chapter 2 Flashcards
how much of us is made up of water
around 70% of our weight
what is a passive role
the structure (hence function) of biomolecules form in response to interaction with water
e.g. protein folding is driven to burt hydrophobic residues
what is a active role
water is a participant in many biochemical reactions
e.g. peptide bond formation releases a water molecule
what does the dipole of a water molecule influence its ability to…
-form electrostatic interactions with charged molecules
-form hydrogen bonds (including with other water molecules)
what are hydrogen bonds
they are electrostatic interations between an electronegative atom with hydrogen covalently linked (donor) to another electronegative atom with a free electron pair (acceptor)
what are two common hydrogen bonders within biomolecules
O and N
does O and N serve as acceptors or donors
both
how do hydrogen bonds compare to covalent bonds
-hydrogen bonds are about double the length
-hydrogen bonds are about only 5% the strength of a covalent bond
what is the strength of A hydrogen bond dependent on
it geometry (better lined up the stronger)
in water what molecules can donate and accept hydrogen bonds
each can donate and accept two hydrogen bonds
how many hydrogen bonds does water molecules have the potential to participate in
within water each molec has potental to partake in four hydrogen bonds with four other molecules
in water each molecule participates in an average of ___ H bonds in ______
3.4, dynamic flickering clusters
what influences the properties of water
the hydrogen bonds between water molecules confering great internal cohesions
what does water like
water
what does the large number if hydrogen bonds within water contribute to
the high heat of vaporization and specific heat capacity of water
what is the heat of vaporization
the amount of heat requires to vaporize a liquid at its boiling temp
what is the specific heat capacity
the amount of heat required to raise the temp of a substance one degree
why do H bonds make it hard for water to vaporize
because the h bonds hold onto each other so tightly
why is the specific heat capacity of water so high
because of complex mesh work of interactions between H2O molecules it allows them to absorb a lot of energy before they increase temp
what is isothermic
regulating and maintaining temp
what organisms are isothermic
most of them
what helps our bodies stay cool or isothermic
the high composition of water within our bodies, coupled with the high specific heat capacity of water
how do water molecules interact with each other in ice
water molecules participate in four hydrogen bonds with other water molecules
because ice participates in four hydrogen bonds with other molecules this leads to
ice having a lower density then liquid water
how many H bonds fours in liquid h2o
3.5
what freezes faster hot or cold water
hot water
what is polywater
-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
what can water molecules do through formations of hydration
they can interact, and dissolve, charged solutes
why does water molecules have great versatility in interacting with + and - charged ions
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)
what kind of ions does water like to interact with
both positive and negative ions
what do biomolecules have that allows them to form hydrogen bonds
functional groups
on biomolecules what can the functional groups “H bond” bond to
these groups can hydrogen bond within the same molecule, other biomolecules or with water
why are water molecules the ideal hydrogen bonding partners
because of there small size and because they can serve as either donors of acceptors
what is the first rule of hydrogen bonding
anything that can forms a hydrogen bond must form a hydrogen bond
what does the solubility of molecules in water depend on
the ability to interact with water molecules
what kind of molecules have the greatest solubility in water
molecules that carry charge (+/-) and/or participate in hydrogen bonds (donor or acceptors)
are hydrophilic polar or non-polar
they are polar
are hydrophobic molecules polar or non-polar
they are non-polar
what are amphiiathic molecules
the contain both hydrophobic and hydrophilic proportions (e.g. fatty acids)
why do we need specialized systems (myoglobin+hemoglobin) to help remove gassed from our body
because many biologically important gasses such as CO2 and )2 are non polar and therefore have limited solubility in water (and blood)
how do we get CO2 and O2 out of our blood
with specialized transport proteins and strategies
what happens when a amphipathic molecules is mixed with water
they hydrophilic regions interact favorably with water but the hydrophobic regions cluster together to present the smallest surface to water
what are hydrophobic interactions
the forces that hold non-polar regions of the molec together
are most biomolecules amphipathic
yes
why is a primary driving force in formation and stabilization of bimolecular structures
hydrophobic drive
non covalent interactions enable:
-transient, dynamic interaction
-flexibility of structure and function
most biomolecules represent stable polymers of what kind of linked building blocks
covalently linked
