Properties of Biological Molecules Flashcards
Properties of Covalent Bonds
strong, short, share electrons
properties of Noncovalent Interactions
weak, long, attraction only (charge-to-charge attraction)
strengths of bonds measured by
energy needed to break the bond and distance between atoms
noncovalent interactions
- charge-charge interactions
- charge-diple
- dipole-dipole
- charge-induced dipole
- dipole-induced dipole
- dispersion (van der Waals or hydrophobic interactions)
- hydrogen bond
charge-charge interactions
an interaction between 2 completely charged ions
ex. ionic bonds (NaCl) and salt bridge (interaction between 2 amino acids in a protein)
Force = positive
repulsion
force = negative
attraction
Dielectric constant
effect of medium that could prevent ions from interacting with each other
energy of interaction =
(kq1q2) / D*r
dipoles involve ____ charges
partial
polar
permanent dipoles
polarizable
induced dipoles
dispersion (van der Waals or hydrophobic interaction)
taking a nonpolar molecule and inducing a dipole so there is something attractive to hold together
highly dependent on distance
ex. benzene ring stacking
hydrogen bonds
sharing proton (hydrogen atom)
hydrogen bond donor
atom that is covalently bonded to hydrogen atom
hydrogen bond acceptor
atom that is accepting the hydrogen
water’s H-bonds in:
solid
liquid
gas
optimal H-bonds
suboptimal H-bonds
No H-bonds
density is measure of
how tightly packed atoms or molecules are
hydrogen bond distances in waters are greater in ____ than in ____
solid
liquid
specific heat capacity
amount of heat needed to change the temperature of 1 gram of a given substance by +/- 1 degree C
(why oceans do not freeze)
heat of vaporization
amount of energy needed to change 1 gram of a given substance from liquid to gas
(why sweating removes body heat)
hydrogen bonds ____ energy to break and ____ energy when they form
use
release
cohesion
attraction to self
water molecules attract each other
adhesion
attraction to other
water and other polar substance attract each other
cohesion creates
surface tension
cohesion and adhesion work together to create
capillary action
charged/polar molecules are hydrophilic and _____ in water
dissolve
nonpolar molecules are hydrophobic and _____ in water
no not dissolve
but rather separate
amphipathic molecules (such as lipids and fatty acids) have both
hydrophilic and hydrophobic parts
noncovalent interactions ____ energy to break and ____ energy when formed
use
release
covalent bonds ____ energy when broken and ____ energy to form
release
use
dynamic equilibrium
same amount being made as destroyed
rate of reactant formed = rate of products formed
no NET formation or destruction
Ka =
[H+] [A-] / [HA]
pKa =
- log Ka
Strong acid:
Ka
pKa
Energy of Interaction
Ka = Larger
pKa= Smaller
Energy of Interaction = Smaller
Weak acid:
Ka
pKa
Energy of Interaction
Ka = Smaller
pKa = Larger
Energy of Interaction = Larger
Water equilibrium =
H2O OH- + H+
Kw = 10^-14 M
[H+] [OH-] / [H2O]
pH =
- log [H+]
pKw =
pH + pOH
pKw = 14
- log Kw
buffer
weak acid or base that can stabilize pH
absorbs change in [H+]
Henderson-Hasselbalch
pH = pKa + log ([A-]/[HA])
or
[A-]/[HA] = 10^pH-pKa
if pH < pKa
then most of the molecules are protonated since [HA] > .[A-]
if pH > pKa
then most of the molecules are deprotonated since [HA] < [A-]
if pH = pKa
then the molecules are just as likely to be protonated as deprotonated
gel electrophoresis
direction of migration based on net charge of molecule
(concerned with pKa of phosphate backbone in DNA- 2 phosphates that are accessible)
at physiological pH –> at least 1 neg charge on every single phosphate
isoelectric point (pI)
the pH where all molecules of a given species in solution have an overall charge of 0
pI = pKa (+1) + pKa (-1) / 2
if pH < pI,
if pH > pI,
if pH = pI,
then the molecule has a positive charge
then the molecule has a negative charge
then (by definition) the molecule has no net charge
pI in context: isoelectric focusing
the pH changes over the length of the gel
proteins stop moving when they are uncharged (pH = pI)
pI in context: protein solubility
if pH > pI or pH < pI then
if pH = pI then
proteins have net charge –> all have same net charge (repulsive to each other but attracted to H2O)
overall net neutral charge, but have local areas that are charged, so proteins are now more attracted to each other than water
first law of thermodynamics
energy is neither created nor destroyed in a closed system
chemical energy
type of potential energy
the potential energy within chemical bonds
when considering something at the atomic level, we see that
atoms are always in motion
the electric charges of protons and electrons in atoms constantly pull and push at each other (potential energy)
closed system
energy cannot leave the system
ex. the universe
open system
energy exchanged between system and surrounds
ex. a cell
universe is considered the surroundings
second law of thermodyanics
disorder is increasing
-increased number of molecules moving around –> increased heat
anabolic reactions
small molecules are assembled into large ones
energy is required
catabolic reactions
large molecules are broken down into small ones
energy is released
results in more disorder
gibbs free energy equation
deltaG = deltaH - TdeltaS
deltaG
change in available/usable energy (gibbs free energy)
deltaH
change in total energy (enthalpy) in the system
T
temperature in Kelvin (degreesC + 273)
deltaS
change in disorder (entropy)
what drives the sign of deltaG
TdeltaS
negative deltaH
energy is released from the system
positive deltaH
energy is added to the system
deltaH = 0
likely to be in closed system
negative deltaS
disorder decreases
positive deltaS
disorder increases
disorder increases in order to create energy for work
deltaS = 0
no net change in disorder
negative deltaG
free energy is released
exergonic rxn
favorable rxn
spontaneous rxn
products favored over reactants
energy is available to do work in system
positive deltaG
free energy required
endergonic rxn
unfavorable rxn
driven rxn
free energy is required to drive reaction forward
reactants favored over products
deltaG = 0
equilibrium
no net forward or reverse rxn
products are made at same rate that reactants are made
what kind of rxn has energy released
exergonic rxn
spontaneous
energy of products is less than energy of reactants
what kind of rxn requires energy
endergonic rxn
not spontaneous
energy of reactants is less than energy of products
state function
value depends only on the initial and final values, not the pathway to get there
ex. deltaG, deltaH, and deltaS
transition state
a high, energy, unstable form of the reactant(s) that is ready to form product(s)
top of curve in rxn diagram
activation energy (Ea or deltaG++)
an energy barrier that must be overcome for the rxn to proceed
enzmes
catalyze rxns by lowering the activation energy
the activation energy is lowered by stabilizing the transition state:
substrate orientation
straining substrate bonds
favorable microenvironment
covalent bonding with substrate
Q
equilibrium constant (when we are not at equilibrium)
Q = K
we are at equilibrium and the rxn proceeds in neither direction
Q < K
the rxn proceeds towards the products
Q > K
rxn proceeds towards reactants
biochemical strategies to drive an unfavorable rxn
- maintain Q < K (create a pathway by using up the products)
- couple it to a highly favorable rxn (e.g. ATP hydrolysis) (couple to exergonic rxn)
chemistry standard state ______ biology standard state
does not equal
