A&P basic chemistry, atoms to ions, bonding, molecules v compounds, water and pH update

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Published on September 13, 2013

Author: jamiehworkman

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Basic chemistry review used for Anatomy and Physiology Students

Anatomy & Physiology Chemistry Review Atomic Theory and Periodic Table Review SPDF orbital electron configuration Ions and Ionic Bonding Covalent Bonding Important Biological Reactions Acid / Base and pH Buffers and buffering mechanism

Matter is anything that has mass and takes up space… Made up of…. Atoms are the basic building blocks of matter All Things Are Made of Matter Chemistry can be thought of as the study of matter, which is “Anything that is.”

Elements are substances made up of 1 kind of atom 6 different elements make up 97% of the mass of compounds that are found in living things There are more than 100 known elements today Elements

The periodic table describes all the different types of known elements; all the different kinds of atoms Elements

Atoms Recall that atoms are comprised of three subatomic particles: Protons (p+) = atomic number; 1 proton = 1 AMU Neutrons (n0) = mass number-atomic number Electrons (e-) = (1/2000 amu) When # of (e-) = # of (P+) atom is neutral. When # of (e-) ≠ # of (P+) an ion When # of (e-) > # of (P+) = anion When # of (e-) < # of (P+) = cation

Element Information - Review This (the electron statement) is only true if we are discussing an atom and NOT an ion

Atoms of the same element that differ in their number of neutrons Isotopes Useful in biological research if radioisotopes Can be used to determine age of fossils

(Neutrons would be at nucleus too) • 1 valence electron • To increase stability, loses valence electron • Forms H+ cation

Bohr Model of Lithium • Lithium • 1 valence electron • Loses valence electron – Forms Li+ cation

Bohr Model of Sodium • Sodium • 1 valence electron, if lost, Na+ cation

Bohr model of Beryllium • 2 valence electrons • Loses valence electrons – Becomes Be2+ cation.

Bohr Model of Magnesium • 2 valence electrons • Loses 2 valence electrons – Forms Mg2+ cation

Anions • Fluorine – 7 valence electrons • Chlorine – 7 valence electrons – Both gain 1 electron – Form -1 anions

SPDF Orbitals – a more modern look

Orbitals

Atoms with 3 or less valence electrons tend to lose them and become positive cations From Atoms to Ions

From Atoms to Ions Atoms with 5 or more valence electrons tend to gain more and become negative anions

Periodic Table of the Elements 1 H 2 He 3 Li 4 Be 5 B 6 C 7 N 8 O 9 F 10 Ne 11 Na 12 Mg 13 Al 14 Si 15 P 16 S 17 Cl 18 Ar 19 K 20 Ca 21 Sc 22 Ti 23 V 24 Cr 25 Mn 26 Fe 27 Co 28 Ni 29 Cu 30 Zn 31 Ga 32 Ge 33 As 34 Se 35 Br 36 Kr 37 Rb 38 Sr 39 Y 40 Zr 41 Nb 42 Mo 43 Tc 44 Ru 45 Rh 46 Pd 47 Ag 48 Cd 49 In 50 Sn 51 Sb 52 Te 53 I 54 Xe 55 Cs 56 Ba 57 La 72 Hf 73 Ta 74 W 75 Re 76 Os 77 Ir 78 Pt 79 Au 80 Hg 81 Tl 82 Pb 83 Bi 84 Po 85 At 86 Rn 87 Fr 88 Ra 89 Ac 104 105 106 107 108 109 110 111 112 +1

