BIOLOGY Chapter 2 THE CHEMICAL FOUNDATION OF LIFE PowerPoint Image Slideshow FIGURE 2.1 Atoms are the building blocks of molecules found in the universe—air, soil, water, rocks . . . and also the cells of all living organisms. In this model of an organic molecule, the atoms of carbon (black), hydrogen (white), nitrogen (blue), oxygen (red), and sulfur (yellow) are shown in proportional atomic size. The silver rods indicate chemical bonds. (credit: modification of work by Christian Guthier) Start With Atoms Atoms are the smallest unit of an element that contains all the properties of that element Atoms are the building blocks of all substances Atoms are composed of electrons, protons and neutrons Atomic Particles • The atomic nucleus contains protons and neutrons • Protons (p+) have a positive charge • Neutrons (n) have no charge • Electrons (e-) have a negative charge and move around outside of the nucleus Atomic Structure proton neutron electron Characteristics of Atoms • Atomic number = the number of protons in the atomic nucleus; is constant and determines the element • Elements consist only of atoms with the same atomic number • Mass number • Total # of protons and neutrons in a nucleus • Used to identify isotopes Isotopes and Radioisotopes • Isotopes • Atoms of the same element, with different numbers of neutrons • Some radioactive isotopes are used in research and medical applications as tracers • Tracer • Any molecule with a detectable substance attached FIGURE 2.3 Carbon has an atomic number of six, and two stable isotopes with mass numbers of twelve and thirteen, respectively. Its atomic mass is 12.11. Periodic Table of the Elements Why Electrons Matter • Atoms may gain, share, or lose/donate electrons • Whether and how an atom will interact with other atoms depends on how many electrons it has FIGURE 2.6 The Bohr model was developed by Niels Bohrs in 1913. In this model, electrons exist within principal shells. An electron normally exists in the lowest energy shell available, which is the one closest to the nucleus. Energy from a photon of light can bump it up to a higher energy shell, but this situation is unstable, and the electron quickly decays back to the ground state. In the process, a photon of light is released. FIGURE 2.8 The s subshells are shaped like spheres. Both the 1n and 2n principal shells have an s orbital, but the size of the sphere is larger in the 2n orbital. Each sphere is a single orbital. p subshells are made up of three dumbbell-shaped orbitals. Principal shell 2n has a p subshell, but shell 1 does not. Atom Interactions • The shell model of electron orbitals diagrams electron vacancies; filled from inside out • First shell: one orbital (2 electrons) • Second shell: four orbitals (8 electrons) • Third shell: four orbitals (8 electrons) • Atoms that lack full outer shells tend to give up, acquire, or share electrons A The first shell corresponds to the first energy level, and it can hold up to 2 electrons. Hydrogen has one proton, so it has 1 electron and 1 vacancy. A helium atom has 2 protons, 2 electrons, and no vacancies. The number of protons in each model is shown. B The second shell corresponds to the second energy level, and it can hold up to 8 electrons. Carbon has 6 protons, so its first shell is full. Its second shell has 4 electrons, and four vacancies. Oxygen has 8 protons and two vacancies. Neon has 10 protons and no vacancies. first shell second shell C The third shell, which corresponds to the third energy level, can hold up to 8 electrons. A sodium atom has 11 protons, so its first two shells are full; third shell the third shell has one electron. Thus, sodium has seven vacancies. Chlorine has 17 pro tons and one vacancy. Argon has 18 protons and no vacancies. 1 proton 1 1 electron hydrogen (H) 2 helium (He) 6 8 carbon (C) oxygen (O) 11 17 sodium (Na) chlorine (Cl) 10 neon (Ne) 18 argon (Ar) Stepped Art Figure 2-5 p26 Chemical Bond An attractive force existing between two atoms when their outermost (valence) electrons interact Molecule = two or more atoms joined in chemical bonds Example: molecular oxygen (O2) Compounds = molecules consisting of two or more elements whose proportions do not vary Example: water (H2O) The Water Molecule…a compound one oxygen atom two hydrogen atoms Types of Bonds The three most common types of bonds in biological molecules: 1. Ionic 2. Covalent 3. Hydrogen bonds Ionic Bond A strong mutual attraction between two oppositely charges ions with a large difference in