Water

Front 1

Water's passive role in biological systems

Back 1

the structures of biomolecules (proteins, membranes, nucleic acids) are formed in response to their interaction with water.

Front 2

Water's active role in biological systems

Back 2

water is a participant in many biochemical reactions. the dependence of life on water shapes the way we look at it and for life. the presence of water on a planet does not ensure life but it is difficult to imagine life ( as we know it ) without water.

Front 3

weak interactions in aqueous solution

Back 3

oxygen is more electronegative than hydrogen. bc of this, water has a permanent dipole (polarity) O has a partial - charge and H has a partial + charge. this polarity is essential in its ability to interact with other water molecules & other biomolecules.

Front 4

the dipole of water will dictate waters ability to:

Back 4

1) form electrostatic interactions with charged molecules, including other water molecules.
2) form hydrogen bonds, including with other water molecules

Front 5

Hydrogen bonds (general)

Back 5

electrostatic interaction (charge charge) between an electronegative atom with a hydrogen linked (donor) to another electronegative atom with a free electron pair (acceptor)
non covalent interaction and are relatively weak. strength depends on its geometry (stronger if O is directly below H as opposed to the side)

Front 6

heat of vaporization

Back 6

the amount of heat required to vaporize a liquid at its boiling temp

Front 7

specific heat capacity

Back 7

the amount of heat required to raise the temp of a substance one degree

Front 8

why is water an effective hydrogen bonder?

Back 8

1) water can accept & donate hydrogen bonds
2) waters small size allows it to adopt optimal positioning for optimal geometry of hydrogen bonding

Front 9

Water and charged solutes

Back 9

water molecules can interact & dissolve charged solutes through formation of layers of hydration
show similar versatility in interacting with both positively & negatively charged groups. ( water interacts favorly with groups that carry a charge&increase solutbility)

Front 10

solubility of molecules in water

Back 10

depends on their ability to interact with water molecules through electrostatic or hydrogen bonding
molecules that carry a charge (+ or -) and/or participate in hydrogen bond ( as either donors or acceptors) will have the greatest solubility in water

Front 11

Hydrophobic vs Hydrophilic

Back 11

hydrophobic (water fearing) are non polar
hydrophilic (water loving) are polar (+/-; acceptor/donor)

Front 12

hydrophobic vs amphipathic effect

Back 12

H: the exclusion of non polar substances by water (critical for protein folding & membrane formation)
A: contain both hydrophobic & hydrophilic portions (ie fatty acids)

Front 13

non-polar amphipathic substances in water

Back 13

the polar hydrophilic region interacts favorbly with water but the non-polar regions cluster together to present the smallest hydrophobic surface to water. hydrophobic interactions hold the molecule togehter.

Front 14

Non-covalent forces include:

Back 14

formation & stabilization of structures of biomolecules. recognition/interactions of one biomolecule with another. binding of reactants to enzymes

Front 15

non-covalent interactions that are of important to biomolecules:

Back 15

hydrogen bonds, ionic interactions, hydrophobic interactions, van der waals interactions

Front 16

Hydrogen bonding as an interaction

Back 16

if it can form a hydrogen bond, it MUST form a hydrogen bond. can form hydrogen bonds with: water, groups within the same molecules (intramolecular), groups within other molecules (intermolecular)
critical determinant of the specificity of biomolecular interactions but not a force formation of their structures.

Front 17

Ionic interactions

Back 17

electrostatic interactions between charged groups. can be attractive (between opp. charged groups) or repulsive (between sim. charged groups)
magnitude of contribution of ionic interactions to biomolecular structures is greatly reduced by the shielding of these groups by water molecules

Front 18

Van der waals forces

Back 18

when two uncharged atoms are brought very close together their surrounding electron clouds influence each other. interaction between permanent & induced dipoles; short range, low magnitude interactions. abundant in the core of protein due to close packing of hydrophobic side chains. attraction is maximal when two atoms are separated by the sum of the van der waals radii

Front 19

hydrophobic interactions

Back 19

association of a relatively non polar molecule or group with other non-polar molecules. (ie. non polar side chains cluster in the interior of the protein, away from water. polar & charged side chains remain on the outer surface facing water.

Front 20

ionization of water

Back 20

in solution, the structure of water is more complicated than h20. water has a limited tendency to ionize to hydrogen ions (H+) + hydroxide ions (OH-).
hydrogen ions in water are often presented as hydronium ions (H3O +)

Front 21

Weak acids & bases

Back 21

strong acids & bases dissociate completely in water. weak acids & bases do not dissociate completely in H2O + the extent of dissociation can be quantified.

Front 22

Titration curves

Back 22

the ratio of the acid to the conjugate base changes over the course of the titration curve.
when pH = pka then [A-] = [HA]
when pH=pka the solution is best able to resist changes in pH.
buffering region extends one pH unit on either side of the pka point

Front 23

buffer

Back 23

a solution that will that will resist changes in pH with the addition of acid or base. the lower the pka, the stronger the acid
arise from weak acids & bases. common in biological systems and are required to maintain physiological pH in cells & tissues (phosphate&bicarbonate)

Front 24

PKA

Back 24

measure of the pH of donating a proton. lower pka = donate your proton from a lower pH to a more acidic environment

protonated: when pH is below the pka
unprotonated: when pH is above pka

Front 25

monoprotic acids

Back 25

one functional group that can pick up & donate electrons. single buffering region, single pka. acetic acid

Front 26

Henderson-Hassel Bach equation

Back 26

describes relationship between:
1) the pH of the solution
2) the pka of the solution
3) the relative concentration of the weak acid (HA) and the conjugate base (A-)

pH= pka + log [(A-)/(HA)]