A Chemical Connection to Biology • Biology is a multidisciplinary science  Living organisms are subject to basic laws of physics and chemistry • Matter consists of chemical elements in pure form and in combinations called compounds • Organisms are composed of matter • Matter is anything that takes up space and has mass • Matter is made up of elements • An element is a substance that cannot be broken down to other substances by chemical reactions • A compound is a substance consisting of two or more elements in a fixed ratio  A compound has characteristics different from those of its elementsFig. 2-3 Sodium Chlorine Sodium chlorideEssential Elements of Life • About 25 of the 92 elements are essential to life • Carbon, hydrogen, oxygen, and nitrogen make up 96% of living matter • Most of the remaining 4% consists of calcium, phosphorus, potassium, and sulfur • Trace elements are those required by an organism in minute quantitiesIntroduction to Biochemistry • Valency and Chemical bonds  electronegativity  types of chemical bonds  Water • Carbon  carbon skeletons  Isomers • Polymerization and macromolecules  monomers and polymers • Biologically important macromolecules  Carbohydrates  Lipids  Proteins  Nucleic AcidsIntroduction to Biochemistry • Valency and Chemical bonds  electronegativity  types of chemical bonds  Water • Carbon  carbon skeletons  Isomers • Polymerization and macromolecules  monomers and polymers • Biologically important macromolecules  Carbohydrates  Lipids  Proteins  Nucleic AcidsEnergy Levels of Electrons • Potential energy is the energy that matter has because of its location or structure • The electrons of an atom differ in their amounts of potential energy • An electron’s state of potential energy is called its energy level, or electron shell Figure 2.8 Energy levels of an atom’s electronsValences for the major elements of organic molecules Hydrogen (valence = 1) Oxygen (valence = 2) Nitrogen (valence = 3) Carbon (valence = 4) H O N C Fig. 4.4 • Valence electrons are those in the outermost shell, or valence shell • The chemical behavior of an atom is mostly determined by the valence electrons • Elements with a full valence shell are chemically inertFig. 2-9 Hydrogen 1H Lithium 3Li Beryllium 4Be Boron 5B Carbon 6C Nitrogen 7N Oxygen 8O Fluorine 9F Neon 10Ne Helium 2He Atomic number Element symbol Electron- distribution diagram Atomic mass 2 He 4.00 First shell Second shell Third shell Sodium 11Na Magnesium 12Mg Aluminum 13Al Silicon 14Si Phosphorus 15P Sulfur 16S Chlorine 17Cl Argon 18ArThe formation and function of molecules depend on chemical bonding between atoms • Atoms with incomplete valence shells can share or transfer valence electrons with certain other atoms • These interactions usually result in atoms staying close together, held by attractions called chemical bonds • A covalent bond is the sharing of a pair of valence electrons by two atoms • In a covalent bond, the shared electrons count as part of each atom’s valence shellElectronegativity • Electronegativity is an atom’s attraction for the electrons in a covalent bond  The more electronegative an atom, the more strongly it pulls shared electrons toward itself o Oxygen = 3.5 o Nitrogen = 3.0 o Sulfur & Carbon = 2.5 o Phosphorus & Hydrogen = 2.1 • In a nonpolar covalent bond, the atoms share the electron equally • In a polar covalent bond, one atom is more electronegative, and the atoms do not share the electron equally  Unequal sharing of electrons causes a partial positive or negative charge for each atom or moleculeHydrogen bonding • A hydrogen bond forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom  In living cells, the electronegative partners are usually oxygen or nitrogen atomsIonic Bonds • Atoms sometimes strip electrons from their bonding partners  An example is the transfer of an electron from sodium to chlorine  After the transfer of an electron, both atoms have charges • A charged atom (or molecule) is called an ion  A cation is a positively charged ion  An anion is a negatively charged ion • An ionic bond is an attraction between an anion and a cation 11 protons 10 electrons 17 protons 18 electronsSalts • Compounds formed by ionic bonds are called ionic compounds, or salts • Salts, such as sodium chloride (table salt), are often found in nature as crystalsMolecular shapes due to hybrid orbitals • A molecule’s shape is very important to its function  Determined by the positions of its atoms’ valence orbitals • Biological molecules recognize and interact with each other with a specificity based on molecular shape  Molecules with similar shapes can have similar biological effectsFig. 2-18 (a) Structures of endorphin and morphine (b) Binding to endorphin receptors Natural endorphin Endorphin receptors Morphine Brain cell Morphine Natural endorphin Key Carbon Hydrogen Nitrogen Sulfur OxygenIntroduction to Biochemistry • Valency and Chemical bonds  electronegativity  types of chemical bonds  Water • Carbon  carbon skeletons  Isomers • Polymerization and macromolecules  monomers and polymers • Biologically important macromolecules  Carbohydrates  Lipids  Proteins  Nucleic AcidsCarbon atoms can form diverse molecules by bonding to four other atoms • With four valence electrons, carbon can form four covalent bonds with a variety of atoms  This tetravalence makes large, complex molecules possible • In molecules with multiple carbons, each carbon bonded to four other atoms has a tetrahedral shape • However, when two carbon atoms are joined by a double bond, the molecule has a flat shapeVariations in carbon skeletonsTypes of IsomersThe pharmacological importance of enantiomers • Enantiomers are important in the pharmaceutical industry  Two enantiomers of a drug may have different effects • Differing effects of enantiomers demonstrate that organisms are sensitive to even subtle variations in moleculesA small number of chemical groups are key to the functioning of biological molecules • Distinctive properties of organic molecules depend not only on the carbon skeleton but also on the molecular components attached to it  A number of characteristic groups are often