electronegativity (no electron transferred) • Example: NaCl (table salt) Ions and Electronegativity • Ion • An atom with a positive or negative charge due to loss or gain of electrons in its outer shell Examples: Na+ a cation; Cl- an anion + ions are cations; - ions are anions • Electronegativity A measure of an atom’s attraction for its electrons electron loss electron gain Sodium atom Chlorine atom 11p+ 11e– 17p+ 17e– charge: 0 charge: 0 Sodium ion Chloride ion 11p+ 10e– 17p+ 18e– charge: +1 charge: –1 Figure 2-6 p27 Ionic Bond: Sodium Chloride ionic bond 11 Sodium ion 11p+, 10e– 17 Chloride ion 17p+, 18e– Sodium Chloride = Table Salt Cl– Na+ a Polar Molecule positive charge negative charge Covalent Bonds • Two atoms sharing a pair of electrons • Can be stronger than ionic bonds • Atoms can share one, two, or three pairs of electrons (single, double, or triple covalent bonds) molecular hydrogen (H2) molecular oxygen (O2) water (H2O) Figure 2-9 p29 Types of Covalent Bonds Nonpolar covalent bond • Atoms sharing electrons equally; formed between atoms with similar electronegativity • CH4 Methane Polar covalent bond • Atoms with different electronegativity do not share electrons equally; one atom has a more negative charge, the other is more positive • H2O Water Polarity of the Water Molecule negative charge positive charge FIGURE 2.12 Whether a molecule is polar or nonpolar depends both on bond type and molecular shape. Both water and carbon dioxide have polar covalent bonds, but carbon dioxide is linear, so the partial charges on the molecule cancel each other out. Table 2-1 p29 Take-Home Message: How do atoms interact in chemical bonds? • A chemical bond forms between atoms when their electrons interact • A chemical bond may be ionic or covalent depending on the atoms taking part in it • An ionic bond is a strong mutual attraction between two ions of opposite charge • Atoms share a pair of electrons in a covalent bond; when the atoms share electrons unequally, the bond is polar Hydrogen Bonding • A weak attraction between a highly electronegative atom and a hydrogen atom taking part in a separate polar covalent bond • Hydrogen bonds do not form molecules and are not true chemical bonds • Hydrogen bonds stabilize the structures of large biological molecules (proteins, DNA) Hydrogen Bonds and Water Overall, water (H2O) has no charge The water molecule is polar • Oxygen atom is slightly negative • Hydrogen atoms are slightly positive Hydrogen bonds form between water molecules • Gives water unique properties a hydrogen bond Figure 2-11a p31 Figure 2-11b p31 Figure 2-11c p31 Water’s Special Properties • Living organisms are mostly water; all the chemical reactions of life are carried out in water • Water is essential to life because of its unique properties • The properties of water are a result of extensive hydrogen bonding among water molecules 1. Cohesion/Adhesion Molecules resist separation from one another Hydrogen bonds give water cohesion • Provides surface tension • Draws water up from roots to the top of plants Water Cohesion and Surface Tension FIGURE 2.16 The weight of the needle is pulling the surface downward; at the same time, the surface tension is pulling it up, suspending it on the surface of the water and keeping it from sinking. Notice the indentation in the water around the needle. (credit: Cory Zanker) FIGURE 2.17 Capillary action in a glass tube is caused by the adhesive forces exerted by the internal surface of the glass exceeding the cohesive forces between the water molecules themselves. (credit: modification of work by Pearson-Scott Foresman, donated to the Wikimedia Foundation) 2. Temperature Stability Temperature is a measure of molecular motion • Water has a high specific heat 3. Polar Solvent • Solvent • A substance (usually liquid) that can dissolve other substances (solutes) • The collective strength of water’s many hydrogen bonds pulls ions apart (dissociation) and keeps them dissolved Water dissolves polar molecules Hydrogen bonds form between water molecules and other polar molecules • Polar molecules dissolved by water are hydrophilic (water-loving) • Nonpolar molecules not dissolved by water are hydrophobic (water fearing) FIGURE 2.15 When table salt (NaCl) is mixed in water, spheres of hydration are formed around the ions. The sodium chloride molecule dissociates into separate sodium and chloride ions. FIGURE 2.13 Oil and water do not mix. As this macro image of oil and water shows, oil does not dissolve in water