Ch. 2.1, 2.2, 2.4 Water Structure & Reactivity, pH & pKa, Osmosis, Diffusion, Buffers

Structure of H2O

electron geometry = tetrahedral, molecular geometry = bent, sp3 oxygen, polar covalent bonds

HIGHLY polar molecule, hydrophilic (interacts with itself), readily dissolves charged & polar molecules.

Biomolecules adopt their shapre based on their ability to interact or NOT interact with H2O (Ex. cell membrane hydrophobic lipids). Liquid medium that transports.

Solvation of ion

Solvent molecules surround and stabilize an ion through favorable interactions. This is called HYDRATION when water is the solvent. The water molecules interacting with the ion/polar group are the waters of hydration. Occurs after dissociation

Dielectric constant

measure of how well a medium reduces (screens) electrostatic interactions between charged particles. How much a solvent weakens attractions between charges. Water has a high dielectric constant.

• Prevents oppositely charged biomolecules from collapsing together

• Enables dissolution of ionic compounds

• Stabilizes solvated ions

• Prevents aggregation and precipitation

All biomolecules adopt their shaped based on their ability to interact/ not interact with

Water

1 water molecule can make how many hydrogen bonding interactions

4 total interactions

2 from hydrogen acceptor oxygen (2 lone pairs)

2 from hydrogen donor hydrogens (2 hydrogens)

Why are hydrogen donors weakly acidic?

The hydrogen involved in a hydrogen bond carry a small partial (+) charge and can be shared electrostatically, but it is not released as a free proton (H+). Weakly acidic means SLIGHTLY willing to give up electron density (to EN atom bonded to). Acidity (Brønsted–Lowry) = ability to donate a proton (H⁺).

What factors influence an atom being a hydrogen acceptor?

ionic state (charge) and resonance, available lone pairs

When are the strongest H-bond observed?

When the donor atom and acceptor atom are oriented ina straight line with one another (180 degrees).attractive force is strongest because it acts along the bond axis

• Any bending reduces how directly the charges face each other.

• The acceptor’s lone-pair orbital overlaps best with the σ* (antibonding) orbital of the X–H bond.

• Electron clouds are best arranged to minimize repulsion.

Hydrophobic interactions

Non-polar groups associating with one another that excludes water. When hydrophobic groups associate/cluster, hydrophobic surface exposed to water decreases and the overall ordering of water decreases since only the lipid edge forces ordering. H2O molecules are released from cages and return to bulk (more disorder means ΔS = (+)). No intermolecular interactions between hydrophilic and hydrophobic…only between the same.

Although individual nonpolar groups cause water molecules to become highly ordered, hydrophobic interactions reduce the total amount of ordered water by clustering nonpolar groups together, thereby increasing disorder and entropy.

What effect plays role in 3-D form adopted by proteins and lipids?

hydrophobic effect

Amphipathic

Molecules that are both hydrophobic and hydrophilic caused by having polar and nonpolar regions within the same molecule.

Phospholipids

• Hydrophilic head (phosphate + charged/polar groups)

• Hydrophobic tails (fatty acid chains)

Fatty acids

• Hydrophilic carboxyl group (–COO⁻)

• Hydrophobic hydrocarbon chain

Proteins

• Hydrophobic amino acids (Leu, Val, Phe)

• Hydrophilic amino acids (Asp, Lys, Ser)

What are hydrophobic interactions and why are these favorable interactions in an aqueous
environment?

Hydrophobic interactions are the association of hydrophobic molecules or regions of
molecules with other hydrophobic molecules. These are favorable interactions in an
aqueous environment since there is an increase in entropy of the water molecules as
compared to having the water molecules in an ordered array around the hydrophobic
regions (since the polar water molecules cannot interact with the nonpolar molecules).

Which forces contribute most to the overall form of biomolecules?

covalent bonding and hydrophobic interactions

Explain why hydrophobic interactions are formed and favorable in a biological system?

Hydrophobic groups interact with one another and exclude water from interacting with the
hydrophobic groups; this interaction would force water into a “Caged” or highly ordered
arrangement around the hydrophobic groups. Hydrophobic interactions are favorable
because it increases the entropy of the water system (lessens the “caged” water formation)
and in biological systems there is an abundance of water

How is an amphipathic molecule able to exist in a mostly water environment?

