Chapter 2-Water: The Solvent for Biochemical Reactions Flashcards
What is the principal component of most cells?
water
electronegativity
the tendency of an atom to attract electrons to itself (so it becomes more negative) in a chemical bond
atoms of the same element have the same electronegativity. why?
because they share electrons equally in a bond
Which pair is more electronegative? Oxygen and Nitrogen or Carbon and Hydrogen
Oxygen and Nitrogen
If atoms of differing electronegativity form a bond, are the electrons shared equally?
No. More negative charge will be found closer to one of the atoms.
Example: In an O-H bond, where are more the electrons located?
near the oxygen because it is more electronegative
difference in electronegativity between hydrogen oxygen and hydrogen in an O-H bond gives rise to…
a partial positive and negative charge (S+/S-)
Polar Bonds
bonds in which two atoms have an unequal share in bonding electrons, so you notice a partial positive and negative charge
Non polar bonds
bonds where two atoms share electrons equally
give an example of a non-polar bond
C-H bond in CH4 (methane)
Can a bond within a molecule be polar and the molecular itself be non polar?
Yes. It all depends on the geometry. For example, carbon dioxide fits this criteria because of the linear nature of the O=C=O.
What is the geometry of water?
bent with a bond angle of 104.3
Dipoles
bonds with positive and negative ends due to an uneven distribution of electrons in bonds
Is water polar or non polar?
polar
Do polar molecules dissolve in polar compounds?
Yes. “Like dissolves like”
what are the strongest type of bonds?
ionic and covalent
does water have a large dipole moment?
yes. think: charge distribution
salt bridges
an interaction that depends on the attraction of unlike charges results from attraction of two side chains that are oppositely charged and in close proximity to eachother
ion-dipole and dipole-dipole interactions both help…
ionic and polar compounds dissolve in water
ion-dipole interactions
ions interacting with molecules that have dipoles example: Cl- & H20
van der waals forces
noncovalent associations based on the WEAK attraction of transient dipoles for one another
how many noncovalent bonds that do not involve electrostatic interaction of a fully charged ion are in van der waals forces?
3
Dipole-dipole interactions
occur between molecules that are dipoles, with the partial positive side attracting the partial negative side
dipole induced dipole interactions occur by…
distorting electron cloud
london dispersion force
an attraction between transient induced dipoles
hydrophilic
water loving
what kind of substances tend to dissolve in water?
ionic and polar
are hydrocarbons polar or non polar?
nonpolar
examples of hydrophilic substances
polar compounds (alcohols and ketones) sugars ionic compounds (KCl) amino acids phosphate esters
examples of hydrophobic substances
nonpolar covalent compounds (hydrocarbons) fatty acids cholesterol
hydrophobic
water-hating does not dissolve in water
why do oil and water mixed together separate into layers?
has both hydrophobic (oil) and hydrophilic (water) properities
amphipathic
molecule that contains an end with a polar, water-soluble group and another end with a non-polar, hydrocarbon group that is insoluble in water (aka hydrophilic and hydrophobic)
hydrogen bonds
noncovalent association formed between a hydrogen atom covalently bonded to one electronegative atom and a lone pair of electrons on another electronegative atom
hydrogen bonding occurs when hydrogen is bonded to
nitrogen, flourine or oxygen (FON)
does ice or liquid water have a lower density
ice
what types of bonds help stabilize DNA, RNA and proteins
hydrogen
acid
proton (H+) donor
base
proton (H+) acceptor
acid strength
the tendency of an acid to dissociate to a hydrogen ion and its conjugate base (H+ and A-); amount of hydrogen ion released when a given amount of acid is dissolved in water
acid dissociation constant
represented by Ka the number that characterizes the strength of an acid
Equation for Ka
Ka= [H+][A-} ______ [HA]
greater the Ka the ______ acid
stronger the acid
ion product constant for water
represents by Kw a measure of the tendency of water to dissociate to give hydrogen ion and hydroxide ion
equation for pH
pH= -log10[H+]
what is a neutral pH
7
what value is considered to be an acidic pH
lower than 7
what value is considered to be an basic pH
higher than 7
pKa
measures acid strength pka= -log10(Ka)
the smaller the pka
the stronger the acid
Henderson-Hasselbalch equation (HH eqn)
mathematical relationship between the pka of an acid and the pH of a solution containing the acid and its conjugate base
HH eqn formula
pH= pka + log [A-]/[HA]
titration
an experiment in which a measured amount of base is added to an acid
equivalence point
the point in a titration where an acid is equally neutralized
pepsin
found in stomach maximum activity at low pH
lysozyme
maximum activity at pH of 5
trypsin
most active at pH of 5
monoprotic acids release _____ hydrogen ion and have _____ ka and ____ pka
1; 1; 1
diprotic acids release _____ hydrogen ion and have _____ ka and ____ pka
2; 2; 2
polyprotic acids release _____ hydrogen ion and have _____ ka and ____ pka
more than 2; more than 2; more than 2
If pH of a solution is less than the pKa, what form dominates? Meaning… pH
protonated (H+ on)
If pH of a solution is greater than the pKa, what form dominates? Meaning… pH>pKa
deprotonated (H+ off)
buffer
something that resists change
buffer solution
-tends to resist change in Ph on addition of moderate amounts of strong acid or strong base -consists of a mixture of a weak acid and its CB
Le Chatelier’s Principle
if stress is applied to a system in equilibrium the equilibrium will shift in the direction that relieves the stress
when the pH is higher than the pKa, the ratio of the conjugate base to form the conjugate acid form is
10
when the pH is higher than the pKa, the ratio is
100 (see table 2.7 on page 52)
why can a buffer maintain the pH at a relatively constant value?
because of the amounts of both acid and the CB (usually met at pH values at or near pKa of the acid)
https://www.youtube.com/watch?v=UnzycyqM0G4
explain the concepts.
- A- is unprotonated form (above 7)
- HA is protonated form (below 7)
- +/- 1 away 90:10 ratio
- +/- 2 away 99:1 ratio
buffering capactity
a measure of the amount of acid or base that can be absorbed by a given buffer solution
how do we make a buffer?
add acid or base to a solution
hemoglobin
oxygen carrying protein in the blood
zwitterions
molecules that have both a positive and negative charge
are zwitterions more or less likely to interfere with biochemical reactions?
less
acidosis
blood pH drops below 7.35
alkalosis
blood pH rises about 7.45
naturally occuring phsophate and carbonate buffers help maintain physiological pH near
7
