2/21/2011. The Chemistry of Life. Matter Anything that has mass and takes up space States of matter? Atoms, Ions and Molecules. Water and Mixtures

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1 The hemistry of Life Atoms, Ions and Molecules Water and Mixtures Energy and hemical Reactions Organic ompounds Matter Anything that has mass and takes up space States of matter? Biochemistry the study of the molecules that compose living organisms carbohydrates, fats, proteins, and nucleic acids 21 The hemical Elements Element simplest form of matter to have unique chemical Atoms particles that make elements 96% of body weight Atomic number of an element number of protons in its nucleus periodic table elements arranged by atomic number elements represented by one or two letter symbols 24 elements have biological role Minerals: inorganic elements 4% human body weight ¾ of this is a and P 23 Atomic Structure The nucleus consists of neutrons and protons Neutrons have no charge and a mass of 1 atomic mass unit (amu) Protons have a positive charge and a mass of 1 amu Electrons are found orbiting the nucleus Electrons negative charge (0 amu) The # protons and electrons for an atom is always equal (by definition: a complete atom) electrically Neutral Atomic number = # Protons Atomic weight = # Protons # Neutrons Isotopes: Atoms with same atomic # but different atomic weights e.g., O atoms all have 8 protons but might have different # of neutrons 1

2 Atomic Structure Planetary Models of Elements Atoms composed of subatomic particles: Proton positive charge Neutron no electrical charge Electron negative charge Neutron (n 0 ) Proton (p ) First Second Third Fourth Nucleus entral part of atom omposed of protons and neutrons Electrons move around the nucleus Electron (e ) Nucleus arbon () 6p, 6e, 6n 0 Atomic number = 6 Atomic mass = 12 Nitrogen (N) 7p, 7e, 7n 0 Atomic number = 7 Atomic mass = 14 Sodium (Na) 11p, 11e, 12n 0 Atomic number = 11 Atomic mass = 23 Potassium (K) 19p, 19e, 20n 0 Atomic number = 19 Atomic mass = 39 Lithium (Li) 7 28 Electrons of an atom occupy regions of space called electron shells which circle the nucleus For atoms with atomic numbers of 18 or less, the following rules apply: The first shell can hold up to 2 electrons The second shell can hold up to 8 electrons The third shell can hold up to 8 electrons 9 Valence shell (electron) outermost shell More farther electrons are from nucleus Lower shells are filled before next shell accepts Electrons 10 Ions ations Anions Ion An atom that gains or loses electrons to become stable An electrically charged atom ation A positively charged ion Formed when an atom loses electrons 11p 12n 0 17p 18n 0 Electrolytes Salts that ionize in water and form solutions capable of conducting an electric current. Electrolyte importance chemical reactivity osmotic effects (influence water movement) nerves and muscle tissue Anion A negatively charged ion Formed when an atom gains electrons Sodium atom (Na) hlorine atom (l)

3 Free Radicals hemical particles with an odd number of electrons Produced by normal metabolic reactions, radiation, chemicals auses tissue damage reactions that destroy molecules causes cancer, death of heart tissue and aging Antioxidants neutralize free radicals Molecules and hemical Bonds Molecule two or more atoms held together by chemical bonds ompound two or more different kinds of atoms chemically bonded together Molecular formulas depict the elements present and the number of each atom present in the molecule 2 612O6 2O Structural Formula of Isomers Isomers molecules with identical molecular formulae but different arrangement of their atoms Structural formulae ondensed Structural formulae Molecular formulae Ethanol O 3 2O 2 6O Ethyl ether O 3O 3 2 6O 216 Figure 2.5 hemical Bonds hemical bonds: hold molecules TABLE 2.3 together, or attract one molecule to another Types of hemical Bonds Ionic bonds ovalent bonds ydrogen bonds Van der Waals force Types of hemical Bonds Ionic Bonds Ionic Bonds An attraction between a cation and an anion Formed when electrons are transferred from one atom to another atom one donates one receives! 11p 17p 12n 0 18n 0 Na l Sodium ion (Na ) hloride ion (l ) 217 Sodium chloride 18 3

4 Ionic Bond: formed by transfer of >1 elecrons from one atom to another ovalent Bonds Formed when atoms share electrons!!!! 2 one donates one receives! Figure 2.5a ydrogen atom ydrogen atom ydrogen atoms form single bonds Oxygen atoms form two bonds Nitrogen atoms form three bonds arbon atoms form four bonds ydrogen molecule O = O N N O = = O 20 ovalent Bonds: atoms share an electron Single Double ovalent Bonds Two pairs of electrons are shared each Figure 2.7a Figure 2.7b Triple ovalent Bonds Nonpolar /Polar ovalent Bonds Nonpolar covalent bond Electrons shared equally (a) O Polar covalent O bond Electrons shared unequally Figure 2.7c (b) Figure

