Jump to Amino Acids - There are 20 amino acids that make up proteins. The main chain has an N terminal which is an amino group (NH2) and a C. Hydrophobic amino acids have nonpolar side chains, such as alkyl groups or aromatic groups. Hydrophilic—neutral—amino acids contain polar side chains, such as hydroxyl, -OH, and sulfhydryl, -SH, groups. Hydrophilic—acidic—amino acids have side chains that contain carboxylic acid, -COOHnegative, C, O, O, H, groups. Chemical structures of pharmaceuticals based on unnatural amino acids. The substructure derived from the unnatural amino acid is highlighted.
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The discrete view sees proteins as separate folds whereas continuous view supports the idea that any arrangement of secondary structures can be possible.
Instead of debating on which of the two is correct, researchers have started to assert that both continuous amino acids organic chemistry discrete views represent a duality in the sense that each view is necessary and present in protein structure space.
Discrete and continuous views are actually complementary, protein structure space is discrete on an evolutionary level but continuous geometrically. Evolutionary connections are made by looking at certain folds as island of structural stability.
Organic chemistry: Amino acids made easy
To view protein structures for their geometric similarities, we see paths that connect any two structures through intermediates. The traditional discrete view was developed under the idea that there are many structural similarities present in protein structures.
This idea was developed by utilizing X-ray crystallography to study the earliest protein structures, myoglobin and hemoglobin. Scientists have found that both myoglobin and hemoglobin have similar structures despite having different sequences.
All of these structures are unique and recognizable. This idea was supported by the fact that most structures matched these commonly seen prototypes of protein amino acids organic chemistry.
23: The Organic Chemistry of Amino Acids, Peptides, and Proteins
The TIM-barrel fold is an example of a prototype. A great number of metabolic enzymes belong in the TIM-barrel fold prototype.
Although most of these families did not show much similarity in terms of sequence, X-ray crystallographers found TIM-barrels in may enzyme families.
These TIM-barrel families are known to have been created from gene duplications and build-up of metabolic pathways. The fold discovered by Michael Rossmann is another example of a prominent structural prototype. There is an evolutionary process that is occurring to evolve into a thermodynamically stable structure.
Amino acids organic chemistry that occur diverge from the evolutionary process by shying away from thermodynamic stability. Thus, these mutated proteins are eliminated by selection. The stabilizing selection that drives evolution makes it so movements between folds are uncommon.
If we look at protein structure space in an evolutionary view, protein discreteness is characteristic of it.
Structural Biochemistry/Organic Chemistry/Proteins
Many publications suggest that structure space is continuous. Similarity metrics like TM-score have allowed scientists to find a connection between any two structures through no more than seven steps. The most common reaction of this group is a reversible oxidation that forms a disulfide.
Oxidation of two molecules of cysteine forms cystineamino acids organic chemistry molecule that contains a disulfide bond.
Amino acid - Wikipedia
When two cysteine residues in a protein form such a bond, it is referred to as a disulfide bridge. Disulfide bridges are a common mechanism used in nature to stabilize many proteins. Such disulfide bridges are often found among extracellular proteins that are secreted from cells.
In eukaryotic organisms, formation of disulfide bridges occurs within the organelle called the endoplasmic reticulum. In extracellular fluids such as bloodthe sulfhydryl groups of cysteine are rapidly oxidized to form cystine.