BIOCHEM 2BB3 Chapter Notes - Chapter 2: Ammonia, Borax, Chief Operating Officer

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Water Molecules and H-Bonds
- Role water: solvent for other molecules, and helps determine their shape and reactivity’s
- Living organisms can be found where there is water
Ex. Methanococcoides burtonii in polar ice caps
Ex. Pyrolobus fumarii in hydrothermal vents
- Can participate up to 4 H-bonds ~tetrahedral geometry during H-bonding
- Ice: Water molecule participates in 4 H-bonds
- Liquid: up to 4 H-bonds, with lifetime of 10-12s = structure of water is continually flickering as molecules rotate, bend
and reorient themselves
H going from liquid solid, is negative
oFlickering: short-lived groups of water molecules due to constant breaking and reforming of H-bonds (the
H from one molecule will move to the next water molecule, and the rest will shift over, constantly)
- High surface tension
- Why it’s liquid whereas similar-sized molecules are gaseous at 25’C
- Less dense when liquid: molecules must interact at a specific orientation
Electrostatic Forces: Covalent stronger > Ionic > H-bond > Van der Waal
Covalent bonds
- Strong covalent bonds define molecular constitution
- Weak noncovalent bonds govern 3D shape and molecular interactions
Electronegativity- measure of an atom’s affinity for electrons
- N—H, O—H, S—H
oCan occur between particles that are polar but not charged (Ex. carbonyl groups)
- 2.8A- 3.0A: distance between radii = in H-bonding
- Carbon does H-bonds; not often but it can- the distance between two C’s with H in the middle is shorter than van der
Waal’s distance => that it’s in H-bonding
- Fluorine doesn't H-bond: it has a longer lifetime than 10^-12 lifetime, and s it’s not really considered H-bonding?
Van der Waal
- Occur b/w dipoles/polar groups due to random fluctuations of charge
oCan occur b/w nonpolar groups (Ex. methyl groups)
Ex. 3.7 A: sum of van der Waal’s radii (when an H is between two electronegative atoms,
the distance between the radii are 3.7 A = they are in van der Waal’s)
Water Dissolving Compounds
Dielectric constant- measure of solvent’s ability to diminish the electrostatic attraction between dissolved ions
- Higher the constant, the lower the ability for ions to interact
Ex. The attraction between the polar water molecules and Na+ and Cl- are > than attraction b/w Na+ and Cl-, NaCl
dissolves (each solute ion is surrounded by water molecules, solvated)
- Molecules with a polar or ionic functional group are readily solubilized
Ex. Glucose: highly soluble in water
Within a cell, there is ~ enough space for 2 water molecules around each solute, acting as a coating, to allow the
molecules slide past each other = maintain a crowded yet fluid state.
- Solubility: thermoenergy makes them move randomly but energetics? Make them want to stay together because their
velocity slows down, making it easier for them to interact and thus, forming dimers, and trimers...
The Hydrophobic Effect
Ex. Benzene in water, benzene will separate out into benzene (nonpolar) phase, and there will be a water phase
-DeltaH can be negative or DeltaS(T) are positive (making a number negative)? It’s TDeltaS
- To go from a polar nonpolar phase, it is driven by TDeltaS- entropy
- Thermodynamically unfavourable to forcefully dissolve a hydrophobic substance water
oEnthalpy needed to break the H-bonds among solvent water molecules in order to create a hold into which
a nonpolar molecule can fit but that energy barrier mostly depends on entropy
When the hydrophobic molecule is hydrated, the water around the solute must orient itself in a
way so that its facing way from the hydrophobic molecule = the constraint on the structure of
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water represents a loss of entropy in the systems, as those water molecules lost some freedom to
form, break and re-from H-bonds with other molecules
- It’s entropy of water that drives hydrophobic effects
oThought that this contributes to protein folding
Hydrophobic effect: the exclusion of nonpolar substances from an aqueous solution
- Therefore, hydrophobic molecules aggregate because entropy-wise, it’s unfavourable otherwise
Amphiphilic Molecules: Hydrophilic and Hydrophobic Effect
The polar groups of amphiphiles orient themselves toward the solvent molecules and are therefore hydrated, while the
nonpolar groups tend to aggregate due to the hydrophobic effect = form a micelle: a particle with a solvated surface and a
hydrophobic core.
- Micelles have 1-tailed lipids, and bilayers have 2-tailed lipids
- Can sometimes form bilayers instead of micelles
oThermodynamically favoured: H-bonding capabilities of the polar heads can interact with solvent water
molecules and the nonpolar tails are hidden from the solvent
oAs T drops, the membrane becomes leaky
The Hydrophobic Core of Lipid Bilayer: Barrier to Diffusion
-Vesicle: lipid bilayer closing up, trapping aqueous solution and hydrophobic solutes (too much energy to pass through
the hydrophobic barrier to leave the vesicle; small, nonpolar can leave easily)
-A barrier such as a bilayer can prevent diffusion from high
low concentrations
oHow cells can maintain [substances] different from external [substances]
Intracellular: [K+] > [Na] and [Cl-]
Extracellular: [K+] < [Na] and [Cl-]
Acid-Base Chemistry
- Aqueous solutions do not have a lone H+ atom, but rather, form a hydronium ion (H3O+), but it’s still somewhat
dissociated in that state => proton jumping
oEffective mobility of H+ in water is greater that the mobility of other ions that must physically diffuse
- Acid-base reaction are faster than biochemical reactions
[H+] and [OH-]
- Kw: the ionization constant of water = 10-14
- pK = -logKa
- The larger an acid’s Ka, the smaller the pK and the stronger the acid
- Polyprotic acid has several Ka values for each H dissociation
oThe first H has the lowest Ka, as subsequent protons are more
difficult to dissociate
pH of a Solution
- pH = -log[H+]
-Acids donate a proton and bases accept a proton
- The pH of a solution of acid depends on the pK and the concentrations of the
acid and its conjugate base
-Henderson-Hasselbalch eqn: pH = pK + log[A-]/[HA]
oPredict pH or [acid] and [its conjugate base] at a given pH
- The functional groups on molecules act as acids and bases
opH < 4: —COOH, —NH3+
Ie. pH below for, carboxylic and amino groups are protonated
o4 < pH < 10: —COO-, —NH3+
opH > 10: —COO-, —NH2
- When the pH is higher than the molecule’s pK, then they start to become
- The affinity of a proton is dependent on what’s attached to it
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