Chapter 2 Notes - Matter, Atoms, and Elements

## Chapter 2 Notes ### Matter, Atoms, Elements, and the Periodic Table Matter has mass and occupies space. - 3 forms of matter: - Solid (e.g., bone) - Liquid (e.g., blood) - Gas (e.g., oxygen) Atom is the smallest particle exhibiting chemical properties of an element. - 92 naturally oc...

## Chapter 2 Notes ### Matter, Atoms, Elements, and the Periodic Table Matter has mass and occupies space. - 3 forms of matter: - Solid (e.g., bone) - Liquid (e.g., blood) - Gas (e.g., oxygen) Atom is the smallest particle exhibiting chemical properties of an element. - 92 naturally occurring elements make up matter. - Organized in periodic table of elements. ### Most common elements of the Human Body | Element | Symbol | %Body weight | |--------------|--------|---------------| | Oxygen | O | 65.5 | | Carbon | C | 18.5 | | Hydrogen | H | 9.5 | | Nitrogen | N | 3.0 | | Calcium | Ca | 1.5 | | Phosphorus | P | 1.0 | Minor elements (less than 1% of body weight): Sulfur (S), Potassium (K), Sodium (Na), Chlorine (Cl), Magnesium (Mg), Iron (Fe). ### Components of an Atom Atoms composed of three subatomic particles. - Neutrons - Mass of one atomic mass unit (amu) - No charge - Located in the nucleus - Protons - Mass of one amu - Positive charge of one (+1) - Located in the nucleus - Electrons - 1/1800th of the mass of a proton or neutron - Negative charge of one (-1) - Located at varying distance from the nucleus in regions called orbitals or shells ### Periodic Table - Chemical symbol - Unique to each element - Usually identified by first letter, or first letter plus an additional letter, e.g., C is carbon - Atomic number - Number of protons in an atom of the element - Located above symbol name - Average atomic mass - Mass of both protons and neutrons - Elements arranged by anatomic number within rows - Shown below the element's symbol on the table ### Determining the number of subatomic particles - Proton number = atomic number - Neutron number = atomic mass - atomic number - Neutron number of Na = 23 - 11 = 12 - Electron number = proton number ### Diagramming atomic structures An atom has “shells” of electrons surrounding the nucleus. - Each shell has given energy level. - Each shell holds a limited number of electrons. - Innermost shell: two electrons, second shell up to eight - Shells close to the nucleus must be filled first. ### Isotopes Isotopes are different atoms of the same element. - Same number of protons and electrons; different number of neutrons. - Identical chemical characteristics; different atomic masses. E.g., carbon exists in three isotopes. - Carbon-12, with 6 neutrons - Most prevalent type - Carbon-13, with 7 neutrons - Carbon-14, with 8 neutrons Weighted average of atomic mass for all isotopes is the average atomic mass. ### Radioisotopes Contain excess neutrons, so unstable. - Lose nuclear components in the form of high energy radiation - Alpha particles - Beta particles - Gamma rays ### Physical half-life - The time for 50% of radioisotope to become stable. - Can vary from a few hours to thousands of years. ### Biological half-life - The time required for half of the radioactive material from a test to be eliminated from the body. ### Clinical View: Medical Imaging of the Thyroid Gland Using Iodine Radioisotopes Radioisotopes introduced into the body during medical procedures. - The time required for half of the radioactive material from a test to be eliminated from the body. - Used by cells in a similar manner to nonradioisotopes. - Can trace products of metabolic reactions that use these elements. - Thyroid gland darker in areas where less radioactive iodine taken up. - Can help locate a nodule. ### Chemical Stability and the Octet Rule Periodic table is organized into periods (horizontal rows) based on increasing atomic number and groups (columns) based on number of electrons in outer or valence shell. - e.g. Column IA shows hydrogen, lithium, sodium, potassium. - All with one electron in their outer shell. - Each consecutive column has one additional electron in outer shell. - Elements in column VIIIA each have a full valence