Module 2: Water, Weak Interactions & Buffers Flashcards
Water has both ____ and ____ roles in Biochem.
passive and active
What is the passive role of water?
Things that happen just cuz water is present. Things occurring in response to water.
The structure/function of biomolecules is formed in response to water (hydrophobic/hydrophilic)
Ex. Proteins folding
What is the active role of water?
When water is a participant in the biochemical reactions it’s playing an active role.
Ex. peptide bonds formation (from amino acids) releases 1 water molecule (sometimes water is needed to initiate rxn)
Possible substitutes for water? (2x)
Ammonia & Formamide
How does water have a permanent dipole?
Oxygen & Hydrogen have diff electronegativities with O = - and H = + so a permanent dipole is created.
What abilities (2x) do the permanent dipole of water impact?
It impacts the ability to form H-bonds
Impacts the ability to form electrostatic interactions with charged molecules
What are H-bonds
they bond to Nitrogen or Oxygen with a H covalently linked to it
What is the ideal H-bond molecule?
Water
____ bonds are less strong than covalent bonds but double the length. The strength of the _____ bond depends on its ______.
H-bond = less strong & double length
Strength of H-bond depends on its geometry
*weak interactions are important to form strong bonds
(enough weak bonds = strong bonds)
List 2 geometric structure H-bond can form; and their pro & con
Anti-parallel beta sheets = geo allows for more H-bonding = stronger
Parallel beta sheets = allows less H-bonds = more flexibility
Which one is better? depends on what biological goal it has
What makes H-bond donor
Your need a H covalently attached to a electronegative (N/O) atom
What makes H-bond acceptor
You need H-bon linked to electronegative (N/O) atom that has a pair of free electrons
How many H-bonds can one water molecule donate/accept?
How many H-bonds can water form with other water?
1 H2O molecule = 2 H donors + 2 H acceptors
1 H2O molecule can form 4 H-bonds with 4 other water
What does “flickering clusters” mean when referring to water?
In liq. form, water molecules move around and continue to change dance partners (with H-bonds) each molecule forms an average 3.4 H-bond at once in liq state.
Since water is held by non-covalent associates = easy to break up
What 2 factors do water molecules influence due to . . . loving to bond with each other (having high internal cohesion)
Then the water molecules don’t want to come apart (hard to break up) which influences heat of vaporization and specific heat capacity
What is Heat of Vaporization?
the amount of heat required to vaporize a liq. at its boiling point/temp
What is specific heat capacity?
amount of heat required to raise the temp of a substance one degree
Water has a ____ melting point, boiling point, and heat of vaporization than most solvents.
Higher than most
Describe water turning to ice?
when the dancing flickering clusters cool down they stop moving (& switching H-bonds) and form 4 stable H-bonds with other water molecules creating solid ice
List 2 abilities that allow water to act as a solvent.
Electrostatic interactions (charged molecules) & H-bonds allow water to be a solvent
Explain how electrostatic interactions (charged molecules) allow water to be a solvent?
Water likes interacting with both +/- charged molecules and can dissolve these charged solutes through the formation of hydration.
Anything with a charge will be hydrophilic / highly soluble + favorable to water
Explain how H-bonding allow water to be a solvent?
Biomolecules have F.G that can form H-bonds, and since water molecules are ideal H-bonding partners, anything with H-bonds possible will be highly soluble
Solubility of molecules depends on how it will interact with water. What 2 factors will give the greatest solubility in water?
Molecules that carry +/- charge & molecules that can form H-bonds will have greatest solubility.
Explain the properties that classify a molecule as Hydrophilic? (charge/no-charge & H-bond/ no H-bond & polar/non-polar)
Hydrophilic = water-loving
Molecular properties: will have a charge (+/-) and the ability to H-bond & is polar = will make it more soluble
Explain the properties that classify a molecule as Hydrophobic? (charge/no-charge & H-bond/ no H-bond & polar/non-polar)
Hydrophobic = water hating
Molecular properties: has no charges and no H-bonding ability & is non-polar
Explain the properties that classify a molecule as amphipathic?
(charge/no-charge & H-bond/ no H-bond & polar/non-polar)
Amphipathic = contains both hydrophilic and hydrophobic parts (they arrange in a way to optimize their position to satisfy both)
Molecular Properties: has both hydrophobic/hydrophilic properties
Ex. Fatty acids
- carboxyl acids (has charge and H-bond) = hydrophilic
- rest of hydrocarbon chain (no charge & H-bond) = hydrophobic
Explain the importance of specialized transport proteins for the solublity of some dissolved molecules?
many biologically imported gases (CO2, O2) are non-polar to water/blood which is problematic for their transport. Which is why we need specialized transport proteins (ex. hemoglobin & myogloban)
List the behaviors of amphipathic substances?
(orientation, force that holds them together, and their importance)
Orient so hydrophilic are outwards towards water & hydrophobic inwards away from water
Non-polar (tails/hydrophic) regions of molecules are held by the hydrophobic interaction force
This hydrophobic drive is the main cause of formation and stableization of biomolecules
For most biomolecules: polymers are _____ linked building blocks. These individual polymers form 3D structures called biomolecules, determined mostly by ______ interactions. Interactions between biomolecules are determined by ______ interactions.
