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Biochemistry Exam One Notes

1.3: Quick Review
Organic Chemistry
o Phenyl




o Carboxyl




o Aldehyde




o Ester




o Ether




o Amine




o Alcohol




o Ketone




o Schiff Base




o Carboxylic Acid




o Phosphate




o Inorganic Phosphate (PI)




o Phosphodiester





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Biology
o DNA RNA Protein
DNA Gene product
General Chemistry
o Atoms
Most (if not all) properties of atoms are defined by valence electrons
Octet rule states that every atom will want to be stable by having 8 electrons.

Ne 1s
2
2s2
2
p
6



F 1s
2
2s
2
2p
5



Fluorine is unstable and wants one more valence electron to complete its octet.
o Molecules
Covalent bonds share electrons equally
Polar bonds share electrons unequally
If the difference in electronegativity is less than .4 than it is a covalent bond
If it is between .5 1.2 than it is a polar bond
If it is greater than 1.21 than it is ionic bonding.
Ex:

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o Molecules interacting with other molecules (InterMolecular Forces)
Van der Waals (induced dipole : induced dipole)
All molecules have VDW
Ex: 2 Alkanes


We will get a partial negative on one end and a partial positive on the adjacent carbon while the other has the opposite charges so that they
may bond.
C4H10 has a lower boiling point than C30H62 because there requires more energy to break apart more
VDW
Hydrogen Bonds (the sharing of a proton)
This bond needs a donor and acceptor







Hydrogen bonds are stronger than VDW
1KJ/mol to break VDW
4-20 KJ/mol to break Hydrogen bonds
350KJ/mol to break covalent bonds
Electrostatic interactions (salt bridges/ionic interactions)
A molecule with a positive or partial positive charge interacts with a molecule with a negative or
partial negative charge.









Hydrophobic interactions
Generates about 7-10 KJ/mol (strongest attraction)
: Nonpolar; no electronegative atoms or polar covalent bonds.


: Polar; negative charge indicates polarity


: Polar; positive charge indicates polarity


: Nonpolar; although the lone pair is present, the molecule is aromatic (stable)
o Nonpolars like nonpolars (hydrophobic) while polar likes polar (hydrophilic).
o Hydrophobic effect: exclusion of nonpolar substances by water
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o S increase in entropy
More disorder = more entropy (positive)
More order = less entropy (negative)
o Alkane in H2O solvent cage


o More alkanes causes more disorder in solvent cage because of VDW forces



o G = H T S
If G is negative then the reaction is spontaeneous
o Amphiles are polar and nonpolar parts of the molecule



o Ketone in H2O






Water





o Water has a high dielectric constant.
o Good for solvating cations and anions by making electrostatic interactions with making ionic bonds weaker

o Water has a high specific heat capacity
o The amount of heat required to raise the temperature of 1g of a substance by 1C is 4.184 J/mol C
o Cohere is to interact with similar molecules
o Adhere is to interact with different molecules
o Capillary Action is the ability to move together
o