Lecture Notes

I. Scientific Method
A. Inquiry Based – based on observation
B. Proceeds logically & serially
C. Initiated by observation
D. Steps:
1. Observation of the action/change/phenomena/etc.
2. Repeatability – is the observed phenomena regular/repeatable?
i. Only if repeatable is it possible to scientifically study the behavior
3. Mechanism – How does it work?
4. Hypothesis: If action is repeatable & mechanism observed – select hypothesis to test
i. Principle of Parsimony – the choice of the easiest hypothesis to test first (Occam’s Razor)
5. Before experimenting map out the possible outcomes
i. Hypotheses:
a. Wrong – choose another experiment
b. Right – hypothesis may be a possible explanation
6. By nature science can disprove but cannot prove
i. There are only increasing probabilities of truth
E. Theory – as close to scientific truth s is possible
II. Chemical Foundations
A. Atomic Theory – protons (+), neutrons, electrons (-)
1. Proton count = atomic number
2. Electrons – their arrangement in discreet outer shells dictate the atom’s chemical properties
3. Atomic mass: protons + neutrons (= baryons – “heavy particles”) (electrons have little mass)
4. Each proton + neutron = 1 Dalton or Atomic Mass Unit
5. Isotope – atom with the same number of protons but differing numbers of neutrons: neutron
count doesn’t change the chemical properties of the element as they’re determined by the
electron arrangement and electron arrangement is determined by the proton count
i. Mass # = single atom weight | Atomic Wt = average of all naturally occurring isotopes
ii. 126 C  Protons + Neutrons = 12 | Protons = 6
6. Charges: p+ , e-
B. Ion – any particle with a net charge: caused by the gain or loss of electrons
1. Cation – positively charged ion
2. anion – negatively charged ion
C. Ionic Bonds – bond formed by attraction of ion charges
1. Atoms have basic desire to complete outer shell to become chemically inert
2. Loss of electron = + charge, gain of electron = - charge
3. These charged particles attract and bond – Ionic Bonding (ex. F- & Na+  NaF)
i. Strength of tendency to form ionic bonds dictated by distance from center of period tbl.
4. Ionic bonds are not molecules – instead form crystals (due to mutual attraction of all + and –
atoms amongst each other)
D. Covalent Bonds – bonds sharing electrons in outer levels – not gaining or losing electrons
1. Symmetrical covalent bond (H2, O2, N2, ) has no polarity - bond shares
electrons 50:50 (diagram )
2. Asymmetrical covalent bond results in one atom having larger pull on
electrons, making the electrons more likely to orbit the heavier
element(s) and less likely to orbit the lighter element resulting in
polarity: A.K.A. electronegativity (see 1st diagram on page 2)
i. Electronegativity – having a greater tendency to pull electrons and thus
partially charge, or polarize, the covalently bonded molecule
 ii. Ex: H2O – Oxygen tends to pull electrons more
strongly, so the probability of shared electrons being in
the O orbits is much more likely and thus is
electronegative
iii. Polarity – the uneven distribution of charge causing
areas of molecules to become partially (δ) charged
E. Polar Bonding
1. Inter-molecular bonding = bonds between different molecules
2. Intra-molecular bonding = bonds within the molecule itself (H & O bonds in H2O)
3. Polarity caused bonding = Hydrogen Bonding (H2O to H2O bonds)
4. Carbon will never form ionic bonds…all C bonds are covalent and can also bond to itself and
as such is the basis for biology
III. Chemistry of Water
A. Boiling = addition of enough energy to rip apart molecules hydrogen bonds
1. Ease of breaking bonds is dictated by the electronegative strength of the molecule
2. Surface tension is another feature of the strength of the H bonds in water
B. Water nature is polar and thus it has attractive & repellent areas of charge
1. These H bonds are responsible for the chemical & physical behavior – results in fairly strong
bonds
2. Has a high surface tension, demonstrating strong cohesion because of these bonds
3. Also has a high latent heat of vaporization (high
thermal capacity)
4. H2O – good solvent for polar substances, especially
ionically bound salts (hydrophilic substances) as water
breaks apart the polar ionic bonds. (see img  )
5. Poor solvent for non-polar substances: waxes, fats, oils,
etc. (hydrophobic substances)
C. PH Scale – measure of the acidity of a system
1. H2O = H–O–H  has a slight tendencty to turn into H+ + OH- ions
i. In ionic form the hydrogen is a lone proton.
ii. H ions are the basis of all acids
2. [H+] = 10-7M and [OH-] = 10-7M concentrations
3. ρ = -Log10 of that number, so:
i. ρ105 = -5  [H+] = 10-7  ρ[H+] = 7  ρH = 7 (also ρOH = 7)
4. Thus acid ρH is lower than 7, meaning an increase in H+ concentration
5. pH 07 = acidic | pH 714 = basic
6. Example: H2SO4: releases hydrogen into solution and thus is acidic, driving pH down
i. NaOH similarly donates OH- into solution, removing the H+ concentration, raising pH
7. pH of a system highly regulated
8. Proton donors function as acid, proton acceptors function as bases: thus H+ not necessarily
needed to be added to function as acid.
