Transcription factors need to have an attraction to DNA in order to stay near or on the DNA the majority of the time. If transcription factors were not attracted to DNA they may float off the DNA and diffuse away. In order to keep transcription factors associated with the DNA, what functional groups on proteins and on DNA may be involved in this attraction? (these are referred to as general interactions=transcription factors being attracted to DNA) ? Transcription factors cannot JUST be attracted to the DNA. They also need to bind to very specific sequences in the DNA in order to properly regulate gene expression. These specific interactions rely on (transcription factors binding to their specific site on the DNA) ?

Answer: → amino acid side chains of the transcription factor proteins

→ base pair residues of DNA functioning as regulatory sequence.

Explanation: These are proteins that recognize and bind to specific short DNA sequence, which leads to gene expression. Examples are TFIIA (transcription factor IIA) and TFIIB (transcription factor II B).

During transcription the transition factors binds to the DNA molecule by chemical interactions of the amino acid side chains of the transcription factor protein with base pair residues of DNA functioning as regulatory sequence. Thus, the functional groups on the protein for binding are

◼the amino side chains of the transcription factor and

on the DNA sequence;

◼ Base pair residues of DNA functioning as regulatory sequence

The chemical reaction above enabled the transcription factors to "read" the genomic sequence. This is the basic mechanisms of sequence recognition function, and template on which informational aspects of all regulatory transactions controlling gene expression depended.

Furthermore; the occupancy of these proteins at their target sites depended

◼on the intrinsic tightness of binding between the transcription factor protein and the DNA target site,

◼ and the concentration at which the transcription factor is present in the nucleus. These parameters together with the above chemical reactions enable the transition proteins to bind with a specific DNA sequence for transcription.

Conclusively, the fundamental ' aspect of transcription factor-DNA interaction is that all transcription factors include basic domains which cause them to be concentrated nonspecifically in the vicinity of the DNA, facilitating the diffusion-limited discovery of their target sites'.