Flashcards in Transcription Deck (99):
What are promoters and where are they located?
It is a region of DNA that initiates transcription of a particular gene and are located near the transcription start sites of genes, on the same strand, and upstream on the DNA (towards 3' region of anti-sense strand). Can be 100-1000 base pairs long.
What are sigma factors?
Subunits of RNA polymerase required for gene transcription to occur.
What is promoter melting?
The denaturization or separation of the two strands of DNA of the promoter region on binding a 3' -> 5' DNA helicase subunit of transcription factor Tfiih.
Why do bacteria transcribe genes and where does it occur?
Bacterial transcription is required to generate RNAs. This transcription process occurs in the cytoplasm.
What enzyme mediates transcription and what are its parts?
RNA polymerase is a multi-subunit enzyme that catalyzes the process of transcription where an RNA polymer is synthesized from a DNA template. It is composed of:
B - upper clamp
B' - lower clamp
a - hinge
_n_ - unknown
o- - sequence specificity
What are components to bacterial promoters?
-35 TTGACA which is recognized by Omega 70
-10 TATAAT which is recognized by Omega ___
What are sigma factors and how do they work?
Sigma factors recognize promoter elements. A sigma factor is a protein needed for initiation of transcription bacteria. IT is a bacterial transcription initiation factor that enables specific biding of RNA polymerase to gene promoters.
What sigma factor signifies normal growth?
What sigma factor signifies nitrogen assimilation?
What sigma factor signifies stationary and oxidative/osmotic information?
What sigma factor signifies a heat shock response?
What sigma factor signifies flagella synthesis?
What sigma factor signifies misfolded proteins in periplasm?
What sigma factor signifies iron transport?
What part of promoters dictates sigma factor binding?
Different sigmas have different binding sites, or promoters, that have their own key characteristics such as low nitrogen conditions, low iron conditions, low nutrient conditions, and stress responses.
What are nanoRNAs and how do they play a role in transcription initiation?
NanoRNAs are a class of small RNAs that can prime transcription initiation in bacteria. NanoRNAs are often degraded by specific nanoRNases; this degradation is harmful for the cell via an unknown mechanism.
What happens during transcription elongation?
1. dNTP comes in the pore at the top of polymerase.
2. Phosphoryl bond transfer, diphosphate leaves.
3. RNA polymerase ratchets over one nucleotide.
Process through which nucleotides are added to the growing RNA chain. Once RNA polymerase is in position at the promoter, the next step of transcription -elongation - can begin. RNA polymerase "walks" along one strand of DNA, known as the template strand in the 3' -> 5' direction. For each nucleotide in the template, RNA polymerase adds a matching (complementary) RNA nucleotide to the 3' end of the RNA strand.
What is the fidelity and the processivity of the transcription machinery in bacteria? How is it different for replication machinery?
Fidelity is the accuracy of polymerase. It is the property of an amino-acid-activating enzyme or a polymerase to correctly charge a tRNA or to correctly place a residue in a growing polypeptide or polynucleotide. It is important because it preserves the genetic identity and prevents accumulation of deleterious mutations. Processivity is how many nucleotides are incorporated as a function of time.
Replication machinery is only semi-conservative
How is transcription terminated in bacteria?
1. Formation of hairpins that slow RNA polymerase.
2. Rho factor that binds to the transcription terminator pause site. It acts at an RNA substrate, binding to nascent RNA at specific Rho-binding sites. It releases RNA and RNA polymerase from DNA.
How is transcription different in archaea?
There are no sigma factors and there is only 1 RNA polymerase because promoter architecture is different.
What kinds of post-transcriptional regulation exist in bacteria?
-Some RNA need to be processed to active form.
-RNase III processes 16S rRNA; RNase G processes 23S
-mRNAs have short half-lives
What occurs during transcription initiation?
