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Tour and quick review of the major compounds important to the human body.

[Study guide covering chapter 5, PDF]

Last edited: 08.04.2019

Important functional groups: those with oxygen, nitrogen, phosphorus, sulfur.

  • Acyl group: the part of the structure that provides the –C=O carbonyl group in an ester/amide linkage. “-yl” ending.
  • Aliphatic: open chains (non-ring).
  • Aromatics/Benzene rings. “Phenyl” if ring is a substituent.

Carbohydrates (sugars).

  • Formula: CnH2nOn. Glucose is C6H12O6.
  • Classified by: carbonyl group (aldose/ketose); # of carbons; positions of the -OH group on the anomeric carbon (D=right/L=left OH position, stereoisomers, epimers); any additional substituents; number of saccharides; how the components are linked (e.g. glycosidic bonds).
  • For n asym centers >> 2^n stereoisomers generally speaking.
  • Humans use D-sugars. “D for Delightful sugars!”
  • Epimer: a pair of stereoisomers that differ only in one position of the OH at a chiral carbon.
  • Epimerases: enzymes that make epimer conversions.
  • Glycoproteins: proteins + sugars.
  • Proteoglycans: proteins that are heavily glycosylated. Many long unbranched polysaccharide chains attached to a protein core. VIP to extracellular matrix, aqueous humor, cells that make mucous secretions, & cartilage.
  • Glycosaminoglycans: polypeptide chains with repeating disaccharide units w/oxidized acid sugars, sulfated sugars, and N-acetylated amino sugars. Structure looks like a bottle brush.
  • https://themedicalbiochemistrypage.org/glycans.php
  • https://www.mdpi.com/1424-8247/11/1/27/pdf
  • Glycosylation: a reaction where a carbohydrate is attached to a hydroxyl or other functional group.
  • Glycolipids: lipids + sugars.
  • In solution, OH on anomeric carbon spontaneously changes (mutarotation) from alpha to beta and back to change from open to ring forms such as chair/boat etc. Chair/boat etc are usually more stable so there’s a greater chance that a compound will be in those configurations.
  • If the anomeric carbon forms a bond with another molecule, those mutarotations cannot happen due to the bond which limits configurational possibilities.
  • Common substituted groups: phosphate, amino, sulfate or N-acetyl.
  • Most free monosaccharides in the body are phosphorylated at the terminal carbons preventing transport out of cell.
  • Galactosamine & glucosamine are examples of an amino group replacing one of the OH groups. Usu. the amino group gets acetylated forming an N-acetylated sugar.
  • Acetylation: adding an acetyl functional group to a compound.
  • Acyl group. http://www.chem.ucla.edu/~harding/IGOC/A/acetyl_group.html
  • https://www.oit.edu/docs/default-source/library-documents/library-publishing/che102-intro-organic-chemistry/chapter-1-7.pdf
  • Sugars can get oxidized at the aldehyde carbon to form “-onic acid” or “-onate”.
  • Uronic (“-uronic acid”) acid forms when the the terminal OH group gets oxidized.
  • Polyol sugar: a sugar where the aldehyde gets reduced where all the carbon atoms have OH. Eg. Sorbitol.
  • Deoxy sugar: a sugar that has reduced such that 1+ carbons contains only H’s. Carbon 2 of deoxyribose.
  • The OH of the anomeric carbon can react with an OH (O glycosidic bonds found in sugar-sugar, sugar-hydroxyl bonds) or NH (N glycosidic bonds found in nucleosides and nucleotides) group to form an alpha/beta glycosidic bond.
  • Alpha glycosidic bond. The Greek alpha looks like a fish which is DOWN in the sea.
  • Beta glycosidic bond. The Greek beta looks like a bird UP in the air.
  • Disaccharide: 2 monosaccharides joined by O-glycosidic bond.
  • Oligosaccharide: 3-12 linked monosaccharides via N or O glycosidic bonds.
  • Polysaccharides: thousands of monosaccharides joined to make chains and/or branches.

Lipids.