The hydrophobic portions associate with one another on the inner part of the molecule
away from the water while allowing the hydrophilic portions of the molecule to interact
with water and be faced outwards towards the water. The interactions between the
hydrophobic outer surface and water make the molecules soluble (able to exist) in a mostly
water environment.

Buffer

Solution that resists changes in pH when small amounts of acid or base are added by neutralizing them. pH changes slightly but buffer minimizes change. Must contain a weak acid and its conjugate base (or weak base and conjugate acid) since they partially dissociate. Additional ions added to the solution will alter the conjugate base to acid ratio and not the pH of the solution.

HA ⇌ (H+) + (A−)

When acid (H⁺) is added:

• Conjugate base (A⁻) absorbs H⁺

• (A−) + (H+) → HA

When base (OH⁻) is added:

• Weak acid (HA) neutralizes OH⁻

• HA + (OH−) → (A−) + H2​O

Added acid/base is “soaked up”

Does not work if too much acid/base is added or too far from its pKa. Work best when pH ~ pKa since Both HA and A⁻ are present in significant amounts…buffer can respond to both acid and base additions.

Henderson-Hasselbalch describes buffer pH:

pH=pKa​+log([A-]/[HA​)​

This tells you:

• pH depends on the ratio, not absolute amounts

• Equal amounts → pH = pKa

You have a buffer if you see:

• Weak acid + salt of its conjugate base

• Weak base + salt of its conjugate acid

• Ex. H₃PO₄ + KH₂PO₄

Polyprotic acids

Some acids donate more than one proton.

Example: phosphoric acid

H3​PO4 ⇌ (H+) + H2​PO4−​ (pKa 1)

H2​PO4−​ ⇌ (H+) + HPO42−​ (pKa 2)

Each step:

• Has its own pKa

• Forms a different buffer pair

Effective buffer range

+1 -1

Why is maintaining pH (Buffers) important?

pH will alter the structure and function of biomolecules

Henderson-Hasselbalch

Finds buffer pH

pH=pKa​+log([A-]/[HA​)​

Phosphate buffer

Phosphoric acid has 3 acidic protons and 3 different pKa values

the pKa2 for phsphate is 7.2

(H2PO4-) ⇌ (HPO4 2-) + (H+)

Most cells have a pH of 6.9—7.4

Good physiological buffer. Bicarbonate (H2CO3 in blood) also good

Bicarbonate buffer

pH of blood ~ 7.4

Bicarbonate = HCO3-

Carbonic acid (H2CO3) is formed by CO2 reacting with water. Can then form bicarbonate ion.

(CO2) + (H2O) ⇌ (H2CO3) ⇌ (H+) + (HCO3-)

High levels of CO2 in the lungs and blood stream = respiratory acidosis

Low levels of CO2 in the lungs and blood stream = repiratory alkalosis

Ka

Equilibrium/acid disociation constant. How much an acid donates a proton in water.

HA + H2​O ⇌ (H3​O+) + (A−)

Ka= [H3O+][A−] / [HA]

• Large Kₐ → lots of dissociation → stronger acid

• Small Kₐ → little dissociation → weaker acid

Tells you how far the equilibrium lies to the right.

pKa= -log(Ka)

• Large Kₐ → small pKₐ → strong acid

• Small Kₐ → large pKₐ → weak acid

Osmosis

movement of WATER (solvent) to region where solute concentration is higher

solute does not move, more controlled passage

Osmotic pressure: pressure is proportional to the concentration of the solute, prevents osmosis

How do cells regulate osmosis?

pump ions or water out of cell

cell wall is effective osmosis regulator for plant and bacteria

Diffusion

Random movement of molecules until concentrations equal (at equilibrium) in two regions

Occurs at different rates depending on

1. distance traveled by molecule to diffuse

2. viscosity (more viscous = slower rate)

Dialysis

Lab teqnique that exploits the principle of diffusion. Controlled diffusion.

Can use dialysis to get a protein or nucleic acid to exchange solvent components of separate from a smaller contaminating molecule.

Why Dialysis?

1. Get purified sample. Can isolate a large molecule from contaminants.

2. Storing a molecule in a way that makes is stable over time. Slowly change a molecules solution to one that’s better for storage (like solution higher in salt or more viscous).