Periodic Table of the Elements 1 H 2 He 3 Li 4 Be 5 B 6 C 7 N 8 O 9 F 10 Ne 11 Na 12 Mg 13 Al 14 Si 15 P 16 S 17 Cl 18 Ar 19 K 20 Ca 21 Sc 22 Ti 23 V 24 Cr 25 Mn 26 Fe 27 Co 28 Ni 29 Cu 30 Zn 31 Ga 32 Ge 33 As 34 Se 35 Br 36 Kr 37 Rb 38 Sr 39 Y 40 Zr 41 Nb 42 Mo 43 Tc 44 Ru 45 Rh 46 Pd 47 Ag 48 Cd 49 In 50 Sn 51 Sb 52 Te 53 I 54 Xe 55 Cs 56 Ba 57 La 72 Hf 73 Ta 74 W 75 Re 76 Os 77 Ir 78 Pt 79 Au 80 Hg 81 Tl 82 Pb 83 Bi 84 Po 85 At 86 Rn 87 Fr 88 Ra 89 Ac 104 105 106 107 108 109 110 111 112 +2

Periodic Table of the Elements 1 H 2 He 3 Li 4 Be 5 B 6 C 7 N 8 O 9 F 10 Ne 11 Na 12 Mg 13 Al 14 Si 15 P 16 S 17 Cl 18 Ar 19 K 20 Ca 21 Sc 22 Ti 23 V 24 Cr 25 Mn 26 Fe 27 Co 28 Ni 29 Cu 30 Zn 31 Ga 32 Ge 33 As 34 Se 35 Br 36 Kr 37 Rb 38 Sr 39 Y 40 Zr 41 Nb 42 Mo 43 Tc 44 Ru 45 Rh 46 Pd 47 Ag 48 Cd 49 In 50 Sn 51 Sb 52 Te 53 I 54 Xe 55 Cs 56 Ba 57 La 72 Hf 73 Ta 74 W 75 Re 76 Os 77 Ir 78 Pt 79 Au 80 Hg 81 Tl 82 Pb 83 Bi 84 Po 85 At 86 Rn 87 Fr 88 Ra 89 Ac 104 105 106 107 108 109 110 111 112 +2 for many; some +1, others +3; several vary

Periodic Table of the Elements 1 H 2 He 3 Li 4 Be 5 B 6 C 7 N 8 O 9 F 10 Ne 11 Na 12 Mg 13 Al 14 Si 15 P 16 S 17 Cl 18 Ar 19 K 20 Ca 21 Sc 22 Ti 23 V 24 Cr 25 Mn 26 Fe 27 Co 28 Ni 29 Cu 30 Zn 31 Ga 32 Ge 33 As 34 Se 35 Br 36 Kr 37 Rb 38 Sr 39 Y 40 Zr 41 Nb 42 Mo 43 Tc 44 Ru 45 Rh 46 Pd 47 Ag 48 Cd 49 In 50 Sn 51 Sb 52 Te 53 I 54 Xe 55 Cs 56 Ba 57 La 72 Hf 73 Ta 74 W 75 Re 76 Os 77 Ir 78 Pt 79 Au 80 Hg 81 Tl 82 Pb 83 Bi 84 Po 85 At 86 Rn 87 Fr 88 Ra 89 Ac 104 105 106 107 108 109 110 111 112 -1

Periodic Table of the Elements 1 H 2 He 3 Li 4 Be 5 B 6 C 7 N 8 O 9 F 10 Ne 11 Na 12 Mg 13 Al 14 Si 15 P 16 S 17 Cl 18 Ar 19 K 20 Ca 21 Sc 22 Ti 23 V 24 Cr 25 Mn 26 Fe 27 Co 28 Ni 29 Cu 30 Zn 31 Ga 32 Ge 33 As 34 Se 35 Br 36 Kr 37 Rb 38 Sr 39 Y 40 Zr 41 Nb 42 Mo 43 Tc 44 Ru 45 Rh 46 Pd 47 Ag 48 Cd 49 In 50 Sn 51 Sb 52 Te 53 I 54 Xe 55 Cs 56 Ba 57 La 72 Hf 73 Ta 74 W 75 Re 76 Os 77 Ir 78 Pt 79 Au 80 Hg 81 Tl 82 Pb 83 Bi 84 Po 85 At 86 Rn 87 Fr 88 Ra 89 Ac 104 105 106 107 108 109 110 111 112 -2