  • Hydrophobic.
  • Usu. straight chains, methyl group at one end (w-carbon) and carboxyl at the other end.
  • Most FA in humans have even number of carbons betw. 16-20.
  • Most common FA in cells are stearic and palmitic FAs.
  • *Special notation for FA’s pg. 69-70.
  • http://rogersal.people.cofc.edu/Lipids.pdf
  • https://www.cs.mcgill.ca/~rwest/wikispeedia/wpcd/wp/f/Fatty_acid.htm
  • https://courses.lumenlearning.com/suny-nutrition/chapter/2-33-fatty-acid-naming-food-sources/
  • https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3646453/
  • https://www.uio.no/studier/emner/matnat/farmasi/nedlagte-emner/FRM2041/v06/undervisningsmateriale/fatty_acids.pdf
  • FA also classified by distance from w-carbon to the double bond.
  • Fatty acids. Esterified to glycerol >> triacylglycerols (triglycerides) or phosphoacylglycerols (phosphoglycerols).
  • Tri acyl glyderols: 3 acyl FA groups attached to glycerol; fat stores in the body.
  • Sphingolipids: FA + sphingosine (serine + palmitate FA). No glycerol backbone.
  • Ceramides (type of amides) = sphingosine + FA attached at the amino group.
  • More sphingolipids formed from attaching substituents onto the OH of the ceramide.
  • Cerebrosides + gangliosides = sugars glycosidically bonded to OH of ceramides.
  • Sphingomyelin = phosphorylcholine + ceramide; vip part of cell membranes and myelin sheath.
  • Glycolipids: lipids + sugar hydroxyl group.
  • Polyunsaturated FA: building blocks of eicosanoids.
  • Eicosanoids: signalling molecules via enZ or non-enZ oxidation of arachidonic acid or other polyunsat. FA. Hormone-like compounds. Polyunsat FA with 20 carbons (eicosa) and have 3-4-or-5 double bonds (e.g. prostaglandins, thromboxanes, leukotrienes).
  • Naturally occurring FA typically cis.
  • There are also trans.
  • Cholesterol: formed from isoprene units.
  • Bile salts.
  • Steroid hormones.
  • Isoprenyl unit: combined in long chains to make structures such as side chains of Coenzyme Q in humans and Vit A in plants.
  • Geranyl groups = 10 carbons & polymers of isoprenyl units.
  • Farnesyl groups = 15 carbons + isoprenyl units.
  • Geranyl and farnesyl groups often get attached to proteins so that proteins can interact w/other cellular structures.
  • Acylglycerols: glycerol with 1+ FAs (acyls via ester linkages). Mono- di- and tri-acylglycerols contain 1, 2, and 3 FA esterified to glycerol. Triacylglycerols don’t usu. have the same FA at all 3 positions (usu. mixed).
  • Phosphoacylglycerols: FA at positions 1 and 2; phosphate group (or substituent attached to phosphate group) at position 3. If it’s only the phosphate group and NO other substituents at position 3, then it’s a phosphatidic acid.
  • Phosphatidylcholine (lecithin) found in membranes. Has polar and nonpolar duality.
  • Lysolipid = phosphoacylglycerols – fatty acyl group
  • Steroids: 4-ring steroid nucleus; cholesterol precursor; diff species made by modifying ring or C20-side chains.
  • Cholesterol hydrophobic can convert to hydrophilic bile salt (eg. cholic acid). Branched 5-carbon units w/1 double bond (isoprenyl unit)
  • Bile salts are on micelles survaces in the intestinal lumen.

Nitrogen Compounds.

Free Radicals.

  • Compounds w/single electron in outer shell.
  • Extremely reactive and unstable.
  • Usually formed as intermediates.
  • Usu. negative effects.

Oxidation/Reduction.

  • Carbon-carbon or carbon-oxygen bonds said to be oxidized or reduced depending on # of electrons around the carbon.
  • LEO: lose electrons (lose H atoms) oxidation.
  • GER: gain (gain H or lose O) electrons reduction.
  • More oxidized from alcohol to aldehyde/ketone to carboxyl.

Acid/Base.

  • Cations are catfabulous (+)! Anions (onions) make you cry (-).
  • Common anionic groups: carboxylate; phosphates (P); sulfates.
  • Common cationic groups: N, amines.

Bond Polarity & Partial Charges.

  • Carboxylate.
  • Phosphate.
  • Sulfate.
  • Ester = carboxylic acid + alcohol – water
  • Thioester = acid + sulfhydryl
  • Amide = acid + amine
  • Phosphoester = phosphoric acid + alcohol
  • Anhydride = acid1 + acid2

Resources.

References.

Lieberman, M., & Peet, A. (2017). Marks’ basic medical biochemistry: A clinical approach(5th ed.). Philadelphia, PA: LWW.