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BMSC 200 > chapter 2 > Flashcards

chapter 2 Flashcards

1
Q

how much of us is made up of water

A

around 70% of our weight

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2
Q

what is a passive role

A

the structure (hence function) of biomolecules form in response to interaction with water
e.g. protein folding is driven to burt hydrophobic residues

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3
Q

what is a active role

A

water is a participant in many biochemical reactions
e.g. peptide bond formation releases a water molecule

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4
Q

what does the dipole of a water molecule influence its ability to…

A

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

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5
Q

what are hydrogen bonds

A

they are electrostatic interations between an electronegative atom with hydrogen covalently linked (donor) to another electronegative atom with a free electron pair (acceptor)

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6
Q

what are two common hydrogen bonders within biomolecules

A

O and N

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7
Q

does O and N serve as acceptors or donors

A

both

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8
Q

how do hydrogen bonds compare to covalent bonds

A

-hydrogen bonds are about double the length
-hydrogen bonds are about only 5% the strength of a covalent bond

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9
Q

what is the strength of A hydrogen bond dependent on

A

it geometry (better lined up the stronger)

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10
Q

in water what molecules can donate and accept hydrogen bonds

A

each can donate and accept two hydrogen bonds

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11
Q

how many hydrogen bonds does water molecules have the potential to participate in

A

within water each molec has potental to partake in four hydrogen bonds with four other molecules

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12
Q

in water each molecule participates in an average of ___ H bonds in ______

A

3.4, dynamic flickering clusters

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13
Q

what influences the properties of water

A

the hydrogen bonds between water molecules confering great internal cohesions

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14
Q

what does water like

A

water

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15
Q

what does the large number if hydrogen bonds within water contribute to

A

the high heat of vaporization and specific heat capacity of water

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16
Q

what is the heat of vaporization

A

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

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17
Q

what is the specific heat capacity

A

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

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18
Q

why do H bonds make it hard for water to vaporize

A

because the h bonds hold onto each other so tightly

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19
Q

why is the specific heat capacity of water so high

A

because of complex mesh work of interactions between H2O molecules it allows them to absorb a lot of energy before they increase temp

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20
Q

what is isothermic

A

regulating and maintaining temp

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21
Q

what organisms are isothermic

A

most of them

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22
Q

what helps our bodies stay cool or isothermic

A

the high composition of water within our bodies, coupled with the high specific heat capacity of water

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23
Q

how do water molecules interact with each other in ice

A

water molecules participate in four hydrogen bonds with other water molecules

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24
Q

because ice participates in four hydrogen bonds with other molecules this leads to

A

ice having a lower density then liquid water

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25
Q

how many H bonds fours in liquid h2o

A

3.5

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26
Q

what freezes faster hot or cold water

A

hot water

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27
Q

what is polywater

A

-soviet physicist was exploring the properties of water through quartz tubes
-resulted in new form of water with higher boiling temp and lower freezing temp and higher viscosity than ordinary water

people were scared

american scientist demoed that his own sweat has simular properties suggesting that unique properties reflected influence of impurities

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28
Q

what can water molecules do through formations of hydration

A

they can interact, and dissolve, charged solutes

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29
Q

why does water molecules have great versatility in interacting with + and - charged ions

A

because of there small size and permanent dipole

(anything w a charge is going to want to interact with water molecs. so they will be hydrophilic and have high solubility)

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30
Q

what kind of ions does water like to interact with

A

both positive and negative ions

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31
Q

what do biomolecules have that allows them to form hydrogen bonds

A

functional groups

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32
Q

on biomolecules what can the functional groups “H bond” bond to

A

these groups can hydrogen bond within the same molecule, other biomolecules or with water

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33
Q

why are water molecules the ideal hydrogen bonding partners

A

because of there small size and because they can serve as either donors of acceptors

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34
Q

what is the first rule of hydrogen bonding

A

anything that can forms a hydrogen bond must form a hydrogen bond

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35
Q

what does the solubility of molecules in water depend on

A

the ability to interact with water molecules

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36
Q

what kind of molecules have the greatest solubility in water

A

molecules that carry charge (+/-) and/or participate in hydrogen bonds (donor or acceptors)

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37
Q

are hydrophilic polar or non-polar

A

they are polar

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38
Q

are hydrophobic molecules polar or non-polar

A

they are non-polar

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39
Q

what are amphiiathic molecules

A

the contain both hydrophobic and hydrophilic proportions (e.g. fatty acids)

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40
Q

why do we need specialized systems (myoglobin+hemoglobin) to help remove gassed from our body

A

because many biologically important gasses such as CO2 and )2 are non polar and therefore have limited solubility in water (and blood)

41
Q

how do we get CO2 and O2 out of our blood

A

with specialized transport proteins and strategies

42
Q

what happens when a amphipathic molecules is mixed with water

A

they hydrophilic regions interact favorably with water but the hydrophobic regions cluster together to present the smallest surface to water

43
Q

what are hydrophobic interactions

A

the forces that hold non-polar regions of the molec together

44
Q

are most biomolecules amphipathic

A

yes

45
Q

why is a primary driving force in formation and stabilization of bimolecular structures

A

hydrophobic drive

46
Q

non covalent interactions enable:

A

-transient, dynamic interaction
-flexibility of structure and function

47
Q

most biomolecules represent stable polymers of what kind of linked building blocks

