EFB325 Cell Physiology

Amino acids and proteins

• Proteins are important as enzymes, structural components, signaling molecules, antibodies, and storage
• Amino acids are the building blocks of the protein polymer=polypeptide
• Specific sequence of amino acids in a protein is critical for its function and is genetically determined according to the sequence of bases in the nucleic acids

Amino acids

• 20 different amino acids, all with same general formula, same in all organisms
• general formula=alpha carbon; amino group; carboxyl group; a hydrogen; and an R group (side chain)
• both the carboxyl and amino groups are charged at biological pH (-COO^-) and (-NH₃⁺)
• the 20 different R groups fit into 4 classes: nonpolar, uncharged polar, negatively charged (acidic), or positively charged (basic)
• can use both a 3-letter and a 1-letter abbreviation

Nonpolar (hydrophobic)

• Gly, Ala, Val, Leu, Ile=hydrophobic with hydrocarbon R groups
• Met=hydrophobic, w/sulfur (thioether); first amino acid in nearly all proteins
• Cys=sulfhydryl group
• Phe, Trp=hydrophobic, aromatic (Phe has phenyl ring, Trp has indole ring)
• Pro=cyclic bond, introduces a kink

Uncharged polar

• Ser, Thr=hydroxyl groups
• Tyr=polar aromatic, w/hydroxyl
• Asn, Gln=amide groups

Negatively charged (acidic)

• Asp, Glu=like Asn, Gln only w/carboxyl groups, (-) charge at biological pH

Positively charged (basic)

• Lys, Arg=basic amino groups, (+) charge at biological pH
• His=imidazole ring, can be neutral or (+), depending on pH (pK=6.5)

Amino acids are linked in the polymer by a special bond between carboxyl carbon and amino nitrogen=peptide bond

• peptide bond is formed between the carboxyl group of one amino acid and the amino group of the next
• polymer is called polypeptide
• amino acids must be activated to be added to the polymer, this is by a covalent bond to a tRNA, bond carries energy from ATP
• confers directionality=amino -> carboxyl
• the atoms in the peptide bond are fixed in a plane, but the bond between the alpha and carbonyl carbon can rotate (except for Pro)
• this allows polypeptides to bend and fold into particular shapes and conformations

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