module 2

Question 1

what is the most abundant molecule in living organisms?

Answer 1

-water
-has both active and passive roles

Question 2

what are the passive roles of water?

Answer 2

-the structure (hence function) of biomolecules form in response to interaction with water
-ex: protein folding is driven to bury hydrophobic residues

Question 3

what are the active roles of water?

Answer 3

-water is a participant in many biochemical reaction
-ex: peptide bond formation releases a water molecule

Question 4

how does water shape the way we look for life?

Answer 4

-difficult to imagine life in the absence of water
-presence of water on other planets is a critical determinant of their habitability by humans
-scientists have started to contemplate alternate liquids, such as ammonia or formamide, that might also be suitable for life

Question 5

what is the structure of water?

Answer 5

-O and H differ in their electronegativities
-O is more electronegative than H, giving water a permanent dipole
-O has a partial negative charge and each hydrogen has a partial positive charge

Question 6

the dipole of a water molecules influences it’s ability to:

Answer 6

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

Question 7

what are hydrogen bonds?

Answer 7

-electrostatic interactions between an electronegative atom with a hydrogen covalently linked (donor) to another electronegative atom with a free electron pair (acceptor)

-O and N are common hydrogen bonders within biomolecules
-O and N can each serve as hydrogen bond donors and acceptor

Question 8

how strong are hydrogen bonds?

Answer 8

-relatively weak, about %5 strength of a covalent bond
-are about double the length of a covalent bond
-depends on its geometry

Question 9

what are parallel and anti-parallel beta sheets?

Answer 9

-anti are more stable that parallel because there is better geometry of hydrogen bonding

Question 10

what are the unusual properties of water?

Answer 10

-each water molecule can donate and accept two H bonds
-each water mole as the potential to participate in four hydrogen bonds with four other water molecules
-the H bonds between water molecules confer great internal cohesion which influences the properties of water
-dont like to come apart

Question 11

in liquid water, how many molecules participate in H bonds?

Answer 11

-average of 3.4 in dynamic “flickering clusters”

Question 12

what is heat of vaporization?

Answer 12

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

Question 13

what is specific heat capacity?

Answer 13

-the amount of heat required to raise the temperature of a substance one degree

Question 14

how does the large number of H bonds within water contribute to?

Answer 14

-the high heat of vaporization and specific heat capacity of water

Question 15

what does water have a higher of than most common solvents?

Answer 15

-melting point, boiling point and heat of vaporization

Question 16

how does the high composition of water within our bodies help us?

Answer 16

-we burn tremendous amounts of energy, a by-product of which is heat
-most living organisms are isothermic, they need to regulate and maintain their temperatures
-STAY COOL

Question 17

what is special about ice?

Answer 17

-each water molecules participate in four hydrogen bonds with other water molecules
-has a lower density than liquid water, ice floats

Question 18

what was polywater?

Answer 18

-a soviet physicist was studying the properties of water forced through quartz tubes
-resulted in the new form of water with a higher boiling point, lower freezing point and much higher viscosity

Question 19

why was polywater a big deal?

Answer 19

-unusual networking of water molecules within polywater was self-propagating and could be used as a weapon
-turned out to be bad science
-other scientist showed that sweat had same properties as polywater

Question 20

what can water interact with?

Answer 20

-interact and dissolve charged solutes through formation of layers of hydration
-by small size and permanent dipole, water molecules have great versatility in interacting with both positively and negatively charged ions

Question 21

how does water act as a solvent around functional groups?

Answer 21

-can form hydrogen bonds
-can HB within the same molecule, other biomolecules or with water
-by small size and ability to serve as either donors or acceptors, water molecules are ideal hydrogen bonding partners

Question 22

what does the solubility of molecules in water rely on?

Answer 22

-depends on the ability to interact with water molecules
-molecules that carry charge and participate in h bonds have the greatest solubility in water

Question 23

what does hydrophilic mean?

Answer 23

water loving
-molecules are polar (carry a charge)

Question 24

what is hydrophobic?

Answer 24

water fearing
-molecules are non polar

Question 25

what are amphipathic molecules?

Answer 25

-contain both hydrophobic and hydrophilic portions (ex: fatty acids)

Question 26

are many biologically important gases very soluble in water?

Answer 26

-CO2 and O2 are non-polar and have limited solubility in water (and blood) -presents a challenge for their transport -specialized transport proteins and strategies are required for transport of CO2 and O2

Question 27

how do amphipathic substances behave?

Answer 27

-when mixed water, form micelles, hydrophobic regions cluster together to present the smallest surface of water -the forces that hold the non-polar regions of the molecule together are called hydrophobic interactions -most biomolecules are -hydrophobic drive is a primary driving force in formation and stabilization of biomolecular structures

Question 28

what are prion diseases?

Answer 28

-infectious proteins -folds differently then duplicate -hard to get rid of because they are always adopting different conformations

Question 29

what do non-covalent interactions enable?

Answer 29

-transient, dynamic interactions -flexibility of structure and function

Question 30

why are non-covalent reactions so important to biomolecules?

