Chapter 13 Flashcards
Toxin ⍺-Amanitin
is a potent inhibitor of RNA polymerase II
- ⍺-Amanitin binds to RNA polymerase and jams the moving parts
of the enzyme, interfering with its ability to move along DNA
The Primary
Structure of RNA
Single stranded
Ribose sugar
Has uracil rather than thymine
The Secondary Structure of RNA
forms by folding
connects by complementary regions
The structures of DNA and RNA compared:Composed of nucleotides
Y,N
The structures of DNA and RNA compared: Type of sugar
Deoxyribosoe, ribose
The structures of DNA and RNA compared: Presense of 2’OH
N,Y
The structures of DNA and RNA compared: Bases
A G C T
A G C U
The structures of DNA and RNA compared: Nucleotides joined by
phosphodiester bonds
Y,Y
The structures of DNA and RNA compared: Double or single stranded
d,s
The structures of DNA and RNA compared: secondary structure
double helix, many types
The structures of DNA and RNA compared: stability
stable, easily degraded
Ribosomal RNA: rRNA
– Make up the ribosome, the site of protein assembly
Messenger RNA: mRNA
– Carries coding instructions for a polypeptide chain from
DNA to a ribosome.
– After attaching to ribosome, an mRNA specifies the
sequence of the amino acids in a polypeptide chain and
provides a template.
pre-messenger RNAs
(pre-mRNAs)
– Large precursor molecules are the immediate products of transcription
in eukaryotic cells.
– Pre-mRNAs are modified before becoming mRNA and
exiting nucleus for translation into protein
Bacterial cells do not possess pre-mRNAs – in
these cells, transcription takes place concurrently
with translation.
Transfer RNA: tRNA
– Serves as the link between the coding sequence of
nucleotides in an mRNA molecule and the amino
acid sequence of a polypeptide chain.
– Each tRNA attaches to one particular type of amino
acid and helps incorporate that into the chain.
Small nuclear RNAs: snRNAs
– Found in the nuclei of eukaryotic cells
– Combine with small protein subunits to form small
nuclear ribonucleoproteins (snRNPs, ‘snurps’)
– Some participate in the processing of RNA, converting pre-mRNA into mRNA.
Small nucleolar RNAs: snoRNAs
–Take part in the processing of RNA
MicroRNAs: miRNAs
Very small and abundant RNA molecules found in the
cytoplasm of eukaryotic cells
– Small interfering RNAs: siRNAs
These carry out RNA interference (RNAi)
RNAi - process in which
small RNA molecules help
trigger the degradation of
mRNA or inhibit its translation
into protein.
Piwi-interacting RNAs: piRNAs
- Found in mammalian testes
- Similar to miRNAs and siRNAs
– Role in suppressing the expression of transposable elements
(DNA sequence that can change it’s position) in reproductive
cells.
Long noncoding RNAS (IncRNAs)
- Found in Eukaryotes
- Relatively long RNA molecules
- Provide a variety of functions, including
regulation of gene expression
CRISPR RNAs (crRNAs)
- Assist in the destruction of foreign DNA molecules
- Found in prokaryotic cells
Transcription Is the Synthesis of an RNA
Molecule from a DNA template
Unlike DNA replication, where all nucleotides
are copied, only parts of the DNA molecule are
transcribed into RNA.
Transcription is a highly selective process:
individual genes are transcribed only as their products
are needed.
Transcription requires three major components:
- A DNA template
- The raw materials (ribonucleotide
triphosphates) to build a new RNA molecule. - The transcription apparatus (consists of
proteins necessary for catalyzing synthesis of
RNA)
Template strand (nucleotide strand used for transcription)
vs. Nontemplate strand (not usually transcribed)
Thus, within a gene, only one of the nucleotide strands is normally transcribed into RNA
Transcription Unit –
stretch of DNA that
encodes an RNA molecule and the sequences
needed for its transcription.
Included within a transcription unit are three
critical regions:
* A promoter
* RNA-coding sequence
* Terminator
Promoter
– DNA sequence that the transcription apparatus
recognizes and binds
RNA-coding Sequence –
sequence of DNA nucleotides
that is copied into an RNA molecule
Terminator
– sequence of nucleotides that signals where
transcription ends.
The Transcription Apparatus
RNA polymerase carries out all the required steps for
transcription.
RNA polymerase actions are enhanced by a number
of accessory proteins that join and leave the
polymerase at different stages.