Polymers = COVALENTLY linked building blocks that are strong in structure
3D structure determined by NON-COVALENT interactions
Interactions of biomolecules determined by NON-COVALENT interactions
T/F :Each covalently liked peptide can form only 1 biomolecule with only 1 higher order function
False - every peptide chain have multiple possible folding outcomes that can occur
List 2 things that non-covalent interactions enable
- Transient, dynamic interactions
- Flexibility of structure & function
List 3 factors that non-covalent interactions influence:
- Formation & stabilization of structure of biomolecules
- Recognition/interactions between biomolecules
3, Binding of reactant to enzymes/proteins
List the 4 types of non-covalent interactions within biomolecules
- H-bonds
- Ionic (electrostatic) iteractions)
- Hydrophobic drive
- Van der Waa;s interactions
T/F: Many functional groups have H-bonding capacity
True
What groups can H bond with? (3x)
- Water molecules
- Groups in the same molecule (intramolecular)
- Groups in other molecules (intermolecular)
What is classic example of H-bonding in us?
Base pairing of nucleotides in DNA
A + T
C + G
H-bonds are critical for ______ of biomolecular structures.
Important for SPECIFICITY - fine tuning details (decides which 2 strands bond together)
T/F: H-bond is the main driving force for the formation of biomolecular structures
False - hydrophobic interactions are main drive for formation
H-bond doesn’t have anything to gain from changing from their default unfolded geometric state, so thats why it is not the driving effect
What are ionic interactions important for?
Important for relationship between biomolecules (attractions/repulsion)
Ionic/Electrostatic interactions between charged groups can have ______ forces (with opposite charge groups) or ______ forces (with similarly charged groups)
attraction = opposite charge
repulsion = same charge
What factor makes Ionic/electrostatic interactions weak instead of strong? (what is the reducing factor of ionic/electrostatic interactions?)
Cuz everything occurs in the context of water. The water creates a hydration layer around charged groups decreasing their charge and ability to interact with other molecules.
What are van der Waals forces? And where are they most abundant in biomolecules?
van der Waal - packing interaction / interactions between permanent & induced dipole (have short range & low magnitude)
Most abundant in the core of proteins
What is the Hydrophobic effect? Why is it important?
drive to have hydrophilic facing water and hydrophobic away from water
Main drive of formation of higher order biomolecular structures
(ex. protein folding)
This folding effect happens spontaneously, decreasing entropy (randomness)
Thermodynamics of Hydrophobic effect:
Introduction of non-polar/hydrophobic molecule results in spontaneous movement that ______ the entropy(randomness) of water. When multiple non-polar/hydrophobic molecules attach they, release water molecules, which ____ the entropy(randomness) of water. Canceling each other out
Hydrophobic introduced = decrease entropy of polypeptide
Polypeptide attach & water molecules released = increase entropy of water
Thermodynamics of Hydrophobic effect:
The folding of a polypeptide ______ the entropy of polypeptide BUT _____ the entropy of the associated water.
DECREASE = polypeptide entropy
INCREASE = water entropy
offset eachother
Ionization of Water:
What is the ion product of water (constant)?
What is the ionization equation of water?
Ion product = Kw = 1.0 x 10^-14 M^2
Eq. H2O <—-> (H+) (OH-)
Water has a limited ability to dissisacotiate into Hydrogen and hydroxyl ions
Kw = [H+] [OH-] OR 1.0 x 10^-14 M^2 = [H+] [OH-]
What does the pH represent?
pH tells you H+ ion con.
The pH of an aqueous solution reflects, on a logarithmic scale, the concentration of hydrogen ions: pH = -log [H+].
Explain the units used in the pH scale
pH is a log scale making a difference in 1 pH = 10x difference in H+ ion con.
What are the characteristics of strong & weak acids/base dissociation in biochem? And which can be calculated?
Strong acid/base = completely dissolve in water (happens mostly in digestive system)
Weak acid/base = partially dissolve/dissociate in water (can be calculated)
Ka= [H+] [CH3COO-] / [CH3COOH] expressed as pKa (pKa = -logKa)
What does pKa represent?
The pKa expresses, on a logarithmic scale, the relative strength of a weak acid or base, pKa = -log Ka.
Titration curves reveal the ____ of weak acids.
the pKa of weak acids
Weak acids occure in 2 forms: _______ weak acid or ______ conjugate base
protonated weak acid or unprotonated conj. base
How do you identify the pKa point on a titration graph? What does this point represent.
pKa point = midpoint of buffering regoin (on the verticle side of graph)
@ pKa point = you have equal amount protonated and unprotonated forms [pH = pKa]
How do you find the buffering regoin on titration curve?
Buffering region is one pH unit up & down from the pKa point on graph
When is a solution best able to resist change in pH?
when its pH = pKa
If your pH is below your pKa point = than your weak acid is in the ______ form (& cannot further donot proton)
pH is below pKa = weak acid in protonated form (no donating)
If your pH is above pKa point, it is in the ______ form already having donated its proton
pH above pKa = unprtotonated conj. acid
What does pKa tell you about a weak acid?
pKa tells us the pH at which the weak acid has been able to donate 1/2 protons
How would you identify the strength of weak acids, if given the pKa?
Higher pKa = weaker acid (it means the acid needs a high pH to donate )
Lower pKa = stronger acid (since it donated protons at such low pH levels)
How does an organism maintain a constant pH? Why is it important to maintain?
By using a buffering system
Changes in pH -> change in protonatino state
–> change strucutre & function
What is a buffer?
A buffer is a solution that resists changes in pH caused by the addition of acid or base.
The Henderson-Hasselback eq. describes the relationship between what parts of a solution?
- pH of the solution
2.pKa of weak acid - con. of weak acid [HA] & and conj base [A-]
