Module 2

Question 1

name four characteristics of water molecules

Answer 1

• they carry a permanent dipole
• they are the most abundant molecule in a living organism
• they are effective at accepting and donating hydrogen bonds
• they are effective solvents for polar molecules

Question 2

What is the buffering range of a weak acid with a pKa of 5.2?

Answer 2

4.2-6.2

Question 3

What is the Henderson- Hasselbalch equation?

Answer 3

pH=pKa + log [A-]/[HA]

Question 4

what side is the hydrogen bond acceptor?

Answer 4

-the one with the dotted line to the hydrogen
- it has a free electron pair

Question 5

which side is the hydrogen bond donor?

Answer 5

the one covalently attached to the hydrogen

Question 6

what is the relationship between the hydrogen atom and the hydrogen bond acceptor ?

Answer 6

the interaction is electrostatic

Question 7

what reduces the strength of electrostatic interactions?

Answer 7

shielding of charged groups by water molecules

Question 8

Which non-covalent forces contribute to the structure and stability of a biomolecule? (4)

Answer 8

• Hydrogen bonds
• Electrostatic interactions
• Hydrophobic interactions
• Van der Waals Interactions

Question 9

What is the most abundant molecule in living organisms ?

Answer 9

water

Question 10

what does a passive role mean regarding water

Answer 10

• the structure of biomolecules form in response to interaction with water
• releases water
  Ex. protein folding is driven to bury hydrophobic residues

Question 11

what does an active role mean in regards to water ?

Answer 11

• water is participating in the biochemical reaction
• needs water
  Ex. peptide bond formation releases a water molecule

Question 12

what abilities does the dipole of a water molecule influence

Answer 12

• form electrostatic interactions with charged molecules
• form hydrogen bonds (including with other molecules)

Question 13

what is a hydrogen bond ?

Answer 13

an electrostatic interaction between an electronegative atom with a hydrogen covalently bonded to another electronegative atom with a free electron pair

Question 14

which atoms can serve as hydrogen bond donors and acceptors ?

Answer 14

oxygen and nitrogen

Question 15

are anti parallel beta sheets or parallel beta sheets more stable ? why?

Answer 15

anti parallel because there is better geometry of hydrogen bonding

Question 16

what impacts the strength of a hydrogen bond ?

Answer 16

its geometry

Question 17

how many hydrogen bonds can a water molecule participate in with others

Answer 17

each molecule has the potential to participate in four hydrogen bonds with four other water molecules

Question 18

what is a flickering cluster?

Answer 18

square dance of water molecules (changing their patterns)

Question 19

what are the unusual properties of water

Answer 19

high heat of vaporization and high specific heat capacity

Question 20

why is it hard to get water apart?

Answer 20

water molecules are attracted to each other

Question 21

how does water act as a solvent?

Answer 21

water molecules can interact, and dissolve, charged solutes through formation of layers of hydration. polar dissolves polar

Question 22

why are water molecules ideal hydrogen bonding partners

Answer 22

their ability to serve as either donors or acceptors

Question 23

are hydrophobic molecules non polar or polar?

Answer 23

non polar

Question 24

what is an amphipathic molecule?

Answer 24

molecules that contain both hydrophobic and hydrophilic portions

Question 25

what is the force that holds the non-polar regions of the molecules together?

Answer 25

called hydrophobic interactions

Question 26

what happens when an amphipathic molecule goes in water

Answer 26

it needs to find some kind of position to get hydrophobic away from water and hydrophilic towards water

Question 27

what are hydrogen bonds critical for? what are they not critical for?

Answer 27

critical for specificity but not critical for formation of bimolecular structures

Question 28

what makes an electrostatic interaction pretty weak

Answer 28

water tends to shield the charged groups, greatly diminishing the strength of the interaction

Question 29

what is a van der waal interaction

Answer 29

interactions between permanent and induced dipoles

Question 30

why does the folding of a protein contradict the second law of thermodynamics

Answer 30

the folding of protein involves creation of a more ordered state