Periodic Table of the Elements 1 H 2 He 3 Li 4 Be 5 B 6 C 7 N 8 O 9 F 10 Ne 11 Na 12 Mg 13 Al 14 Si 15 P 16 S 17 Cl 18 Ar 19 K 20 Ca 21 Sc 22 Ti 23 V 24 Cr 25 Mn 26 Fe 27 Co 28 Ni 29 Cu 30 Zn 31 Ga 32 Ge 33 As 34 Se 35 Br 36 Kr 37 Rb 38 Sr 39 Y 40 Zr 41 Nb 42 Mo 43 Tc 44 Ru 45 Rh 46 Pd 47 Ag 48 Cd 49 In 50 Sn 51 Sb 52 Te 53 I 54 Xe 55 Cs 56 Ba 57 La 72 Hf 73 Ta 74 W 75 Re 76 Os 77 Ir 78 Pt 79 Au 80 Hg 81 Tl 82 Pb 83 Bi 84 Po 85 At 86 Rn 87 Fr 88 Ra 89 Ac 104 105 106 107 108 109 110 111 112 -3

Periodic Table of the Elements 1 H 2 He 3 Li 4 Be 5 B 6 C 7 N 8 O 9 F 10 Ne 11 Na 12 Mg 13 Al 14 Si 15 P 16 S 17 Cl 18 Ar 19 K 20 Ca 21 Sc 22 Ti 23 V 24 Cr 25 Mn 26 Fe 27 Co 28 Ni 29 Cu 30 Zn 31 Ga 32 Ge 33 As 34 Se 35 Br 36 Kr 37 Rb 38 Sr 39 Y 40 Zr 41 Nb 42 Mo 43 Tc 44 Ru 45 Rh 46 Pd 47 Ag 48 Cd 49 In 50 Sn 51 Sb 52 Te 53 I 54 Xe 55 Cs 56 Ba 57 La 72 Hf 73 Ta 74 W 75 Re 76 Os 77 Ir 78 Pt 79 Au 80 Hg 81 Tl 82 Pb 83 Bi 84 Po 85 At 86 Rn 87 Fr 88 Ra 89 Ac 104 105 106 107 108 109 110 111 112 +3

Periodic Table of the Elements 1 H 2 He 3 Li 4 Be 5 B 6 C 7 N 8 O 9 F 10 Ne 11 Na 12 Mg 13 Al 14 Si 15 P 16 S 17 Cl 18 Ar 19 K 20 Ca 21 Sc 22 Ti 23 V 24 Cr 25 Mn 26 Fe 27 Co 28 Ni 29 Cu 30 Zn 31 Ga 32 Ge 33 As 34 Se 35 Br 36 Kr 37 Rb 38 Sr 39 Y 40 Zr 41 Nb 42 Mo 43 Tc 44 Ru 45 Rh 46 Pd 47 Ag 48 Cd 49 In 50 Sn 51 Sb 52 Te 53 I 54 Xe 55 Cs 56 Ba 57 La 72 Hf 73 Ta 74 W 75 Re 76 Os 77 Ir 78 Pt 79 Au 80 Hg 81 Tl 82 Pb 83 Bi 84 Po 85 At 86 Rn 87 Fr 88 Ra 89 Ac 104 105 106 107 108 109 110 111 112 No ions for noble gases.

Common Cations (+) and Anions (-) +1 +2 Transition metals – mult. oxidation states +3 4 -3 -2 -1

Matter – Atoms and Combinations of Atoms Sometimes atoms of elements combine into MOLECULES and / or COMPOUNDS

Compounds are substances which contain 2 or more different types of elements chemically combined in a fixed ratio Compounds H2O C2H4OH

Molecules are substances which contain 2 or more atoms, and are the most basic unit of a substance Molecules can contain atoms of the same element or different types of elements Molecules

The Point of Reactions and Bonding is…. Why Bonds Form Types of Bonds Reactions and Equations Energy! Chemical Bonds and Reactions

Why Do Chemical Bonds Form? Atoms are most stable when their outermost energy level is filled with electrons In order to have a full valence atoms can share or transfer electrons among their nuclei. This results in formation of bonds. A Bohr Model or electron configuration can be used to determine the number of electrons in the outer shell (valence shell) of any atom

Bohr Models? Electron configuration? How?

