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Cellular Composition > Water, pH and buffers > Flashcards

Water, pH and buffers Flashcards

1
Q

why is water unusual?

A

its melting and boiling point don’t follow periodic table trends

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2
Q

heat of vaporisation

A

energy needed to go from solid to gas

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3
Q

energy needed to go from solid to gas

A

heat of vaporisation

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4
Q

heat of vaporization of water and the significance of this

A

40.71
higher than expected when following periodic table trends

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5
Q

lone pairs of electrons on an oxygen atom

A

2

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6
Q

why does water form?

A

its energetically favourable for oxygen to bind to two hydrogens to have eight electrons in its outer shell

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7
Q

what type of molecule is water?

A

polar

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8
Q

what does it mean if a molecule is polar?

A

one end of the molecule is different to the other and can be polarised and has directionality

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9
Q

bond energy

A

to break the bond we need to put in this much energy per mole of it

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10
Q

how many covalent bonds are in water?

A

2

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11
Q

bond energy of the O-H in water and the significance of this

A

460
a lot (compare to 30 for atp)

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12
Q

put the different types of bonds in order of decreasing strength

A

covalent
hydrogen
hydrophobic interactions
van der waal interactions

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13
Q

where are lone pairs of electrons found in water?

A

two lone pairs on the oxygen atom

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14
Q

van der waals radius

A

radius of the whole atom/molecule

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15
Q

radius of the whole atom/molecule

A

van der waals radius

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16
Q

approximate van der waals radius of oxygen

A

1 Angstrom

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17
Q

O-H covalent bond approximate distance

A

1 Angstrom

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18
Q

1 Angstrom

A

1x10^-10m

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19
Q

shape of water

A

not linear

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20
Q

what allows hydrogen bonds to form in water?

A

the lone pair of electrons on water have a significant effect on the properties of water. We have an EN and an electropositive region and this polarity allows hydrogen bonds to form

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21
Q

hydrogen bonds

A

when a hydrogen atom is shared between two electronegative atoms such as oxygen or nitrogen. electrostatic, weak.

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22
Q

describe hydrogen bonds

A

electrostatic, weak

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23
Q

how do we represent hydrogen bonds?

