Introduction to Cell Biology & Biochemistry

Recap of Amino Acids

  • 4 Main Groupings of Amino Acid Side Chains:

    • Hydrophobic: Glycine (G), Alanine (A), Valine (V), Isoleucine (I), Leucine (L), Phenylalanine (F), Proline (P), Tryptophan (W), Methionine (M)

    • Polar but uncharged: Serine (S), Threonine (T), Tyrosine (Y), Cysteine (C), Asparagine (N), Glutamine (Q)

    • Positively charged (basic): Lysine (K), Arginine (R), Histidine (H)

    • Negatively charged (acidic): Aspartic acid (D), Glutamic acid (E), Tyrosine (Y), Cysteine (C)

  • Amino Acid Structure:

    • Contains a chiral α-carbon bonded to four different groups:

    • Amine group (positively charged)

    • Carboxylic acid group (negatively charged)

    • Hydrogen atom

    • R groups (20 different)

Classification of Amino Acids

  • Chemical Nature of R Groups:

    • Amino acids can be categorized based on the chemical composition of their R groups.

  • Multiple Classification Criteria:

    • A single amino acid can belong to different categories based on various classification criteria.

Aliphatic R Groups

  • Definition: R groups containing only carbon (C) and hydrogen (H) bonds with no double bonds.

  • Notable Amino Acids:

    • Glycine (G): Smallest amino acid, non-chiral (two hydrogen atoms attached to the α-carbon).

    • Alanine (A), Valine (V), Leucine (L) and Isoleucine (I): Stabilize protein structure via hydrophobic interactions, located generally in the protein interior.

    • Proline (P): Unique structure where its side chain (3 CH2) links back to the amino nitrogen, making it the only amino acid with a secondary amine.

Aromatic R Groups

  • Key Amino Acids:

    • Phenylalanine (F or Phe)

    • Tyrosine (Y or Tyr)

    • Tryptophan (W or Trp)

  • Features:

    • Contain aromatic rings:

    • Phenylalanine: benzene ring

    • Tyrosine: phenol ring

    • Tryptophan: indole ring

UV Absorbance of Amino Acids

  • Observation:

    • UV absorbance scale is logarithmic and non-linear.

    • Important for protein isolation.

    • Aromatic amino acids (W, Y, F) strongly absorb UV light in the order: W > Y > F.

Protein and DNA UV Spectra

  • Peak Absorbance:

    • Proteins: 280 nm

    • DNA: 260 nm

  • Concentration Impact:

    • DNA solutions absorb more UV than protein at the same concentration.

Side Chains with Alcohols (-OH)

  • Key Alcohol-Containing Amino Acids:

    • Serine (S or Ser)

    • Threonine (T or Thr)

    • Tyrosine (Y or Tyr)

Sulfur-containing Amino Acids

  • Included Amino Acids:

    • Methionine (M or Met)

    • Cysteine (C or Cys)

  • Chemical Structure:

    • Cysteine can form disulfide bonds.

Disulfide Bond Formation

  • Two Cysteine Residues:

    • Can undergo oxidation to yield cystine:

    • NH2-CH( ext{CH}2)-SH + HS-CH_2-CH( ext{COOH}) o ext{Cystine} + 2H^+ + 2e^-

    • The resulting disulfide bond is essential for protein structure and protein-protein interactions.

Basic Amino Acids

  • Positively charged at pH 7:

    • Lysine (K or Lys)

    • Arginine (R or Arg)

    • Histidine (H or His)

  • Basic Group Behavior:

    • Basic group (R-NH2) is positively charged only at pH below its pKa.

  • pKa Understanding:

    • pK_a defines the ratio between protonated (-NH3+) and unprotonated (-NH2) forms.

    • At high pH (alkaline), basic groups lose protons and become uncharged.

Acidic Amino Acids

  • Included Amino Acids:

    • Aspartate (D or Asp)

    • Glutamate (E or Glu)

  • Properties:

    • Negatively charged at pH 7 due to the presence of carboxylic acid groups.

    • Amide forms include Asparagine (N or Asn) and Glutamine (Q or Gln).

Acid-Base Behavior of Amino Acids

  • Acidic Conditions:

    • Acid groups (-COOH) remain protonated and uncharged at low pH.

  • Ionization:

    • As pH rises, acid groups become deprotonated and negatively charged.

  • pKa Measurement:

    • Defines acid strength: lower pKa means stronger acid.

Atypical Amino Acids

  • Examples:

    • UGA (opal) and UAG (amber): recognized by rare tRNAs, usually act as stop codons.

Post-Translational Modifications of Amino Acids

  • Post-Translational Modifications:

    • Many amino acids can be modified after their incorporation into proteins resulting in significant cellular functions.

    • Example: Ca2+ binding in prothrombin, stability in collagen.

Charged Forms of Amino Acids

  • Behavior in Solution:

    • Amino acids exist in uncharged or charged forms, typically ionized in solution.

  • Zwitterionic Form:

    • Represents a hybrid form where amino acids can donate or accept protons.

Summary of Zwitterion Concept

  • Definition:

    • The term 'zwitterion' derives from the German word for 'hybrid'. The molecule carries both positive and negative charges but is overall neutral.

  • Behavior:

    • Can act as both proton donors and acceptors depending on the pH of the surrounding environment.