A

covalently linked

48
Q

what is a down side to covalently bonded building blocks

A

they are strong but interms of biological activity they are worthless

49
Q

what gives stable polymers of covalently liked building blocks there biological functions

A

the 3D structures formed by these polymers that are held through non covalent forces

50
Q

what do non-covalent forces influence

A

-formation and stabilization of structures of biomolecules
-recognization/interactions between biomolecules
-binding of reactions to enzymes

51
Q

non covalent interaction within biomolecules include…

A

-hydrogen bonds
ionic interactions
hydrophobic interaction
van der waals interactios

52
Q

many functional groups with biomolecs have H bonding capacity. these groups can form hydrogen bonds with…

A

-water molecules
-groups in the same molecule (intramolecular)
-groups in other molecules (intermolecular)

53
Q

why does are ionic bonds weaker in water

A

the water tends to sheild the charges groups, diminishing the stranth of interaction

54
Q

in ionic bonds what does the strength of electrostatic interactions depend on

A

the distance separating the atoms and the nature os the intervening medium

55
Q

what are electrostatic interaction

A

interactions between charged group

56
Q

hydrogen bonds are critical for _____ of bimolecular interactions but not the ___ of bimolecular structures

A

specificity, formation

57
Q

what are van der waals forces

A

the interaction between parmanet and induced dipoles; short range, low magnitude interations

58
Q

how do van der waals forces interact

A

atoms want to be close to each other but not too close. they have optional spaces and so they will attract according to that

59
Q

how do hydrophobic interactions work

A

they drive to have polar groups interacting with water and non polar regions shielded away from water

60
Q

what is an example of hydrophobic interactions that break the second rule of thermodynamics

A

the folding of proteins

61
Q

when you add a non-polar molecule to water what does this to to entropy

A

it decreases it

62
Q

why does adding a non-polar molecule decrease entrophy

A

the water molecules aroud hydrophobic molecules are more ordered then they would be in pure water

63
Q

the association of non-polar molecules releases some of the ordered water molecules resulting in…

A

an increase in entropy of water

64
Q

what does the folding of polypeptides do to entropy of the polypeptide and the associated water

A

it decreases the entropy of the polypeptide but increases the entropy of associated water

65
Q

what does water have the tendency to ionize into

A

H+ and OH- ions

66
Q

what is the keq of water

A

Keq=[H+][OH-]/[H2O]=1.8x10-16 M

67
Q

what is the concentration of H2O

A

[H2O]=55.5 M

68
Q

what equals the concentration of H+ and OH-?

A

1.8x10-16 M [55.5M]=[H+][OH-]

69
Q

what is the Kw formula

A

[H+][OH-]=1.0x10-14 M^2

70
Q

what is Kw

A

it is the ion product of water

71
Q

what is the most convenient way to express [H+]

A

and pH

72
Q

how do you get the pH

A

pH=-log [H+]

73
Q

in biochemistry when we deal with pH changes ho major are they

A

the pH changes are settle in biochem

74
Q

what do strong acids and bases do in water

A

they fully dissociate in water

75
Q

what do weak acids and bases do in water

A

they do not dissociate fully in water and the extent of dissociation can be quantified

76
Q

how is the amount of acid that has dissociated quantified

A

with the ka

77
Q

how is Ka calculate

A

Ka=[H+][CH3COO-]/[CH3COOH]

78
Q

How is (p)Ka expressed

A

how Ka values are offten expressed (pKa=-log Ka)

79
Q

what are titration curves

A

thy reveal the pKa of weak acids

80
Q

when is a solution best able to resist changes in pH

A

when pH=pKa

81
Q

how long does the buffering region in a titration curve extend for

A

one pH unit on either aide of pKa

82
Q

what is the buffering region

A

where weak acid donates a proton

83
Q

what is the pKa

A

the pH in which a weak acid can donate its protons at. so the lower the pKa the more acidic it’ll donate

84
Q

how can you look at the pKa and tell which one is the strongest or weakest acid

A

the higher the pKa the weaker the acid
the lower the pKa the stronger the acid

85
Q

what is the only amino acid with out a alpha carbon

A

glycene

86
Q

if you have a amino acid with two different functional groups and have different pKas how does this work

A

functional groups retain characteristics independent of molecular context. so they will each donate protons at different times

87
Q

what is thr protonated form that weak acids can exist in

A

the HA form

88
Q

what is the conj base form weak acids

A

when they have donated there proton into solution

89
Q

when pH=pKa then…

A

[A-]=[HA]

90
Q

why are buffers important to biological systems

A

because living organisms need to be able to maintain constant pH

91
Q

what could changes to pH do to protonation states of bio molecules

A

it could change the protonation states potentially changing there structure and function

92
Q

how is the the pH in our blood maintained

A

by a bicarbonate buffer system

93
Q

what are the benefits of CO2 and H2O reacting in your blood stream

A

-to convert CO2 into a more soluble form to get from muscles to your lungs
-the product acts as a buffer to control pH

94
Q

what does CO2 and H2O turn into

A

the more polar H2CO3

95
Q

what does H2CO3 turn into to act as a buffing system

A

HCO3- and H+

96
Q

if you are above the pKa then you have more…

A

unprotonated A- (conjigate base)

97
Q

if you are below the pKa then you have more…

A

protonated form (HA)

98
Q

how does the logarithm scale work say if your 10x, 100x, 1000x less then the pH

A

10x=1 unit
100x=2 units
1000x=3 units

BMSC 200 (10 decks)

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