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BIOC 299 > Water, pH, acids/bases > Flashcards

Water, pH, acids/bases Flashcards

1
Q

What are the 4 classes of biomolecules?

A

Nucleic acids
carbohydrates
proteins
lipids

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2
Q

Why does H2O have a dipole moment?

A

The oxygen is highly electronegative, where the two hydrogens are not - the oxygen pulls the electrons from the hydrogens and creates a partial negative charge on the O and a partial positive charge on each H

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3
Q

T or F: water is highly cohesive and binds easily to itself

A

true - due to the dipole moments

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4
Q

What kind of bond holds two water molecules together?

A

hydrogen bond between the O of one molecule and the H of a second molecule

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5
Q

How many bonds can 1 water molecule form?

A

up to 4

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6
Q

in its liquid form, how many hydrogen bonds can a water molecule form?

A

an average of 3.4 per molecule

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7
Q

Describe flickering clusters

A

the H-bonds between water molecules are constantly changing partners due to high entropy

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8
Q

in its solid form (ice) what is the maximum number of H-bonds a water molecule can form?

A

4

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9
Q

T or F: water in its solid form is less dense than its liquid form

A

True. this allows ice to float on water

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10
Q

What are the 2 ways atoms and molecules can interact?

A

covalent and non-covalent bonds

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11
Q

Describe covalent bonds

A

occur when atoms SHARE one or more pairs of electrons

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12
Q

Are covalent bonds stable or unstable?

A

stable

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13
Q

How are molecules formed?

A

by stable covalent bonds between their atoms

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14
Q

T or F: covalent bonds are constantly breaking and reforming

A

false - they are stable and strong

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15
Q

What are the backbones of macromolecules?

A

covalent bonds

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16
Q

Which is the strongest form of interactions between atoms/molecules?

A

covalent bonds

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17
Q

How are interactions between molecules usually mediated?

A

by relatively weak non-covalent interactions

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18
Q

Explain why weak interactions are important?

A

while individual interactions are weak, they can occur in large numbers and contribute a lot of strength

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19
Q

What are the 3 types of weak interactions?

A

Electrostatic (ionic/salt bridges)
Hydrogen bonds
Van der Waals

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20
Q

Describe electrostatic interactions

A

they occur between two electrical charges on atoms aka they are charge-charge interactions

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21
Q

How are electrostatic interactions disrupted?

A

by water and Brownian (random) motion

ie., increasing entropy

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22
Q

What does the strength of electrostatic interactions depend on?

A

size of charges

type of charges (ex. positive-positive, positive-negative)

distance between charges

dielectric constant of the media/buffer solution

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23
Q

T or F: increasing entropy is favourable

A

true

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24
Q

What is the bond distance in electrostatic interactions?

A

3A

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25
Q

Describe hydrogen bonds

A

When a hydrogen atom bonds to a nearby highly electronegative atom

there is always a H-bond donor (not EN) and an H-bond acceptor (highly EN)

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26
Q

What molecular structure creates stronger H-bonds?

A

linear (as opposed to non-linear)

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27
Q

Which atom will be the H-bond donor?

A

the atom with the partially positive charged H

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28
Q

Which atom will be the H-bond acceptor?

A

the highly electronegative atom

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29
Q

What are two indicators a molecule will be the H-bond donor?

A

-OH
-NH

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30
Q

What are two indicators a molecule will be the H-bond acceptor?

A

O-
N-

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31
Q

What does the strength of H-bonds depend on?

A

the molecular structure

linear = stronger
nonlinear = weaker

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32
Q

What is the distance of a H-bond?

A

1.5-2.6A

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33
Q

What is a major example of H-bonds in molecular biology?

A

H-bonding holds the two strands of DNA together through the base pairs

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34
Q

What are 3 common hydrogen bonds?

A
  1. between H2O and a hydroxyl group of an alcohol
  2. between H2O and a carbonyl group of a ketone
  3. between H2O and an amino group of an amine
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35
Q

When H-bonding occurs between H2O and an alcohol, which is the donor and which is the acceptor?

A

donor: the H from the hydroxyl group (-OH)

acceptor: the O from H2O

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36
Q

When H-bonding occurs between H2O and a ketone, which is the donor and which is the acceptor?