IV. Carbon Chemistry
A. Covalent bonding only
B. Shares four pairs of e-
C. Naturally forms symmetrical tetrahedron 
D. Will bond to itself, giving rise to variety of structures: methane, ethane,
propane, butane, pentane, hexane, septane, octane, nonane, etc.
1. Can also form ringed structures: Cyclohexane, benzene ring, etc.
2. Double bonding = ending in “ene”
E. Isomerism – same molecular formula but differing arrangements of atoms
 1. Structural Isomers
i. C4H10 – can be both butane or isobutane
ii. C3H7OH – can be propyl alcohol or isopropyl alcohol
2. Geometric Isomoers (cis/trans) – appear with double bonds only
i. Trans have juxtaposed bonds, while cis isomers have bonds on the same
side of the double bond
3. Stereoisomers/Enantisomers – mirror images of each other 
i. Occurs when there are 4 different structures around the Carbon atom
F. Functional Groups
1. Hydroxyl Groups – OH group, alcohols
i. Hydroxyl group becomes polar due to presence of O2 and is thus very soluble in H2O.
ii. OH group adds an “ol” ending: methanol, ethanol, propanol, butanol, etc.
2. Alkyl Group – simple C-H based groups: methyl, ethyl, alkyl, etc.
i. Formula is: CnH2n+1
3. Carbonyl Group – CHO
i. Contains a double bonded oxygen at the end of a molecule
(polar)
ii. Found in sugars, amino acids, nucleotides
iii. An aldehyde if at end of C backbone (-CHO)
iv. A keytone if attached to interior of C backbone (>CO)
4. Carboxyl group – COOH
i. In amino acids, fatty acids; highly polar, tends to release H+,
functions as an acid
5. Amino group – NH2
i. In amino acids and certain nucleotide bases
ii. Water soluble, acts as a weak base (proton acceptor) to become NH3+ (ionized)
6. Sulfhydryl group – SH
i. In amino acid cysteine; helps to stabilize proteins (acting as disulphide bridge –S–S–)
7. Phosphate group – PO4-3
i. In nucleotides (ATP), DNA, RNA, many proteins,
phospholipids, etc.
ii. Water soluble, acidic
G. Organic Composition
1. Polymer – large molecule consisting of many similar bonded smaller units, or monomers.
i. Connection of monomers: condensation/dehydration reactions
a. Dehydration/condensation – reaction in which
two molecules become covalently bonded to each
other through the loss of a small molecule, usually
H2O
ii. Disassembly of polymers: hydrolosis – type of
cleavage reaction using water to split a polymer, attaching a hydroxyl group and a H atom
derived from a water molecule to the exposed site. Essentially the opposite of a
dehydration reaction.
iii. Enzymatic action assist in both hydrolysis and dehydration synthesis reactions
H. Carbohydrates – consist of sugars and their polymers
1. Monosaccharides – the simplest sugars, usually with molecular formulas that are a multiple
of CH2O (ex. Glucose, most common monosaccharide – C6H12O6)
i. Most sugars form rings in aqueous solutions – serve as major nutrients for cells
2. Disaccharide – double sugar, consisting of two monosaccharides joined by a glycosidic
linkage
 i. Ex: maltose = glucose + glucose; lactose = glucose + galactose; sucrose = glucose +
fructose
3. Polysaccharides – very large carbohydrates, joining hundreds to thousands of monomers
I. Biological Polymers
1. Monomers – the base, or “repeating, unit
2. Condensation, a.k.a. dehydration synthesis, reactions form most polymers from base
monomers
3. Formation of poly-“sugars” (a.k.a. polysaccharides)
i. Starch – storage sugar/polysaccharide of plants made up entirely of glucose monomers
(through 1-4 linkages, number 1 C to number 4 C)
a. Because of the angles of the bonds the polymer forms a helical shape
ii. Glycogen – storage sugar/polysaccharide of animals
a. More extensively branched than that of plants
iii. Cellulose – structural polysaccharide that comprises cell walls of plant cells
a. Consists of glucose monomers, but all C-OH bonds between glucose monomers are
of the β form.
b. Cell walls of plants are many parallel cellulose molecules held together by hydrogen
bonds between the hydroxyl groups of the glucose monomers (arranged as
microfibrils)
J. Lipids – grouped together for their hydrophobic properties – waxes, oils, fats, etc.
1. Fats – large molecules, but not polymers.
i. Consist of one glycerol backbone and three fatty acids – Glycerol is an
alcohol with three carbons, each bearing a hydroxyl group 
ii. Fatty acids have long carbon skeleton with a carboxyl group at one end
(thus giving it the “acid”
nomenclature)
iii. Three fatty acids joined by ester
linkage (C-O-C bond between
the glycerol’s hydroxyl group
and the fatty acid’s carboxyl group) results in a triglyceride, a.k.a. fat.
iv. Ester bonds between the glycerol & fatty acids produce H2O, and are condensation synth.
v. Fatty acid with no double bonds, all being single C-H bonds, is saturated
vi. Fatty acid with double bonded C within the chain is
unsaturated (mono, poly, etc)
2. Phospholipids
i. Composed of two fatty acids rather than three, with the
third hydroxyl group of the glycerol molecule joined to
a phosphate group (quite polar)
ii. Tail end of phospholipid is a fatty acid hydrocarbon,
and hydrophobic
iii. Head end of phospholipids is very polar phosphate
group, and thus hydrophilic
3. Steroids (sterol-based lipids) ex.
Cholesterol
i. Comprised of C skeleton of four
interconnected rings (fig. )
4. Waxes – long chain fatty acids tightly packed and bonded to long chain alcohols or carbon
rings. Are malleable and hydrophilic.
