BIO 311 Chapter Notes - Chapter 4: Stereoisomerism, Amine, Side Chain

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Amino acids and peptides
• Aio aids ae the ooes, o uildig loks, of polpeptides ad poteis
• Aog all the possile aio aids, ol 0 ae usuall foud i poteis
• The geeal stutue of aio aids iludes a aio goup ad a carboxyl
goup, oth of hih ae oded to a α-carbon
• The HN+ ad COO- ionic forms of the amino group and carboxyl group,
respectively, predominate at a pH of 7
• The α-carbon is also bonded to a hydrogen and to a side chain group,
represented by the letter R
• The side hai, o ‘ goup, deteies the idetit ad popeties of the aio
acid, as well as the overall structure and function of proteins
• It is ipotat to eogize that aio aids ae thee-dimensional - in biology
Fig. 3-1, p. 66
Amino acids
Amino acids and Stereochemistry
• Ma ipotat iooleules ae said to e hial
• This eas that to oleules ae o-superimposable mirror images of each
other, e.g. left and right hands
• No-superimposable mirror image molecules are referred to as enantiomers or
stereoisomers
• A feuetl eouteed hial ete i iooleules is a ao ato ith
four different groups attached to it
• Suh a hial ete ous i all aio aids eept fo glie - glycine has
two hydrogen atoms oded to its α-carbon, as its R group is hydrogen, and thus
has symmetry
• I all the othe aio aids the α-carbon has four different groups bonded to it,
giving rise to two non-superimposable mirror images or stereoisomers
Fig. 3-2, p. 66
Amino acids and Stereochemistry
• The to steeoisoes of the hial iooleules glealdehde ad alaie ae
shown
• The to steeoisoes of eah aio aid ae desigated as L- and D-amino
acids
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• The L- form of glyceraldehyde has a hydroxyl group on the left side of the
molecule while the D- form has it on the right side
• The positio of the aio goup o the left o ight side of the α-carbon
determines the L or D designation - the amino acids that occur in proteins are all
in the L form
Summary 3-1, p. 66
Amino acids: Structure and properties
• The ‘ goups, ad thus the idiidual aio aids, ae lassified aodig to
several criteria, two of which are particularly important
• The fist of these is the pola o opola atue of the side hais
• The second depends on the presence of an acidic or basic group in the side
chain
• Othe useful iteia ilude the pesee of futioal goups othe tha aidi
or basic ones in the side chains and the nature of those groups, e.g. thiol group
(-SH) in cysteine
• Side hai ao atos ae desigated ith lettes of the Geek alphaet,
outig fo the α-carbon
• These ao atos ae i tu the β-, -, -, ad -carbons - a terminal carbon
ato is efeed to as the ω-carbon
• Aio aids ae efeed to by three-letter or one-letter abbreviations of their
names (**we will use the one-letter code)
Table 3-1, p. 69
Amino acids: Abbreviations
Non-polar (hydrophobic) amino acids (Group I)
• I seeal ees of this goup A, V, L, I eah side hai is a aliphatic hydrocarbon
group (aliphatic refers to the absence of a benzene ring)
• Polie has a aliphati li stutue, ad the itoge is oded to to a
Fig. 3-3a (2), p. 68
Non-polar (hydrophobic) amino acids
• I phelalaie F, the hydrocarbon group is aromatic rather than aliphatic - it contains a
cyclic group similar to the benzene ring
• I tptopha W, the side hai otais a idole ig, hih is also aoati
• I ethioie M, the side hai otais a sulfu ato i addition to aliphatic hydrocarbon
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