Gene Structure and Protein-Nucleic Acid Interactions

Gene Structure and Protein-Nucleic Acid Interactions 

Brief digestion of chromatin with micrococcal nuclease results in the production of discrete units termed nucleosomes (nu bodies). On electron microscopy, these protein-DNA particles are approximately 10-13 nm long, linked by shorter (2-4 nm) DNA sequences. Further details of chromatin structure may be found in Chapter 7. 

The amount of DNA in the eukaryotic cell is approximately 500 times that found in prokaryotes (Watts and Watts, 1975). Since there has not been a commensurate increase in the number of proteins manufactured in the eukaryotic cell, this potential information explosion in the size of the genome must be accounted for in ways other than by structural genes. In fact, only 2-15% of the total information in the genome is expressed in differentiated cells. The interaction of the genome with its cellular environment, and the change in that environment introduced upon fertilization must eventually be incorporated into any theory of differentiation. 

Proteins which interact with DNA do so either by recognizing specific nucleotide sequences or by disregarding the nucleotide sequence. Such binding must involve several points of attachment so as to provide sufficient discrimination and free energy for the fruitful interaction to take place. In general, proteins binding to DNA carry out one of two functions (1) they mediate or facilitate information expression in the DNA sequence or (2) they inhibit or stop such information expression. 

A number of enzymes which bind polyanions such as DNA may be separated broadly into those which recognize special sequences with higher affinity than bulk DNA and those which bind nonspecifically. The first group includes RNA polymerases, repressors, cAMP receptor protein (CRP), the rho factor, restriction endonucleases, and methy-lases the second group includes histones and DNA-unwinding proteins. 

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B. Gene Structure and Protein-Nucleic Acid Interactions... 

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