The Genetic Code-More Than Just a Table

被引:13
作者
Berleant, D. [1 ]
White, M. [2 ]
Pierce, E. [1 ]
Tudoreanu, E. [1 ]
Boeszoermenyi, A. [3 ]
Shtridelman, Y. [4 ]
Macosko, J. C. [4 ]
机构
[1] Univ Arkansas, Dept Informat Sci, Little Rock, AR 72204 USA
[2] Rafiki Inc, Bloomington, IN USA
[3] Karl Franzens Univ Graz, Graz, Austria
[4] Wake Forest Univ, Dept Phys, Winston Salem, NC 27109 USA
关键词
Genetic code; Codon table; Biological pedagogy; Code optimization; Point mutation; BLOSUM62; PAM250; FREE PROTEIN-SYNTHESIS; CHEMICAL-SHIFT; E-COLI; SELENOCYSTEINE; USAGE; INSERTION; DEPENDENCE; EVOLUTION; CODONS; ORIGIN;
D O I
10.1007/s12013-009-9060-9
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The standard codon table is a primary tool for basic understanding of molecular biology. In the minds of many, the table's orderly arrangement of bases and amino acids is synonymous with the true genetic code, i.e., the biological coding principle itself. However, developments in the field reveal a much more complex and interesting picture. In this article, we review the traditional codon table and its limitations in light of the true complexity of the genetic code. We suggest the codon table be brought up to date and, as a step, we present a novel superposition of the BLOSUM62 matrix and an allowed point mutation matrix. This superposition depicts an important aspect of the true genetic code-its ability to tolerate mutations and mistranslations.
引用
收藏
页码:107 / 116
页数:10
相关论文
共 52 条
[1]   CodonO: codon usage bias analysis within and across genomes [J].
Angellotti, Michael C. ;
Bhuiyan, Shafquat B. ;
Chen, Guorong ;
Wan, Xiu-Feng .
NUCLEIC ACIDS RESEARCH, 2007, 35 :W132-W136
[2]  
BALTIMORE D, DNA IS REALITY METAP
[3]   A common periodic table of codons and amino acids [J].
Biro, JC ;
Benyó, B ;
Sansom, C ;
Szlávecz, A ;
Fördös, G ;
Micsik, T ;
Benyó, Z .
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 2003, 306 (02) :408-415
[4]   Whence the genetic code? Thawing the 'frozen accident' [J].
Carter, C. W., Jr. .
HEREDITY, 2008, 100 (04) :339-340
[5]  
Church G., 2009, Safeguarding biology, Seed, V20, P84
[6]   Protein backbone angle restraints from searching a database for chemical shift and sequence homology [J].
Cornilescu, G ;
Delaglio, F ;
Bax, A .
JOURNAL OF BIOMOLECULAR NMR, 1999, 13 (03) :289-302
[7]   Silent mutations affect in vivo protein folding in Escherichia coli [J].
Cortazzo, P ;
Cerveñansky, C ;
Marín, M ;
Reiss, C ;
Ehrlich, R ;
Deana, A .
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 2002, 293 (01) :537-541
[8]   ORIGIN OF GENETIC CODE [J].
CRICK, FHC .
JOURNAL OF MOLECULAR BIOLOGY, 1968, 38 (03) :367-&
[9]   Large scale features in DNA genomic signals [J].
Cristea, PD .
SIGNAL PROCESSING, 2003, 83 (04) :871-888
[10]   Selenium metabolism and bioavailability [J].
Daniels, LA .
BIOLOGICAL TRACE ELEMENT RESEARCH, 1996, 54 (03) :185-199