A

donor: one of the Hs from H2O

acceptor: the O from carbonyl (-C=O)

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37
Q

When H-bonding occurs between H2O and an amine, which is the donor and which is the acceptor?

A

donor: the H from the amino group (-NH)

acceptor: the O from H2O

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38
Q

Describe Van der Waals interactions

A

interactions that occur between uncharged and non-polar molecules

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39
Q

What mediates Van der Waals interactions?

A

transient asymmetries in electric charges between molecules

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40
Q

T or F: Van der Waals interactions are the weakest interactions

A

true but they can accumulate and be stronger

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41
Q

List the types of interactions from strongest to weakest

A

covalent (C-H)

covalent (O-H)

electrostatic (ionic/salt bridges)

ion-dipole

hydrogen bonds

Van der Waals

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42
Q

Describe the hydrophobic effect

A

the spontaneous association of non-polar molecules in aqueous solution

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43
Q

What drives the hydrophobic effect?

A

entropy

44
Q

What is entropy?

A

the disorganization of a system

45
Q

What are 3 examples of the hydrophobic effect?

A

lipids and formation of membranes

protein folding

molecular interactions

46
Q

What happens when water reaches a hydrophobic surface?

A

no favourable interactions occur and water molecules will form a highly ordered structure around the hydrophobic surface

47
Q

What are lipids? (hydrophobic, -philic, or amphipathic)

A

amphipathic molecules

48
Q

Which part of a lipid molecule is hydrophilic/phobic?

A

the head group is hydrophilic

the tail is hydrophobic (alkyl group)

49
Q

Why is the hydrophobic effect important?

A

H2O molecules form a highly ordered structure surrounding the hydrophobic molecule (lipid), lowering the entropy

the effect increases entropy and allows organized structures to form

50
Q

How does the hydrophobic effect increase entropy?

A

it brings the hydrophobic surfaces of multiple lipids together so water molecules surrounding individual lipid molecules can be released. This causes increase in entropy

51
Q

Why would increasing entropy be a good thing?

A

increasing entropy due to the hydrophobic effect can allow for organized structures to form such as lipid bilayers

52
Q

What is an example of the hydrophobic effect on lipids?

A

it allows organized structures such as a lipid bilayer to form

53
Q

How does the hydrophobic effect drive protein folding?

A

it splits up the amino acids of proteins and brings together the hydrophobic ones together and prevents them from interacting with water, while allowing the hydrophilic ones to interact with each other or water

54
Q

How does the hydrophobic effect promote molecular interactions?

A
55
Q

Describe electronegativity

A

the property of some atoms to attract electrons to itself in a chemical bond (ex. O and N are highly EN)

56
Q

Describe polarity

A

when two atoms of differing EN bond, the electrons are not shared equally and are more often located near the more EN atom

this gives the molecule a partial negative and partial positive charge

57
Q

Give an example of a polar bond

A

O-H

O has a partial -
H has a partial +

58
Q

Give an example of a non-polar bond

A

C-H

negligible difference in EN

59
Q

What is a dipole moment?

A

when a molecule has an uneven distribution of charge

60
Q

T or F: bonds of a molecule can be polar, but the molecule itself can be non-polar

A

true, because of the molecule’s geometry

61
Q

give an example of a molecule that is non-polar but has polar bonds

A

CO2

O = C bonds are polar (partial - on O, partial + on C)

but the molecule CO2 is planar O = C = O, so the partial charges cancel out

62
Q

T or F: water is polar

A

true

63
Q

T or F: water is a solvent

A

true

64
Q

What does it mean for water to be a solvent?

A

both polar (ex. partial charges) and ionic compounds (ex. full charges) will dissolve in water

and nonpolar molecules will not easily dissolve in water if at all

65
Q

What happens to nonpolar molecules in water?

A

they aggregate

66
Q

What is the main reason oil and water do not mix?

A

entropy of water increases when lipids interact with each other

67
Q

Does entropy of water increase or decrease when lipids interact with one another?

A

increase

68
Q

What is an acid?

A

a molecule that acts as a proton donor

69
Q

What is a base?

A

a molecule that acts as a proton acceptor

70
Q

What happens to strong acids in water?

