focus chapter 2 (water, bonding, and buffers)

Question 1

Describe the chemical structure of water

Answer 1

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

Question 2

Bond breaking process is

Answer 2

exothermic

Question 3

exothermic

Answer 3

energy is released

Question 4

bond forming process is always

Answer 4

endothermic

Question 5

endothermic

Answer 5

Energy must be added to form the bond

Question 6

six types of chemical bonds found in macromolecules

Answer 6

nonpolar covalent (strong), polar covalent (strong), ionic, hydrogen(relatively weak), van der waals (Weak), hydrophobic

Question 7

nonpolar covalent bonds

Answer 7

the two atoms are identical, the electrons are shared equally

Question 8

polar covalent bonds

Answer 8

• the two atoms are different and one has a higher affinity for electrons than the other

Question 9

ionic/ electrostatic

Answer 9

-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.)

Question 10

Hydrogen bonds

Answer 10

Hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom (nitrogen or oxygen)

Question 11

Van der waals interactions

Answer 11

•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

Question 12

Hydrophobic interactions

Answer 12

•Water fearing
•It is the most important non-covalent interaction for proteins in aqueous environment
•Come into play at closer distances than ionic interactions

Question 13

Equilibrium constant

Answer 13

Represent the ratios between forms of chemical species at equilibrium

Question 14

Dissociation constant

Answer 14

dissociation species on top, associated species on the bottom

Question 15

Association constant

Answer 15

associated species on top, dissociated species on the bottom

Question 16

acid dissociation constant

Answer 16

equilibrium dissociation constants of protons dissociating from molecules, and it would apply to the example on the left since it concerns proton dissociation

Question 17

Henderson-Hasselbalch equation

Answer 17

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

Question 18

When you have equal amounts of the protonated and deprotonated forms of the acid

Answer 18

—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

Question 19

Ka is the dissociation constant for a

Answer 19

weak acid
 Describes protons coming on and off a certain spot on a molecule

Question 20

if the carboxyl group of an amino acid has a pka of 2 and your solution is at ph=2

Answer 20

 half the molecules will be proton associated (COOH)
 half the molecules will be proton dissociated (COO-)

Question 21

if the carboxyl group of an amino acid has a pka of 2 and your solution is at ph>2

Answer 21

the molecules will be proton dissociated (COO-)

Question 22

if the amino group on an amino acid has a pka of 9 and your solution is at ph=9

Answer 22

 half molecules will be proton associated and the other half will be proton dissociated
• H3N+, H2N

Question 23

if the amino group on an amino acid has a pka of 9 and your solution is at ph<9

Answer 23

 the molecules will be proton associated
• H3N+

Question 24

An amino group is basic

Answer 24

The proton is relatively reluctant to dissociate form the molecule. At ph 7, the proton is present and group will have a positive charge

Question 25

a carboxyl group is acidic

Answer 25

the proton readily dissociates from the molecule. At ph 7, the proton is absent and the group will have a negative charge

Question 26

A buffer system consists of a

Answer 26

weak acid, HA and its conjugate base, A-

Question 27

State the useful pH range for a biological buffer relative to the pKa of that buffer

Answer 27

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