Lectures 4.2–4.4: Proteins, Nucleic Acids & Lipids

Protein

The workhorse molecules

Amino acid

Protein's monomer — central carbon + amino group (-NH3+) + carboxyl group (-COO-) + H + R-group

R-group

The variable "side chain" of an amino acid — its properties decide how the protein folds

Zwitterion (at pH 7)

Amino acids have +NH3 on one end and -COO on the other

Peptide bond

Links amino acids together (condensation reaction); chain has an N-terminus and a C-terminus

Primary (1°) structure

The SEQUENCE of amino acids; held by peptide bonds

Secondary (2°) structure

Alpha-helices and beta-pleated sheets; held by H-bonds BETWEEN THE BACKBONE only (NOT the R-groups!)

Tertiary (3°) structure

The overall 3D fold of ONE polypeptide; held by R-group interactions (H-bonds, ionic, disulfide bridges, hydrophobic effect)

Quaternary (4°) structure

Two or more polypeptides assembled together (e.g., hemoglobin = 4 subunits)

Disulfide bridge

A strong covalent S-S bond between two cysteines that locks a protein's shape

Hydrophobic effect in folding

Oily R-groups hide in the protein's center; polar ones face the water — this drives 3D shape

Denaturation

Unfolding a protein (by heat, pH change, urea) — it loses its function, like an egg white cooking

Sickle cell disease

ONE amino acid change (glutamate → valine) in hemoglobin → whole protein misfolds → disease. One residue matters!

Prion

A misfolded protein that makes OTHER proteins misfold too (dangerous!)

Chaperonin

A helper protein that gives new proteins a safe space to fold correctly

Nucleic acid

DNA and RNA — store, transmit, and express genetic information

Nucleotide

Monomer of nucleic acids = 5-carbon sugar + phosphate group + nitrogenous base

Purine

Double-ring bases — A and G (mnemonic

Pyrimidine

Single-ring bases — C, T, and U

DNA vs RNA bases

DNA = A, T, G, C | RNA = A, U, G, C (U replaces T)

Phosphodiester bond

Links nucleotides (5' phosphate to 3' OH); makes the sugar-phosphate backbone

5' end vs 3' end

5' end has a phosphate; 3' end has an -OH group — chains have DIRECTION

Chargaff's rule

In DNA, A = T and C = G (always pairs a big purine with a small pyrimidine)

A-T vs G-C H-bonds

A-T pairs with 2 hydrogen bonds; G-C pairs with 3 → GC-rich DNA is more heat-stable

Antiparallel

The two DNA strands run in opposite directions (one 5'→3', one 3'→5')

Complementary base pairing

A always with T (or U), C always with G — the secret behind DNA replication and transcription

Central Dogma

DNA → (transcription) → RNA → (translation) → protein. Information NEVER flows backward (protein can't make DNA/RNA)

DNA

Double-stranded, deoxyribose sugar, long-lived, hereditary, lives in chromosomes (humans = 46)

RNA

Single-stranded, ribose sugar, short-lived working copy; can fold into shapes (like tRNA) and some even act as enzymes (ribozymes)

Practice problem — 20% A, how much G?

A=20%, so T=20%. Leftover 60% splits evenly

Practice problem — complement of 5'-TAGCTCGAT-3'

5'-ATCGAGCTA-3' (complement AND reverse it!)

Other nucleotide jobs

ATP (energy), GTP, cAMP (signals), NADH (carries electrons)

Lipid

Not a polymer! Defined by being hydrophobic and made of hydrocarbons — fats, oils, phospholipids, steroids, waxes

Fatty acid

A long hydrocarbon chain with a carboxyl head (polar head, nonpolar tail)

Saturated fatty acid

NO double bonds — straight chains that pack tightly → SOLID at room temp (animal fats like butter)

Unsaturated fatty acid

Has double bonds that KINK the chain → can't pack → LIQUID at room temp (plant oils)

Polyunsaturated

Multiple double bonds (like linoleic acid)

Trans fat

An unsaturated fat straightened out so it packs like a saturated fat (the unhealthy kind)

Why is butter solid but olive oil liquid?

Packing! Saturated fats stack tightly; kinked unsaturated ones don't

Triglyceride

Glycerol + 3 fatty acids; joined by condensation forming ESTER bonds; stores 2x more energy per gram than carbs

Ester bond

The bond linking fatty acids to glycerol in fats

Phospholipid

Amphipathic molecule — hydrophilic HEAD + hydrophobic TAILS

Amphipathic

Having both a water-loving part and a water-fearing part

Phospholipid bilayer

In water, phospholipids form a double layer (heads out, tails hidden in) — this IS the cell membrane!

Micelle

A single-layer ball of lipids with tails hidden inside

Steroid

Lipids built from 4 fused rings — cholesterol (membranes), testosterone, cortisol, vitamin D

Hormone

A chemical messenger that travels through the bloodstream to control distant body parts