L1-2: Properties of Biological Molecules Flashcards
covalent bonds
strong
short
share electrons
noncovalent bonds
weak
long
attraction only
name of bond between monomers: carbohydrates lipids proteins nucleic acids
glycosidic bond
ester
peptide
phosphodiester
strength of a bond is the measure of ?
the energy needed to break the bond
strength also depends on distance between atoms
examples of electrostatic interactions and definition
an interaction between 2 completely charged ions
ionic bonds NaCl
salt bridges
what is a salt bridge
interaction between 2 amino acids in a protein
how do we measure how attractive the 2 ions are to each other? in vacuum
in a vacuum we would use coulomb’s law to calculate it
using variables: force ion charges k constant distance between nuclei
how do we measure how attracted 2 ions are to each other in biological environments?
we would use coulomb’s law but add the relative permittivity to it
by using D - dielectric constant – used to account for the other things in the environment that could prevent their interaction
F > 0 means ?
F < 0 means ?
F = force between ions
>0 = repulsion <0 = attraction
define energy of interaction
the energy required to separate two ions
dipole
means having a partial charge when covalently bonded
can be permanent/polar
or
induced/polarizable
dispersion forces
also called van der waals forces
contact distance interactions
ex. stacking of nucleotides
hydrogen bonding
sharing a hydrogen bond between two atoms
hydrogen donor and
hydrogen acceptor
distance of hydrogen bonds
between donor and acceptor usually around 3 A
range = 2.6 - 3.7
O - H = 2.0A
N - H = 0.9A
H bond breaking and forming
take nrg to break
release nrg when formed
explain water’s strange physical properties
are explained by it’s ability to form H bonds and create an electric dipole
ice
less dense than liquid
H bond distances are greater in solid than in liquid
density
a measure of how tightly packed atoms or molecules are
specific heat capacity
the amount of heat needed to change the temp of 1g of a given substance by 1 Celsius
heat of vaporization
the amount of nrg needed to change 1g of a given substance from liquid to gas
cohesion
attraction to self
water molecules attract each other
adhesion
attraction to other
water and other polar substances attract each other
cohesion creates _____.
surface tension
cohesion and adhesion work together to create ?
capillary action
water is the universal _____.
solvent
charged/polar molecules are ______ and will ______ in solution.
hydrophilic
dissolve
nonpolar molecules are _____ and will _____ in solution.
hydrophobic
separate
amphipathic molecules
have both hydrophilic and hydrophobic parts
most rxns are ?
reversible
chemical rxns = ?
making and/or breaking chemical bonds
equilibrium does not mean equal ?
concentrations
Ka is the ____ constant
dissociation constant of acids
relate the Ka and pKa of strong vs weak acids
strong acid = larger Ka
weak acid = larger pKa
same for strong base/weak base pKb’s
formula for pKa/pKb
pKa = - log Ka
same for pKb
Kw and pKw
equilibrium constant of water
pKw = -logKw = 14
also
pKw = pH + pOH
pH formula
pH = -log[H+]
buffers
are weak acids or weak bases that can stabilize pH
Henderson-Hasselbalch Variation conclusions:
pH < pKa
pH > pKa
pH = pKa
then most of the molecules are protonated since [HA]>[A-]
most are deprotonated
[HA] < [A-]
molecules are just as likely to be protonated as deprotonated
Gel electrophoresis – direction of migration is based on ?
net charge of molecule
define isoelectric point
the pH where all molecules of a given species in solution have an overall average charge of 0
what are the results of the following?
pH < pI
pH > pI
pH = pI
the molecule has + charge
the molecule has - charge
then the molecule has no net charge – by definition
pI in context of isoelectric focusing
the pH changes over the length of the gel
proteins stop moving when they are uncharged
–when pH = pI
first law of thermodynamics
energy is neither created nor destroyed in a closed system
define kinetic energy
motion
performing work
define potential energy
position, potential to do work
chemical energy – the potential nrg w/in chemical bonds
closed vs open system
ex. universe vs a cell
nrg cannot leave the universe but nrg can leave the cell to matrix and back into the cell
which type of metabolic rxns create more disorder? anabolic or catabolic
catabolic because nrg is released
anabolic – takes nrg to happen
gibbs free nrg equation
deltaG = dH - TdS
d = delta
deltaG is an example of a _____ function. meaning ?
state function
its value depends only on the initial and final values
and not the only pathway to get there
delta H values
-
nrg is released
+
nrg is added to system
0
closed system
delta S values
- disorder decreases \+ disorder increases 0 no net change in disorder
delta G values
- free nrg released \+ free nrg required 0 equilibrium