but forms droplets instead. This is due to it being a nonpolar compound. (credit: Gautam Dogra). Take-Home Message: What gives water the special properties that make life possible? • The polarity of a water molecule gives rise to extensive hydrogen bonding among water molecules • Hydrogen bonding among water molecules imparts cohesion to liquid water, and the ability to stabilize temperature and dissolve many substances Acids and Bases • pH is a measure of the number of hydrogen ions in a solution • The more hydrogen ions, the lower the pH • pH 7 is neutral (pure water) • Most biological processes occur within a narrow range of pH, typically around pH 7 • Concentration refers to the amount of a particular solute that is dissolved in a given volume of fluid —0 battery acid —1 gastric fluid —3 more acidic —2 —4 acid rain lemon juice cola vinegar orange juice tomatoes, wine bananas beer bread black coffee urine, tea, typical rain —5 corn —6 butter milk pure water —7 blood, tears egg white seawater —8 — 10 toothpaste hand soap milk of magnesia — 11 household ammonia — 12 — 13 — 14 more basic —9 baking soda detergents Tums hair remover bleach oven cleaner drain cleaner Figure 2-12 p32 Biological Reactions Occur In Water • Water molecules (H2O) can separate into hydrogen ions (H+) and hydroxide ions (OH-) H20 ↔H + + OH- Acids and Bases • Acids donate hydrogen ions in a water solution • pH below 7 • Bases accept hydrogen ions in a water solution • pH above 7 Salts • Salt • A compound that dissolves easily in water and releases ions other than H+ and OH- HCl (acid) + NaOH (base) → NaCl (salt) + H20 Buffers Against Shifts in pH • Buffer • A set of chemicals (a weak acid or base and its salt) that can keep the pH of a solution stable OH- + H2CO3 (carbonic acid) → HCO3- (bicarbonate) + H20 H+ + HCO3- (bicarbonate) → H2CO3 (carbonic acid) FIGURE 2.20 This diagram shows the body’s buffering of blood pH levels. The blue arrows show the process of raising pH as more CO2 is made. The purple arrows indicate the reverse process: the lowering of pH as more bicarbonate is created. Take Home Message: Why is hydrogen important in biological systems? • pH reflects the number of hydrogen ions in a fluid. Most biological systems function properly only within a narrow range of pH • Acids release hydrogen ions in water; bases accept them • Salts release ions other than H+ and OH– • Buffers help keep pH stable. Inside organisms, they are part of homeostasis Carbon – The Stuff of Life • Organic molecules are complex molecules of life, built on a framework of carbon atoms • Carbohydrates • Lipids • Proteins • Nucleic acids • All molecules of life are built with carbon atoms Carbon – The Stuff of Life • Carbon atoms can be assembled and remodeled into many organic compounds • Carbon can bond with one, two, three, or four other atoms • Carbon can form polar or nonpolar bonds • Carbon can form chains or rings FIGURE 2.21 Methane has a tetrahedral geometry, with each of the four hydrogen atoms spaced 109.5° apart. FIGURE 2.24 Molecules that have the same number and type of atoms arranged differently are called isomers. (a) Structural isomers have a different covalent arrangement of atoms. (b) Geometric isomers have a different arrangement of atoms around a double bond. (c) Enantiomers are mirror images of each other. FIGURE 2.26 D-alanine and L-alanine are examples of enantiomers or mirror images. Only the Lforms of amino acids are used to make proteins. Representing Structures of Organic Molecules • Ball-and-stick models show positions of atoms in three dimensions; elements are coded by color glucose From Structure to Function • The function of organic molecules in biological systems begins with their structure • The building blocks of carbohydrates, lipids, proteins, and nucleic acids bond together in different arrangements to form different kinds of complex molecules • Any process in which a molecule changes is called a reaction Assembling Complex Molecules • Monomers (one unit) • Molecules used as subunits to build larger molecules (polymers) • Polymers (many units or monomers) • Larger molecules that are chains of monomers What Cells Do to Organic Compounds • Metabolism • Activities by which cells acquire and use energy to construct, rearrange, and split organic molecules • Allows cells to live, grow, and reproduce • Requires enzymes (proteins that increase the speed of reactions) FIGURE 2.27 The functional groups shown here are found in many different biological molecules.
