83 Questions
What is the function of RNA molecules that are usually non-coding?
They function as structural or regulatory molecules
What is the role of RNA polymerase in transcription initiation?
It binds to the dsDNA and initiates transcription at promoters
Where are promoters located in relation to the coding region of genes?
Upstream to the 5'-side of the coding region
What is responsible for interacting with the DNA in the '-helical region?
Basic amino acids
How many times is the structure repeated in TFIIIA, the RNA Pol III transcription factor?
Nine
How many C2H2 zinc fingers are usually required for DNA binding?
Three
What is the first step in gene expression?
Transcription
Which enzyme complex catalyzes transcription in prokaryotes?
RNA polymerase
What are the ribonucleotides required for transcription?
A, U, C, G
In which direction does RNA synthesis occur?
5' to 3'
Which strand of DNA carries the gene sequence that will be copied into an RNA molecule?
Sense strand
What is the enzymatic synthesis of protein from a transcribed gene sequence?
Translation
What is the function of the holoenzyme formed by the association of the σ factor?
It binds to specific promoter sequences with a 100-fold increase in affinity
What is used at very active gene promoters to help with the melting of the DNA duplex?
Negative supercoiling
What can initiate RNA synthesis without a primer?
RNA polymerase
What is present at the 5’-most end of almost all RNA?
Guanine (G)
What is the primary function of RNA Polymerase III?
Transcribing tRNAs
Which statement accurately describes the initiation of transcription?
It is initiated by the binding of RNA polymerase complex to a specific regulatory sequence on the dsDNA.
What distinguishes the promoters of different genes in terms of transcription initiation efficiency?
The conservation of elements and their ability to be stimulated by bound proteins.
In eukaryotes, which RNA Polymerase is responsible for transcribing most rRNA?
RNA Polymerase I
What is the function of promoters in transcription initiation?
Promoters help RNA polymerase bind to the dsDNA to initiate transcription
What is the role of the template strand in transcription?
It serves as the template for ribonucleotides to base-pair during RNA synthesis
What is the function of RNA polymerase in transcription initiation?
Initiating the binding of an RNA polymerase to dsDNA at promoters
What is the physiological function of Thiogalactoside transketolase (lacA) in lactose metabolism?
Its physiological function in lactose metabolism is unknown.
What is the role of the lac repressor (Homotetramer) in the lac operon?
It is responsible for low-level expression of lacZYA.
How many zinc ions does one group of DNA-binding proteins utilize for correct protein folding?
One Zn2+ ion
What is the function of Zn2+ ions in DNA-binding proteins?
To maintain correct protein folding
What does the lac operon structure consist of?
LacZYA transcription cassette, PlacI, and LacZ
In the absence of lactose, what is the status of the lac repressor (Homotetramer) in the lac operon?
Always ON
What is the role of the σ-factor in E.coli transcription?
Causing the polymerase to move forward and clear the promoter
What happens when the polymerase reaches a termination sequence in E.coli transcription?
It dissociates from the DNA
In E.coli transcription, what is the effect of stalling the polymerase at the termination sequence?
A dissociation of the core enzyme
What is the significance of the 12 bp hybrid between the template strand and the mRNA in E.coli transcription?
It keeps a constant area of RNA-DNA helix unwound
What is the function of GTP or ATP in initiating E.coli transcription?
To start the chain for mRNA synthesis
Why does a fast growth rate in E.coli sometimes lead to queuing of the next polymerase holoenzyme?
The next polymerase holoenzyme is queued awaiting the next initiation
What are the two forms of zinc finger domain?
C2H2 and CH
Where do most regulatory proteins bind on the DNA?
Major groove
What kind of proteins bind to the regulatory region of DNA to 'turn on' or 'off' the gene?
Eukaryotic transcription factors
What is the structure in the zinc finger domain that anchors the loop of amino acids?
Two cysteine and two histidine residues
What are the differences between the promoters of different genes responsible for?
Differing efficiencies of transcription initiation and involvement in their regulation.
In prokaryotes, how many RNA polymerase enzymes are present and which RNAs do they transcribe?
There is a single RNA polymerase, and it transcribes most rRNA (ribosomal RNAs).
What is the specific responsibility of RNA Polymerase II in eukaryotes?
Transcription of all protein-coding genes.
Where does the binding of RNA polymerase complex occur during the initiation of transcription?
To a specific regulatory sequence(s) on the dsDNA upstream of the gene to be transcribed.
What is the significance of the σ factor in transcription initiation?
Promoter recognition and formation of the initiation complex
What is the role of the holoenzyme in the transcription process?
Initiation of RNA synthesis and elongation complex formation
What is the composition of the complete holoenzyme in terms of subunits and bound ions?
DNA σ, two $ subunits, # subunit, #¿ subunit, and & subunit with Mg2! and Zn2! ions
What is the process that occurs stochastically over several nucleotide additions in transcription?
Dissociation of the σ factor from the core–DNA–RNA One -subunit
What is the physiological function of Thiogalactoside transketolase (lacA) in lactose metabolism?