1. Sigma binds to RNA polymerase
2. RNA polymerase slides along DNA to find promoter
3. -10 region melted
4. RNA polymerase uses dNTPs or nanoRNAs to prime
What happens during transcription termination - the rho-independent model?
1. Hairpin of GC rich region directly upstream of polyA tail
2. NusA binds to hairpin
3. RNA polymerase pauses as hairpin folds while sitting over the poly A tail
4. Weak A-T bonds of polyA tail lower the energy of destabilization of the RNA-DNA duplex and unwind the hybrid strands
5. RNA polymerase falls off
What happens during transcription termination - the rho-dependent model?
1. Rho binds to binding site on nascent RNA and processes along it
2. RNA polymerase stalls at transcription terminator site
3. Rho binds to RNA polymerase and dissociates the RNA-DNA duplex
4. RNA polymerase falls off
What is a gene?
Unit of heredity, encodes RNA molecule - codes for proteins and responsible for transcription via RNA polymerase.
How does Gene Expression regulation work?
Signals in DNA sequence tell RNA polymerase where to start and stop and how much RNA to make.
How does initiation of transcription work?
Via a promoter -> tells RNA polymerase where gene is and where to start transcription.
What direction does RNA polymerase work in?
5' to 3' direction
What does a promoter do?
What is mRNA?
Messenger RNA, codes for proteins
What is rRNA?
Ribosomal RNA, forms the basic structure of a ribosome and catalyzes protein synthesis.
What is tRNA?
Transfer RNA. Central to protein synthesis as adaptors between mRNA and Amino Acids
What is reverse transcriptase?
From RNA to DNA
How many RNA polymerase do prokaryotes have?
More transcription equals?
Less proteins via transcription
Prokaryotes can have how many templates and what do they code for?
Both the DNA strands act as templates which code for different genes
In prokaryotes, the expression of genes depend on?
What is a promoter?
Sequences that dictate transcription rate and regulates genes
Each gene is regulated by?
A specific promoter
5' and 3' ends of bacteria mRNA are unmodified because?
RNA polymerase initiates and terminates transcription at these ends
Bacteria mRNA's contain genes that?
Code for several different proteins
In prokaryotes, what is a complex/holoenzyme and what does it do?
RNA polymerase + sigma factor. It recognizes and binds promoter sequence (TATAAT-Pribnow box) to specify start site of transcription.
In prokaryotes what is AUG?
First codon read for transcription to begin
What is a Sense Strand?
5' to 3' strand
What is a Anti-Sense Strand?
3' to 5' DNA strand
Single mRNA can code for?
What are RNases?
Also known as ribonucleases. Are enzymes that breakdown RNA
What are Ribozymes?
RNA molecules that have catalytic properties that function in self-splicing. Cut itself, no protein necessary.
What is methylated as specific bases during Pre-rRNA processing?
The 30S RNA precursor
What gets liberated during the cleavage process during the processing of Pre-rRNA?
Precursors of rRNAs and tRNAs
What enzymes carry out the cleavage process during the processing of Pre-rRNA?
RNase III, RNase P, and RNase E
RNase P is a _? What does that mean?
Riboenzyme. It has self-catalytic abilities
The final products from the processing of pre-rRNA from the action of specific nucleases are?
16S, 23S, and 5S RNA
What are additional tRNA gene segments in copies during the pre-rRNA processing?
Between 16S and 23S rRNA at the 3' end of the primary transcript
How do the copies of genes in pre-rRNA chromosome differ?
Number, location, and identity of tRNAs included in primary transcripts
What is Rifampin?
Binds to B Subunit of Prokaryotic RNA polymerase preventing it from working
What is Dactinomycin?
Binds tightly and specifically to double-delical DNA and thereby preventing it from being an effective template for RNA synthesis
In Eukaryotes what is Higher Order of Organization?
Chromatin gets unfolded from transcription to allow access to proteins and enzymes by post-transitional modification
What is a Histone?
Positively charged proteins due to being rich in lysine and arginine. They neutralize negatively charged DNA phosphate groups.
