Lecture 1/2: Water Flashcards
Water!
Water has a ____ moment.
Dipole
Since water is so ____, it takes a lot of ____ to break bonds bw H2O molecules.
Since water is so polar, it takes a lot of energy to break bonds bw H2O molecules.
What is a disordered collection of clusters?
When is it not in clusters?
Bc of this it is known to have what type of structure?
- Liquid H2O
- When there are individual molecules of water @ BP
- Flickering
Liquid H2O’s collection of clusters explains:
- ?
- ?
- ? (?)
- Viscosity
- High BP (when compared to molecules of similar MW)
- Extraordinarily high heat capacity (thermal mass)
How many H-bonds are possible per H2O molecule?
Liquid water?
Ice?
4
Liquid water: 3.4 H-Bonds
Ice: 4 H-Bonds
Which is ice and water?
Why?
Left: Water
Right: Ice
- Due to less dense structure, allows it to float
Due to accessible melting point, H2O:
- Occurs in a ____ ______ compatible with life
- Facilitates ____ _______: (AKA- ice ……. = )
- Occurs in a temperature range compatible with life
- Facilitates biological turnover: (AKA- ice expands and rips apart cellulosic & woody plant = Carbon Cycle!)
Due to low boiling point: H2O
- Permits ____ & ____ ____
- _____ keeps atmosphere moist
- Permits evaporation & heat loss
- Vapor keeps atmosphere moist
Due to other aspects of polarity: H2O
- Readily accomodates ____/_____ substances
- Also affect the interactions of _____ groups (called?)
- Strongly affects biochemical _______
- Readily accomodates polar/ionic substances
- Also affect the interactions of apolar groups (called? Hydrophobic Interactions)
- Strongly affect biochemical thermodynamics
H2O deactivates _____ rxns.
- ____ rxns work best in _____ ______ solvents. (EX:)
- Water binds to _____ and ______ greatly deactivating them.
H2O deactivates nucleophilic rxns.
- Nucleophilic rxns work best in polar organic solvents. (EX: Acetone, DMF, THF)
- Water binds to nucelophiles and electrophiles greatly deactivating them.
Why are the deactivating effects of H2O towards nucleophilic rxns extemely beneficial, tho it seems disadvantageous?
Nonenzymatic rxns are extremely slow under physiological conditions (salty water, neutral pH, moderate temps)
H2O deactivates nucelophilic rxns and explains vital role that ____ play?
H2O deactivates nucelophilic rxns and explains vital role that enzymes play?
Due to H2O deactivating nueclophilic rxns, this explains the vital roles ezymes play which allows them to:
- ?
- ?
- bind substrates
- behave as virtual on/off switches
Enzymes bind substrates:
- Increasing their ____ ____
- Orienting them to maximize ______
- Stabilizing rxn _____-_____
- Making rxns go ______
- Increasing their local concentration
- Orienting them to maximize reactivity
- Stabilizing rxn transition-states
- Making rxns go much faster
Enzymes behave as virtual on/off switches:
- No rxn in _____ of _____
–> rxn too slow = water _____
- ______ potentially toxic ____-____
- Allows for highly effective ______
- No rxn in abscence of enzyme
–> rxn too slow = water suppresses
- Reduces potentially toxic side-rxns
- Allows for highly effective regulation
Ezymes ____ reactivity so that metabolism can proceed under _____ conditions.
EX: ?
Ezymes increase reactivity so that metabolism can proceed under physiological conditions.
EX: Glucose Phosphorylation
What is the breaking apart of molecules by H2O?
- ?
- ? (? attached)
- Ionic Hydrolysis: solid/gas and breaking into hydrated ions
- Covalent Hydrolysis: (phosphate attached) bring in water and hydrolved glucose and phosphate and breaking covalent bond
What refers to the continuous exchange of water w/in the hydrosphere?
AKA:
Bw? (6)
Water/Hydrologic Cycle
Bw: atmosphere, soil water, surface water, groundwater, plants, and animals
Water moves thru each region by what 4 transfer processes?
- Evaporation
- Transpiration
- Precipitation
- Runoff
What is the water transfer process from oceans and other water bodies into the atmosphere?
Evaporation
What is the water transfer process from land plants and animals into the atmosphere?
Transpiration
What is the water transfer process from water vapor condensing and falling to the earth/ocean?
Precipitation
What is the water transfer process from the land and reaching the sea?
Runoff
Life getting started was incredibly slow due to lack of _____.
catalysts
Life most likely began in _____/____ ____.
Why?
Life most likely began in desert/mt. slopes bc molecules such as peptides, oligosaccharides and metabolic intermediates (ie ATP) ONLY form upon loss of water.
