Lecture: Basic Chemistry
I. Matter and Energy
A. Matter - fundamental building blocks of nature
1. elements - basic units of matter
B. Energy - capacity to do work (put matter into motion
1. potential energy - energy stored in a structure
a. water stored in a lake uphill
b. chemical bonds of glucose molecule
2. kinetic energy - energy in an object in motion
a. water in a stream - allows mill to grind corn
b. broken glucose bonds -> ATP -> muscles work
3. Forms of Energy
a. chemical energy - energy in chemical bonds
I. ATP (adenosine triphosphate) - stores energy
b. electrical energy - energy of separated charges
I. battery - + pole and - pole separate charge
ii. nervous impulse run just like a battery
c. mechanical energy - energy of matter in motion
I. bowling ball transfers energy to move pins
ii. muscle motion - ATP -> contraction of muscle
d. electromagnetic energy - energy traveling in waves (light, X-rays, UV rays)
I. electromagnetic spectrum - visible light, UV light, radio waves, X-rays
C. First Law of Thermodynamics
1. "Energy can change from one form to another, but it can never be created or destroyed" (Total Energy In = Total Energy Out)
examples: Car Engine vs. Human Body
a. Car Engine - gasoline used to run motor to move car
Chemical Energy (gas) ---> motion (20%) + heat (79%) + sound (1%)
b. Human Body - food used to move body, digest, think, etc.
Chemical Energy (food/glucose) ---> physiology (80%) + heat (20%)
II. Organization of Matter (Atoms - Elements)
A. Atomic Particles
Mass Charge Characteristics
proton 1 +1 defines element
neutron 1 neutral defines isotopes
electron 0 -1 determines element bonding properties
B. Organization of Periodic Table
1. # protons = atomic number (unique for each element)
2. # protons + # neutrons = atomic mass
3. isotope - same element; different # neutrons
# protons + # neutrons = atomic mass
Carbon-12 (99%) 6 6 12
Carbon-13 (0.9%) 6 7 13
Carbon-14 (0.1%) 6 8 14
4. # electrons - dictates the NET CHARGE of an atom
# protons # electrons NET CHARGE
H 1 1 0
H+ 1 0 +1
H- 1 2 -1
ion - any atom with a positive or negative charge
anion - atom with a NEGATIVE charge
cation - atom with a POSITIVE charge
III. Electron Shells, the Periodic Table, and Chemical Bonds
A. Electron Shells - electrons occupy "shells" as they orbit around the nucleus (2, 8, 8, ...)
B. The Periodic Table of Elements is organized by electron shells
H1 He2 SHELL 1 2 e-
Li3 Be4 B5 C6 N7 O8 F9 Ne10 SHELL 2 8 e-
Na11 Mg12 Al13 Si14 P15 S16 Cl17 Ar18 SHELL 3 8 e-
C. Chemical Bonds are formed so that each atom can have the outermost electron shell filled
1. Ionic Bond - one atom donates electron(s) to another
a. Example: Sodium Chloride (table salt) Na+Cl-
2. Covalent Bond - two atoms share one/more electrons
a. Example: Methane (CH4), Carbon Dioxide (CO2), and Ammonia (NH3)
a. Polar Molecule - electron sharing is unequal in the bonds
Example: Water (H2O)
b. Non-polar Molecule - electron sharing is almost equal
Example: Methane (C02)
IV. Elements other than C,H,O,N in Humans
Primary Elements (3% of all body weight)
Calcium Ca Bones,teeth, muscle and nerve action, blood clotting
Phosphorus P Bones and Teeth, DNA, RNA, ATP. Important in energy transfer
Trace Elements (Less than 1% of body weight altogether)
Potassium K Osmotic balance; cell voltage, muscle and nerve action
Sulfur S Component of proteins (cysteine) and other organic molecules
Sodium Na Osmotic balance; cell voltage, muscle and nerve action
Chlorine Cl Osmotic balance; cell voltage, muscle and nerve action
Magnesium Mg Co-factor for many enzymes
Iron Fe Hemoglogin and many enzymes
Copper Cu Co-factor of many enzymes
Zinc Zn Co-factor of many enzymes
Manganese Mn Co-factor of many enzymes
Cobalt Co Co-factor of many enzymes and vitamin B12
Chromium Cr Co-factor of many enzymes and potentiates Insulin
Selenium Se Required for normal liver function
Molybdenum Mo Co-factor of many enzymes
Flourine F Tooth and bones
Tin Sn Promotes growth (unknown mechanism)
Silicon Si Growth, bone mineralization, connective tissue synthesis
Vanadium V Promotes growth and reproduction
V. Chemical Reactions
A. Patterns of Chemical Reactions
1. Chemical Equation - # of atoms of each element same for reactants and products
C6H12O6 + 6O2 ------> 6H2O + 6CO2
2. Synthesis - smaller molecules form larger molecule
A + B ----> AB (anabolic process)
amino acid 1 + amino acid 2 + ...... ----> peptide (protein)
sugar 1 + sugar 2 + sugar 3 + ...... -----> polysaccharide (glycogen)
3. Decomposition - larger molecule broken down into smaller molecules
AB ----> A + B
glycogen ----> glucose + glucose + glucose + ......
4. Displacement - one part is exchanged
AB + C -----> A + BC
glucose + adenosine-P-P-P (ATP) ------> glucose-P + adenosine-P-P (ADP)
B. Exergonic vs. Endergonic Reactions
1. Exergonic - energy is released during the reaction
A + B ------> C + D + ENERGY
glucose + oxygen ----> water + carbon dioxide +ENERGY (trapped by ATP)
2. Endergonic - energy required for reaction to proceed
A + B + ENERGY ------> C
amino acid 1 + amino acid 2 + ... + ENERGY ---> peptide (protein)
C. Chemical Equilibrium
1. Reversible Reactions
A + B ------> AB and AB ------> A + B
2. Chemical Equilibrium
A + B <=====> AB
D. Rates of Chemical Reactions
1. size of reactants species (smaller means faster)
2. temperature (speeds up the particles)
3. concentration (more likely to come together)
4. catalysts (enzymes) - make reacting more convenient
VI. Acid- Base Chemistry and the pH Scale
A. Water normally exists in an equilibrium reaction with some dissociation
H2O <======> H+ + -OH
in a beaker of pure water, the ratio of H+ to H2O is about 1/10,000,000
pH = -log10[H+] = -log10[10-7] = -(-7) = 7
pH = relative concentration of H+ in a solution of water
B. Acids - compounds which increase the concentration of H+ (pH = 1 to 6)
C. Bases - compounds which decrease the concentration of H+ (pH = 8 to 14)
D. Buffer - compound that prevents large changes in pH of a solution (pH “shock absorber”)