Foundations: Water, pH & Buffers

BCH 100 — Introductory Biochemistry · Dr. Radi

build Jul 17 · 18:59 · CC BY-NC-SA 4.0 · owned figures (RDKit / matplotlib / PyMOL)
Dr. Radi

By the end of this unit, you can…

  • Explain water's polarity and hydrogen bonding, and identify H-bond donors and acceptors
  • Describe the hydrophobic effect and its role in protein folding and membranes
  • Work with acids, bases, pH, pKa, the Henderson–Hasselbalch equation, titration curves, and buffer capacity
  • Explain how physiological buffers (bicarbonate) hold blood at pH 7.4
Dr. Radi

Today's route 🗺️

  1. Water — Polarity & Hydrogen Bonding
  2. The Hydrophobic Effect
  3. pH, Acids, Bases & pKa
  4. The Henderson–Hasselbalch Equation
  5. Titration Curves & Buffers
  6. Buffer Capacity & Blood
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1 · Water — Polarity & Hydrogen Bonding

"See why the bent, polar water molecule — and the hydrogen bonds it makes — is the stage every reaction in you plays out on."

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Water is bent, and that changes everything

Life happens in water. The molecule is bent, and oxygen hogs the shared electrons — so the O end goes slightly negative (δ−) and the H's go positive (δ+). A tiny magnet with a + end and a − end.

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The hydrogen bond

Point one water's δ+ hydrogen at another water's δ− oxygen and they stick — a hydrogen bond. The O–H is the donor; the O with its lone pairs is the acceptor. Each water can make four.

Spot the donor and acceptor — you'll see the exact same bond holding DNA's strands together and folding every protein.
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Water's superpowers all come from H-bonds

That one bond, multiplied by trillions, gives water its whole personality: ice floats (the open lattice is less dense), it's cohesive (surface tension, capillary rise), and it's the universal solvent that dissolves the salts and sugars of life.

Snowflake: Alexey Kljatov, CC BY-SA 4.0 · Water strider: Tim McCormack, CC BY-SA 3.0 (Wikimedia Commons)
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2 · The Hydrophobic Effect

"See why oil and water don't mix — and how that same push folds every protein and builds every membrane."

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Why oil and water refuse to mix

Drop something nonpolar in water and the water can't hydrogen-bond to it — so it wraps the intruder in an ordered cage. Cages cost entropy. So the nonpolar bits clump together, shrinking the surface and setting the trapped water free. Entropy wins.

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This is what folds a protein

That same shove is the main driver of protein folding: the greasy side chains bury themselves in a hydrophobic core, away from water, while the polar ones face out. Water isn't a bystander here — it's the force doing the folding.

Same logic builds every membrane — lipid tails hide from water, heads face it.
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3 · pH, Acids, Bases & pKa

"Set up the language of acids and bases — the pH scale, conjugate pairs, and what pKa really tells you."

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The pH scale

pH = −log[H⁺], so a low number means more H⁺ and more acidic. Each step is a 10× change — pH 2 has a hundred times the H⁺ of pH 4. Your blood sits tight at 7.4.

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Acids, bases & conjugate pairs

An acid gives up a proton (H⁺); a base takes one. Lose the proton and an acid becomes its conjugate base — the two differ by exactly one H⁺, so they always come as a pair.

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Strong vs weak — and what pKa means

A strong acid dissociates completely; a weak acid only partly, leaving most molecules intact. pKa measures that eagerness: a lower pKa = a stronger acid. Biochemistry runs almost entirely on weak acids and bases.

Weak is the point — only a partial giver can act as a buffer.
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4 · The Henderson–Hasselbalch Equation

"Turn the acid–base ratio into a pH with one equation — and see why pH = pKa is the magic point."

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One equation ties pH, pKa, and the ratio

The Henderson–Hasselbalch equation says the pH of a buffer is just its pKa plus the log of the ratio of base to acid. The punchline: when [A⁻] = [HA], that log is zero, so pH = pKa.

KNOW HOW TO USE THIS. Given any two of pH, pKa, and the ratio, you can always find the third.
Dr. Radi

Try one: an acetate buffer

Acetic acid has pKa 4.76. Mix in ten times as much acetate as acid — what's the pH?

pH = 4.76 + log(10/1) = 4.76 + 1 = 5.76
more conjugate base than acid → pH climbs one unit above the pKa
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5 · Titration Curves & Buffers

"Read a titration curve — find the pKa at half-equivalence, spot the buffer zone, and see how a buffer soaks up acid or base."

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The titration curve tells you the pKa

Add base to a weak acid and the pH climbs — but not evenly. At half-equivalence, half the acid is deprotonated so [A⁻] = [HA], which means pH = pKa right there. The flat stretch around it is the buffer zone; the steep jump is the equivalence point.

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What a buffer actually is

A buffer is a weak acid and its conjugate base sitting together. Throw in H⁺ and the A⁻ mops it up; throw in OH⁻ and the HA neutralizes it. Either way the pair absorbs the hit and the pH barely moves.

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6 · Buffer Capacity & Blood

"See when a buffer works best (pH near its pKa) and how your blood holds 7.4 with the bicarbonate system."

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A buffer works best near its pKa

A buffer's capacity — how much acid or base it can swallow — peaks when pH = pKa and fades fast on either side. The useful range is about pKa ± 1. Outside it, one side of the pair runs out and the pH lurches.

So you pick a buffer whose pKa is close to the pH you want to hold.
Dr. Radi

How your blood holds pH 7.4

Blood runs on the bicarbonate buffer: CO₂ + H₂O ⇌ H₂CO₃ ⇌ H⁺ + HCO₃⁻. Two organs steer the same equilibrium — the lungs blow off CO₂ in seconds, the kidneys tune HCO₃⁻ over hours. Together they pin blood at pH 7.4.

Inside cells the phosphate buffer (pKa ~6.8) and proteins do the job. Bicarbonate's low pKa (6.1) works only because it's an open system — lungs and kidneys keep topping it up.
Dr. Radi

Can you…?

  • ☐ explain water's polarity and hydrogen bonding, and identify H-bond donors and acceptors?
  • ☐ describe the hydrophobic effect and its role in protein folding and membranes?
  • ☐ work with acids, bases, pH, pKa, the Henderson–Hasselbalch equation, titration curves, and buffer capacity?
  • ☐ explain how physiological buffers (bicarbonate) hold blood at pH 7.4?

If any box stays empty, the practice site has a drill for it. 🧪

Dr. Radi