Protein DNA Interactions
Every cell in the human body contains the same genes, however, not all of the genes are transcribed at the same time and depending on the type of tissue different genes are transcribed and other are never turned on. For example all cell types contain the gene for hemoglobin, but it is only transcribed in red blood cells. There a number of factors which control transcription. Control is exerted by proteins which can bind to DNA . Since specific binding is possible to the outside of the double helix, DNA does not need to unwind for this interaction. There several common binding motifs:
In the helix - turn -helix motif two alpha helix domains of the regulatory protein interact with the double helix DNA . One of the alpha helices called recognition helix, binds to the major or minor groove , whereas the other helix stabilizes the interaction.
In the Zinc Finger motif a protein forms a finger like loop, held in place through complexation with Zn ions. This Zn finger can interact with specific DNA sequences, and thus control their transcription.
The Leucine Zipper motif consists of two recognition alpha helices, attached to a coiled portion of the protein. The two recognition alpha helices can interact with the DNA major groove.

The Homeodomain uses a helix-turn-helix motif to interact with DNA.

Schematic diagrams of the motifs are shown below ( taken from Raven and Johnson) .

Lac Operon
We will use the example of the breakdown of lactose into galactose and glucose by the enzyme beta galactosidase, to illustrate the control mechanisms in the transcription of a gene. The mechanism was worked using the bacterium E. coli . The DNA region, which contains the genes for all control proteins as well as enzymes involved in the breakdown of lactose is called the lac operon . A schematic diagram of the lac operon is shown below

If a gene is to be transcribed into a m-RNA, the enzyme RNA polymerase must be able to bind to DNA. It will not just bind to any site on the DNA but to a specific base sequence which is located in front of the sequence of the actual gene. The region to which RNA polymerase can attach is called promoter. In case of the lac operon three genes are transcribed, the gene for beta galactosidase (Z), a permease (Y) which is a transporter protein for lactose and the gene for the enzyme transacetylase (A), which is important in the metabolism of lactose. The promotor region for the transcription of these gene is designated P_lac.
Sometimes the promoter site in not accessible to the RNA polymerase. In such a case a transcription activator protein has to binds to the promoter region, exposing the site so that RNA polymerase can attach and begin the transcription. One such transcription activator protein is CAP. CAP itself does not attach to the promoter site, only after binding to cAMP, the CAP/cAMP complex can bind to the transcription site making it accessible to RNA polymerase. As you can see the CAP- site is just upstream of the promoter site. Adjacent to the promoter site is the so called operator (O) site. This is a regulatory site to which a repressor protein (I) can bind, preventing RNA polymerase to transcribe the DNA strand, even if CAP/cAMP has exposed the promoter site. The structural gene for this repressor protein is located upstream of the lac promoter site (P_lac). The repressor has also its own promoter site (P_I). Now we know all the components of the lac operon, let’s se how it works.

The bacterium can use either glucose or lactose as carbon and energy source. When glucose levels are high the repressor protein (I) is tightly bound to the operator region and since cAMP levels are low during high glucose concentrations, the CAP protein does not bind to its site. These are the conditions which block transcription, as shown below.

If the glucose levels drop, as a cellular response the cAMP levels increase. The CAP protein can now form a complex with cAMP, which promotes the attachment of RNA polymerase to its promoter site. But this is not enough for the lac genes (Z, Y and A) to be transcribed. It is necessary that lactose is actually present. If lactose is present it can form a complex with the repressor protein (I) This frees the operator site and RNA polymerase can now transcribe the lac genes Z Y and A. This is illustrated in the scheme below.

Thus, for the lac genes to be transcribed, glucose levels have to be low and lactose has to be present. If lactose and glucose are present transcription does not begin, because the CAP protein is not active (low cAMP levels).

trp Operon
A second example of transcription control is the trp operon , which contols the biosynthesis of the amino acid tryptophan. ( Fig. 13.8. )

Transcription in eukaryotes
( Fig. 14.14. ) The transcriptional control in eukaryotes is more complex than in bacteria. Before RNA polymerase can bind to the promoter region of the DNA a number of proteins called transcription factors have to attach to the site. Togther with the RNA polymerase they form a complex which binds to a highly conserved promoter sequence TATAAT, called Pribnow box or TATA box. Changes (mutations) in the Pribnow box affect transcription and can either enhance or decrease promoter activity. Since so many different transcription factors are involved in the formation of the RNA polymerase complex, a multitude of transcription control points exist. The regulatory proteins so far discussed interact with DNA through their DNA binding motifs, for example, some repressor proteins bind to DNA through a helix - turn - helix interaction.
Another type of regulatory proteins interact with transcription factors, to enhance their binding activity toward RNA polymerase and thus speeding up the transcription. These enhancer or activator regulatory proteins can attach to specific DNA sites which do not need to be in close proximity of the promoter region. Through their protein interaction domain they can control the activity of the RNA polymerase complex. The advantage of such a regulation is that the enhancer can exert transcriptional control from distant sites on the DNA. That means a distant gene can influence the transcription of another gene.

