Information Technology Reference
In-Depth Information
Ta b l e 4 . 1
Protein functions
Transformation
Regulation
Recognition
Signal
Transport
Movement
Structure
regular expressions where
P
C
.
The 20 amino acids are encoded by 61 codons while the remaining codons (UAG,
UGA, UAA) encode the
stop
character. The codon AUG both codes for methionine
and serves as an initiation signal for translation. In fact, the first AUG in an mRNA's
coding region is where translation into protein begins. A circular representation of
genetic code is given in Fig. 4.3.
=
U
+
C
,
Q
=
A
+
G
,
N
=
P
+
Q
,
¬
G
=
U
+
A
+
Ta b l e 4 . 2
The amino acids with their codons and regular expressions
Amino acid
Name
Letter
Codons
Regular expression
Arg
Arginine
R
{
CGU
,
CGC
,
CGA
,
CGG
,
AGA
,
AGG
}
CGN
+
AGQ
Leu
Leucine
L
{
UUA
,
UUG
,
CUU
,
CUC
,
CUA
,
CU G
}
CU N
+
UUQ
Ser
Serine
S
{
UCC
,
UCU
,
UCA
,
UCG
,
AGU
,
AGC
}
UCN
+
AGP
Ala
Alanine
A
{
GCU
,
GCC
,
GC A
,
GC G
}
GC N
Gly
Glycine
G
{
GGU
,
GGC
,
GGA
,
GGG
}
GGN
Pro
Proline
P
{
CCU
,
CCC
,
CCA
,
CCG
}
CCN
Thr
Threonine
T
{
ACU
,
ACC
,
AC A
,
AC G
}
AC N
Val
Valine
V
{
GU U
,
GU C
,
GU A
,
GU G
}
GU N
Ile
Isoleucine
I
{
AU U
,
AU C
,
AU A
}
AU
¬
G
Asn
Aspargine
N
{
AAU
,
AAC
}
AAP
Asp
Aspartate
D
{
GAU
,
GAC
}
GAP
Cys
Cysteine
C
{
UGU
,
UGC
}
UGP
His
Hystidine
H
{
CAU
,
CAC
}
CAP
Gln
Glutamine
Q
{
GAA
,
GAG
}
GAQ
Glu
Glutamate
E
{
CAA
,
CAG
}
CAQ
Lys
Lysine
K
{
AAA
,
AAG
}
AAQ
Phe
Phenilananine
F
{
UUU
,
UUC
}
UUP
Tyr
Tyrosine
Y
{
UAU
,
UAC
}
UAP
Met
Methionine
M
{
AU G
}
AU G
Trp
Tryptophan
W
{
UGG
}
UGG
RNA molecules are obtained by transcription from DNA and after that they are
translated by specific complexes of proteins and RNA which are called ribosomes.
They are particular translation machines, called transducers, in the sense of formal
language theory. A transducer is an extension of a finite automaton which reads one
letter per transition, possibly changing its internal state, but also replacing the letter
by a suitable string (in dependence from its current state). For example, the
iterated
transducer
given in Fig. 4.1 generates the tri-somatic language. It translates the
string in input (in the initial state on the top) in the string of the same language that