How many histones are in a nucleosome?
H2a, H2b, H3, and H4 (times 2)
How many nucleotides in a nucleosome?
How many base pairs in a linker DNA?
What is Histone 1?
Functions to hold chromatin into higher order structure
Where do modifications occur?
Acetylation of lysine?
Turns on gene expression via removal of positive charge
Acetylation occurs through what?
When Histone Acetyltransferase, or (HATs), Charge becomes negative and the tails open
Deacetylation occurs through what?
When Histone Deacetylase, or (HDs), charge becomes positive and tails become closed.
Methylation on Lysine?
Turns Gene Expression on or off depending on location of lysine and number of methyl groups by binding to transcriptional regulators.
Phosphorylation of Serine and Threonine?
Regulates chromatin/chromosome structure. Mitotic chromosome condensation and DNA repair.
What is ADP?
Ribosylation on arginines - DNA repair
Acetylation and phosphorylation causes what?
Alters interactions of Histones with DNA. Affects chromatin structure due to negative charge. Relaxes chromatin by regulating transcription and binding regulators of gene expression.
Initiation of transcription in Eurkaryotes is done by?
RNA Polymerase 1, 2, and 3
What is RNA polymerase 1?
5.8S, 18S, and 28S rRNA genes
What is RNA polymerase 2?
All protein coding genes, mRNA. Transcribe around nucleosome and require transcription factors such as TFIIA, TRIIB
What is RNA polymerase 3?
tRNA genes, 5s rRNA genes
Where are RNA Polymerase compartmentalized?
What sequences are recognized by RNA polymerase 2?
CAAT box and TATA box as well as tissue-specific promoters. Position RNA polymerase at start site.
What is the TATA box?
Promoter-sequence bound by transcription factor TFIID which enables binding of TFIIB
How does TFIIH pry apart DNA double helix at the transcription start point?
With ATP allowing transcription to begin
Where do transcription factors and RNA polymerase assemble?
At the promoter
What does each globin combine with and what does it form and where?
Combines with A-globin chain to form hemoglobin in Red Blood Cells
What are enhancer sequences and where are they located?
DNA sequences that increase rate of transcription. Can be located thousands of base pairs away. It tells cells to produce a lot of RNA.
What are silencer sequencers?
Bound by repressor proteins. Sequences that prevent transcription of a gene. Code for whether gene should do faster or slower.
What signals termination of transcription?
AAUAAA sequence which is transcribed into pre-mRNA by RNA polymerase 2.
What sits of AAUAAA sequences?
CstF - Cleavage stimulation factor
CPSF - Cleavage and polyadenylation specificity factor
What is a consensus nucleotide?
Sequence that directs cleavage and polyadenylation to form the 3' end of a eukaryotic pre-mRNA
Where are the consensus nucleotide sequences encoded? How are they recognized?
In the genome and recognized by proteins as RNA after being transcribed.
What is the post-transcriptional modifications 5' methyl cap?
1st modification of eukaryote pre-mRNA added soon after transcription begins.
What does the 5' methyl cap do?
Identifies the mRNAs from other types of RNA and binds protein complex for RNA processing, export and translation.
What is RNA Splicing?
Removes introns in most pre-mRNA (most genes have introns)
What does a consensus sequence identify?
What are the three steps in transcription?
Initiation, elongation, and termination
What role do sigma factors play in bacterial transcription?
Sequence recognition and promoter melting
What are the core components of the bacterial promoters?
-35 and -10 regions for sigma 70 or the -24/-12 regions for sigma 54
What are the functions of B', B, a, w subunits?
B and B' contain the active site, a and w subunits are for assembly and stabilization, a also recognizes some promoters
What are nanoRNAs?
2-5 nt RNAs produced during transcription initiation that may function in priming/regulation
What is fidelity and processivity?
Fidelity - error rate
Processivity - incorporation rate
How is transcription terminated in bacteria?