shell. - Results in chemical stability. - Helium, neon, etc., chemically inert noble gases. ### Organization of the Periodic Table Based on Valence Shell Electrons Elements tend to lose, gain, or share electrons to obtain complete outer shells with eight electrons. - Known as the octet rule. ### Ions and Ionic Compounds #### Chemical compounds - Stable associations between two or more elements combined in a fixed ratio. - Classified as ionic or molecular. #### Ionic compounds - Are structures composed of ions held together in a lattice by ionic bonds. #### Ions - Atoms with a positive or a negative charge. - Produced from loss or gain of one or more electrons. - Significant physiological functions. - E.g., K+ is used to sports drinks to replace the K+ lost in sweat. - E.g., K+ in a large dose is used in some states for lethal injection. #### Losing electrons and the formation of cations Sodium can reach stability by donating an electron. - Now satisfies the octet rule. - Now has 11 protons and 10 electrons. - Charge is +1 #### Cations - Are ions with a positive charge. #### Gaining electrons and the formation of anions Chlorine reaches stability by gaining an electron. - Now satisfies the octet rule. - Now has 17 protons and 18 electrons. - Charge is -1. #### Anions - Are ions with negative charge. #### Polyatomic ions - Are anions with more than one atom. - E.g., bicarbonate ion and phosphate ion. ### Ionic Bonds - Cations and anions bound by electrostatic forces. - Form salts. - E.g., table salt (NaCl) - Each sodium atom loses one outer shell electron to a chlorine atom. - Sodium and chlorine ions are held together by ionic bonds in a lattice crystal structure (ionic compound). - E.g., magnesium chloride. - Each magnesium atom loses one electron to each of the two chlorine atoms. ### Covalent Bonding, Molecules, and Molecular Compounds #### Covalently bonded molecule - Electrons shared between atoms of two or more different elements. - Termed molecular compounds. - E.g., carbon dioxide (CO2), but not molecular oxygen (O2) #### Molecular formula - Indicates number and type of atoms. - E.g., carbonic acid (H2CO3). #### Structural formula - Indicates number and type of atoms. - Indicates arrangement of atoms within the molecule. - E.g., O=C=O (carbon dioxide). - Allows differentiation of isomers. - Same number and type of elements, but arranged differently in space. #### Isomers - May have different chemical properties. ### Covalent Bonds #### Covalent bond - Atoms share electrons. - Occurs when both atoms require electrons. - Occurs with atoms with 4 to 7 electrons in outer shell. - Formed commonly in human body using - Hydrogen (H) - Oxygen (O) - Nitrogen (N) - Carbon (C) #### Number of covalent bonds an atom can form - Simplest occurs between two hydrogen atoms. - Each sharing its single electron - Oxygen needs two electrons to complete outer shell. - Forms two covalent bonds. - Nitrogen forms three bonds. - Carbon forms four bonds. #### Single, double, and triple covalent bonds - **Single covalent bond** - One pair of electrons shared. - E.g., between two hydrogen atoms. - **Double covalent bond** - Two pairs of electrons shared. - E.g., between two oxygen atoms. - **Triple covalent bond** - Three pairs of electrons shared. - E.g., between two nitrogen atoms. #### Carbon needs four electrons to satisfy octet rule - Can be obtained in a number of ways. - Forms straight chains, branched chains, or rings. - Carbon present where lines meet at an angle. - Additional atoms are hydrogen. ### Nonpolar and polar covalent bonds #### Electronegativity - Relative attraction of each atom for electrons - Determines how electrons are shared in covalent bonds. - Two atoms of same element have equal attraction for electrons. - Resulting bond is nonpolar covalent bond. #### Nonpolar and polar covalent bonds - Sharing of electrons unequally = polar covalent #### In periodic table, electronegativity increases: - From left to right across row. - From bottom to top in column. #### For 4 most common elements composing living organisms; - From least to greatest electronegativity - hydrogen < carbon < nitrogen < oxygen #### Electrons have negative charge. - More electronegative atom develops a partial negative charge. - Less electronegative atom develops a partial positive charge. - Written using Greek delta (δ) followed by superscript plus or minus. #### Exception to rule of polar bond forming between two different atoms: - Carbon bonding with hydrogen #### Covalent bonds may be polar or nonpolar: - **Nonpolar molecules** contain nonpolar covalent bonds. - E.g., O-O and C—H are nonpolar bonds. - **Polar molecules** contain polar covalent bonds. - E.g., O—H is a polar bond in the polar molecule water (H2O). #### Nonpolar molecules may contain polar covalent bonds: - If the polar covalent bonds cancel each other. - E.g., carbon dioxide. #### Amphipathic molecules - Large molecules with both polar and nonpolar regions. - E.g., phospholipids. ### Intermolecular attractions - Weak chemical attractions between molecules. - Important for shape of complex molecules. - E.g., DNA and proteins. - **Hydrogen bond** - Forms between polar molecules. - Attraction between partially positive hydrogen atom and a partially negative atom. - Individually weak, collectively strong. - Influences how water molecules behave. ### Nonpolar, Polar, and Amphipathic Molecules ### Water: A Neutral Solvent - Water spontaneously dissociates to form ions. - Bond between oxygen and hydrogen breaks apart spontaneously. - 1/10,000,000 ions per liter. - OH group hydroxide ion (OH-). - Hydrogen ion transferred to a second water molecule. - Hydronium ion (H3O+). - Equal numbers of positive hydrogen ions and negative hydroxyl ions produced. - Water remains neutral. - H2O + H2O → H3O+ + OH- - simplified to - H2O → H+ + OH- ### Acids and Bases - Acid dissociates in water to produce H+ and an anion. - Proton donor. - Increases concentration of free H+. - More dissociation of H+ with stronger acids. - E.g., HCl in the stomach. - Less dissociation of H+ with weaker acids. - E.g., carbonic acid in the blood. ### Substance A (an acid in water) → H+ + Anion Base accepts H+ when added to solution - Proton acceptor. - Decreases concentration of free H+. - More absorption of H+ with stronger bases. - E.g., ammonia and bleach. - Less absorption of H+ with weaker bases. - E.g., bicarbonate in blood and in secretions released into small intestine. ### Substance B (a base in water) + H+ → B─H ### pH, Neutralization, and the Action of Buffers - pH is a measure of H+. - Relative amount of H+ in a solution. - Range between 0 and - Water dissociates to produce 1/10,000,000 of H+ and OH– ions per liter. - Equal to 1 x 10-7 or to 0.0000001 - pH and H+ concentration are inversely related. - Inverse of the log for a given H+ concentration. - As H+ concentration increases, pH decreases. - As H+ concentration decreases, pH increases. ### Interpreting the pH scale - Solutions with equal concentrations of H+ and OH-. - Are neutral. - Have a pH of 7. - Solutions with greater H+ than OH-. - Are acidic. - Have a pH < 7. - Solutions with greater OH- than H+. - Are basic (alkaline). - Have a pH > 7. - Moving from one increment to next is a 10-fold change. - E.g., a pH of 6 has 10 times greater concentration of H+ than pure water. ### Neutralization - When an acidic or basic solution is returned to neutral (pH 7). - Acids neutralized by adding base. - E.g., medications to neutralize stomach acid must contain a base. - Bases neutralized by adding acid. ### Buffers - Help prevent pH changes if excess acid or base is added. - Act to accept H+ from excess acid or donate H+ to neutralize base. - Carbonic acid (weak acid) and bicarbonate (weak base) buffer blood pH. - Both help maintain blood pH in a critical range (7.35 to 7.45). ### Water Mixtures - Mixtures are formed from combining two or more substances. - Two defining features: - Substances mixed are not chemically changed. - Substances can be separated by physical means. - E.g., evaporation or filtering. ### Categories of Water Mixtures - Three categories of water mixtures: - **Suspension:** material larger in size than 1 mm mixed with water. - E.g., blood cells within plasma or sand in water. - Does not remain mixed unless in motion. - Appears cloudy or opaque; scatters light. - **Colloid:** smaller particles than a suspension, but larger than those in a solution. - E.g., fluid in cell cytosol and fluid in blood plasma. - Remains mixed when not in motion. - **Solution:** homogeneous mixture of material smaller than 1 nanometer. - Dissolves in water. - Does not scatter light; does not settle if solution not in motion. - E.g., sugar water, salt water, blood plasma. - **Special category of suspension-emulsion.