Steps of first life?
- Drought concentrates _____, allowing them to _____ –> loss of _____
- Solutes ____ by rain, relocating and ____ elsewhere
- Drought concentrates solutes, allowing them to combine –> loss of H2O.
- Solutes diluted by rain, relocating and reacting elsewhere
After a few billion years, everything changed upon the appearance of small ____ of _______.
After a few billion years, everything changed upon the appearance of small oligomers of ribonucelotides.
RNA molecules were incredibly special bc they could:
- fold into ___-___ 3D _____.
- act as ____.
- ____ information.
- eventually, _____ themselves.
- fold into well-defined 3D structures.
- act as catalysts.
- store information.
- eventually, replicate themselves.
Simply put, Life is a ____-____ system, able to ____ & ____ _____. (Rudimentary form of life became this)
Simply put, Life is a self-adaptive system, able to evolve & gain options.
Life “evolving and gaining options” refers to?
Which eludes to _____, the search algorithm for change.
Learning and adjusting
Mutation
This is an image of water undergoing rapid H+ _____/_____ @ equilibrium.
AKA?
Water undergoes rapid H+ dissociation/reassociation.
AKA: autocrotolysis
In reality there are no free H+’s; instead H+ ____ w/ neighboring _____ to form _____ ions. (= ?)
In reality there are no free H+’s; instead H+ combines w/ neighboring H2O to form hydronium ions. (= H3O+)
In liquid H2O, ____ ____ occurs; the fast transfering of one H+ to water, creating hydronium ion.
____ ____ creates a “___ wire” to facilitate rapid H+ transfer in/out of active site.
In liquid H2O, proton hopping occurs; the fast transfering of one H+ to water, creating hydronium ion.
Carbonic Anhydrase creates a “proton wire” to facilitate rapid H+ transfer in/out of active site.
In pH Acid/Base Rxns:
pH = (rxn?)
Kw = ?rxn = ?M
–> Measure of?
[H+] = ?
[A] = ?
[HA] = ?
pH = -log10[H3O+]
Kw = [H3O+][OH-] = 10-14 M2
–> Measure of dissocation constant for water reacting w/ self
[H+] = proton
[A] = anion/ base
[HA] = acid
Neutrality of pH Acid/Base Rxns require x = ?
[H3O+] = [OH-] = x
What do pH meters measure?
Where ___ is the activity coefficient and (H+) =
pH meters measure proton activity (H+)
Where A is the activity coefficient and (H+) = A[H+]
Since pH meters are standardized by using solutions of known concentration and activity, pH of pure water is _____, but not _____ _____.
Since pH meters are standardized by using solutions of known concentration and activity, pH of pure water is ~7.00 but not exactly 7.00.
Ka =
units?
Henderson-Hasselbalch Equation?
Ka = [H+][A-]/[HA]
pH = pKa + log ([A-]/[HA])
When: what are the concentration of anions to acids?
pH = pKa
pH = pKa + 1
pH = pKa - 1
[A-] = [HA]
[A-] = 10 x [HA]
[A-] = 0.1 x [HA]
On the basic/acid side of the pKa, what is the concentration of acid to anion?
Basic Side: [HA] < [A-]
Acidic Side: [HA] > [A-]
Understanding biochemical processes and acid/base rxns are important when considering:
- _____ have acid/base groups
- Enzymes have acids and bases in _____ sites
- DNA & RNA are ________
- Metabolites have acid/base groups
- Enzymes have acids and bases in active sites
- DNA & RNA are polyelectrolytes
What are weak acids & bases that help stabilize pH?
Buffers
Buffers obey __ ______ Principle, which states:
“a ____ system compensates to a _____” meaning: ?
Add H+ & they readjust–> ?
Add OH- & they readjust–> ?
Buffers obey Le Chatelier’s Principle, which states:
“a dynamic system compensates to a stress” meaning:
adjusts equilibrium ratios in accordance to stabilize system
Add H+ & they readjust–> A- + H+ = HA
Add OH- & they readjust–> HA + OH- = A- + H2O
Buffers are most effective near their ___ values, bc that’s where there is a sufficiently large pool of ___ the weak ___ and its conjugate ___.
Buffers are most effective near their pKa values, bc that’s where there is a sufficiently large pool of both the weak acid and its conjugate base.
What is the largest biological buffer in the body that is the conjugate base of phosphoric acid?
Orthophosphate
What is the second largest biological buffer that is located in cells, helps oxidize foods and creates CO2?
Bicarbonate
What buffers are the biggest contributions of pH control, due to many metabolites are weak acids/bases?
