Lecture 1&2: Kincaid Flashcards
Covalent bonds
Sharing of a pair of electrons
Electrostatic. Interactions
A charged group can attract an oppositely charged group
Hydrogen bonds
Hydrogen atom covalently bonded to one EN atom is also attracted to another
Van dear walls interactions
Results from the asymmetrical distribution of electrons in molecules or atoms
Common COVALENT c-c bond distance and energy:
1.54 angstroms; 355 kJ mol-1 (85kcal)
Common electrostatic interaction length
3 angstroms; 5.86 kJmol-1
Common hydrogen bond length
1.5 -2.6 angstrom; 4-20 kJ mol-1
How to combine sugar and amino acid moieties:
Dehydration rxn
Which carbon in DNA is “deoxy”
2’ carbon
Nuceloside
Sugar+nitrogenous base(NO phosphate group)
Adenine and thymine have___ bonds; Guanine and cytosine have ____ bonds.
2; 3
Properties of water:
Polarity, cohesion, moderation of temperature, expansion upon freezing, versatility as a solvent
Hydrophobic effect
Nonpolar to cluster together to exclude water in aq. Environment
Guanine: pKa =9.7 what’s this mean?
Above this pH, you lose H’s…DNA becomes single stranded
PH=pKa then:
Protonated = deprotonated
PKa =
The susceptibility of proton removal
PH is lower than pKa:
Hydrogen bonds remain intact
Buffers:
Regulate pH in organisms and in lab; weak acid and its conjugate base
Buffers are most effective at pH:
near their pKa
Dynamic equilibrium
Rate of the forward reaction = rate of reverse; [ ] of R / P don’t have to be =
Catabolic pathways
Release energy by breaking bonds of complex molecules to simpler.
Anabolic pathway
Consume energy to build complex molecules from simpler ones.
Kinetic energy
Asso. W/ motion
Thermal energy
Also. W/ random movements of atoms/molecules
Potential energy
Energy in matter that is present d/t location or structure
First law thermodynamics
Total energy of a system and environment is constant. “Can’t be created or destroyed”
Second law thermodynamics
Entropy of system and environment always increases. Spreading
IF disorder increases, why does an organized DNA helix form?
The heat released by helix formation increases the entropy of the surrounding.
Free energy:
A living organisms energy that can do work
3 types work from cell:
Chemical, transport, mechanical
ATP
Cells energy shuttle
Phosphates are removed from ATP via
Hydrolysis
Can exergonic rxn’s be used to drive end endergonic rxn’s?
Yes
Free energy of activation:
Initial energy needed to start a chemical reaction
Do enzymes affect the changes in free energy?
NO
How do enzymes work?
Lower activation energy
How does enzyme active site lower activation energy?
Orienting substrates,straining substrate bonds, making favorable environment, covalently bonding to substrate
