Bio 1&2: Biomedical Importance of Water (Adalel Almotamyz College of Medical Sciences) PDF

# Adalel Almotamyz College Of Medical Sciences ## المقرر الدراسي : الكيمياء الحيوية 1 ### القسم العلمي / الفصل : الرابع. للفصل الدراسي : خريف 2024 – 2025 ### المحاضرة : الأولى. ### استاذ المقرر : عودة طلحة خوجلي عباس. ## Molecular Base of Life Water (Vital of life ### BIOMEDICAL IMPORTANCE:...

# Adalel Almotamyz College Of Medical Sciences ## المقرر الدراسي : الكيمياء الحيوية 1 ### القسم العلمي / الفصل : الرابع. للفصل الدراسي : خريف 2024 – 2025 ### المحاضرة : الأولى. ### استاذ المقرر : عودة طلحة خوجلي عباس. ## Molecular Base of Life Water (Vital of life ### BIOMEDICAL IMPORTANCE: - Water is the predominant chemical component of living organisms. - Water has the ability to solvate a wide range of organic and inorganic molecules from water's dipolar structure and exceptional capacity for forming hydrogen bonds. - Water is a reactant or product in many metabolic reactions. - Water has a slight propensity to dissociate into hydroxide ions and protons. - Bicarbonate and other buffers normally maintain the pH of extracellular fluid between 7.35 and 7.45. Suspected disturbances of acid base balance are verified by measuring the pH of arterial blood and the CO2 content of venous blood. Causes of acidosis (blood pH < 7.35) include diabetic ketosis and lactic acidosis. Alkalosis (pH > 7.45) for example, follows vomiting of acidic gastric contents. ### NOTE: WATER IS AN IDEAL BIOLOGIC SOLVENT. #### Water Molecules Form Dipoles: A water molecule is an irregular, slightly skewed tetrahedron with oxygen at its center (Figure). The two hydrogens and the unshared electrons of the remaining two sp3 -hybridized orbitals occupy the corners of the tetrahedron, the 105-degree angle between the hydrogens. Water is a dipole; the strongly electronegative oxygen atom pulls electrons away from the hydrogen nuclei, leaving them with a partial positive charge, while its two unshared electron pairs constitute a region of local negative charge. Its strong dipole and high dielectric constant enable water to dissolve large quantities of charged compounds such as salts. #### Water Molecules Form Hydrogen Bonds: An unshielded hydrogen nucleus covalently bound to electron-withdrawing oxygen or nitrogen atom can interact with an unshared electron pair on another oxygen or nitrogen atom to form a hydrogen bond. Since water molecules contain both of these features, hydrogen bonding favors the self-association of water molecules into ordered arrays (Figure 2–2). Hydrogen bonding profoundly influences the physical properties of water and accounts for its exceptionally high viscosity, surface tension, and boiling point. Hydrogen bonding enables water to dissolve many organic biomolecules that contain functional groups which can participate in hydrogen bonding. ### Physiochemical properties of water: #### Physical Properties of water: - Colorless - Odorless - Tasteless Solvent: also have important implications for the structure and functions of biological molecules. ### Structure of water: Consist of two hydrogen atoms bonded to an oxygen atom (figure 1). The O - H bond distance is 0.958A° (1A° =10¯¹ºm) and the angle formed by the three atoms is 104.5° (figure 1 water structure). Water molecules form hydrogen bonds. Water is a polar molecule: Oxygen atom with its unshared electrons carries partial negative change and the hydrogen atoms each carry partial positive charge. The resulting directional intermolecular association is known as hydrogen bond (figure of hydrogen bond). Single water can participate in a maximum of four hydrogen bonds with other water molecules. Energy of individual hydrogen bond (-20KJ.mol¯¹), energy of covalent bond O –H (460kJ.mol¯¹). ### Ice is a crystal of hydrogen- bonded water molecules: Each water molecule is tetrahedrally surrounded by four nearest neighbors to which it is hydrogen bonded. (Figure ice structure at 0°c) Liquid water density =1.00g.ml¯¹ Whereas ice density =0.92g .ml¯¹ ### Structure of liquid water is irregular: - Trimer - Tetramar - Pentamer These net works continually break up and reform every 2(1011) Second. Note that water can serve simultaneously both as a hydrogen donor and as a hydrogen acceptor. ### Hydrogen Bonds and Other Weak Interactions in Biological Molecules: #### Self-ionization of water: Dissociation of H20 is through a breakage of an – oH bond H2O → H+ + OH¯ (at 25°c). {H+} {oH®}= 10-14mol/L2. Where {H+} and {oH} are the concentration of the two ions in mole per liter. ## المقرر الدراسي : الكيمياء الحيوية .1 ### القسم العلمي / الفصل : الرابع للفصل الدراسي : خريف 2024 - 2025 ### المحاضرة : الثانية. ### استاذ المقرر : مودة طلحة خوجلي عباس. ## PH It is more convenient to refer to the hydrogen ion concentration in whole numbers. To do this -log of [H+] is used (-log is called (p)) thus: PH= - log[H+] There for when [H+] =[OH+] . The PH=7. i.e., the neutral pH below 7 solutions are acidic, and above 7 solutions are basic Alkaline. In the body the PH is varies, depending on the function of the compartment. In the cell cytoplasm the PH is 7.2. In the stomach where food is digested by acid, The PH is about 1. In small intestine it is about 8 and in lysosomes it is about 5. ## Acids and Bases An acid is any molecule that can release proton, and gain a negative charge (Anions). And the base is a substance that can accept a proton. And again