module 2 Flashcards
what is the most abundant molecule in living organisms?
-water
-has both active and passive roles
what are the passive roles of water?
-the structure (hence function) of biomolecules form in response to interaction with water
-ex: protein folding is driven to bury hydrophobic residues
what are the active roles of water?
-water is a participant in many biochemical reaction
-ex: peptide bond formation releases a water molecule
how does water shape the way we look for life?
-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
what is the structure of water?
-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
the dipole of a water molecules influences it’s ability to:
-form electrostatic interactions with charged molecules
-form hydrogen bonds (including with other water molecules)
what are hydrogen bonds?
-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
how strong are hydrogen bonds?
-relatively weak, about %5 strength of a covalent bond
-are about double the length of a covalent bond
-depends on its geometry
what are parallel and anti-parallel beta sheets?
-anti are more stable that parallel because there is better geometry of hydrogen bonding
what are the unusual properties of water?
-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
in liquid water, how many molecules participate in H bonds?
-average of 3.4 in dynamic “flickering clusters”
what is heat of vaporization?
-the amount of heat requires to vaporize a liquid at its boiling temp
what is specific heat capacity?
-the amount of heat required to raise the temperature of a substance one degree
how does the large number of H bonds within water contribute to?
-the high heat of vaporization and specific heat capacity of water
what does water have a higher of than most common solvents?
-melting point, boiling point and heat of vaporization
how does the high composition of water within our bodies help us?
-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
what is special about ice?
-each water molecules participate in four hydrogen bonds with other water molecules
-has a lower density than liquid water, ice floats
what was polywater?
-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
why was polywater a big deal?
-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
what can water interact with?
-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
how does water act as a solvent around functional groups?
-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
what are van der waal forces?
-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
how does the hydrophobic effect work in protein folding?
-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)
what is the ionization of water?
-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
what acids and bases dissociate completely in water?
-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
re draw the midpoint of titration graph?
-the line in red=weakest acid
-the line in blue=strongest acid
-the lower the pKa, the stronger the acid
what is an example of weak acids that serve to buffer biological systems
-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
what is the henderson-hasselbalch equation? what does it describe?
describes
-the pH of the solution
-the pKa of the weak acid
-the relative concentrations of the weak acid (HA) and conjugate base (A-)