what is a down side to covalently bonded building blocks
they are strong but interms of biological activity they are worthless
what gives stable polymers of covalently liked building blocks there biological functions
the 3D structures formed by these polymers that are held through non covalent forces
what do non-covalent forces influence
-formation and stabilization of structures of biomolecules
-recognization/interactions between biomolecules
-binding of reactions to enzymes
non covalent interaction within biomolecules include…
-hydrogen bonds
ionic interactions
hydrophobic interaction
van der waals interactios
many functional groups with biomolecs have H bonding capacity. these groups can form hydrogen bonds with…
-water molecules
-groups in the same molecule (intramolecular)
-groups in other molecules (intermolecular)
why does are ionic bonds weaker in water
the water tends to sheild the charges groups, diminishing the stranth of interaction
in ionic bonds what does the strength of electrostatic interactions depend on
the distance separating the atoms and the nature os the intervening medium
what are electrostatic interaction
interactions between charged group
hydrogen bonds are critical for _____ of bimolecular interactions but not the ___ of bimolecular structures
specificity, formation
what are van der waals forces
the interaction between parmanet and induced dipoles; short range, low magnitude interations
how do van der waals forces interact
atoms want to be close to each other but not too close. they have optional spaces and so they will attract according to that
how do hydrophobic interactions work
they drive to have polar groups interacting with water and non polar regions shielded away from water
what is an example of hydrophobic interactions that break the second rule of thermodynamics
the folding of proteins
when you add a non-polar molecule to water what does this to to entropy
it decreases it
why does adding a non-polar molecule decrease entrophy
the water molecules aroud hydrophobic molecules are more ordered then they would be in pure water
the association of non-polar molecules releases some of the ordered water molecules resulting in…
an increase in entropy of water
what does the folding of polypeptides do to entropy of the polypeptide and the associated water
it decreases the entropy of the polypeptide but increases the entropy of associated water
what does water have the tendency to ionize into
H+ and OH- ions
what is the keq of water
Keq=[H+][OH-]/[H2O]=1.8x10-16 M
what is the concentration of H2O
[H2O]=55.5 M
what equals the concentration of H+ and OH-?
1.8x10-16 M [55.5M]=[H+][OH-]
what is the Kw formula
[H+][OH-]=1.0x10-14 M^2
what is Kw
it is the ion product of water
what is the most convenient way to express [H+]
and pH
how do you get the pH
pH=-log [H+]
in biochemistry when we deal with pH changes ho major are they
the pH changes are settle in biochem
what do strong acids and bases do in water
they fully dissociate in water
what do weak acids and bases do in water
they do not dissociate fully in water and the extent of dissociation can be quantified
how is the amount of acid that has dissociated quantified
with the ka
how is Ka calculate
Ka=[H+][CH3COO-]/[CH3COOH]
How is (p)Ka expressed
how Ka values are offten expressed (pKa=-log Ka)
what are titration curves
thy reveal the pKa of weak acids
when is a solution best able to resist changes in pH
when pH=pKa
how long does the buffering region in a titration curve extend for
one pH unit on either aide of pKa
what is the buffering region
where weak acid donates a proton
what is the pKa
the pH in which a weak acid can donate its protons at. so the lower the pKa the more acidic it’ll donate
how can you look at the pKa and tell which one is the strongest or weakest acid
the higher the pKa the weaker the acid
the lower the pKa the stronger the acid
what is the only amino acid with out a alpha carbon
glycene
if you have a amino acid with two different functional groups and have different pKas how does this work
functional groups retain characteristics independent of molecular context. so they will each donate protons at different times
what is thr protonated form that weak acids can exist in
the HA form
what is the conj base form weak acids
when they have donated there proton into solution
when pH=pKa then…
[A-]=[HA]
why are buffers important to biological systems
because living organisms need to be able to maintain constant pH
what could changes to pH do to protonation states of bio molecules
it could change the protonation states potentially changing there structure and function
how is the the pH in our blood maintained
by a bicarbonate buffer system
what are the benefits of CO2 and H2O reacting in your blood stream
-to convert CO2 into a more soluble form to get from muscles to your lungs
-the product acts as a buffer to control pH
what does CO2 and H2O turn into
the more polar H2CO3
what does H2CO3 turn into to act as a buffing system
HCO3- and H+
if you are above the pKa then you have more…
unprotonated A- (conjigate base)
if you are below the pKa then you have more…
protonated form (HA)
how does the logarithm scale work say if your 10x, 100x, 1000x less then the pH
10x=1 unit
100x=2 units
1000x=3 units