Biological Buffers
What is the 3rd largest biological buffer that has high concentration in the heart?
ATP
What is the 4th largest biological buffer that is located in all cells, especially cytoplasm, and contains carboxyl and amino groups?
Proteins
What are the smallest biological buffers that are located in muscles and helps controls ATP in cells?
Creatine Phosphate
What is arguably the most important buffer system for acid/base homeostasis in humans that is found in all areas of the body?
- Takes advantage of ____ production
- Maintains a relatively constant __ pH by countering changes in ___, ____, ____, ____ _____, etc
Bicarbonate Buffer System
- Takes advantage of CO2 production
Maintains a relatively constant plasma pH by countering changes in acids, bases, anions, metal ions, etc
*
What is the equation for the Bicarbonate Buffer System?
- ___ combines with ____ to form ____, which rapidly dissociates to form ___ ion and ____.
- Rxn catalyzed by ____ _______
CO2 + H2O = H2CO3 (minor species) = H+ + HCO3-
CO2 combines with water to form carbonic acid, which rapidly dissociates to form hydrogen ion and bicarbonate.
Rxn catalyzed by carbonic anhydrase
When the Bicarbonate Buffer sytem is partered with _____ ______ it becomes a powerful acid-base regulator.
When the Bicarbonate Buffer sytem is partered with respiratory compensation it becomes a powerful acid-base regulator.
What is the term that modifies circulating CO2 to create altered breathing rates?
- What decreases CO2 levels by bringing in more O2 and expelling CO2?
- What method increases CO2 levels by inhaling the previously expelled CO2?
- Respiratory Compensation
- Hypervenilating
- Taking a paperbag and breathing in and out CO2
Increasing the breathing rate and expelling excess CO2 results in?
Occurs by pulling even more ____ toward production of ___
Excess acid is essentially “____”
- Respiratory Alkalosis
- Occurs by pulling even more protons toward production of CO2
- Excess acid is essentially “exhaled”
Cells also buffer ____: In acid-base disturbances, shifts of H+ or HCO3- bw cells and ___ are mainly balanced by movements of Na+, K+, and Cl-
Cells also buffer ECF: In acid-base disturbances, shifts of H+ or HCO3- bw cells and ECF are mainly balanced by movements of Na+, K+, and Cl-
Protonation/Deprotonation of ___ molecules is rapid
Protonation/Deprotonation of small molecules is rapid
_____ means that the rxn rate is determined by how fast reactants collide
___ molecules collide quickly
Diffusion-limited process means that the rxn rate is determined by how fast reactants collide
Small molecules collide quickly
Protonation/deprotonation of macromolecules:
- Acid/base groups on _____ react immediately
- Acid/base groups ____ _____ may never ionize
- H-Bonds of buried helices and ß-sheets require the “____ ______” - (___ _____)
Acid/base groups on surface react immediately
Acid/base groups deep inside may never ionize
H-Bonds of buried helices and ß-sheets require the conformational breathing” - (local unfolding)
What is a digestive enzyme secreted into gastric juice in the stomach, which allows it to act optimally @ a pH ~1.5?
Pepsin
What is a digestive enzyme that acts in the small intestine and has a pH optimum that matches the neutral pH in the lumen of the small intestine?
Trypsin
What is a hydrolytic enzyme that operates well enough at neutral pH of intestine?
Alkaline phosphatase
Label the peaks of the graph with the appropriate enzyme.
What type of interactions are very important for biomolecules in aqeous solvent?
- ?
- ?
- ?
- ?
Noncovalent “Weak” Interactions
- H-Bonds
- Ionic Interactions
- Hydrophobic Interactions
- Van der Waals Interactions
“Weak” noncovalent interactions are individually ____, but the ________ is very significant.
“Weak” noncovalent interactions are individually weak, but the aggregate is very significant.
What allows proteins and nucleic acids to fold & unfold?
“Weak” noncovalent interactions
What type of “Weak” Noncovalent bond is this?
H-Bond bw neutral groups
What type of “Weak” Noncovalent bond is this?
H-bond bw peptide bonds
What type of “Weak” Noncovalent bond is this?
Ionid Attraction Interaction
What type of “Weak” Noncovalent bond is this?
Ionic Repulsion Interaction
What type of “Weak” Noncovalent bond is this?
Hydrophobic Interactions
What type of “Weak” Noncovalent bond occurs bw any 2 atoms in close proximity, is the longest and weakest and is due to “flickering dipoles”?
van der Waals interactions
With Gibbs Free energy (deltaG):
energy needs to be ______ to make a bond
and
_______ to break a bond.
With Gibbs Free energy (deltaG):
energy needs to be released to make a bond
and
added to break a bond.
