Download Study Guide for Transcription.

Study Guide for Transcription.
--RNA vs. DNA:
Ribose instead of deoxyribose
Uracil instead of thymine
RNA is usually single stranded
RNA is usually short compared to DNA
RNA is much less stable than DNA
--in RNA, U and G can base-pair. There are also other unusual pairings that occur in RNA but not in DNA
--single stranded RNA has secondary structure: stem-loops form when bases pair up. Also, a
pseudoknot forms when the bases of a loop pair with a different part of the RNA molecule.
--RNA molecules that can catalyze chemical reactions (that is, act as enzymes) are called ribozymes.
Most ribozymes are part of RNA/protein hybrid structures: ribosomes are a good example.
--The RNA World hypothesis: the idea that the first “living” things on Earth were RNA molecules that
can both store information and catalyze chemical reactions. No real evidence for this theory, but
ribozymes are often found in important and widespread mechanisms, such as ribosome splicing,
telomere maintenance, and protein synthesis.
--transcription is performed by the enzyme RNA polymerase. It uses ribonucleoside triphosphates
(rNTPs or just NTPs) as raw materials.
--RNA polymerase binds to a promoter sequence on DNA and starts transcribing. Unlike DNA
synthesis, RNA synthesis does not require a double stranded primer to get started.
--the promoter is a consensus sequence: a group of similar sequences that all function as
promoters.
--the promoter is located just upstream (5’ to) the start of transcription.
--in bacteria, RNA polymerase has a special subunit called the sigma factor, which recognizes the
promoter and causes RNA polymerase to bind. Once transcription gets started, the sigma factor falls
off. There are several different sigma factors, which recognize different genes and are used under
different conditions.
--RNA is synthesized from 5’ to 3’: the first nucleotide of a new RNA molecule has a free 5’ end, and the
last base has a free 3’ end. New nucleotides are added to the 3’ end.
--The DNA strand that RNA polymerase uses as a template is called the template strand or the
anti-sense strand. The other strand, which is not used by RNA polymerase, is called the coding strand
or sense strand, because the nucleotide on it match the nucleotides of the RNA.
--in bacteria, transcription is terminated in 2 possible ways: rho-independent and rho-dependent. Rho is
a protein
--rho-independent termination occurs when a stem-loop structure in the RNA is immediately
followed by a sequence of U’s. Since A-U base pairs are weaker than G-C base pairs (because A-U has 2
hydrogen bonds while G-C has 3), the RNA polymerase is only weakly held onto the DNA template. As
the stem-loop forms, it pushes the RNA polymerase off the DNA, terminating RNA synthesis.
--in rho-dependent termination, the rho protein moves from 5’ to 3’ on the RNA, the formation
of a stem-loop in the RNA slows RNA polymerase down. This allows rho to catch up to the RNA
polymerase, which causes it to fall off the DNA, ending transcription
--there are 3 different RNA polymerases in eukaryotes (only 1 in bacteria). RNA polymerase 2 (pol2) is
the one that transcribes protein-coding genes.
--initiation in eukaryotes is very similar to bacteria: RNA polymerase binds to a promoter sequence with
the help of various transcription factors (which are proteins that bind to the DNA at the start of
transcription). The initiation complex goes from a closed complex to an open complex when a helicase
enzyme unwinds the DNA at the promoter to create a short single-stranded region.
--in eukaryotes, transcription is not terminated at a definite site. Instead, the RNA is cut at a
polyadenylation site, and 100-200 A nucleotides are added to the 3’ end: this is a poly-A tail.
--in eukaryotes (but not bacteria), RNA is processed before it can be translated. The exact copy of the
gene made by RNA polymerase in the nucleus is called the primary transcript. After being processed,
the RNA is called messenger RNA (mRNA).
--RNA processing involves 3 steps: 1. Adding a cap to the 5’ end. The cap is 7-methyl guanine,
and it is attached through a 5’-5’ linkage to the RNA. 2. Adding a poly-A tail to the 3’ end. 3. Splicing out
introns.
--Introns are sequences found in the primary transcript that are removed before the RNA is translated
into protein. Exons are the sequences in the primary transcript that become part of the messenger RNA
that is transported into the cytoplasm.
--most but not all eukaryotic genes have introns.
--introns are spliced out by spliceosomes, which are assembled from several snRNPs, which are
protein/RNA hybrids that bind to splicing signals on the RNA.
--some genes use several different splicing patterns: sequences that are spliced out as introns in
one cell type can be used as exons in a different cell type. The different proteins produced by these
alternate splicings are called isoforms.
--Transport of mRNA out of the nucleus is a controlled process: mRNA is transported only if it is carrying
proteins that indicate a proper 5’ cap, 3’ poly A tail, and correct intron splicing.
--RNA editing is a process by which the nucleotide sequence of an RNA is altered, by chemically
modifying specific bases, or by adding in new bases. It is a relatively rare process. In one example, a CAA
sequence is modified by deaminating the C to U. This changes the sequence to UAA, which is a stop
codon.
--RNA polymerase 1 transcribes 3 of the 4 ribosomal RNAs. All 3 are transcribed as a single RNA
molecule, which is then cut up. The ribosomal RNA genes occur in large tandem arrays on several
different chromosomes. Ribosomes are assembled in the nucleolus, an organelle in the nucleus, which
sits on top of the ribosomal RNA genes.
--RNA polymerase 3 transcribes transfer RNA genes, the 4th ribosomal RNA gene, and several other
small functional RNAs. Several nucleotides in transfer RNA are modified by enzymes into non-standard
bases. The promoters for RNA polymerase 3 genes are downstream from the transcription start site,
within the transcribed region.