1

Cell Molecules Cell Molecules continuo..continuo..

2

• 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 neighborsfour neighbors.

Fig. 3.1, Page 42Fig. 3.1, Page 42

3

• The solution The solution المحلولالمحلول:: 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 The solvent المـذيبالمـذيب:: Is the dissolving agent • The solute The solute المذابالمذاب:: Is the substance that is dissolved

– In the above example, water is the solvent, and sugar is the solute.

• The aqueous solution The aqueous solution المائى المائى المحلول ::المحلول is the solution in which water is the solvent.

5. Water is the solvent of life5. Water is the solvent of life

4

• Water is an effective solvent because it forms hydrogen bonds with charged and polar covalent molecules.

Fig. 3.7, Page 45

For example, when a crystal of salt (NaCl) is placed in water, the Na+ cations form hydrogen bonds with partial negative oxygennegative oxygen regions of water molecules. While, the Cl- anions form hydrogen bonds with the partial positive partial positive hydrogen regionshydrogen regions of water molecules.

5

• Hydrophilic:Hydrophilic:• Is any substance that has an affinity for water is.Is any substance that has an affinity for water is.

• Hydrophobic: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.

6

• The acid:The acid: Is a substance that increasesincreases the hydrogen ion concentration in a solution.

– When hydrochloric acid is added to water, hydrogen ions dissociate تنفصل from chloride ions:

• HCl -> H+ + Cl-

• Addition of an acid makes a solution more acidic.Addition of an acid makes a solution more acidic.

• The base:The base:• Is any substance that reducesreduces 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+ + OH- OH- + H+ -> H2O

• Solutions with more OHOH-- than HH++ are basic solutions.

1. Organisms are sensitive to changes in pH1. Organisms are sensitive to changes in pH

Page 47

7

– In a neutral solution, pH = 7pH = 7.– Values for pH decline تقل as [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 HH++ and OHOH--

Fig. 3.9, Page 48

8

• To maintain cellular pH values at a constant level, biological fluids have buffers.

• Buffers resist تُـوازن changes 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 Buffers accept hydrogen ions from the solution when they are in excess and donate hydrogen ions when they have been depleted.and donate hydrogen ions when they have been depleted.

– One important buffer in human blood and other biological solutions is One important buffer in human blood and other biological solutions is carbonic acidcarbonic acid..

9

• Isomers:Isomers:• are compounds that have the same molecular formula but different are compounds that have the same molecular formula but different

structures, and therefore, different chemical properties.structures, and therefore, different chemical properties.– For example, butanebutane and isobutaneisobutane have the same molecular formula C4H10, but

butane has a straight skeleton and isobutane has a branched skeleton.

• 1- 1- structural isomersstructural isomers The two butanes are, The two butanes are, molecules with the same molecules with the same molecular formula but differ molecular formula but differ in the covalent arrangement in the covalent arrangement of atoms. of atoms.

Fig. 4.6a, Page 56Fig. 4.6a, Page 56

2- Geometric isomers:2- Geometric isomers:Are compounds with the same covalent partnerships that differ in their arrangement around a carbon-carbon double bond.

10

• 3- Enantiomers3- 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, Fig. 4.6c, Page 56Page 56

11

• Functional groups: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 testosteronetestosterone (male hormone) and estradiolestradiol (female hormone) is identical.

1. Functional groups contribute to the molecular diversity 1. Functional groups contribute to the molecular diversity of lifeof life

Page 57

12

• There are six functional groups that are most important to the chemistry of life:

• hydroxyl, carbonyl, carboxyl, amino, hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, and phosphate.sulfhydryl, and phosphate.– All are hydrophilic and increase solubility of organic

compounds in water.

Page 57

13

• 1- Hydroxyl group (-OH):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.

Page 58

14

• 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.

Page 58

15

• 3- carboxyl group (-COOH):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+).

Page 58

16

• 4- Amino group (-NH4- Amino group (-NH22):): 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.

Page 58

17

• 5- Sulfhydryl group (-SH):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.

Page 58

18

• 6- Phosphate group (-OPO6- Phosphate group (-OPO332-2-):):

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.

Page 58