In a _____ noncovalent interaction, intrinsically polar bonds interact.
H-Bonds
In a _____ noncovalent interaction, opposite charges attract and like repel.
Electrostatic
In a _____ noncovalent interaction, H-Bonding and electrostatic interactions combine.
Salt Bridge
In a _____ noncovalent interaction, displacement of water is driven by favorable entropy.
Hydrophobic interactions
In a _____ noncovalent interaction, stacking of aromatic rings occur due to greater e- delocalizations.
Pi Stacking
In a _____ noncovalent interaction, very weak forces occur bw oscillating dipoles.
van der Waals interactions
What is the order of Noncovalent interactions according to their strengths?
- ?
- ?
- ?
- ?
- ?
- ?
- Salt Bridge
- H-Bonds
- Electrostatic
- Hydophobic
- Pi Stacking
- van der Waals
What is fundamentally an “acid/base” interaction?
H-Bonds
H-Bonds require proton donors = electro+/-?
H-Bonds require proton donors = electro+
H-Bonds require proton acceptors = electro+/-?
H-Bonds require proton acceptors = electro-
When are H-Bonds the strongest?
When they are linear.
H-Bonds are found throughout nature bw:
- ?
- ?
BUT, it depends on the ___ of the attached molecules and group
H-Bonds are found throughout nature bw:
- Peptide groups in polypeptides
- Complementary bases of DNA
BUT, it depends on the EN of the attached molecules and group
H-Bonds are found throughout nature:
- Exploit the properties of the universal ______
- Improve _______
- Essential for biospecific ________
- Easy to make & break bond to allow fast ______
H-Bonds are found throughout nature:
- Exploit the properties of the universal solvent
- Improve solubility
- Essential for biospecific recognition
- Easy to make & break bond to allow fast kinetics
Why are the stabilizing interactions in Hydrophobic Interactions NOT true bonds?
There is no overlapping of atomic/molecular orbitals, which allows apolar groups to weakly interact.
Wha is the Gibbs Equation?
In hydrophobic interactions, water binds tightly to apolar groups so that:
Delta H <>> for water-binding and water-release?
Hydrophobic interaction results in the release of water molecules which (in/de)creases randomness?
Increases randomness (Delta S >> 0)
As temperature strongly influences Delta G, when is it favorable vs unfavorable?
At low T: > 0, unfavorable
High T: < 0, favorable
_____ groups facilitate protein folding:
- protein folding ______ local entropy of protein
- water release ____ entropy of overall system
Hydrophobic groups facilitate protein folding:
- protein folding decreases local entropy of protein
- water release increases entropy of overall system
______ in hydrophobic interactions can swivel w/ ease, facilitating ______ ______.
________ maximizes packing within the protein, thereby maximizing release of bound ______.
Side-chains in hydrophobic interactions can swivel w/ ease, facilitating protein folding.
Variety in side-chains maximizes packing within the protein, thereby maximizing release of bound water.
Strength of hydrophonic interaction is determined by:
Strength of hydrophonic interaction is determined by the number of water molecules released per interaction.
What is a measure of the number of water molecules needed to cover a particular hydrophobic side-chain?
Water Accessible Area
Hydrophobic interactions also play a dominant role in stabilizing _______ __________ ________.
Hydrophobic groups on the surface interact with apolar lipid ________ of the inner ______ _______.
Hydrophobic interactions also play a dominant role in stabilizing membrane bilayer structure.
Hydrophobic groups on the surface interact with apolar lipid side-chains of the inner membrane bilayer.
Amphipathic molecules possess BOTH:
- _______ region (water-like, polar or charged)
- _______ region (apolar)
Long-chain fatty acids have very hydrophobic alkyl chains, each of which is surrounded by a layer of highly ordered ______ molecules.
Amphipathic molecules possess BOTH:
- hydrophilic region (water-like, polar or charged)
- hydrophobic region (apolar)
Long-chain fatty acids have very hydrophobic alkyl chains, each of which is surrounded by a layer of highly ordered water molecules.
LABEL!
What occurs with amphipathic molecules in water?
In amphipathic molecules in water:
What does clustering together in micelles do to the fatty acid molecules?
Due to this, how many and where do water molecules form the shell of the ordered water?
What stabilizes the micelle?
In amphipathic molecules in water:
What does clustering together in micelles do to the fatty acid molecules?
Reduce the hydrophobic SA exposed to water
Due to this, how many and where do water molecules form the shell of the ordered water?
Fewer water molecules are req’d to form the shell of ordered water around a hydrophobic surface
What stabilizes the micelle?
The energy gained by freeing immobilized water molecules as entropy increases.
