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The Biomolecules (Protein, CHO, Lipids)
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  • Course
  • Biochemistry
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  • Ateneo De Manila University
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  • Harper\'s Illustrated Biochemistry Thirty-First Edition

Lecture notes study book Harper's Illustrated Biochemistry Thirty-First Edition of Victor Rodwell, David Bender - ISBN: 9781259837944, Edition: 31, Year of publication: - (medicine notes)

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  • August 27, 2022
  • 6
  • 2021/2022
  • Class notes
  • Dr.
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Subjects

  • biomolecules
  • proteins
  • carbohydrates
  • lipids
  • biochemistry
  • harpers biochemistry
  • medicine

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MODULE 2: The Biomolecules (Protein, CHO, Lipids)

AMINO ACIDS, PEPTIDES & PROTEINS

1. Differentiate / define common L-a amino acids and unusual L-amino acids
- Monomer units from which polypeptide chains of proteins are constructed
- Only L-a-AA occur in proteins, though both D-AA and non amino acids occur in nature
- Subset of only 20 AA constitute monomer units from which polypeptide backbones of proteins are constructed
- All proteins contain varying proportions of the 20 L-a-AA
1.1. Unusual AA and proteins where they are found
- Arise by posttranslational processing (occurs after formation of polypeptide backbone) methylation, formylation, acetylation…
- Cysteine -> oxidation of –SH group of 2-cysteine to an S-S disulfide bond
- amino terminal glutamate of glutathione -> protein folding and metabolism of xenobiotics linked to cysteine by non peptide bond
- amino terminal of glutamate of thyrotropin-releasing hormone (TRH) is cyclized to pyroglutamic acid and the arboxyl group of the carboxyl terminal prolyl
residue is amidated.
- The non protein AA D-phenylalanine and ornithine are present in the cyclic peptide antibiotics (tyrocidin & gramidin S)
- Hepapeptide opioids dermorphin and deltophorin in the skin of South American tree frogs contain tyrosine and D-alanine
1.2. Describe how these unusual AA are formed
- linked by non peptide bonds / atypical peptide bonds

Common L-a AA & important roles in metabolic processes:
a. Ornithine, citrulline, argininosuccinate -> urea synthesis
b. Tyrosine -> formation of thyroid hormones
c. Glutamate -> neurotransmitter biosynthesis

Naturally occurring D-AA
a. free D-serine & D-aspartate -> brain tissue
b. D-alanine and D-glutamate -> cell wall of G(+) bacteria
c. D-AA -> peptides, antibiotics

*pH low enough to protonate carboxyl group, the amino group would also be protonated
pH sufficiently high for uncharged amino group to predominate, a carboxyl group will be present as R-COO(-)
uncharged -> no protonic equilibria

2. Describe the general structure of L-a AA
- absolute configuration L-glyceraldehyde
- dextrorotatory – R, levorotatory – L

Function of L-a AA:
a. nerve transmission
b. biosynthesis of porphyrins, purines, pyrimidines, urea
c. neuroendocrine system (hormones, hormone-releasing factors, neuromodulators…)

AA contain both amino and carboxylic acids function groups. In L- amino acid, both are attached in the same carbon atoms. Although some AA found in proteins
are dextrorotatory and some levorotatory at pH 7.0, all have the absolute configuration of L- glyceraldehyde and hence are L- amino acids.

3. Classify the 20 amino acids on the basis of their polarity and charge of the R group at physiologic pH
Nonpolar / Hydrophobic Polar / Hydrophilic
With Aliphatic Side Chains –HC R group Basic groups (-)
Glycine Arginine
Alanine Lysine
Isoleucine Histidine
Leucine Acidic groups and amides (+)
Valine Aspartic acid
With –S atoms Glutamic acid
Methionine With –OH groups
Cysteine Serine
With aromatic rings Threonine
Phenylalanine Tyrosine
Trytophan Neutral
Tyrosine Asparagine
Glutamine

4. Discuss the physical and chemical proteins of AA
4.1. Optical activity
- can rotate the plane of the plane-polarized light due to the tetrahedral orientation on the 4 different groups attached to 1 C atom
- AA are “chiral” (except glycine); achiral = symmetric
- d/t lack of a plane of symmetry = 2 stereoisomers* of AA (*one is non-superimposable mirror image of another)
4.2. Solubility
- reflects ionic character; in H2O, ionic attractions between ions in the solid AA are replaced by strong attractions between polar H2O molecules &
zwitterions* (molecules that contain equal number of ionizable groups of opposite charge& bear no net charge; internal transfer of H ion from –COOH to
–NH2 to leave an ion with both (+) and (-) charge)
- extent and nature of solubility varies, depending on size and nature of R group
- lack of solubility in non polar organic solvents such as HC is because of lack of attraction between solvent molecules and zwitterions
- soluble in polar solvents – H2O, ethanol
- insoluble in non-polar solvents – benzene, hexane, ether HC




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