A

dashed lines

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24
Q

distance between 2 EN atoms

A

about 3 Angstroms

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25
what holds water molecules a certain distance apart?
the fact that the distance between 2 EN atoms is always about 3 Angstroms
26
how many hydrogen bonds can water form?
2
27
what are the strange properties of water explained by?
water behaving as a larger molecule than it is. only water forms hydrogen bonds hence the melting point etc.
28
what does hydrogen bonding make water be a good one of?
a good solvent
29
what is it that makes water a good solvent?
hydrogen bonding
30
explain why water is a solvent for urea?
urea is polar and so can hydrogen bond with water and so water is a solvent for urea
31
in what situation can water be a solvent for something?
if it can hydrogen bond with that thing
32
what repel water?
non-polar molecules
33
example of a non-polar molecule
fatty acids
34
what does free energy, G, tell us?
whether or not a reaction will occur spontaneously
35
what happens to free energy in spontaneous reactions?
decreases
36
if free energy has decreased in a reaction, what does it mean?
the reaction is spontaneous
37
spontaneous reaction
no energy as to be put into the reaction
38
can we measure free energy straight up?
no, it's only possible to measure changes in free energy
39
non-spontaneous reaction
endergonic
40
is a spontaneous reaction exer or endergonic?
exergonic
41
delta G for non-spontaneous/endergonic reactions
higher than zero
42
endergonic reactions
non-spontaneous
43
what does it mean if delta G = 0?
reaction at equilibrium
44
delta G for exergonic/spontaneous reactions
less than zero
45
spontaneous reactions in terms of entropy
increase in entropy
46
if we have a big entropy value, describe the change in free energy
negative
47
if we have a negative change in free energy, describe this in terms of entropy values
big entropy
48
what does an increase in entropy mean in terms of a reaction occuring?
spontaneous reaction
49
entropy
universe tending towards chaos
50
what does a smaller entropy (less chaos) mean in terms of free energy?
higher free energy
51
what does a lower free energy mean in terms of entropy?
larger entropy (more chaos)
52
Gibbs free energy equation + definitions
deltaG = deltaH - TdeltaS deltaG = free energy deltaH = change in enthalpy T = temperature deltaS = change in entropy
53
units in the gibbs free energy equation
deltaG = kJmol-1 deltaH = kJmol-1 T = K deltaS = JK-1mol-1 (must change unit to kJmol-1 before starting)
54
what do we need to do in terms of units before starting a Gibbs free energy calculation?
change delta S to kJmol-1 before starting
55
explain how big of an effect each component of the gibbs free energy equation has on it
enthalpy has a relatively small effect, temperature has a big effect but doesn't tend to change that much since human life takes place under a small range of temperatures. Therefore, the major component in the change in Gibbs free energy is the entropy.
56
why does temperature not tend to change that much in the gibbs free energy equation?
since human life takes place under a small range of temperatures
57
major component in the change in gibbs free energy
entropy
58
what's the most important thing driving biological interactions and why?
change in entropy due to the effect of water and solvent
59
example of hydrophobic molecules in biochemistry
protein or dna
60
what type of a molecule is dna?
hydrophobic
61
explain how hydrophobic interactions dominate protein structure
water molecules close to the surface of hydrophobic molecles have few opportunities to exchange hydrogen onds with other water molecules. consequently, many water molecules form ordered ice-like "shells" around the protein this system has a low entropy (deltaS is small) and so the gibbs free energy is high ordered shells have an energetic cost if the hydrophobic surface area is minimised, the number of ordered water molecules is reduced. the increase in deltaS (entropy) reduces the deltaG (Gibbs free energy) - the hydrophobic effect drives hydrophobic molecules together. it is the dominant force in protein folding.
62
what's wrong with having ordered shells?
energetic cost
63
explain why its energetically favourable for a hydrophobic protein in water to be compact
large surface area when extended = interacts with more water molecules = imposes order on the water molecules = doesn't allow them to occupy a certain space in space more compact = less order = more entropy = free energy is less on RHS = change in free energy is negative = spontaneous this is driving the shape of the macromolecules in the body. all molecules take the shape they do because of their interactions in water and the entropic effects that take place.
64
when do we see the hydrophobic effect taking place?
when we place a hydrophobic molecule (e.g - protein) int polar solvent (e.g - water)
65
what type of solvent is water?
polar
66
what does every protein in the body have around it?
a "water shell"
67
explain why proteins would fall apart without water
if you took protein out of water and put it in a different solvent with different properties, it would fold differently and become denatured
68
is it common that water dissociates?
no
69
what does water form when it (uncommonly) dissociates?
hydronium ion hydroxyl ion
70
can the covalent bond between oxygen and hydrogen in water be broken?
it's strong but it still breaks sometimes
71
what happens when the covalent bond between oxygen and hydrogen in water breaks?
water is dissociating - water molecules grab another hydrogen atom to form a hydronium ion and a hydroxyl ion
72
show the dissociation of water in equation form
H2O --><-- H+ + OH-
73
concentrations of H+ and OH- in pure water
[H+] = [OH-]
74
when does [H+] = [OH-]?
in pure water
75
[H+] at 25 degrees celcius
10^-7mol.L-1
76
define pH
pH = -log10[H+]
77
what is the concentration of water?
"how many molecules of H2O per litre?" RMM of H2O = 18 so, 1 mole of H2O = 18g 1g H2O = 1/18 = 0.0556 moles the density of H2O = 1g/mL (at 4 degrees celcius) 1mL water contains 0.0556 moles 1L water contains 55.6 moles the concentration of water = 55.6mol/L
78
equilibrium dissociation constant for K
[H+][OH-]/[H2O]
79
Ka
dissociation constant for pure water at 25 degrees celcius
80
work out Ka
[H+][OH-]/[H2O] 10^-7M x 10^-7M/55.6M
81
Kw value + working out
(Ka x 55.6) = ([H+][OH-]) = (10^-7 x 10^-7) = 10^-14
82
[H+][OH-] = 10^-14 what is this valid for?
any aqueous solution
83
Ka
the equilibrium constant
84

Cellular Composition (2 decks)

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