Eukaryotic RNA Polymerases
Most Eukaryotic cells possess three distinct types of RNA
polymerase, each responsible for transcribing a different
class of RNA
RNA polymerase I – transcribes rRNA
RNA polymerase II – transcribes pre-mRNAs, snoRNAs,
some miRNAs, and some snRNAs
RNA polymerase III – transcribes other small RNA
molecules (tRNAs, small rRNAs, some miRNAs, and
some snRNAs
Bacterial Transcription
Initiation
– transcription apparatus assembles on the
promoter and begins synthesis of RNA
Bacterial Transcription
Elongation
– DNA is threaded through RNA polymerase
and the polymerase unwinds the DNA, adding new
nucleotides(to the 3’ end of the growing strand
Bacterial Transcription
Termination
– recognition of the end of transcription and
separation of the RNA molecule from the DNA template
Initiation comprises all necessary steps to
begin RNA synthesis:
1.Promoter recognition
2.Formation of a transcription bubble
3.Creation of the first bonds between rNTPs
4.Escape of the transcription apparatus from
the promoter
Consensus sequences
sequences that possess
considerable similarity.
Consensus sequences usually imply an important function!
Almost all bacterial promoters have –10 consensus
sequence (~10 bp upstream of the start site) sometimes
called the
Pribnow box:
– 5’ TATAAT 3’
– 3’ ATATTA 5’
Also common: –35 consensus sequence:
TTGACA
Initiation
– Initial RNA synthesis: no primer is required.
– The location of the consensus sequence
determines the position of the start site.
Elongation
– RNA elongation is carried out by RNA polymerase.
– RNA polymerase does have the ability to do some
backtracking and proofreading as well
Termination
– Transcription stops after the terminator region
has been transcribed.
There are two types of terminators:
- Rho-dependent: requires
an ancillary protein
rho factor (⍴)
It detaches due to helicase unzipping, want DNA and RNA to seperate - Rho-independent:: also
referred to as intrinsic
terminators, are able to
cause termination
without rho.
Hairpin structure
formed by inverted
repeats, followed by a
string of uracils
Which of the following phrases does not
describe a function of the promoter?
Signals where transcription ends
Eukaryotic Transcription and Bacterial
Transcription Differences
Eukaryotic cells possess three different RNA Polymerases
– Each recognizes a different promotor
- Promoter recognition and initiation are also different!
– Many accessory proteins take part in the binding of eukaryotic
RNA polymerases to DNA templates
– Different types of promoters require different proteins! - Chromatin structure in eukaryotes needs to be modified before
transcription can begin. A more open configuration is required for
the machinery access to begin transcription!
Termination: The three RNA polymerases use different
mechanisms for termination
– RNA polymerase I: Requires a terminator factor similar to rho
factor (unlike rho, this termination factor binds to a DNA
sequence downstream of the terminator)
– RNA polymerase II: Does not occur at specific sequences
(will look at more detail in Ch. 14)
– RNA polymerase III: Ends transcription after transcribing a
terminator sequence that produces a string of uracil
nucleotides in the RNA molecule.
Recent research suggests that secondary structures
(hairpin, etc) are necessary
Eukaryotic Transcription and Bacterial
Transcription Differences Initiation:
– Transcription in eukaryotes is initiated through the
assembly of the transcription machinery on the promoter
Eukaryotic RNA Polymerases
Most Eukaryotic cells possess three distinct types of RNA
polymerase, each responsible for transcribing a different
class of RNA.
RNA polymerase I – transcribes rRNA
RNA polymerase II – transcribes pre-mRNAs, snoRNAs,
some miRNAs, and some snRNAs
RNA polymerase III – transcribes other small RNA
molecules (tRNAs, small rRNAs, some miRNAs, and
some snRNAs)
Polymerase I and III Promoters
RNA polymerase I and RNA polymerase III each
recognize promoters that are distinct from those
recognized by RNA polymerase II.
Promoters for small rRNA and tRNA genes,
transcribed by RNA polymerase III, contain
internal promoters that are downstream of the
start site and are transcribed into the RNA
Regulatory promoter
: located immediately upstream of the core
promoter.
Variety of different consensus sequences may be found in the
regulatory promoters.
enhancers
Transcription activator proteins may also regulate transcription by
binding to more distant sequences
Eukaryotic Promoters
Promoters recognized by RNA polymerase II – which transcribes
the genes that encode proteins.
– Core promoter is located immediately upstream of the gene,
(the site where basal transcription apparatus binds).
– TATA box TATAAAA – one of the most common promoter
sequences ( –25 to –30 bp), bound by transcription factors
Transcriptional activator
proteins
– another class
of accessory proteins,
bind specific DNA
sequences and bring
about higher levels of
transcriptions by
stimulating assembly of
basal transcription
apparatus at the start site.
TATA box gets it started and box helps assemble apparatus
One class of accessory
proteins comprises
general transcription
factors, which along with
RNA polymerase form the
basal transcription
apparatus
group of proteins that assemble near transcription start site
and initiates minimal
levels of transcription.