a positive charge (Cations). The –COOH group of nucleic acids tend to hold on to its protons (i.e. remain largely unionized). While a weak base will take up protons (i.e. Ionize). In a basic solution, weak acids will ionize, while weak base are only partially ionized NAs ionize by releasing proton and become negatively charged. Amino acids contain both basic (-NH2) and acidic (-cooH) groups and become positively or negatively charged or both. ### Ionization of amino acids: Amino acids have -cooH groups which can release protons, and they have NH2 groups which can accept protons, Therefore, depending on the pH of the solution, amino acids can exist as weak acids or bases .Since proteins may have unequally balanced numbers of -cooH and -NH2 groups, changes in PH of the solution they are dissolved will cause change in the ratio of changed acidic and basic groups. For the different amino acids, the pH at which the -cooH and -NH2 groups exactly balance each other to create no net charge on the molecule is called the isoelectric PH of the molecule. In chemical terms, any molecule that has both negatively and positively charged groups is called zwitterions. ## The Henderson- Hasselbalch equation: The -cooH group ionizes thus cooH↔ coo¯+ H+....... (1) At equilibrium: K= {coo] {H+} / {cooH} (2) Where K(also sometimes called Ka) is the equilibrium. Constant for equation....(3) Pk is defined as as the PH at which 50% of the-cooH (or - NH2) groups are ionized,clearly, K will depend on the numbers of these groups that the amino acid has, Similary, the -NH3+ is deprotonated thus: NH3+↔ NH2+ H+ .......(3) Figure (titration curve) A titration curve for the -cooH and -NH2 groups occurs over a pH range, and the pH at which 50% of the groups are deprotonated is the pk., the protonated forms predominate; at PH values above the pk, the deprotonated forms pre dominate .It follows that a stronger acid has a lower pk, ie. It readily loses protons. (Figure titration curve). Using equation 2, we can derive one which enables us to predict the state of ionization of a given amino acid if we know k and pH of the solution. 1-Rearrange and take the log of both sides log k=log (H+) +log= {coo} / {cooH} .....(4) 2- Convert to -log and rearrange -log {H+} =-log {k} + log.ooo........ (5) Express in terms to p (-log): the Henderson- Hasselbalch equation PH= PK+ Log {coo}/ {cooH} (6) Equation (6) allows us to predict, for example, the degree of ionization of the-cooH group of drugs for absorption through biological members, which are lipophilic and allow only the unionized form of the drug to pass through easily. For example, aspirin is a weak acid, with a pk of 3.5 the reader is invited (PH 1.5) and in the small intestine (PH8) from this result, the theoretical site of greater absorption may be predicted. ## Buffers: Buffer solutions are those that resist a change in pH even when H+ ions are added to, or removed from the solution. Thus, they protect the solutes within the buffers from sharp changes in pH that could for example, inhibit a chemical reaction. In the absence of a buffering mechanism, the pH of a solution will change much more when acids or alkalis are added to the solution. Mechanism of buffer action: The weak acid, acetic acid (cH3cooH) and its salt sodium acetate (cH3cooNa) provide an example of buffering system. The acid has a pk of 4.75.achange of 2pH units in the solution from 5.75 to 3.75 causes a change from about 10% cH3cooH in the unionized form to about 90% unionized CH3c00H. The ability of a weak acid and its salt to buffer a solution is greatest over the PH range pk-1 to pk+1 when CH3cooH and CH3cooNa are present together in solution. They ionize as follows CH3COOH ↔ CH3c00¯ +H+ CH3COONa ↔ CH3coo¯+Na+ Although the acid ionizes only partially, salts ionize virtually completely. Therefore, there will be a large concentration of cH3coo and Na+ ions in solution. The increased concentration of CH3coo ions from the salt suppresses even further the ionization of CH3c0oH, If more H+ ions are added to the solution they will combine with CH3coo ions to form even more of the largely undissociated CH3cooH. A new equilibrium is established. And the resulting liberation of H+ ions is relatively slight. If oH ions are added, they will combine with H+ ions to form neutral H20. Thus at pH values close to its pk. a weak acid is a useful buffering agent when mixed with its salt. ### Biological buffer: Note: The system will lose its buffering capacity sharply at Ph values more than 1 pH value away from the pK. In a strongly basic solution the weak acid itself ionizes virtually completely, so cannot exist in the unionized form. And it strongly acidic solutions it cannot exist in the ionized form. ## In cell: Buffering of physiological fluids is achieved largely through the ionization of phosphoric acid (H3PO4), to form phosphates. H3PO4 can exist in three forms, depending on the PH of the solution: PK=2.1 H3PO4 → H2PO4 +H+ PK=7.2 H2PO4 →HPO42+H+ PK=12.7 HPO4²¯ ↔PO4³¯+H+ Note: At cytoplasmic PH, phosphate can act as buffering systems. In plasma buffering and interstitial fluid, the CO2 bicarbonate (HCO3) system is very important it prevents the development of dangerous of acid or base imbalance, and works as follows. CO2+H2O → H2CO3 Ionizes H2CO3↔ H+ +HCO3 H2CO3 ionizes so rapidly that for our purposes the reaction of importance can be considered to be CO2+H2O → H++HCO3¯.