3. Measure how strongly 2 molecules interact with one another based on how easy it is to separate them using dialysis.

Hydrolysis Reaction

Water molecule consumed as another molecule is broken apart

Ex. destruction of a protein by breaking the amind bond and releasing individual amino acids, break down of ATP to ADP and Pi

When water is used and breaks bonds

hydrolysis

When water is made and makes bonds

condensation

Condensation Reaction

Water molecule is produced and two separate molecules are joined by a covalent bond

Ex. formation of a protein by amino acids forming an amide bond, formation of ATP from ADP an Pi

Phosphoanhydride bond

HYDROLYSIS

water consumed, phosphate bond broken, ADP and Pi formed

ATP + H₂O → ADP + Pi (inorganic free phosphate group)

anhydride=phosphate to phosphate

occurs throughout the cell wherever energy is required

ATP → ADP

Hydrolysis

Phosphate ester bond

HYDROLYSIS

water consumed, phosphate carbon bond broken (dephosphorylation), alcohol and Pi formed

R–O–PO₃²⁻ + H₂O → R–OH + Pi

Ester=attached to carbon

Carboxylate ester bond

HYDROLYSIS

water consumed, carboxylic acid and alcohol formed

Ester + H₂O → Carboxylic acid + Alcohol

Acyl phosphate bonds

HYDROLYSIS

water consumed, carboxylic acid and Pi formed

Reactivity of water

water “neutral”, but theres also water molecules that constantly react with one another

H2​O ⇌ (H+) + (OH−)

Free H+ does not exist by itself in water.

Instead, it instantly binds to another water molecule:

(H+) + H2​O → H3​O+

Hydronium (H3O+) = the true “acid” in water

Why do acid-base reactions in water occur quickly?

proton hopping along a string of H-bonds

Kw (Keq)

Ionization/dissociation constant of water

H2​O ⇌ (H+) + (OH−)

Kw= [H+][OH-]

Kw= 1.0×10^-14

Kw= [1.0×10^-7][1.0×10^-7]

• Water ionizes very weakly

• Only a tiny amount of (H+) and (OH−) exist at any moment

Pure water

[H+] = [OH-]

pH

concentration of hydrogen (H+) ions in solution. reflects how acidic or basic a solution is.

pH= -log[H+]. If [acid]>10^-6, ignore water ionization. If acid has lower concentration than this, add concentration of water (1.0×10^-7M), then solve for pH.

[OH−]=10^−pOH

[H+]=10^−pH

Ionization of H2O

1.0×10^-7M

Acid

1. Arrhenius: produces H+ ions in water (only aq solutions)

2. Bronsted-Lowry: proton (H+) donor.

3. Lewis: electron pair acceptor.

Base

1. Arrhenius: produces OH- ions in water (only aq solutions)

2. Bronsted-Lowry: proton (H+) acceptor.

3. Lewis: electron pair donor.

pKa

pKₐ = −log₁₀(Kₐ)

Measures acid strength. How tightly an acid holds onto its proton.

• Low pKₐ → lets go easily → strong acid

• High pKₐ → holds tightly → weak acid

• If pH < pKₐ → acid is mostly protonated

• If pH > pKₐ → acid is mostly deprotonated

• If pH = pKₐ → 50% protonated / 50% deprotonated

• Acetic acid: pKₐ ≈ 4.8

• Hydrochloric acid: pKₐ ≈ −7 (very strong)

• Water: pKₐ ≈ 15.7 (very weak)

Proton donor

Acid

Proton acceptor

Base

Conjugate acid

Gains H+

Conjugate base

Loses H+

Ka

Acid dissociation constant

Ka​= [HA][H+] / [A−]​

• Large Ka​ → acid dissociates a lot → strong acid

• Small Ka​ → little dissociation → weak acid

Acid type	Ka	What it means
Strong acid	Ka ≫ 1	Mostly dissociated
Weak acid	Ka < 1	Mostly remains HA

DAB

Donate = Acid, Accepts = Base

Monoprotic acid

can donate 1 proton

CH₃COOH

Only the H on the OH is acidic and can be donated

pH ≈ pKₐ

If pH= pKa + log([A-]/[HA]

and pH ~ pKa

then log([HA]/[A−]​) ≈ 0

[HA]/[A−] ​≈ 1

[A⁻] ≈ [HA], the solution can:

• Neutralize added acid (A⁻ grabs H⁺)

• Neutralize added base (HA donates H⁺)

This is the point of maximum buffering capacity.