Interactions of Chemical Substances

structure of cytosine:

• Pyrimidine ring (six-membered ring with two nitrogens).

• Key functional groups:

  • Amine group (-NH₂) at C4

  • Keto group (=O) at C2

  • Nitrogens at positions 1 and 3.

How does hydrogen bonding affect boiling point?

✅ Effect:

• Hydrogen bonding creates strong intermolecular forces.

• More energy (heat) required to break these bonds → higher boiling point.

What is Fractional Distillation?

Fractional distillation is a separation technique used to separate a mixture of liquids with different boiling points.

Threonine structure:

Side chain (R group): CH(OH)CH₃ (hydroxyl + methyl group)

Serine structure:

"Serine is Simple" → Side chain is just –CH₂OH (simpler than threonine’s branched OH + CH₃).

isoleucine structure:

"Iso = Isomer of Leucine" → Isoleucine is a structural isomer of leucine (same formula, different arrangement).

structure of glucose:

• Aldehyde group (–CHO) at carbon 1 → makes glucose an aldose.

• 6 carbons with hydroxyl (–OH) and hydrogen (–H) groups in specific orientation.

Why is fluorine a stronger electron-withdrawing group than chlorine?

"F is Fierce (pure EWG), Cl is Compromise (EWG + resonance)."

Tryptophan structure:

Side chain (R group): CH₂ connected to an indole ring (aromatic).

How is pH related to hydronium ion concentration?

• pH = –log[H₃O⁺]

• [H₃O⁺] = 10^(–pH)

• Lower pH → higher [H₃O⁺] (acidic).

• Higher pH → lower [H₃O⁺] (basic)

What is a Colloid?

A colloid is a mixture where small particles (1–1000 nm) are dispersed throughout another substance, but they do not settle out or separate upon standing.

Ionic Solids and Electrolytes:

• Ionic solids (e.g., NaCl, KBr) consist of positive and negative ions held together by strong electrostatic forces.

• When dissolved in water (a polar solvent), these ionic bonds break due to ion-dipole interactions, separating into free ions.

• These free ions allow the solution to conduct electricity, forming an electrolyte solution.

weak vs. strong electrolyte:

• Strong electrolytes: Fully dissociate (e.g., NaCl, HCl).

• Weak electrolytes: Partially dissociate (e.g., CH₃COOH).

What is a Monoprotic Acid?

A monoprotic acid is an acid that can donate only one proton (H⁺) per molecule in an aqueous solution.

What are Strong Acids?

Strong acids are acids that completely dissociate (ionize) in water, releasing all of their protons (H⁺) and forming hydronium ions (H₃O⁺).

What are strong acids? Name the common ones.

Climb High in Chemistry, No Problems

(Cl: HCl, H: HBr, I: HI, C: HClO₄, N: HNO₃, P: H₂SO₄).

What are weak acids?

Weak acids are acids that partially dissociate (ionize) in water, releasing only some of their protons (H⁺).

Give examples of weak acids:

"A Funny Penguin Can Bake Cookies"

• A – Acetic acid (CH₃COOH)

• F – Hydrofluoric acid (HF)

• P – Phosphoric acid (H₃PO₄)

• C – Carbonic acid (H₂CO₃)

• B – Benzoic acid (C₆H₅COOH)

• C – HCN (Cyanide acid)

Is citric acid a strong or weak acid?

Citric acid is a weak, triprotic acid (not strong)

how is pka related to ph?

1. When pH = pKa:

   • The acid is 50% dissociated (equal acid and conjugate base concentrations).

   • This is the buffering point.

2. When pH < pKa:

   • Solution is more acidic (protonated form HA dominates).

3. When pH > pKa:

   • Solution is more basic (deprotonated form A⁻ dominates).

Henderson–Hasselbalch Equation:

pH = pKa+ log([HA/][A−]​)

Where:

• pKa = acid dissociation constant (strength of acid)

• [A⁻] = conjugate base concentration

• [HA] = undissociated acid concentration

what does a high and low pka mean?

• Low pKa → Strong acid (dissociates easily).

• High pKa → Weak acid (holds onto protons).

what is pKa?

acid dissociation constant (Ka) expressed on a logarithmic scale.

determines the strength of an acid - how easily it donates a proton (H⁺). How easily is dissociates.

What is pH?

a measure of how acidic or basic (alkaline) a solution is, based on the concentration of hydrogen ions (H⁺)/ hydronium ions (H₃O⁺) in the solution.

What is a Buffer?

A buffer is a solution that resists changes in pH when small amounts of acid (H⁺) or base (OH⁻) are added.

How Does a Buffer Work?

• Buffers are usually made of:

  • A weak acid (HA) and

  • Its conjugate base (A⁻).

• The weak acid neutralizes added base, and the conjugate base neutralizes added acid, keeping pH stable.

why does a triprotic acid have three pkas?

A triprotic acid has three pKa values because it can donate three protons (H⁺), each at a different stage of dissociation.

Which nucleotides are purines and which are pyrimidines?

Purines:

• Adenine (A)

• Guanine (G)
  → Two-ring structures

Pyrimidines:

• Cytosine (C)

• Thymine (T) (DNA)

• Uracil (U) (RNA)
  → One-ring structures

What determines the stability of DNA and RNA folded structures?

The number of G-C (guanine–cytosine) base pairs greatly affects the stability of both DNA and RNA.
This is because G≡C has three hydrogen bonds, compared to A=T (or A=U in RNA), which has only two.

What is Tm (melting temperature) in the context of DNA/RNA structure?

Tm is the temperature at which 50% of the nucleic acid molecules are denatured (unfolded) and 50% remain folded.
It reflects the thermal stability of the molecule — higher Tm means more stable structure.

What does it mean that galactose is a C-4 epimer of glucose?

Galactose and glucose are both six-carbon aldoses (hexoses), but they differ in the configuration around carbon 4 (C-4).
That’s why galactose is a C-4 epimer of glucose.

What are oxidation and reduction in organic/biological chemistry?

• Oxidation = Loss of electrons (or gain of oxygen / loss of hydrogen)

• Reduction = Gain of electrons (or gain of hydrogen / loss of oxygen)

Why is adding hydrogen a reduction?

• A hydrogen atom (H) consists of 1 proton and 1 electron.

• When a molecule gains hydrogen, it also gains the electron that comes with it.

• Gaining electrons = reduction.

What is NADH redox cycling, and why is it important?

NADH redox cycling refers to the continuous reduction and oxidation of NAD⁺/NADH in metabolic pathways:

• NAD⁺ is reduced to NADH when it accepts electrons (and a proton) during catabolic reactions like glycolysis and the citric acid cycle.

• NADH is oxidized to NAD⁺ when it donates electrons to the electron transport chain or during fermentation.