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Cell Molecules continuo.. 1 • Water has a variety of unusual properties because of attractions between its polar molecules. – The slightly negative regions of one molecule are attracted to the slightly positive regions of nearby molecules, forming a hydrogen bond. – Each water molecule can form hydrogen bonds with up to four neighbors. Fig. 3.1, Page 42 2 5. Water is the solvent of life • The solution المحلول: Is a liquid that is a completely homogeneous mixture of two or more substances. – A sugar cube in a glass of water will eventually dissolve to form a uniform mixture of sugar and water. • The solvent المـذيب: Is the dissolving agent • The solute المذاب: Is the substance that is dissolved – In the above example, water is the solvent, and sugar is the solute. • The aqueous solution المحلول المائى: is the solution in which water is the solvent. 3 • Water is an effective solvent because it forms hydrogen bonds with charged and polar covalent molecules. For example, when a crystal of salt (NaCl) is placed in water, the Na+ cations form hydrogen bonds with partial negative oxygen regions of water molecules. While, the Cl- anions form hydrogen bonds with the partial positive hydrogen regions of water molecules. Fig. 3.7, Page445 • Hydrophilic: • Is any substance that has an affinity for water is. • Hydrophobic: • Is the substances that have no affinity for water are. These substances are dominated by non-ionic and nonpolar covalent bonds. – Because there are no consistent regions with partial or full charges, water molecules cannot form hydrogen bonds with these molecules. • Hydrophobic molecules are major ingredients of cell membranes. 5 1. Organisms are sensitive to changes in pH • The acid: Is a substance that increases the hydrogen ion concentration in a solution. – When hydrochloric acid is added to water, hydrogen ions dissociate تنفصلfrom chloride ions: • HCl -> H+ + Cl- • Addition of an acid makes a solution more acidic. • The base: • Is any substance that reduces the hydrogen ion concentration in a solution. • Some bases reduce H+ directly by accepting hydrogen ions. • Other bases reduce H+ indirectly by dissociating to OH- that combines with H+ to form water. – NaOH -> Na+ + OHOH- + H+ -> H2O • Solutions with more OH- than H+ are basic solutions. Page 47 6 – In a neutral solution, pH = 7. – Values for pH decline تقلas [H+] increase. – While the pH scale is based on [H+], values for [OH-] can be easily calculated from the product relationship. – Acidic solutions have pH values less than 7 and basic solutions have pH values more than 7. – Most biological fluids have pH values in the range of 6 to 8. – A small change in pH actually indicates a change in H+ and OH- Fig. 3.9, Page 48 7 • To maintain cellular pH values at a constant level, biological fluids have buffers. • Buffers resist تـُوازنchanges to the pH of a solution when H+ or OH- is added to the solution. – Buffers accept hydrogen ions from the solution when they are in excess and donate hydrogen ions when they have been depleted. – One important buffer in human blood and other biological solutions is carbonic acid. 8 • Isomers: • are compounds that have the same molecular formula but different structures, and therefore, different chemical properties. – For example, butane and isobutane have the same molecular formula C4H10, but butane has a straight skeleton and isobutane has a branched skeleton. • 1- structural isomers The two butanes are, molecules with the same molecular formula but differ in the covalent arrangement of atoms. 2- Geometric isomers: Are compounds with the same covalent partnerships that differ in their arrangement around a carbon-carbon double bond. 9 Fig. 4.6a, Page 56 • 3- Enantiomers are molecules that are mirror images of each other – Enantiomers are possible if there are four different atoms or groups of atoms bonded to a carbon. – They are like left-handed and right-handed versions. – Usually one is biologically active, the other inactive. Fig. 4.6c, Page 56 10 1. Functional groups contribute to the molecular diversity of life • Functional groups: • Are the components of organic molecules that are most commonly involved in chemical reactions, and give each molecule its unique properties. – Functional groups are attachments that replace one or more hydrogen atoms to the carbon skeleton of the hydrocarbon. – For example, the basic structure of testosterone (male hormone) and estradiol (female hormone) is identical. Page 57 11 • There are six functional groups that are most important to the chemistry of life: • hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, and phosphate. – All are hydrophilic and increase solubility of organic compounds in water. Page 57 12 • 1- Hydroxyl group (-OH): a hydrogen atom forms a covalent bond with an oxygen which forms a covalent bond to the carbon skeleton. – Organic compounds with hydroxyl groups are alcohols and their names typically end in -ol. 13 Page 58 • 2- Carbonyl group (=CO): consists of an oxygen atom joined to the carbon skeleton by a double bond. – If the carbonyl group is on the end of the skeleton, the compound is an aldelhyde. – If not, then the compound is a ketone. 14 Page 58 • 3- carboxyl group (-COOH): consists of a carbon atom with a double bond with an oxygen atom and a single bond to a hydroxyl group. – A carboxyl group acts as it releases hydrogen as an ion (H+). 15 Page 58 • 4- Amino group (-NH2): consists of a nitrogen atom attached to two hydrogen atoms and the carbon skeleton. – Organic compounds with amino groups are amines. – The amino group acts as a base because ammonia can pick up a hydrogen ion (H+) from the solution. – Amino acids, the building blocks of proteins, have amino and carboxyl groups. 16 Page 58 • 5- Sulfhydryl group (-SH): consists of a sulfur atom bonded to a hydrogen atom and to the backbone. – This group resembles a hydroxyl group in shape. – Organic molecules with sulfhydryl groups are thiols. – Sulfhydryl groups help stabilize the structure of proteins. 17 Page 58 • 6- Phosphate group (-OPO32-): consists of phosphorus bound to four oxygen atoms (three with single bonds and one with a double bond). – A phosphate group connects to the carbon backbone via one of its oxygen atoms. – Phosphate groups are anions with two negative charges as two protons have dissociated from the oxygen atoms. – One function of phosphate groups is to transfer energy between organic molecules. 18 Page 58