Transcription Flashcards
What is transcription?
- Transcription is the first step of gene expression.
- Transcription is the mechanism by which a template strand of DNA is utilized by
specific RNA polymerases to generate one of the four classes of RNA
It is also called DNA directed synthesis of RNA.
Describe the types of RNA
1. Messenger RNAs (mRNAs): This class of RNAs are the genetic coding templates used to determine the order of amino acids incorporated into an elongating polypeptide in the process of translation.
2. Transfer RNAs (tRNAs): This class of small RNAs form covalent attachments to
individual amino acids and recognize the encoded sequences of the mRNAs to
allow correct insertion of amino acids into the elongating polypeptide chain.transfers amino acids to the site of protein synthesis
3. Ribosomal RNAs (rRNAs): This class of RNAs are assembled, together with
numerous ribosomal proteins, to form the ribosomes. Ribosomes engage the mRNAs and form a catalytic domain into which the tRNAs enter with their
attached amino acids. The proteins of the ribosomes catalyze all of the functions
of polypeptide synthesis. forms part of the structure of ribosomes which are site of protein synthesis.
4. Small RNAs: This class of RNAs includes the small nuclear RNAs (snRNAs)
involved in RNA splicing and the microRNAs (miRNAs) involved in the modulation
of gene expression through the alteration of mRNA activity.
What are the similarities between transcription and replication?
- its fundamental chemical mechanism
- its polarity during synthesis is the same-: they are both in the 5’ → 3’ direction
- its use of a DNA template
- it has 3 phase :- initiation, elongation, and termination phases
What are the differences between transcription and replication?
Transcription differs from replication in;
1. it does not require a primer while replication requires a primer
2. involves only limited segments of a DNA molecule while replication the entire chromosome is copied
3. only one DNA strand serves as a template while in replication both strands are used as templates.
4. ribonucleotides are used in RNA rather than deoxyribonucleotides
5. U replaces T as the complementary base pair for A in RNA
Differentiate between a template strand and non-template strand
The strand that serves as template for RNA synthesis is called the template strand.
The DNA strand complementary to the template, the non-template strand, or
coding strand, is identical in base sequence to the RNA transcribed from the gene,
with U in the RNA in place of T in the DNA
What is a primary transcript?
The RNA being transcribed is called the primary transcript.
The information in the DNA is being read in the 3’→ 5’ direction, and the transcript is being synthesized in the 5’→ 3’ direction
Describe the types of RNA polymerases
RNA polymerase I - catalyzes synthesis of ribosomal RNA. is responsible for the synthesis of only one type of RNA, a transcript called pre-ribosomal RNA (or pre-rRNA), which contains the precursor
for the 18S, 5.8S, and 28S rRNAs.
RNA polymerase II- catalyzes synthesis of messenger RNA and
some specialized RNAs. RNA polymerase II requires an array of other proteins, called transcription factors, in order to form the active transcription complex.
RNA polymerase III- catalyzes synthesis of transfer RNA, the 5S rRNA, and some other small specialized RNAs.
Briefly list the functions of sequence elements
- Shows where transcription is suppose to start from
- Contributes to the mechanisms that control how frequently transcription is to
occur.
* Mutations in these regions reduce the frequency of transcriptional.
* Typical of these DNA elements are the GC and CAAT boxes, so named because of
the DNA sequences involved. - A third class of sequence elements can either increase or decrease the rate of
transcription – called enhancers or suppressors depending on their effect.
Describe the function of a sequence element in relaation to a TATA box
- Shows where transcription is suppose to start from.
* Most mammalian genes have a TATA box that is usually located 25–30 bp upstream
from the transcription start site.
* Mutation or inactivation of the TATA box markedly reduces transcription of genes.
* A small number of genes lack a TATA box. In such instances, two additional
elements, an initiator sequence (Inr) and the so-called downstream promoter
element (DPE), direct RNA polymerase II to the promoter.
* The proteins that bind to Inr in order to direct pol II binding include TFIID.