5 ydrogen Bonds ydrogen bond a weak attraction between a slightly positive hydrogen atom in one molecule and a slightly negative oxygen or nitrogen atom in another. Water molecules are weakly attracted to each other by hydrogen bonds relatively weak bonds ydrogen Bonds very important to physiology protein structure DNA structure 225 Figure 2.10a Van der Waals Forces Van der Waals Forces weak, brief attractions between neutral atoms Fluctuations in electron density in electron cloud of a molecule creates polarity for a moment, and can attract adjacent molecules in the region for a very short instant in time Only 1% as strong as a covalent bond when two surfaces or large molecules meet, attraction between large numbers of atoms can create a very strong attraction important in protein folding important with protein binding with hormones association of lipid molecules with each other 227 Water and Mixtures Mixtures substances physically blended, but not chemically combined body fluids are complex mixtures of chemicals each substance maintains its own chemical properties Most mixtures in our bodies consist of chemicals dissolved or suspended in water Water 5075% of body weight depends on age, sex, fat content, etc. 228 Water 1. Solvency Water s polar covalent bonds and its Vshaped molecule gives water a set of properties that account for its ability to support life. 1. solvency 2. cohesion 3. adhesion (to same molecules stick together) 4. chemical reactivity 5. thermal stability 229 Solvency ability to dissolve other chemicals water is called the Universal Solvent ydrophilic substances that dissolve in water molecules must be polarized or charged ydrophobic substances that do not dissolve in water molecules are nonpolar or neutral (fat) Virtually all metabolic reactions depend on the 230 solvency of water 5

6 2. Water as a Solvent Oxygen (a) 105 ydrogen (b) Na l Polar water molecules overpower the ionic bond in Na l (polar molecule) forming hydration spheres around each ion Figure 2.9 water molecules: negative pole faces Na, positive pole faces l 231 Please note that due to differing operating systems, some animations will not appear until the presentation is viewed in Presentation Mode (Slide Show view). You may see blank slides in the Normal or Slide Sorter views. All animations will appear after viewing in Presentation Mode and playing each animation. Most animations will require the latest version of the Flash Player, which is available at 3. Adhesion and ohesion Adhesion tendency of one substance to cling to another ohesion tendency of like molecules to cling to each other water is very cohesive due to its hydrogen bonds surface tension 4. hemical Reactivity of Water is the ability to participate in chemical reactions water ionizes into and O water ionizes other chemicals (acids and salts) water involved in hydrolysis and dehydration synthesis reactions 5. hemical Reactivity of Water eat capacity of water buffer Solution particles of matter (solutes) mixed with a more abundant substance (usually water) (solvent) Solute can be gas, solid or liquid Solutions Acids, Bases, and Salts Electrolytes substances that release ions in water Nal Na l Acids a proton donor: a molecule that dissociate to release hydrogen ions () in water l l (a) (b) (c) (d) Ken Saladin 235 Figure 2.10 (1) Bases a proton acceptor: substances that release ions that can combine with hydrogen ions () NaO Na O proton acceptor Salts electrolytes formed by the reaction between an acid and a base l NaO 2 O Nal 36 6

7 Acids and Bases Acids release and are therefore proton donors Bases take up and are proton acceptors Acidic solutions have higher concentration and therefore a lower p (= more acidic) Alkaline solutions have lower concentration and therefore a higher p (= less acidic Neutral solutions have equal and O concentrations AcidBase oncentration (p) Acidic: p Basic: p Neutral: p 7.00 A change of one number represents a 10 fold change in concentration p 4.0 is 10 times as acidic as p of 5.0 Figure 2.13 p Scale Milk, Pure water Bread, saliva (7.0) Egg white Wine, black Bananas, ( ) (8.0) vinegar coffee Gastric juice tomatoes ( ) (5.0) ( ) (4.7) Lemon juice 1 M (2.3) ydrochloric Acid (0) ousehold bleach ousehold (9.5) ammonia ( ) Oven cleaner, lye (13.4) 1 M sodium hydroxide (14) Buffers Systems (chemicals) that resist abrupt and large swings in the p If are in excess (acidic) they bond with them to increase Ph (lower acididity) if are depleted (basic) they can donate ions to lower Ph (increase acidity) Neutral 0 14 Figure