions in solution available for ionization although not ionized at time  Alkalis (Hydroxyl Ion Donors) are Substances that Give Hydroxyl Ion in Solution May be; Strong Alkali which Dissociate (ionizes) Completely in Solution i.e. give Large Number of Hydroxyl Ions Weak Alkali which Dissociate (ionizes) Slightly in solution i.e. give Low Number of Hydroxyl Ions  Base (Proton Acceptor) are Substances that Accept Protons (hydrogen ions) in solution e.g. Na, Uracil N.B. All alkalis are Bases But Not All Bases are Alkalis  Conjugate Base is Part of Acid which Remain after Removal of Proton Amphoteric Substance is a Substance which act as an Acid (Proton Donor) or as Base (Proton acceptor)  Law of Mass Action Rate (Velocity) of Reversible Reaction is Directly Proportional to Concentrations of Reacting Substances V1 A+B C+D V2 V1 is Proportional to [A] × [B] V2 is Proportional to [C] × [D]  V1 is Proportional to [A] × [B] V1 = CONSTANT (K1 ) × [A] × [B] V2 is Proportional to [C] × [D] V2 = CONSTANT (K2 ) × [C] × [D] At equilibrium V1 = V2 (K1 ) × [A] × [B] = (K2 ) × [C] × [D] K1 [C] × [D] Keq = = Constant Eq K2 [A] × [B] Dissociation Constant of Acid = Ka pK of an Acid= Negative Log of Ka at Base 10 Strong acid ~ Bigger Ka Strong acid ~ Smaller pK pH= Negative Log of [H+] to base 10 At Equilibrium of Water H 2o H+ + OH Amount of Ions Present in Sample of Pure Water is Very Small Dissociation Constant of Water= Kw Smaller pH ~ Increasing acidity Higher pH ~ Increasing alkalinity pH= Negative Log of [H+] to base 10 [H+] 10 0 10-1 10-2 10-3 10-4 10-5 10-6 10-7 10-8 10-9 10-10 10-11 10-12 10-13 10-14 pH Zero 1 2 3 4 5 6 7 8 9 10 11 12 13 14 A c i d i t y A l k a l i n i t y Neutral  pH of the Blood is Normally 7.4 ± 0.03 (7.37 – 7.43) Very Narrow Range due to Presence of Buffers Acedemia Acidosis 7.37 - 7.43 Alkalosis Alkalemia Death 7. 1 7.37 - 7.43 7. 8 Death any Slight Change in Blood pH will affect the Function of the Body e.g. any Enzyme needs Special pH for its Maximum action Henderson- HasselBalch Equation  Represent Relationship Between pH & pK of a Weak Acid pH = Negative Log of [H+] to base 10 pK = Negative Log of Ka at base 10 [HA] acid pH = pK - Log [A-] Conjugate Base  Buffer is a Solution that Resist change in pH when Acid or Alkali is added to it Composed of a Mixture of Weak Acid with Salt of Strong Base or Weak Base with Salt of Strong Acid e.g. Carbonic acid with Na or K Bicarbonate H2CO3 / NaHCO3 or H2CO3 / kHCO3  Mechanism of Action of Buffers: If Buffer is H2CO3 / NaHCO3 When Alkali (NaOH) is Added React with H2CO3 To Form NaHCO3 & HOH When Acid (HCL) is added React with NaHCO3 To Form H2CO3 & NaCL  In Either case the Change in pH (Hydrogen ion Concentration) is Relatively Smaller (Narrow Range Suitable for Life 7.4 ± 0.03 (7.37 – 7.43)) than if the Buffer was Not Present Body Buffer Present in Plasma, Extracellular tissue & inside RBCs  Plasma Buffers: 1-Bicarbonate Buffer ( H2CO3 / NaHCO3 ) 2- Phosphate Buffer (Na2HPO4 / NaH2PO4) 3- Plasma Protein Buffer (Na Proteinate / H Protein) RBCs Buffers: 1- Bicarbonate Buffer (H2CO3/k HCO3) 2- Haemoglobin Buffer ( KHb / HHb ) 3- OxyHaemoglobin Buffer (KHbO2/HHbO2)  Solutions, Units of Mass & Units of Concentrations Solute + Solvent = Solution NaCL + Water = Na CL Solution Mass is Expressed in Terms (gm, Mole, Equivalent) One mole is Amount of Substances (Weight in Grams) Equal to its Molecular Weight N.B. Molecular Weight is the Sum of all Atomic Weights of all Atoms in a Compound NaCL + Water = Na