The figure below (taken for Raven & Johnson) illustrates the action of a eukaryotic transcription complex

Activators: Proteins that bind to Enancer sites which helps the RNA polymerase to position properly to begin transcription
Repressor: Protein that interferes with the binding of activators. This action will slow or prevent transcription
Basal factors: Proteins which position RNA polymerase over the beginning of the structural gene. Once positioned, the transcription complex releases the RNA polymerase and transcription begins
TATA box (or Pribnow box): Highly preserved DNA sequence (part of the promoter) upstream of the structural gene. A TATA binding protein attaches to the site, which is essentially the first step in the binding of the entire transcription complex. Transcription factors: Can sense the correct positioning of activators. If aligned properly, basal factors will release RNA polymerase and transcription begins.

Termination of transcription in eukaryotes
In most cases transcription stops when a certain nucleotide sequence is encountered. The transcribed sequence has sections which are rich in G C causing complementary binding of this sections in the m-RNA. This results in a hairpin formation (see below) which dislodges the m-RNA from the DNA strand, terminating transcription.

RNA splicing
In prokaroytic organisms the m-RNA is an exact complementary copy of the gene inscribed in DNA. In eukaryotic organisms certain sections of the newly synthesized m-RNA (called introns) are excised by specific enzymes. The remaining sections are called exons and they make up the final m-RNA, whose sequence is translated into protein. Introns are formed because certain sections of the m-RNA are self complementary and they can form hair pins. (these hair pins are not recognized as a termination signals by the RNA polymerase). Depending on what enzymes are present some hairpins are not excised. Thus, the same structural gene can produce different m-RNAs (= different proteins) depending on what excision enzymes are active.

Telomeres
The 3' ends of a double stranded DNA contain highly repetitive sequences (TTAGGG). These regions of the DNA are called telomeres. When DNA is replicated the 3' end of each strand can not be completely replicated since the DNA polymerase can not attach outside the of the strand to synthesize the last Okazaki fragment. This is illustrated in the figure below. ( The section on telomeres and the action of telomerases as described and illustrated in your textbook is very confusing at best )

At an eukaryotic replication origin, DNA is replicated in both directions. Because DNA polymerase can add only nucleotides to the 3' end, the 5' ends of each newly replicated strand has a gap. Through the action of a telomerase the 5' end is elongated. Telomerase is an enzyme that has a nucleotide domain with a base sequence that is complementary to the base sequence on the 3' end of the DNA to be copied (illustrated below).

After attachement of the telomerase to the 3' end of the original strand, the original is elongated. Now there is room for the primase and the 5' end of the newly synthesized strand is elongated as shown above. Without a telomerase a cell can divide about 20 times before the replicated DNA becomes too short to be still functional. Rapidly dividing cells such as bone marrow have active telomerases. It is theorized that cancer cells have also very active telomerases.

Transposon
Certain Indian corns (maize) have cups in which individual kernels have different color (they are spotted ). One might expect that the kernels should be of the same color since they are derived from the same plant. In the 1950ies Barbara McClintock proposed that transposons (small fragments of DNA) could jump from one position in a gene to another. The role of transposons in the color of corn kernels is illustrated below.

Early in the history of the corn plant a transposon inserted itself via insertion sequences into the allele which codes for a brown color. As a result of such insertions the gene produced a faulty enzyme and the kernels show no color ( = yellow). While the plant is growing (during DNA replication) it is possible that the transposon moves out of the gene, resulting in a new allele. This may happen in a few cells which make up the kernel. These cells have now the original color allele and produce the brown color. As a result the kernels appear spotted.
Transposons had been discovered originally in bacteria by Lederberg and Tatum, where genetic exchange via the F-plasmid between different organisms was observed.

There two fundamentally different mechanisms by which transposons move to different locations :"cut and paste" of a DNA section ( Fig. 14.5. ) and transcription of a DNA segment into RNA, followed by reverse transcription. In both cases the resulting DNA fragment is inserted into a different location on a chromosome. The human genome has a large number of moderately repeated sequences. (Alu and L1 families), which transpose via RNA. It is estimated that there are about 500,000 copies of transposable L1 sequences (6000 bases long) in the nuclear DNA. What is the function of these DNA sequences? Possibly "junk DNA", but concequences of their presence are: linking of previously unlinked genes, formation of new genes (telomerase is believed to be derived from a transposase) and domain properties of enzymes. Alus contain a hormone response element in their promoter region , if an Alu transposes, hormone sensitivity can be transferred to a gene. Alus have been implicated in Leukemia, Alzheimer's and Multiple Sclerosis