Cell Bio Lecture 3

Alanine

Ala A

Arginine

Arg R

Asparagine

Asn N

Aspartate

Asp D

Cysteine

Cys C

Glutamate

Glu E

Glutamine

Gln Q

Glycine

Gly G

Histidine

His H

Isoleucine

lle I

Leucine

Leu L

Lysine

Lys K

Methionine

Met M

Phenylalanine

Phe F

Proline

Pro P

Serine

Ser S

Threonine

Thr T

Tryptophan

Trp W

Tyrosine

Tyr Y

Valine

Val V

D vs L Amino Acids

• Proteins are composed almost exclusively of L-amino acids

• D- vs L- refers to the stereochemistry (orientation) around the α-carbon, NOT the amino acid identity

• Aspartate (Asp) vs Leucine (Leu) = different amino acids

• D vs L = mirror-image forms of the SAME amino acid

Important Notes:

• L-amino acids → used in ribosomally synthesized proteins

• Some D-amino acids have biological functions, but are NOT incorporated into human proteins

  • Examples:

    • Bacterial cell walls (peptidoglycan)

    • Neurotransmission/modulation (rare in humans)

Exam Tip 🧠:

If the question is about protein structure or synthesis → choose L-amino acids

Glycine

(Gly, G) Nonpolar, hydrophobic

• R-group: H (smallest amino acid)

• Achiral (only amino acid without chirality)

• Provides flexibility in protein

Alanine

(Ala, A)Nonpolar, hydrophobic

• R-group: CH₃

• Small, commonly found in α-helices

Valine

(Val, V) Nonpolar, hydrophobic

• R-group: branched isopropyl

• Branched-chain amino acid (BCAA)

Leucine

(Leu, L) Nonpolar, hydrophobic

• R-group: branched isobutyl

• BCAA, very hydrophobic

Isoleucine

• Nonpolar, hydrophobic

• R-group: branched alkyl

• BCAA, chiral side chain

Methionine

• Nonpolar, hydrophobic

• R-group: sulfur-containing thioether

• Start codon (AUG) amino acid

Phenylalanine

• Nonpolar, hydrophobic

• R-group: benzyl (aromatic)

• UV absorbance contributor

Tryptophan

• Nonpolar, hydrophobic

• R-group: indole ring

• Strong UV absorbance (280 nm)

Proline

• Nonpolar, hydrophobic

• R-group: cyclic, binds amino group

• Helix breaker (rigid structure

Serine

• Polar, uncharged HYDROPHILIC

• R-group: –CH₂OH

• Phosphorylation site

Threonine

• Polar, uncharged HYDROPHILIC

• R-group: –CH(OH)CH₃

• Phosphorylation site

Cysteine

• Polar, uncharged HYDROPHILIC

• R-group: –SH (thiol)

• Forms disulfide bonds

Tyrosine

• Polar (aromatic) HYDROPHILIC

• R-group: phenol

• Phosphorylation site, UV absorbance

Asparagine

• Polar, uncharged HYDROPHILIC

• R-group: amide

• N-linked glycosylation site

Glutamine

• Polar, uncharged HYDROPHILIC

• R-group: amide

• Nitrogen donor in metabolism

Aspartate

• Polar, charged, HYDROPHILIC

• Negatively charged (acidic)

• R-group: carboxylate (–CH₂–COO⁻)

• Frequently found in enzyme active sites

Glutamate

• Polar, charged, HYDROPHILIC

• Negatively charged (acidic)

• R-group: longer carboxylate (–CH₂–CH₂–COO⁻)

• Major excitatory neurotransmitter

Lysine

• Polar, charged, HYDROPHILIC

• Positively charged (basic)

• R-group: long alkyl chain ending in –NH₃⁺

• Common in DNA-binding proteins

Arginine

• Polar, charged, HYDROPHILIC

• Positively charged (basic)

• R-group: guanidinium group

• Strongest base among amino acids

Histidine

• Polar, charged, HYDROPHILIC

• Weakly basic (can be + or neutral at physiologic pH)

• R-group: imidazole ring

• Important for pH buffering & enzyme catalysis

How pH Affects Amino Acid Side-Chain Ionization

• pH determines the protonation state of ionizable side chains

• Ionizable amino acids: D, E, R, K, H, C, Y, S, T

• Each ionizable group has a pKa

  • pH < pKa → protonated

  • pH > pKa → deprotonated

Key Concepts:

• Titration curve shows stepwise loss of protons as pH increases

• Plateaus = buffering regions (near pKa values)

• Isoelectric point (pI):

  • pH where net charge = 0

  • Occurs between pKa values surrounding the neutral species

Charge Trends:

• Acidic side chains (D, E):

  • Low pH → neutral

  • High pH → negative

• Basic side chains (K, R, H):

  • Low pH → positive

  • High pH → neutral

Exam Tip 🧠:

Compare pH to pKa to predict charge — don’t memorize charge blindly