BIOC 2580 week 1

general things to remember

What are the four major classes of biomolecules?

Proteins, Nucleic acids, Carbohydrates, Lipids.

Which element is the backbone of biomolecules and why?

Carbon — forms 4 covalent bonds and stable chains/rings.

What are the three major types of weak interactions in biological systems?

Hydrogen bonds, van der Waals interactions, ionic (electrostatic) interactions.

Why are weak interactions essential in biochemistry?

They are easily reversible and allow molecular recognition (e.g., enzyme–substrate, DNA base pairing).

What drives macromolecular folding?

The hydrophobic effect — nonpolar molecules cluster to minimize contact with water.

What is the structure of water?

Bent molecule (104.5°), polar covalent bonds, capable of forming 4 H-bonds per molecule.

What are hydrophilic vs hydrophobic substances?

Hydrophilic = polar/ionic; hydrophobic = nonpolar (e.g., hydrocarbons).

Define amphipathic molecules.

Contain both polar (hydrophilic) and nonpolar (hydrophobic) regions (e.g., phospholipids).

pH formula

pH= -log[H+]

Henderson–Hasselbalch Equation

pH=pKa+log[De]/[Pro]

Dep/Pro = a/1-a

Deprotonated=protonated

50/50

If pH > pKa, which form predominates?

Deprotonated

If pH < pKa, which form predominates?

Protonated

General structure of an α-amino acid?

Central (α) carbon bonded to H, carboxyl (–COOH), amino (–NH₂), and R-group side chain.

What are the 5 categories of amino acids based on R-group polarity?

• Nonpolar (hydrophobic)

• Moderate non polar

• Polar uncharged

• Acidic (negatively charged)

• Basic (positively charged)

Which amino acid has no chiral center?

Glycine 

Which amino acid forms disulfide bonds?

Cysteine

What is the significance of Proline’s cyclic structure?

Restricts backbone flexibility; introduces kinks.

What is the isoelectric point (pI)?

The pH where the amino acid has a net charge = 0.

Formula for pI (neutral amino acids):

pI= pKa1​+pKa2​​/2

At pH < pI → amino acid is mostly

Positively charged (protonated).

At pH > pI → amino acid is mostly

Negatively charged (deprotonated).

What is a zwitterion?

Molecule with both positive (NH₃⁺) and negative (COO⁻) charges but overall neutral.

What reaction forms a peptide bond?

Condensation (dehydration) between α-COOH and α-NH₂ → releases H₂O.

Peptide bond characteristics?

Planar, partial double bond (resonance), usually trans configuration.

What reaction breaks a peptide bond

hydrolysis water is added

Direction of peptide chain?

N-terminus → C-terminus.

Amino acids that are protonated = to 0 de protonated = to -1

Aspartate

Glutamate

Tyrosine

Cysteine

Amino acids that are protonated = to +1 de protonated = to 0

Histidine

Lysine

Arginine

Proteins are

chain of amino acids

# of amino acids

# of amino acids = Protein MW/ 110

# of hydrogen bonds

n-4