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RNA Polymerase II : The Reader of the Secret Code!
St. Dominic Middle School SMART Team
18105 W. Capitol Drive, St Dominic, WI 53045
How Does RNA Pol II Work?
Bridge Helix
Magnesium Ion
Last nucleotide added
to growing mRNA
Images are based on
PDB File 1I6H.
RNA Polymerase II synthesizes a messenger RNA
copy of the DNA template strand. In the image above
and to the right the DNA template strand is cyan and
the mRNA being made is magenta. When the mRNA
copy of a gene is complete, it is translated into a
protein by ribosomes in the cytoplasm of the cell.
Diseases Associated with RNA Pol II
• Werner's Syndrome is a rapid aging disease
that starts in adolescence and causes death
around 50 years old. In cells with two bad
copies of Werner’s protein, RNA Pol II
transcription rates are half the normal rate of
3000 nucleotides per minute.
•Alpha-Amanitin Poisoning causes death within
10 days unless the patient is treated
immediately. Alpha-amanitin reduces
transcription rates to 5 or 6 nucleotides per
minute and that’s not enough to sustain the life
of a cell.
•Cockayne Disease is a rapid aging disease
that causes death in the early teens. In this
disease RNA Pol II cannot backtrack to fix
mistakes in the DNA, although it can carry out
transcription at normal rates.
Primary Citation
1. Structural Basis of Transcription: An RNA Polymerase II Elongation
Complex at 3.3 Angstrom Resolution, Averell L. Gnatt, Patrick Cramer,
Jianhua Fu, David A. Bushnell, Roger D. Kornberg, Science, Volume 292,
page 1876
Other References
2. Structural Basis of Transcription: α-Amanitin-RNA Polymerase II
Cocrystal at 2.8 angstrom resolution, David A. Bushnell, Patrick Cramer,
and Roger D. Kornberg, PNAS, online Jan. 22, 2002
DNA Template Strand
Messenger RNA
The diagram on the right
(adapted from [1]) shows
the process translocation
proposed by Roger
Kornberg and his research
group. The DNA template
strand is cyan, the mRNA is
red, the bridge helix is
yellow, and the magnesium
ion is pink. In the first
picture, we see a nucleotide
added to the mRNA strand.
In the second picture the
magnesium ion is
connecting the nucleotide to
the mRNA. The third picture
shows the bridge helix in a
changed conformation
(violet) to brace the mRNA
nucleotide that has just
been added. Notice that the
DNA/RNA hybrid has
translocated (moved) with
respect to the magnesium
ion. In the final picture the
bridge helix moves back to
its original position, opening
up a space to add the next
nucleotide to mRNA.
A SMART Team project supported by the National Institutes of Health (NIH) – National Center for Research Resources Science Education Partnership Award (NCRR-SEPA)
ABSTRACT
RNA polymerase II is essential to life in cells. Found in the nucleus of a cell, this molecule is a multi‐subunit protein. RNA Pol II makes messenger RNA (mRNA) copies of genes. This process is called transcription and is the first step in protein synthesis. Genes are made of DNA and contain the codes for making proteins. Since DNA is unable to leave the nucleus, RNA Pol II makes an mRNA copy that can leave the nucleus. Ribosomes then attach to and read the mRNA. They synthesize a protein by joining amino acids in the correct order. RNA Pol II has 12 subunits and the two largest, Chain A and Chain B, contain the active site where the enzyme adds fifty to ninety nucleotides per second to the growing mRNA strand. Pol II is very accurate, only making about 1 mistake every 10,000 nucleotides. When it does make a mistake or finds DNA damage, it can backtrack to correct the error. Roger Kornberg and his research group hypothesize that during transcription the bridge helix changes shape to ratchet the DNA template and transcript through the active site while holding the end of the transcript in place. When the poison alpha‐amanitin found in the Death Cap Mushroom paralyzes the bridge helix , transcription slows from 50 to 90 nucleotides per second to 2 to 3 nucleotides per minute. At this slow transcription rate, mRNA copies of genes do not get made, protein synthesis stops, and cells die. Untreated alpha‐amanitin poisoning usually causes death within 10 days. Members:
Grace Buting, Teddy Delforge, Meg Donovan, Erika Engel, Teddy Esser, Ellen Fink, Maura King, Meredith Klinker, Billy MacDonald, Katie Mark, Stephanie McGavin, Vince Moldenhauer, Paige Pichler, Nathan Rein, Katie Rieger, Hailey Rowen, Stephanie Seubert, Rachel Sladky, Ariana van Willigen
Teacher: Donna LaFlamme
Scientist Mentor: Dr. Vaughn Jackson Medical College of Wisconsin
α - Amanitin
The figure above (adapted from [2]) shows RNA Pol II in
the process of transcription and also where the poison,
α-amanitin, inserts under the bridge helix.
The blue strand represents the template strand of DNA.
The red strand is the mRNA. The green strand is the
non-coding strand of DNA. The pink dot is the
magnesium ion which binds the nucleotides that enter
through the funnel to the growing mRNA strand. The
mRNA is directed out the exit by the rudder. The DNA
enters through the jaw, is then braced by the bridge
helix, and then leaves the molecule by exiting between
the lid and the clamp. It is directed to the lid by the wall.