CL Solution Molecular Weight of NaOH is 23 + 16 + 1 = 40 gm One Mole of NaOH is 40 gram Units of Concentration Concentration is Expressed in Molarity or Normality Molar Solution is the Solution that Contain One Mole of Solute dissolved in One Liter of Solvent Molar Solution of NaOH is 40 gm Na OH Dissolved in One Liter Water  Normal Solution is the Solution that contain One Equivalent of Solute Dissolved in One Liter of Solvent. Molecular Weight of H2SO4 is 98 (1+1+32+(16×4)) & it contain 2 Hydrogen Atoms Normal Solution of H2SO4 = 98/2 = 49 grams H2SO4 dissolved in one liter of water  Crystalloids, Colloids & Suspensions Less Than Particle Size Ranged from More Than 1.0 nm 1 : 100 nm 100 nm Crystalloids Colloids Suspensions Emulsoids Suspensoids e.g. Blood Crystalloid: is a Solution in which the Particle Size is Less Than 1.0 nm (NanoMeter) Colloid: is a solution in which the Particle Size is Ranged from 1 : 100 nm (NanoMeter) they are either Emulsoid or Suspensoid Suspension: is a Solution in which the Particle Size is More than 1oo nm (NanoMeter)  Colloid: is a Solution in which the Particle Size is Ranged from 1 : 100 nm (NanoMeter) they are Either Emulsoid or Suspensoid Particles of Solutes (Dispersed Phase) are Distributed in a Solvent (Dispersion Medium) Two Types of Colloids (Emulsoid & Suspensoid)  Emulsoids: - Colloids are - called Lyophilic colloids or Hydrophylic colloids (if Water is Dispersion Medium) - Dispersed Particle is Surrounded by 2 Stability Factors (Charges (+ or -) & Shell of Dispersion Medium which may be Water) - Stable (Not Easily Precipitated) - Precipitation can be occurred by Removal of Two Stability Factors By Dehydration Followed by Neutralization of Present Charges Suspensoids: are - Colloids - called Lyophobic Colloids or Hydrophobic Colloids (if Water is Dispersion Medium) - Dispersed Particle is Surrounded by One Stability Factors (Charges Only (+ or -)) - Not Stable ( Easily to be Precipitated) - Precipitation can be Occurred by Removal of the Only Stability factor by Neutralization General Properties of Colloids: - Tyndall Effect: Solution appear Cloudy if Light Beam is Passed through It (due to Reflection of Light) - Brownian Movements: Continuous & Strong Vibratory Movement due to Bombardment of Colloidal Particles by the Molecules of Solvent - Viscosity: More in Suspensoids - Small Osmotic Pressure: due to Large Particle Size - Gel Formation: on Cooling e.g. Gelatin - Imbibition: Ability of Some colloids to take Water & Swell. - Syneresis: on concentration can Squeeze Fluid out - Colloidal Stabilizers: Soap, Saponine, Gelatin  Emulsoids Suspensoids 1 Lyophic Lyophobic 2 Two Stability Factors One Stability Factor 3 Difficult to Precipitate Easy to Precipitate 4 More Viscous Less Viscous 5 Tyndal Effect: More Marked Tyndal Effect: Less Marked 6 Brownian movements: Brownian movements: Less marked More marked 7 Examples: Starch Solution Examples: Colloidal Gold Protein Solution Colloidal Iron Solutions Phenomena: Diffusion: Distribution of Particles by Simple Agitation i.e. All Molecules are in State of Agitated Motion by which Diffusion Occur. Osmosis: Passage of Solvent Molecule from Lower to Higher Concentration through Semi-Permeable Membrane (Membrane Pores Allow Passage of Solvent Particle (small) & Prevent Passage of Solute Particle (Large)). Osmotic Pressure: Hydrostatic Pressure Needed to Prevent Osmosis. Which can be Affected By: - Number of Dissolved Particles (Crystalloid Pressure have High Osmotic Pressure due to Small Particle Number) - Number of Ions (Ionizable Molcules have higher osmotic pressure than Non-Ionizable Particles) (if we have Three Types of Same Number of Molecules) 1- Non-Ionizable Glucose have One Osmotic Pressure. 