V. Proteins
 A. Amino acid – an amino group (-NH3+), a carboxyl group (-COO-), the H+ atom, and one or more
atoms called it’s R group
1. Amino acids are the monomers that polymerize into protein polymers
2. 21 amino acids of human biological concern
3. Bonds between amino acids are peptide bonds ( –C–N–C– bonds, like esters but using N)
i. Dehydration synthesis/condensation reaction joins the amino acids
ii. Grouping of multiple amino acids is a polypeptide (chain)
iii. In peptide bond production there is always a carboxyl group (COOH) at one end and a
nitrogen (-NH2) left over at the other – C terminus & N terminus
B. Structure
1. The sequence of amino acids in the polypeptide chain is the Primary Structure
2. Secondary Structure is the regular H bonding in the chain, resulting in either α helix or β
pleated sheet
3. Tertiary structure – domain formation, irregular bonding from Hydrogen bonds, disulfide
bridges (of the sulfhydryl group), ionic bonding and hydrophobic interactions
4. Quaternary structure – the final structure of the polypeptide chain, which determines the
function of the protein.
C. Denaturation
1. Any change or disruption of the 4th protein structure (change of heat, pH, etc) disables the
protein from doing its job
D. Nucleotides
1. All nucleotides comprised of a sugar-phosphate backbone and one nitrogenous base
i. ATP – contains three phosphate groups attached to its sugar.
ii. Because the phosphate groups are very polar the release of those
bonds is extremely exegetic
2. Nucleic Acids
i. Formed by nucleotide monomers – covalent bonds form between the sugar of one
nucleotide and the phosphate group of the next
ii. DNA –
a. made up of 4 deoxyribonucleotide monomers (the nitrogenous bases are what
differentiate them) Adenine, Guanine, Thymine, Cytosine
b. pentose (5 C sugar) bonded to nitrogenous base (AGTC) and to phosphate group
c. DNA contains the instructions for day to day operation and reproduction of the cell
d. Secondary structure of DNA, formed by H bonding, is what forms the double helix
iii. RNA – composed of ribonucleotide monomers
a. Single stranded – integral in protein synthesis
b. Substitute thymine base of DNA for uracil base

VI. Cell Theory

A. Cell – functional unit of all living things – the smallest unit with the properties of life
1. All have a region of DNA, all have cytoplasm, all have plasma membrane
B. Types
1. Prokaryotic – primitive cells – no membranous fixed inner structure or nucleus
2. Eukaryotic – has a true nucleus and is a more complex cell. Plant & animal cells are
eukaryotes
C. Cell Structure – General Cellular Parts
1. Plasma membrane – selective barrier allowing passage of oxygen, nutrients and waste to cell
i. Consists of a lipid bilayer that selectively prevents water soluble substances from
crossing
2. Nucleus – contains the DNA of eukaryotes – directly communicates with the (rough) ER
 i. Nucleolis – mass of proteins & copies of genes coding
for ribosomal RNA
3. Nucleoid – region of cytoplasm in prokaryotes containing
DNA
4. Endoplasmic Reticulum (ER)
i. Smooth ER – assists in the packaging and transport of
materials in the cell
ii. Rough ER – contains protein clumps (ribosomes) on
membrane wall, synthesizes lipids,
5. Ribosomes – contained on wall of rough ER and in
cytoplasm – assist in TRANSLATION of proteins
6. Mitochondria – primary ATP manufacturer of the cell (thus “powerhouse”) – have their own
DNA and divide on their own
7. Golgi Body – manufacture & packaging of inner & extra cellular materials (proteins &
lipids)
8. Vesicles – membrane bound grouping of cellular material act as cellular material transporters
i. Lysosomes – type/subset of vesicle that can open up and release digestive enzymes
breaking down cells
ii. Peroxisomes – hold enzymes for digesting fatty acids, amino acids and H2O2
9. Chloroplasts (plant cell) – photosynthetic cell, transfers sunlight & water into ATP
10. Central Vacuole (plant cell) – stores amino acids, sugars, ions and waste, takes up 50 to 90%
of the plant cell interior
11. Cytoskeleton – structurally supports, gives shape to and moves eukaryotic cell (not present in
prokaryotes)
i. Microtubules – largest skeletal elements, regulates cell organelle placement and
movement
ii. Microfilaments – smallest skeletal elements, reinforce cell shape, reconfigure surface, etc
iii. Intermediate filaments – mid sized elements, help reinforce the nucleus