Element Information - Review This (the electron statement) is only true if we are discussing an atom and NOT an ion

Types of Bonds Chemical Bonds Form When Atoms Share or Transfer Electrons Covalent Bonds form when an electron (or electrons) are shared between atoms Ionic Bonds forms when an electron (or electrons) is transferred from one atom to another Type of bond formed is dependent on the relative electronegativities of atoms involved

Ionic Bonds Draw a Bohr Model of Sodium (Na) and Chlorine (Cl) How does each atom become most stable with a full outer shell of electrons? The strong attraction between the positive sodium ion and the negative chloride ion creates an ionic bond

Ionic Compounds These are compounds typically compounds of a metal element and a nonmetal element. – The metal loses electrons to become a + ion (Cation), and the nonmetal gains electrons to become a – ion (Anion); the non metal element has a significantly higher electronegativity – The + and – ions are attracted to each other in a ratio so that the resulting compound is neutral in charge; ionic bonds. NaCl MgF2 are examples. – The formula unit is the simplest ratio of ions. – These have unique names formed from naming the cation followed by the anion with an “ide” ending.

Ionic Compounds - Formulas Examples (don’t show charges in compound) Na & F Na+1 F-1 Na & O Na+1 O-2 Ca & N Ca+2 N-3 K+1 & NO2 -1 NaF Na2O Ca3N2 KNO2

Ionic Compounds - Nomenclature Simple Ionic Compounds Name + then – ions and change ending to “ide.” If a polyatomic ion is present, then name it. Examples: NaCl = Sodium Chloride BaI2 = Barium Iodide Na3P = Sodium Phosphide Al2O3 = Aluminum Oxide AlF3 = Aluminum Fluoride Mg3N2 = Magnesium Nitride

Polyatomic Ions Multi-atom Ions Usually are negative Usually contain oxygen Names often end in -ite or -ate Charges and formulas cannot be predicted from Periodic Table

Polyatomic Ions • Nitrate = NO3 - – One N plus three oxygens; total charge = -1 • Carbonate = CO3 -2 – One carbon plus three oxygens; total charge = -2 • Sulfate = SO4 -2 – One S plus four oxygens; total charge = -2 • Hypochlorite = ClO- – One Cl plus one oxygen; total charge = -1

Combining Ions Rules are the same; charges add to zero. Magnesium nitrate Mg+2 and NO3 -1 Mg(NO3)2 +2 -1 -1 Note: where more than one polyatomic ion occurs, it must be enclosed in parentheses. A subscript always follows the closed parenthesis.

Covalent Bonds Non-polar covalent bonds form if the electrons are shared equally Polar covalent bonds form if the electrons are not shared equally

Valence The number of chemical bonds an atom can form. Usually calculated by subtracting the number of valence shell electrons from 8 (or 2 in the case of H and He) Helps to predict chemical formula Examples: HCl H2O NH3 CH4

Electronegativity The affinity an atom has for electrons Electronegativity and Bonding Rules 1. Extreme differences in electro- (group 1 or 2 with group 6 or 7) results in ionic bonds. 2. C and H very little difference in electro- results in nonpolar covalent bond. 3. 2 atoms of the same element have no difference in electro- results in nonpolar covalent bond. 4. O or N with C or H, moderate difference in electronegativity. Electrons pulled toward O or N, results in polar covalent bond

A chemical reaction involves the making or breaking of chemical bonds (ionic or covalent) Chemical reactions are necessary for life: • To establish stable atomic structures • To form new molecules that cells need •To manage cellular energy (energy release, usage, and storage) Chemical Reactions and Equations

