BCEM 393 Chapter Notes - Chapter 3: Fischer Projection, Alpha And Beta Carbon, Amine

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Amino Acids
- Some amino acids function as signal molecules (eg. neurotransmitters), and all amino acids
are precursors to other biomolecules (eg. hormones, nucleic acids, lipids, and proteins)
- Two Different Ways of Depicting Biomolecules Will Be Used
- Proteins and biochemicals in general, derive their array of functions from the ability to form
3D structures
- When visualizing the constituent atoms of a molecule, such as carbons and hydrogens, is
more important than seeing the shape of the molecules, use a depiction called a Fischer
projection
- In a Fischer projection, every atom is identified and the bonds to the central carbon atom
are represented by horizontal and vertical lines
- By convention, the horizontal bonds are assumed to project out of the page, whereas the
vertical bonds are assumed to project behind (or into) the page
- When emphasis is on a molecule’s function, visualization of the shape of the molecule is
more important
- In such instances, stereochemical renderings are used because they convey an
immediate sense of the molecule’s structure and, therefore, a hint about its function
- Stereochemical renderings also simplify the diagram, thereby making the function of a
molecule clearer
- Carbon and hydrogen atoms are not explicitly shown unless they are important to the
activity of the molecule
3.1 PROTEINS ARE BUILT FROM A REPERTOIRE OF 20 AMINO ACIDS
- An alpha-amino acid consists of a central carbon atom, called the alpha carbon, which is
bonded to an amino group, a carboxylic acid group, a hydrogen atom, and a side chain (R-
group)
- Most Amino Acids Exist in Two Mirror-Image Forms
- Alpha amino acids are chiral1 because they have four different groups connected to the
tetrahedral alpha carbon atom
- L amino acids are the only constituents of proteins
- Evidence shows that pure L and D amino acids are slightly more soluble than a stable DL
crystal
- Therefore, if simply by chance, there were a small excess of the L amino acid, this small
solubility difference could have been amplified over time so that the L isomer became
dominant in solution
- All Amino Acids Have at Least Two Charged Groups
- Free amino acids in solution at neutral pH exist predominantly as dipolar ions (also known
as zwitterions)
- In the dipolar form, the amino group is protonated (NH3+) and the carboxyl group is
deprotonated (COO-)
1 To be chiral means to be able to exist in one or the other of two mirror-image forms, called the
L isomer and the D isomer
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Document Summary

Some amino acids function as signal molecules (eg. neurotransmitters), and all amino acids are precursors to other biomolecules (eg. hormones, nucleic acids, lipids, and proteins) Two different ways of depicting biomolecules will be used. Proteins and biochemicals in general, derive their array of functions from the ability to form. When visualizing the constituent atoms of a molecule, such as carbons and hydrogens, is more important than seeing the shape of the molecules, use a depiction called a fischer projection. In a fischer projection, every atom is identified and the bonds to the central carbon atom are represented by horizontal and vertical lines. By convention, the horizontal bonds are assumed to project out of the page, whereas the vertical bonds are assumed to project behind (or into) the page. When emphasis is on a molecule"s function, visualization of the shape of the molecule is more important.

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