Here are some very brief guidelines as to what I would like you to know for Quiz 1.
•The meanings of ∆G, ∆H and ∆S
• ∆G is called Gibbs free energy and is is composed of both enthalpy and entropy.
• ∆H is the component enthalpy and is the equivalent to the heat content of the system in
• ∆S is the component entropy and is a measure of how the energy is dispersed within the
sytem in question (a measure of a system’s disorder or randomness).
•The implications of the equation ∆G = ∆H -T∆S for biological reactions
• T represents temperature in Kelvin and is a coefficient of entropy because entropy varies
with temperature, entropy increases when it’s warmed because thermal energy has
dispersed throughout the system.
• When heat is released from a system ∆H < 0, and when energy is absorbed ∆H > 0.
• Similarly ∆S can be both posative and negative.
•Spontaneous and nonspontaneous reactions
• For a spontaneous reaction ∆G < 0, for a nonspontaneous reaction ∆G > 0.
•Oxidation state and reactivity
• Reduction is achieved by the gain of electrons through the addition of hydrogen or the
removal of oxygen.
• Oxidation is the loss of electrons through the addition of oxygen or removal of hydrogen.
•Bacteria (eubacteria), Archaea (archaebacteria), Eucarya (eukaryotes) and the evolution of
• Life began through polymerization from inorganic molecules
• Organic molecules formed into photosynthetic organisms that could photosynthesize
• Natural selection would favor those organisms that could replicate and were contained in
• The rise in oxygen levels would have forced these organisms into microenvironements
that had a lesser oxygen concentration
• Present day organisms are of two types:
o Prokaryotes: small unicellular organisms that lack a nucleus and don’t usually
contain an internal membrane system. And also Archaea: organisms that inhabit
exteme environments, but are found most everywhere
o Eukaryotes: usually larger than prokaryotic cells and contain a nucleus and
membrane-bound cellular compartments. They may be unicellular or
• Eukaryotic cells probably developed from prokaryotic cells which grew together to form
the structures found within a eukaryotic cell.
• This would have allowed for the division of labor within the cell and consequent
development of multicellular organisms.
•Properties of water: polarity and the ability to form hydrogen bonds (H bonds)
• The molecule has tetrahedral geometry
• Central oxygen atom has two unshared electron pairs
• Molecule is charged with oxygen bearing the negative charge and both hydrogens
bearing posative charges
• Neighboring water molecules will orient themselves so that the partially positive hydrogen atoms align with the partially negative oxygen atom to form a hydrogen bond
• Each water molecule can engage in four simultaneous hydrogen bonds, two with the
hydrogen atoms and two with the unpaired electrons on the oxygen atom
• Hydrogen bonding gives water the ability to form a crystalline structure in ice
•Noncovalent bonds in macromolecular structure
• Though covalent bonds define molecular constitution, noncovalent bonds, though
weaker, govern the final 3D structure
• Second strongest noncovalent bond, forms between H attached to O, S, or N and forms
between open O, S, or N
• Form between two ions, the stongest noncovalent bond.
van der Waals interactions
• Also known as dipole-dipole interaction, the weakest noncovalent bond, forms between
two stongly polar groups.
solubility of ionic and polar molecules; effect of dielectric constant
• Dielectric constant is the measure of a solvent’s ability to diminish the electrostatic
attraction between dissolved ions, water has a high dielectric constant
• molecules with polar or ionic functional groups are readily solubilized
• molecules that lack polar groups are insuluble in water and said to be hydrophobic
• The exclusion of nonpolar substances from an aqueous solution is the hydrophobic
relationship to formation of internal core of globular proteins
• hydrophobic molecules will be in the center of globular proteins
relationship to formation of micelles, vesicles and membranes
• Amphiphilic molecules will form these with the hydrophillic head on the outside and
hydrophobic tail in the center of a bilayer
pH and pK; definitions
• pH is the measure of the hydrogen ion concentration, pH=-log[H+]
• pK is the convinient form of the acid dissociation constant Ka, pK=-log[Ka]
How to use Henderson-Hasselbalch Equation
• This relates the pH of a solution to the pK of an acid and the concentration of the acid
(HA) and its conjugate base (A-), pH=pK+log([A-]/[HA])
usefulness of weak acids (and bases) for buffers
• When a stong acid such as HCl is added to water with a weak acid in equilibruim, the pH
doesn’t change dramatically because some of the added protons combine with the
conjugate base to re-form acid and therefore don’t contribute to an increase in pH, same
goes when using bases as buffers
•Experimental basis for model of DNA double helix (in a very general sense)
• A & T and G & C are present in the same concentrations in DNA Franklin's x-ray crystallography
• Showed that DNA was in a double helix form
•Know chemical structure of bases, nucleosides and nucleotides found in DNA and RNA
• Nucleotides o
•Chemical structure of nucleic acids, i.e., the phosphodiester backbone
• phosphodiester backbone
•Base pairing and base stacking in the formation and stability of double-stranded DNA and RNA
• A:T & G:C
• Base pairs are 11A wide reguardless of the pair
• In DNA bases stack 3.4A apart
•Properties of DNA double helix
• single turn is 34A (10 bp)
• The entire helix is 20A wide
• There is a major and minor groove
• It’s twisted in a right hand fashion • The sugar phosphate backbone is on the outside and binds with Mg2+ ions in solution to
minimize the negativity of the backbone and stabalize it
• The core of the helix is solid because of base stacking
•Peculiarities of RNA secondary (base-pairing) and tertiary (three-dimensional) structure
• RNA usually single stranded
• can fold back on itself so that base pairs form between complementary segments of the
• Can also bind a ssDNA to form RNA-DNA hybrid helix
o wider and flatter than DNA double helix (26A wide)