** - Water and a nonpolar liquid substance. - E.g., oil and vinegar salad dressing or breast milk. - Does not mix unless shaken. ### Other amphipathic molecules form a micelle. - Hydrophilic substances dissolve in water. - Hydrophobic molecules do not dissolve in water. - Amphipathic molecules partially dissolve in water. ### Molecular Structure of Water - **Hydrogen Bonding** - Composes two-thirds of the human body by weight. - Polar molecule. - One oxygen atom bonded to two hydrogen atoms. - Oxygen atom has two partial negative charges. - Hydrogens have single partial positive charge. - Can form four hydrogen bonds with adjacent molecules. - Central to water's properties. ### Phases of water - 3 phases of water, depending on temperature: - Gas (water vapor) - Substances with low molecular mass. - Liquid (water). - Almost all water in the body. - Solid. - Liquid at room temperature due to hydrogen bonding. ### Functions of liquid water: - Transports - Substances dissolved in water move easily throughout body. - Lubricates - Decreases friction between body structures. - Cushions - Absorbs sudden force of body movements. - Excretes wastes - Unwanted substances dissolve in water are easily eliminated. ### Cohesion, surface tension, and adhesion - **Cohesion** - Attraction between water molecules due to hydrogen bonding - **Surface tension** - Inward pulling of cohesive forces at surface of water. - Causes moist sacs of air in lungs to collapse. - **Adhesion** - Attraction between water molecules and a substance other than water. - Surfactant, a lipoprotein, prevents collapse. ### High specific heat and high heat of vaporization - **Temperature** - Measure of kinetic energy of atoms or molecules within a substance - **Specific heat** - Amount of energy required to increase temperature of 1 gram of a substance by 1 degree Celsius. - Water's value extremely high due to energy needed to break hydrogen bonds. - Contributes to keeping body temperature. - **Heat of vaporization** - Heat required for release of molecules from a liquid phase into a gaseous phase for 1 gram of a substance. - Water's value very high due to hydrogen bonding. - Sweating cools body. - Excess heat dissipated as water. ### Water as the Universal Solvent - **Water-solvent** of the body. - **Solutes** are substances that dissolve in water. - Water is called **universal solvent** because most substances dissolve in it. ### Substances that dissolve in water - **Polar molecules and ions** - Hydrophilic means “water-loving". - Water surrounds substances, forms a hydration shell. - Some substances dissolve but remain intact. - E.g., glucose and alcohol. - **Nonelectrolytes** remain intact but do not conduct current. - **Electrolytes** can conduct current - Substances dissolve and dissociate (separate) - NaCl dissociates into Na+ and Cl- ions. - Acids and bases, such as HCI. - **Nonpolar molecules** - Hydrophobic means "water-fearing" - Hydrophobic exclusion-cohesive water molecules “force out” nonpolar molecules. - Hydrophobic interaction—“excluded molecules" - E.g., fats and cholesterol are unable to dissolve within - Hydrophobic substances require carrier proteins to be transported within the blood. ### Substances that partially dissolve in water - Amphipathic molecules have polar and nonpolar regions. - Polar portion of molecule dissolves in water. - Nonpolar portion repelled by water. - Phospholipid molecules are amphipathic. - Polar heads have contact with water. - Nonpolar tails group together. - Results in bilayers of phospholipid molecules. - E.g., membranes of a cell. ### Other amphipathic molecules form a micelle