Amino Acids & Proteins

Amino Acids & Proteins

Learning Objectives

• Describe the basic structure of an amino acid.

• Understand amino acid stereochemistry.

• Classify amino acids based on chemical properties.

• Differentiate between essential and non-essential amino acids.

• Relate the role of amino acids to protein structure and function.

Biomolecules

• Proteins, nucleic acids, polysaccharides, lipids are biomolecules.

• All contain carbon.

• Building blocks of proteins = Amino Acids.

Amino Acids

• Most common organic molecule in the body.

• 20 commonly found in mammalian proteins.

Amino Acid Structure

• Except for proline (an imino acid), amino acids have:

  • Carboxyl group

  • Amino group

  • R group (side chain)

• Function of amino acids depends on these groups.

Structure Breakdown

• Amine group: -NH_2

• Variable group: R

• Carboxyl group: -COOH

Chirality of Amino Acids

• Enantiomers are nonsuperimposable mirror images.

• Alanine example shows L and D forms.

Glycine: An Exception

• Glycine is achiral because its R group is H.

• Structure: H_2N-C-COOH

Amino Acid Stereochemistry

• Focus on the position of the amine group.

• D-amino acids are more common in bacterial cell walls.

• L-amino acids are more common in human proteins.

Amino Acid Stereochemistry and pH

• Alanine in acid, neutral, and basic solutions.

• Form I (acid solution, pH < 2): Net charge = +1

• Form II (neutral solution, pH ≈ 6, isoelectric form): Net charge = 0

• Form III (basic solution, pH > 10): Net charge = -1

• pK1 = 2.3 and pK2 = 9.1

Amino Acid Abbreviations

• AAs with a unique 1 letter code:

  • Cysteine - Cys, C

  • Histidine - His, H

  • Isoleucine - Ile, I

  • Methionine - Met, M

  • Serine - Ser, S

  • Valine - Val, V

• Commonly occurring AAs:

  • Glycine - Gly, G

  • Alanine - Ala, A

  • Leucine - Leu, L

  • Proline - Pro, P

  • Threonine - Thr, T

• AAs with phonetic abbreviations:

  • Arginine - Arg, R (aRginine)

  • Asparagine - Asn, N (asparagiNe)

  • Aspartic Acid - Asp, D (asparDic acid)

  • Glutamic Acid - Glu, E (glutEmic acid)

  • Glutamine - Gln, Q (Qtamine)

  • Phenylalanine - Phe, F (Fenylalanine)

  • Tyrosine - Tyr, Y (tYrosine)

  • Tryptophan - Trp, W (tWiptophan)

  • Lysine - Lys, K (letter Klose to L)

Classification of Amino Acids

• Hydrophobic:

  • Aliphatic: Gly, Ala, Val, Leu, Ile, Pro, Met

  • Aromatic: Trp, Phe, Tyr

• Hydrophilic:

  • Hydroxyl (-OH): Ser, Thr, Tyr

  • Sulfhydryl (-SH): Cys

  • Carboxyamide: Asn, Gln

• Ionic:

  • Acidic: Asp, Glu

  • Basic: Lys, His, Arg

Hydrophobic Amino Acids

• Aliphatic R-groups: Glycine, Alanine, Valine, Leucine, Isoleucine, Proline, Methionine

• Aromatic R-groups: Tryptophan, Phenylalanine

Hydrophilic Amino Acids

• Hydroxyl R-groups (-OH): Serine, Threonine, Tyrosine

• Sulfhydryl R-groups (-SH): Cysteine

• Carboxyamide R-groups: Asparagine, Glutamine

Ionic Amino Acids

• Acidic R-groups: Aspartic acid, Glutamic acid

• Basic R-groups: Arginine, Lysine, Histidine

• BAAD = Bases Accept H^+, Acids Donate H^+

Essential, Semi-, and Non-Essential Amino Acids

• Essential:

  • Not synthesized in the body, needed in the diet.

  • Phe, Val, Thr, Trp, Leu, Ile, Met, His, Lys

  • PVT TIM HALL

• Semi-essential:

  • Needed in adolescents, but not in adults.

  • Arg

  • PVT TIM HALL, always ARGues, never TYRes

• Non-essential:

  • Synthesized in the body, not needed in the diet.

  • Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, Pro

  • All other amino acids

Peptide Bonds

• Formed through dehydration (condensation).

• Bond between the carboxyl group of one amino acid and the amino group of another.

Importance of Amino Acids

• Structural proteins: Collagen (rich in glycine and proline)

• Neurotransmitters: Glutamate (excitatory NT of CNS), Glycine (inhibitory NT of spinal cord)

• Signaling proteins: Insulin (contains cysteine)

• Precursors for important compounds: Tyrosine → dopamine, Tryptophan → serotonin, melatonin

Quick Quiz

• Glycine's side chain is a hydrogen atom, hence it is achiral. (AmiNo)

• Most amino acids in the human body are in the L-configuration. (AmiYes)

• Tryptophan contains an indole ring, making it the largest amino acid. (AmiYes)

Summary

• Amino acids are fundamental units of proteins.

• Their structure, stereochemistry, and classification determine their function.

References

• Ferrier DR. Lippincott Illustrated Reviews: Biochemistry. 7th ed. Philadelphia, PA: Wolters Kluwer; 2017.

• Garrett RH, Grisham CM. Biochemistry. 7th ed. Boston, MA: Cengage Learning; 2016.

• King MW. Integrative Medical Biochemistry: Examination and Board Review. New York, NY: McGraw-Hill Education; 2014.

• Lecturio Biochemistry. [Internet]; 2023. Available from: https://www.lecturio.com. Accessed 2025 Mar 1.

• LibreTexts Chemistry. The Peptide Bond [Internet]. LibreTexts; 2020. Available from: https://chem.libretexts.org/Courses/AmericanRiverCollege/CHEM309%3AAppliedChemistryfortheHealthSciences/09%3AProteins_-
  _AnIntroduction/9.03%3AThePeptideBond. Accessed 2025 Mar 4.