Thiogalactoside transketolase (lacA) is responsible for converting thiogalactosides into glycogen or galactose-6-phosphate.
What is responsible for interacting with the DNA in the '-helical region?
The holoenzyme formed by the association of the σ factor is responsible for interacting with the DNA in the '-helical region.
What is the function of RNA polymerase in transcription initiation?
RNA polymerase is responsible for unwinding the DNA duplex to form an open complex with the holoenzyme during transcription initiation.
In the absence of lactose, what is the status of the lac repressor (Homotetramer) in the lac operon?
In the absence of lactose, the lac repressor (Homotetramer) binds to the operator, preventing transcription of the lac operon genes.
What is the enzymatic synthesis of RNA from a DNA template called?
Transcription
What is the process of making proteins from genetic information known as?
Translation
What enzyme complex catalyzes transcription in prokaryotes?
RNA polymerase
What are the ribonucleotides required for transcription?
ATP, GTP, CTP, UTP
In which direction does RNA synthesis occur?
5' to 3'
What are the two types of DNA strands used in transcription, and what are their respective functions?
Sense strand - carries the gene sequence; Antisense strand - template for generating a copy of the sense strand
What type of proteins bind to the regulatory region of DNA to 'turn on' (and off) the gene?
Gene Regulatory Proteins N1 – Eukaryotic transcription factors
Where do the regulatory proteins bind to the DNA?
The major groove
What is the composition of the zinc finger domain in terms of anchored amino acids and bound ions?
It has a loop of 12 amino acids anchored by two cysteine and two histidine residues that tetra-coordinate a zinc ion.
What are some of the opportunities for interactions provided by the exposed edges of the base pairs in the major groove?
Hydrogen bonding and hydrophobic interactions
What are the differences between the promoters of different genes responsible for?
Differences in transcription initiation efficiency and regulation
What are the responsibilities of RNA Polymerase I, II, and III in eukaryotes?
Polymerase I transcribes most rRNA, Polymerase II transcribes all protein-coding genes, Polymerase III transcribes tRNAs
What is the process involved in the initiation of transcription?
Binding of RNA polymerase complex to the dsDNA, binding to specific promoter sequences
How many RNA polymerase enzymes are present in prokaryotes, and what is their responsibility?
There is a single RNA polymerase in prokaryotes responsible for transcription
What is the structure that binds in the major groove of DNA in the zinc finger motif?
The "-helix
How many times is the zinc finger motif structure repeated in TFIIIA, the RNA Pol III transcription factor?
Nine times
What type of proteins are formed by over 100 steroid hormone receptor transcription factors, and how do they bind to DNA?
Homo- or hetero-dimers; by the insertion of one "-helix from each monomer into successive major grooves
What is the role of the template strand in transcription?
Serves as the template to which ribonucleotides base-pair for the synthesis of RNA
Where does the binding of RNA polymerase complex occur during the initiation of transcription?
At sites called promoters
What is the physiological function of Thiogalactoside transketolase (lacA) in lactose metabolism?
Thiogalactoside transketolase (lacA) plays a role in lactose metabolism
What process is responsible for the dissociation of the σ factor from the core–DNA–RNA One -subunit to form the elongation complex?
Transcription initiation
What experiment demonstrated the ability of the σ factor to join with another core to form a new initiation complex?
Burst of RNA synthesis on addition of core enzyme to a transcribing reaction mixture
What are the colors of the two $ subunits in the complete holoenzyme?
Yellow and green
Which ions are represented by red and orange spheres in the X-ray structure of Tth core RNAP?
Mg2+ and Zn2+ ions
What is the process called when the resulting increased size of the transcription bubble in the downstream direction must somehow be accommodated within the RNAP?
scrunching
What is the specific term for the process when the RNAP fails to escape the promoter and instead relieves the conformational tension by releasing the newly synthesized fragment?
abortive initiation
What is the main function of the holoenzyme formed by the association of the σ factor?
initiation of transcription
What is the name of the process where the RNAP reinitiates transcription from the same position after relieving the conformational tension?
reinitiation
What are the responsibilities of RNA Polymerase I, II, and III in eukaryotes?
RNA Polymerase I transcribes most rRNA, Polymerase II is responsible for the transcription of all protein-coding genes, Polymerase III transcribes tRNAs
What is the significance of the σ factor in transcription initiation?
The σ factor is responsible for the initiation of transcription by recognizing and binding to the promoter sequence on the DNA.
What distinguishes the promoters of different genes in terms of transcription initiation efficiency?
The differences between the promoters of different genes give rise to differing efficiencies of transcription initiation and can be switched on weakly or strongly based on the sequence elements present.
What is the primary function of RNA Polymerase III?
The primary function of RNA Polymerase III is to transcribe tRNAs (transfer RNAs).
Test your knowledge about the formation of a holoenzyme and its association with the σ factor, as well as the process of transcription initiation including the unwinding of DNA. Understand the steps involved in the formation of the closed complex awaiting stimulation at specific promoter sequences.
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