2- Ionizable NaCL into Na & CL ions have Two Osmotic Pressures. 3- Ionizable CaCL2 into Ca & 2 CL ions have Three osmotic pressures Importance of Osmotic Pressure: 1- Formation of Urine: inside the Glomerular Capillaries, there are 2 Opposing Forces: Filtration force (caused by Capillary Blood Pressure & Equal +35) Reabsorbtion force (Caused by Osmotic Pressure of Plasma Protein & Equal -20) so Net Filtration is 35 – 20 = 15 mmHg which Allow Formation of Urine Under Shock Condition where Capillary Blood Pressure is much Decreased than 35, this leads to Stop Filtration & Anuria occurred Untill Blood Pressure is Restored. Importance of Osmotic Pressure: 2- Formation & Reabsorption of Interstitial Fluid: Formation of Interstitial Fluid by Filteration of Blood Plasma at Arterial End of Blood Capillaries (30 – 25 = 5 mmHg) Blood Pressure at Arterial end – Osmotic Pressure of Plasma Protein i.e. Net Filtration is 5 mmHg, thus Oxygen go out. & its Reabsorption of Interstitial Fluid at Venous End (15 – 25 = -10 mmHg). Blood Pressure at Venous end – Osmotic Pressure of Plasma Protein i.e. Net Filtration is -10 mmHg (in Opposites Direction), thus CO2 go inside. Importance of Osmotic Pressure: 3- Hemolysis: RBCs are Isotonic with 0.9% NaCL Solution (N.B. 0.9% NaCL solution has Same Osmotic Pressure as that of RBCs SO RBCs Neither Swell nor Shrink) - if RBCs are Put in Hypertonic Solution (Solution has Higher Osmotic Pressure than Cells) RBCs will Loss Water & Become Crenate (Shrink) - if RBCs are put in Hypotonic Solution (Solution has Lower Osmotic Pressure than Cells) RBCs will absorb Water & Swell then Hemolysis Occur Solutions Phenomena: Viscosity: (Unit is the Poise) Resistance Offered by the Fluid to Flow Due to Internal Friction between Fluid Molecules Viscosity can be affected by Temperature: ‫تناسب عكسى‬ Solute Concentration & Size: ‫تناسب طردى‬  Blood Viscosity is due to Plasma Protein, Red & White cells Blood viscosity Determine Blood Pressure - During Anemia, HypoProteinemia: Viscosity Decreased. - During Polycythemia: Viscosity Increased Absolute Viscosity of water at 25°C is 0.895 poise  Solutions Phenomena: Surface Tension: is the Force which Hold Surface Molecules of the Liquid Together & Attract them Toward the Body of the Liquid Molecules of Surface of the Liquid is Attracted Down Only But Molecules of Interior of the Liquid is Attracted in All Directions  Solutions Phenomena: Emulsification: is the Breakdown of Large Fat Globules in Water into Small Ones to form Emulsion. Emulsifying Agents: Substance which can Lower Surface Tension of water e.g. Bile Salts, Soap, Proteins  Solutions Phenomena: HydroTrophy: Capacity of Certain Substance to Convert water Insoluble substances into more Soluble e.g. Bile Salts render fats soluble in water to facilitate its absorbtion through Missell formation Hydrotropic Factors: Substance which Make Water Insoluble Substances More Soluble in Water e.g. Bile salts, Phospholipids, Glucorunic acids Lipotropic Factors; help Fat Mobilization from Liver, so Prevent Fatty Liver e.g. Methionine, Choline, Inositol  Solutions Phenomena: Adsorption: Capacity of Substance to Make Other Substance Closely Attached to its Surface (adsorbed on it) due to Presence of Attractive Forces on the Surface