* Promoters that have both a TATA box and an Inr may be stronger than those that
have just one of these elements
Explain the initiation phase of transcription
The sequence of bases on DNA where transcription is supposed to start from are called promoters.
The promoters have an initiator sequence or a TATA box. The sequence of bases at the TATA box TATAAA in the 5’ →3’ direction and ATATTTT in the 3’→ 5’ direction.
The following bind to the TATA box to create a transcription initiation complex( Transcription bubble). TATA binding proteins, transcription factors and RNA polymerases.
RNA polymerase then starts transcription.
Describe the assembly of RNA polymerase and transcription factors at a promoter in order for initiation to occur
- The formation of a closed complex begins when the TATA-binding protein (TBP)
binds to the TATA box. - Transcription factor IIB (TFIIB) then binds to TBP-TATA box.
- TFIIA binding (although not always essential) stabilize the TFIIB-TBP complex on the
DNA. - The TFIIB-TBP complex is next bound by another complex consisting of TFIIF and Pol
II. TFIIF helps Pol II bind to the promoters. - TFIIE and TFIIH bind to create the closed complex.
* TFIIH has DNA helicase activity that promotes the unwinding of DNA near the RNA
start site thereby creating an open complex. Hydrolysis of ATP is required
Describe the elongation phase of transcription
As the RNA polymerase moves along the DNA, it untwists the double helix.
The enzyme then adds nucleotides at the 3’ end of the growing strand.
Behind the point of RNA synthesis, the double helix re forms and the RNA molecule peels off.
2. Elongation: DNA unwinding occurs in order to provide access for appropriate base
pairing to the nucleotides of the template strand.
* During elongation, the activity of the polymerase is greatly enhanced by proteins
called elongation factors.
* The elongation factors suppress pausing during transcription.
* The extent of this transcription bubble (i.e., DNA unwinding) is constant
throughout transcription and has been estimated to be about 20 bp per
polymerase molecule.
* Topoisomerase both precedes and follows the progressing RNAP to prevent the
formation of superhelical complexes.
* Elongation involves the addition of ribonucleotides to the 3’–OH of the elongating
RNA with the release of pyrophosphate.
Describe the termination phase of transcription
- Termination: Termination of the synthesis of the RNA molecule is signaled by a
sequence in the template strand of the DNA molecule—a signal that is recognized
by a termination protein, the rho (ρ) factor.
* Rho is an ATP-dependent RNA-stimulated helicase that disrupts the nascent RNADNA complex.
* In E. coli transcriptional termination occurs by both ρ-dependent and ρ-
independent means
What post transcriptio modifications occur?
Post transcription modification.
1. 5’ capping: This takes place in mRNA where guanine is added to the 5’ end to protect mRNA from hydrolytic enzymes (ribonucleases) and is also the point of attachment to the ribosomes.
2. Addition of poly A to the 3’ end : This also happens in the mRNA. The 3’ end is cleaved, and 80 to 250 A residues are
added to create a poly(A) “tail.” The poly (A) tail help protect mRNA from enzymatic destruction. Many prokaryotic mRNAs also acquire poly (A) tails, but these tails stimulate decay
of mRNA rather than protecting it from degradation
3. Splicing of mRNA: the primary transcript of mRNA contains non coding segments(introns) and coding segments( exons). In splicing, the introns are removed from the primary transcript and the exons are joined to get a continuous coding sequence that specifies a functional polypeptide.
Which drugs/substances cause selective inhibition in RNA polymerases?
- The elongation of RNA strands by RNA polymerase in both bacteria and eukaryotes
is inhibited by the antibiotic actinomycin D.
* The planar portion of this molecule inserts (intercalates) into the double helical
DNA between successive G-C base pairs, deforming the DNA. This prevents
movement of the polymerase along the template. - Acridine inhibits RNA synthesis in a similar fashion.
- Rifampicin inhibits bacterial RNA synthesis by binding to the β subunit of bacterial
RNA polymerases, preventing the promoter clearance step of transcription. - The mushroom Amanita phalloides produces α-amanitin, which disrupts mRNA
formation in animal cells by blocking Pol II and, at higher concentrations, Pol III
