focus chapter 2 (water, bonding, and buffers) Flashcards
Describe the chemical structure of water
o One oxygen and two hydrogens
o Hydrogen bonding
o Linked by covalent bonds
o Oxygen is slightly negative charged and the hydrogen atoms are slightly positive charged
Bond breaking process is
exothermic
exothermic
energy is released
bond forming process is always
endothermic
endothermic
Energy must be added to form the bond
six types of chemical bonds found in macromolecules
nonpolar covalent (strong), polar covalent (strong), ionic, hydrogen(relatively weak), van der waals (Weak), hydrophobic
nonpolar covalent bonds
the two atoms are identical, the electrons are shared equally
polar covalent bonds
• the two atoms are different and one has a higher affinity for electrons than the other
ionic/ electrostatic
-High electronegativity difference between the 2 atoms, and one atom actually strips electrons away from the other
-Electron transfer creates ions (charged atoms)
-Ionic bonds can be found in substances such as salts (sodium chloride, etc.)
Hydrogen bonds
Hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom (nitrogen or oxygen)
Van der waals interactions
•Weak interactions result from the fluctuations in the electronic charge around the atoms
•The can be substantial when summed over many atoms
•If atoms are too far apart, these forces aren’t much of a factor, but if they are too close, their electron clouds repel each other
—-Thus there is an optimal distance for these interactions called the van der waals contact distance
Hydrophobic interactions
•Water fearing
•It is the most important non-covalent interaction for proteins in aqueous environment
•Come into play at closer distances than ionic interactions
Equilibrium constant
Represent the ratios between forms of chemical species at equilibrium
Dissociation constant
dissociation species on top, associated species on the bottom
Association constant
associated species on top, dissociated species on the bottom
acid dissociation constant
equilibrium dissociation constants of protons dissociating from molecules, and it would apply to the example on the left since it concerns proton dissociation
Henderson-Hasselbalch equation
o The equation tells you how far a weak acid solution’s ph is from the pka based on how much acid is in the protonated state, and how much is in the deprotonated state
When you have equal amounts of the protonated and deprotonated forms of the acid
—Base (A-) divided by acid (HA)
• If they both have equal values, that equals one
o. Log of 1 is zero
o So ph = pka
Ka is the dissociation constant for a
weak acid
Describes protons coming on and off a certain spot on a molecule
if the carboxyl group of an amino acid has a pka of 2 and your solution is at ph=2
half the molecules will be proton associated (COOH)
half the molecules will be proton dissociated (COO-)
if the carboxyl group of an amino acid has a pka of 2 and your solution is at ph>2
the molecules will be proton dissociated (COO-)
if the amino group on an amino acid has a pka of 9 and your solution is at ph=9
half molecules will be proton associated and the other half will be proton dissociated
• H3N+, H2N
if the amino group on an amino acid has a pka of 9 and your solution is at ph<9
the molecules will be proton associated
• H3N+
An amino group is basic
The proton is relatively reluctant to dissociate form the molecule. At ph 7, the proton is present and group will have a positive charge
a carboxyl group is acidic
the proton readily dissociates from the molecule. At ph 7, the proton is absent and the group will have a negative charge
A buffer system consists of a
weak acid, HA and its conjugate base, A-
State the useful pH range for a biological buffer relative to the pKa of that buffer
o From one pH above to one pH unit below the pka
This is due to consumption of the two forms of the buffer: either the protonated form as the pH rises, or the deprotonated form as the pH lowers
