Chapter 18

Amino acids and primary

structure of proteins

Biochemistry for non-majors

(CHEM 283)
Dr. Nayla Munawar

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Proteins are the foundation of the working cell

• Catalysis (Enzymes, e.g. Carbonic anhydrase CO2 + H2O H2CO3)

• chemical storage and transport (Hemoglobin/O2)

• structure (Collagen in nails/hair)
• mechanical work (Actin/Myosin in Muscles)
• information storage and retrieval (DNA polymerase)
• intercellular communication (Hormones, e.g. Insulin)
• defense (Antibodies, e.g. IgG (Immunoglobin G))

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 Amino Acids
Amino acids: building blocks of the proteins
About 500 amino acids occur in nature, 20 of them found in proteins.

Amino acids have four groups or atoms

attached to α carbon

1. Amino group: (NH2), except proline

2. Carboxyl group: (COOH)
3. Hydrogen atom: (H)
4. Distinctive side chain: (R)

At physiological pH (7.4) the carboxyl group is

dissociated forming a negatively charged
carboxylate ion (-COO-) and a amino group is
protonated, forming positively charged ion (-
NH3+).
 Zwitterion and Isoelectric point
A Zwitterion is a dipolar ion with both
positive and negative charges in
different parts of the molecule.

Isoelectric point (PI): pH at which

amino acids exist as Zwitterion ions
(neutral charge)
 Twenty different amino acids make up proteins

• Ala alanine • Met methionine

• Cys cysteine • Asn asparagine
• Asp aspartate • Pro proline
• Glu glutamate • Gln glutamine
• phe phenylalanine • Arg arginine
• Gly glycine • Ser serine
• His histidine • Thr threonine
• Ile isoleucine • Val valine
• Lys lysine • Trp tryptophan
• Leu leucine • Tyr tyrosine

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General chemical structure of an amino acid

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 Optical Stereoisomers (D/L)
For amino acids: COOH, R, NH2 and H (where R is a variant carbon chain) are arranged
around the chiral center carbon atom.

Starting with the hydrogen atom away from the viewer, if these groups are arranged
clockwise around the carbon atom, then it is the D-form. If counter-clockwise, it is
the L-form.

Any molecule containing a chiral carbon can exist as a pair of enantiomers.

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 D and L amino acids

Levorotatory…………left hand side----------anti-clockwise

Dextrorotatory……..right hand side----------clockwise

Cells contain L-amino acids

D-amino acids occur in cell wall of bacteria
Classes of amino acids
a) non-polar:
P V FW MAIL
GAP FILM VW

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b) Neutral polar:

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c) Basic amino acids:

d) Acidic amino acids:

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Keep in mind that:

▪ Sulfur containing amino acids: Methionine (Met) and Cysteine (Cys).

▪ Aromatic amino acids: Phenylalanine (Phe), Tyrosine (Tyr) and Tryptophane

(Trp). They all absorb UV.

▪ Amide containing amino acids: Asparagine (Asn) and Glutamine (Gln).

(contains a carbonyl group (C=O) linked to a nitrogen atom (N))

▪ Histidine (His): has an imidazole group side chain which is a heterocyclic

aromatic amine.

▪ Proline (Pro): is unique among the 20 protein-forming amino acids in that the
α-amino group is secondary. The distinctive cyclic structure of proline gives it
an exceptional conformational rigidity compared to other amino acids.

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Peptide bond formation

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Polypeptides

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 Disulfide bond formation

• Disulfide bond formation is reversible

• disulfide bonds form in proteins and help stabilize their structures15