A

they completely dissociate (lose protons)

71
Q

What happens to weak acids in water?

A

they do not completely dissociate

72
Q

What is Ka?

A

the acid dissociation constant

73
Q

Will Ka be larger or smaller for stronger acids?

A

larger

74
Q

What is the equation for Ka?

A

Ka = [H+][A-]/[HA]

75
Q

What is pH?

A

a scale to measure the concentration of protons (H+) in a solution

76
Q

What is the reaction for the ionization of water?

A

H2O + HA <–> H3O+ + A-

where H3O+ is the con acid to H2O and A- is the con base to HA

77
Q

What is Kw?

A

the ion product constant for water (ie., the molar concentration of water in ionization is a constant)

78
Q

What is the equation for Kw?

A

Kw = Ka x 55.5 or

Kw = [H+][OH-]

79
Q

What is the concentration of [H+] and [OH-] in the Kw equation?

A

[H+] = [OH-] = 10^-7 M

80
Q

What does Kw equal?

A

Kw = 10^-14

81
Q

What is the equation for pH?

A

pH = -log[H+]

82
Q

What is the scale for pH units?

A

10x

ie., a difference of 1 pH unit = 10x difference in [H+]

83
Q

if there is a 1 unit difference in pH, what is the difference in [H+]?

A

10x

84
Q

Calculate the pH for the following solution given that 1x10^-3 M HCl is added to pure water ([H+] = 1x10^-7)

A

1x10^-3 M

pH = -log(1x10^-3)
pH = 3

85
Q

Acidic solutions have pH…

A

lower than 7

86
Q

basic solutions have pH…

A

higher than 7

87
Q

physiological pH is

A

7

88
Q

What is pKa?

A

a constant that’s used to measure the strength of weak acids

89
Q

The smaller the pKa, the ____ the acid.

A

stronger

90
Q

What is the equation for pKa?

A

pKa = -log(Ka)

91
Q

Give examples of a strong and weak acid

A

weak: HCO3- has pKa = 10.20

strong: HCOOH has pKa = 3.75

92
Q

What is the Henderson-Hasselbalch equation?

A

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

93
Q

When should you use the HH equation?

A

if given:

pH and ratio concentrations = solve for pKa

pKa and concentration ratio = solve for pH

pH and pKa = solve for ratio

94
Q

Why is the HH equation useful in biochem?

A

it can be used to predict properties of buffer solutions to control pH and help in picking an appropriate buffer

95
Q

What is a buffer solution?

A

a solution that resists changes in pH when a strong acid or base is added to a mixture

96
Q

What is a buffer composed of?

A

a weak acid and its con base

97
Q

What range of pH values are buffers effective at?

A

+- 1 pH unit of the pKa (ranges 2 units)

98
Q

At pH values below pKa, does the acid or base form of the buffer predominate?

A

acid

99
Q

At pH values above pKa, does the acid or base form of the buffer predominate?

A

base

100
Q

How do you convert number of molecules to moles?

A

molecules / 6.02x10^23 (Avo’s number)

101
Q

If 1 mL of 0.1M HCl is added to 99mL of pure water (pH=7), determine the [H+] and pH

A

*note: HCl is a strong acid, so the 0.1M will dissociate completely to form 0.1M H+

  1. determine [H+]

1mL HCl = 1x10^-3 L

[H+] = 1x10^3 L * 0.1 mol/L
= 1x10^-4 mol H+

dilute to 100mL volume total (0.1L)

[H+] = 1x10^4 mol/0.1 L
= 1x10^-3 M

  1. determine pH

pH = -log[H+]
pH = -log(1x10^-3) = 3

102
Q

What does low buffering capacity mean?

A

the buffer contains low concentrations of both the acid and base forms of the buffer (takes less addition of the strong acid/base to use up the buffer)

103
Q

What does high buffering capacity mean?

A

the buffer contains appropriate concentrations of both the acid and base forms

104
Q

What is an example of buffering in real life?

A

the dissociation of carbonic acid (H2CO3) in human blood

105
Q

If pH > pKa, what is the protonation state?

A

H+ off, molecule is deprotonated

BIOC 299 (16 decks)

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