Chemical equations describe a chemical reaction Chemical equations provide the following information: The different elements involved in the reaction The number of atoms involved in the reaction The reactants and products of the reaction Chemical Reactions and Equations

Reading a chemical reaction….. Carbon dioxide and water react (in the presence of sunlight and chlorophyll) to produce carbohydrate (glucose) and oxygen Chemical Reactions and Equations

Other information from the equation…. Coefficient tells # of molecules of reactants and products: 6 CO2 6 H2O 1 C6H12O6 6 O2 Chemical Reactions and Equations

Law of Conservation of Matter In a chemical reaction matter cannot be created or destroyed, but it may change form

Five general types of reactions 1. Synthesis / Combination (Anabolism) 2. Decomposition (Catabolism) 3. Combustion 4. Single Replacement 5. Double Replacement Exchange

Classify each of the following as one of your 5 from the previous slide. Add to or adjust your list as necessary. 1. A + B  AB 2. AB  A + B 3. A + O2  CO2 + H2O 4. A + BC  AC + B 5. AB + CD  AD + CB

Reactions can be reversible

Oxidation Reduction

The Chemistry of Water

The Structure of Water Surface tension and capillary action Temperature moderation Low density of ice Water as a solvent The Importance of Water

The Structure of Water Two hydrogen atoms are each joined to an oxygen atom by a single polar covalent bond Hydrogen Bond The weak attraction between the hydrogen atom of one molecule and a slightly negative atom within another molecule The Importance of Water

Surface Tension

The tendency of molecules of the same kind to stick to one another is called cohesion. The type of attraction that occurs between unlike molecules is called adhesion. Surface Tension and Capillary Action

Temperature Moderation Water has a better ability to resist temperature change than most other substances •Oceans and large lakes moderate the temperatures of nearby land areas •Water also moderates temperature through evaporation, such as when you sweat

Low Density of Ice

When NaCl dissolves in water the ionic bonds are broken. The sodium cation is attracted to the slightly negative part of the water molecule and the chloride anion is attracted to the positive part of the water molecule. Water is an excellent solvent

Water is an excellent lubricant

Solutions Solute A solid that dissolves in a solution Solvent The liquid that does the dissolving Hydrophilic Any substance that will dissolve in water. Ionic Compounds Molecules with polar covalent bonds Electrical charges attract to partial charges on water molecule Salt, sugar, proteins Hydrophobic Any substance that will not dissolve in water Molecules with nonpolar covalent bonds Majority of atoms are C and H Oils, fats, waxes (lipids)

When a covalent compound such as water is converted to ions, there are H+ and OH- ions in solution The presence and abundance of these ions is critical to the functioning of the cell in terms of its biochemistry The relative abundance of H+ and OH- ions in solution is measured by the…. pH Scale Ions and Living Cells

A pH of 7 [H+] = [OH-] ions in solution A pH less than 7 [H+] > [OH-] ; acid A pH greater than 7 [H+] < [OH-] ; base Ions and Living Cells

Acid Bases and Salts HF  H+ + F- HCl  H+ + Cl- H2SO4  2H+ + SO4 2- NaOH  Na+ + OH- KOH  K+ + OH- Mg(OH)2  Mg2+ + 2OH- KCl  K+ + Cl- MgF2  Mg2+ + 2F- Acids Donate H + + to solution Lower pH Bases Donate OH- to solution Raise pH Salts Donate neither H + + nor OH- to solution; do not affect pH

The functioning of living cells can be affected by a change in pH Because the very reactions of life cause pH changes, there is a need for cells to be able to regulate the pH of the intracellular fluid Ions and Living Cells

Buffers Biological fluids resist changes to pH because of buffers Buffers work by accepting H+ from solution when they are in excess and donating H+ when they have been depleted Most Buffers are weak acids and bases

Bicarbonate buffer system

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