adsorbing agent. Elution: Recovery of Adsorbed Material from Adsorbing Agent  Solutions Phenomena: Dialysis: is the Separation of Colloids from Crystalloids by Using Semi-Permeable Membrane Crystalloids CAN PASS through Semi-Permeable Membrane But Colloids can not due to Large particle size this Technique used to Separate Mixture of Proteins (colloids) & Salts (crystalloids) used in cases of Renal Failure (Renal Dialysis) to Get Ride of Waste Products (Crystalloids) & Preserve Plasma Proteins (Colloids)  Solutions Phenomena: Osmolarity: Term used to Define Relationship Between Concentration of Substance & Volume of Solvent. i.e. Concentration of Substance per Volume Solution. Concentration of Substance / Liter of Water as the Volume Varies with the Change of Temperature, so Osmolarity Depends on Temperature.  Solutions Phenomena: Osmolality: Term used to Define Relationship Between Concentration of Substance & Mass of Solvent. i.e. Concentration of Substance per Mass Solution. Concentration of Substance / kg water Osmolality can be Measured by OsmoMeter  Covalent Bond: ‫رابطه تساهميه‬ is Formed by Sharing of Electrons in the Outer Atomic Orbit  Oxygen atom have 2 Electrons in Inner shell & 6 electrons in outer shell. Chemical reaction occurred between 2 electrons of outer shell of each oxygen atom. Outer shells of two atoms become Sharing by four electrons , two from each atom Covalent Bonds hold atoms within an individual Molecule Together. Covalent Bonds tend to be Very Stable & require Much Energy to Break or Rearrange Non-Covalent Bonds: ‫رابطه غير تساهميه‬ are Much Weaker than Covalent Bonds. Play an Important role in Determining many Properties of the Molecules Types Include: 1 - Hydrogen Bonds 2 - Ionic Interactions 3 - Hydrophobic Interactions 4 - Van Der-Waals Forces Hydrogen Bonds Water Molecules (Hydrogen Polar Molecules) have a Weak Partial Negative Charge at One Region of the Molecule (O2 atom in Water) & a Partial Positive Charge ElseWhere (Hydrogen atoms in Water).  i.e. when Water Molecules are close together, their Positive & Negative Regions are Attracted (Force of Attraction) Each Water Molecule is hydrogen bonded to Four others. Multiple Hydrogen Bonds - hold Two Strands of DNA. - Hold Polypeptides Together in Protein Secondary Structure (Alpha Helix & Beta Conformation) - help Binding of Enzymes to their substrates. - help Binding of Antibodies to their antigens. - help Binding of Transcription Factors to each others. - help Binding of Transcription factors to DNA.  Non-Covalent Bonds Ionic interactions At any pH, Protein have Charged groups that Participate in Binding them to Each Other or to Other Types of Molecules. e.g. Negatively charged Carboxyl groups (COO- e.g. Aspartate or Glutamate) May be Attracted by Positively charged Amino groups (+H3N e.g. Lysine or Arginine) Ionic Bonds are Highly Sensitive to changes in pH.  NonCovalent Bonds: Hydrophobic Interactions Side chain R of Amino Acids e.g. Phenylalanine & Leucine are Non Polar So it can Interact Poorly with Polar Molecules Like Water.  For this Reason Many of Non-polar Residues in Globular protein are Directed Toward the Interior of Molecules. Hydrophobic Bonds are Not Affected by Change in pH  NonCovalent Bonds: Van Der Waals forces Forces that Exist Between are Molecules of the Same Substance. N.B. Electrostatic Forces that Keep a Molecule Intact are Existent in Covalent & Ionic Bonds But not Van Der Waals Forces. Famous Example is Dipole Dipole Interaction End Of Show