Answer 30

-most biomolecules represent stable polymers of covalently linked building blocks -the 3 dimensional structures formed by these polymers are largely determined through non-covalent interactions -interactions between biomolecules are also largely determined by non-covalent interactions

Question 31

what do non-covalent forces influence?

Answer 31

-formation and stabilization of structures of biomolecules -recognition/interactions between biomolecules -binding of reactant to enzymes

Question 32

what do non-covalent interactions within biomolecules include?

Answer 32

-hydrogen bonds -ionic (electrostatic) interactions -hydrophobic interactions -van der Waals interactions

Question 33

many func group with biomolecules have h bond capacity, functional groups can form hydrogen bonds with:

Answer 33

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

Question 34

why are hydrogen bonds critical?

Answer 34

-for the specificity of biomolecular interactions but not for the formation of biomolecular structures -in the unfolded state, these groups can hydrogen bond with water, a nearly perfect hydrogen boner

Question 35

what are electrostatic (ionic) interactions between?

Answer 35

-between charged groups can be attractive (oppositely charged groups) or repulsive (similar charged groups)

Question 36

what reduces the contribution of ionic interactions to biomolecular structures?

Answer 36

-by the shielding of these groups by water molecules -water tends to shield the charged groups, greatly diminishing the strength of the interaction

Question 37

what does the strength of electrostatic interactions depend on?

Answer 37

-on the distance separating the atoms and the nature of the intervening medium

Question 38

what are van der Waals forces between?

Answer 38

-interactions between permanent and induced dipoles; short range, low magnitude interactions (packing)

Question 39

when is the attraction maximal during van der waal forces?

Answer 39

-when two atoms are separated by the sum of the van der waal radii

Question 40

what are van der waal forces?

Answer 40

-when two surfaces of complementary shapes come together a large number of atoms are brought into van der waal contact -abundant in the core of folded proteins -ex: standing close to someone ur talking to or far away -dont want gaps, but not too close or too far

Question 41

what is the hydrophobic effect?

Answer 41

-drive to have polar groups interacting with water and non-polar regions shielded away from water -ex: protein folding

Question 42

how does the hydrophobic effect work in protein folding?

Answer 42

-non-polar side chains cluster in the interior of the protein, away from water -polar and charged side chains remain on the outer surface facing water -involves the creation of a more ordered state, which seems to be in contradiction of the second law of thermodynamics (greater disorder)

Question 43

what are the thermodynamics of the hydrophobic effect?

Answer 43

-water molecules around hydrophobic molecules are more ordered that they would be in pure water, the introduction of the non-polar molecule causes a decrease in the entropy of water -the association of non-polar releases some of the ordered water molecules, resulting in an increase the entropy of water -the folding of a polypeptide decrease the entropy of the polypeptide but increases the entropy of the associated water -cheerio affect

Question 44

does water have a memory?

Answer 44

-paper reported that an extreme dilution of a biomolecule retained biological activity -extent of dilution was no possibility that even a single molecule remained -author suggest water molecules "remember" -turned out to be BS

Question 45

how can bad science be big businesses?

Answer 45

-homeopathic remedies are prepared by repeatedly diluting a chosen substance: often 30 sequential dilutions of 1 in 100 -countless investigations have failed to find any scientific merit to homeopathy and yet selling water as medicine remains a multi-billion dollar industry

Question 46

what is the ionization of water?

Answer 46

-in solution, the structure of water is more complicated than H2O -water has a limited tendency to ionize to hydrogen ions (H+) and hydrox9de ions (OH-) -Kw is the ion product of water -concentration of water is a constant

Question 47

what is the pH scale?

Answer 47

-pH is a long scale such that the difference of 1 pH unit equals a 10-fold difference in H+

Question 48

what acids and bases dissociate completely in water?

Answer 48

-strong acids and bases dissociate completely in water -weak acids and bases do not dissociate completely in H2O and the extent of the dissociation can be quantified -K values often expressed as pKa's (pKa=-logKa) -pKa when HA=A

Question 49

how does titration curves reveal the pKa of weak acids? what are buffering regions?

Answer 49

-the ratio of the acid to the conjugate base changes over the course of the titration curve -when pH=pKa then A-=HA -when pH=pKa, the solution is best able to resist changes in pH -buffering region extends one pH unit on either side of the pKa point

Question 50

re draw the midpoint of titration graph?

Answer 50

-the line in red=weakest acid -the line in blue=strongest acid -the lower the pKa, the stronger the acid

Question 51

why are buffers important to biological systems?

Answer 51

-organisms need to be able to maintain a constant pH -change to pH could alter the protonation state of biomolecules, potentially changing their structure and function -a number of weak acids that serve to buffer biological system?

Question 52

what is an example of weak acids that serve to buffer biological systems

Answer 52

-the pH within blood is maintained by a bicarbonate buffer system -compensatory respiratory alkalosis serves to maintain the ratio of H2CO3/HCO3- to maintain a constant pH

Question 53

what is the henderson-hasselbalch equation? what does it describe?

Answer 53

describes -the pH of the solution -the pKa of the weak acid -the relative concentrations of the weak acid (HA) and conjugate base (A-)