Card Set Information
A gene is defined as...
a segment of DNA that is used to make a functional product, either an RNA molecule or a polypeptide.
Transcription is the act of...
"making a copy"
In Transcription, you synthesize ____ from ____.
RNA from DNA
Transcription adds nucleotides to...
the growing 3' end of an RNA chain
In DNA, a promoter is...
The site for RNA polymerase binding.
What signals the begining of transcription?
What signals the end of transcription?
What is the three steps in the "central dogma" of genetics?
1) DNA Replication
DNA replication produces..
Chromosomal DNA stores....
information in units called genes
Messenger RNA is a...
temporary copy of a gene that contains information to make a polypeptide
Polypeptides become a part of...
functional protein that contributes to an organism's trait
List the flow os genetic infromation in the central dogma of genetics from start to finish.
1) DNA Replication
2) Chromosomal DNA
4) Messenger RNA
What is gene expression at the molecular level?
The overall process by which the information within a gene is used to produce a functional product.
What causes RNA synthesis to occur within a defined location?
The promoter and terminator sites
What are the regulatory sequences of DNA?
sites for binding of regulatory proteins.
What is the role of regulatory proteins?
to influence the rate of transcription.
The DNA strand that is copied is termed the...
Template Strand (non coding)
The opposite DNA strand is called the...
Coding strand (sense strand)
The base sequecne of the coding strand is _________ the RNA transcript
RNA Polymerase is..
The enzyme that catalyzes the synthesis of RNA
in a transcription bubble there is about ____ bp of DNA/RNA hybrid.
In a transcription bubble there is about ____ bp of unpaired DNA.
What is a core enzyme?
a RNA Polymerase without the sigma factor
What are the four subunits of the core enzyme?
two alphas, A beta and a beta prime (a2bb')
In addition to the four subunits, what are the two other subunits that the core enzyme may include?
δ and ω (delta and omega)
What is capable of transcribing DNA into RNA randomly?
The core enzyme is capable of transcribing DNA into RNA......
What is a holoenzyme?
A holoenzyme is a core enzyme with an added sigma factor
What is specificity?
When the subunit allows RNA polymerase to recognize promoters
Core enzyme does not recognize...
What are the three stages of transcription?
What happens in Intiation?
The promoter functions as a recognition site for initiation
What happens in Elongation?
RNA polymerase slides along the DNA in an open complex to synthesize the RNA transcript in the 5’ to 3’ direction
What happens in termination?
A termination signal is reached that causes RNA polymerase to dissociated from the DNA.
In intiation, Following the binding of RNA polymerase to the promoter, the DNA is..
denatured into a bubble known as the open complex.
Promoters are DNA sequences that __________ gene expression.
Promoters direct the exact location for the initiation of transcription by....
telling RNA polymerase where to bind on the DNA
_________ direct the exact location for the initiation of transcription by telling RNA polymerase where to bind on the DNA
The position in DNA where the RNA chain starts is called...
DNA 5' to the start site is called..
DNA 5' to the ________ is called Upstream.
______ to the start site is called upstream.
Upstream is given ______ values.
Downstream is given _____ values
DNA to the 3' side is called ....
DNA to the ____ side is called downstream.
The sigma subunit recognizes the ____ and the ___ regions of a promotoer on both DNA strands.
-10 and -35
The sigma subunit recognizes the -10 and -35 regions of a promoter on....
Both DNA strands
what is the promoter region consists of from left to right?
-35 sequence, 16-18bp, -10 sequence
what is to the right of the promoter?
Transcriptional start site
The first nucleotide that acts as a template for transcription is located at the...
transcriptional start site
The first nucleotide that acts as a template for transcription is called...
The nucleotide that is immediately to the left of the +1 nucleotide is numbered..
the nucleotide that is immediately to the right of the +1 nucleotide is numbered..
There is no ____ nucleotide in the promoter numbering system.
The binding of the RNA polymerase to the promoter forms...
the closed complex
the open complex is formed when...
~17 bp of DNA in the vicinity of the TATAAT box is unwound
What is abortive initiation?
When Many short RNAs (2-10 nucleotides) are made within the open complex without any movement of RNA polymerase.
What is promoter clearance?
When RNA polymerase eventually moves away from the promoter 5’ to 3’
When is the sigma factor released?
when promoter clearance takes places
What marks the end of initiation?
When the sigma factor is released
What are the 4 steps of transcription initiation?
1) Binding of RNA polymerase holoenzyme to form a closed complex
2) Formation of an open complex
3) Release of sigma factor
4) Promoter clearance
RNA is snythesized in a 5' to 3' direction using _______ as a precursor
When RNA is snythesized, ______ is released.
why is pyrophosphate released when RNA is snythesized?
because ribonuceloside triphophates are used as a precursor
In the synthesis of the RNA transcript, The RNA polymerase slides along the DNA creating an ________ as it moves.
In the synthesis of the RNA transcript, The __________ slides along the ______ creating an open complex as it moves.
In the synthesis of the RNA transcript, The DNA strand known as the template strand is used to make....
a complementary copy of RNA as an RNA-DNA hybrid.
In the synthesis of the RNA transcript, The DNA strand known as the ___________ is used to make a complementary copy of RNA as an RNA-DNA hybrid.
In the synthesis of a RNA transcript, RNA polymerase moves along the template strand in a ________ direction.
3′ to 5′
What are the two different mechanisms for transcription termination?
Intrinsic termination and rho-dependent
Which transcription termination only requires sequences in the DNA -> RNA?
Which transcription termination is factor independent?
Which transcription termination is rho independent?
Which transcription termination is rho dependent?
Intrinsic termination depends on....
two sequences in the RNA
What are the two sequences in RNA that intirnsic termination depends on?
1) A uracil rich sequence located at the 3' end of the RNA
2) A stem-loop structure upstream of the Us
What acts as the recognition site for the binding of the rho protein?
a sequence upstream from the terminator, called the rut site.
What are the three steps in rho-dependent termination
1) rho-protein binds to the rut site in RNA and moves toward the 3' end.
2) RNA polymerase reaches the terminator and a stem-loop causes RNA polymerase to pause
3) RNA polymerase pauses due to its interaction with the stem-loop structure and the rho protein catches up to the open complex and separates the RNA-DNA hybrid
What happens in intrinsic termination?
The stem-loop causes RNA polymerase to pause and the U-rich sequence is not able to hold the RNA-DNA hybrid together. (termination occurs)
In intrinsic transcription termination, The DNA template strand goes through ________ to make RNA transcript.
In intrinsic transcription termination, The DNA template strand goes through transcription to make .....
In intrinsic transcription termination, the RNA transcript goes through _________ to make folded RNA.
Rapid RNA Folding
In intrinsic transcription termination, the RNA transcript goes through Rapid RNA folding to make...
In intrinsic transcription termination, _______ helps cause chain termination
In intrinsic transcription termination, Folded RNA helps cause....
In bacteria, what event marks the end of the initiation stage of transcription?
The release of the sigma factor
A consensus sequence is...
is the calculated order of most frequent residues in nucleotides
An Up-promoter mutation is..
Any mutation allowing a mutated nucleotide in the core promoter sequence to look more like the consensus sequence
A down-promoter mutation is..
Any mutation allowing a mutated nucleotide in the core promoter sequence to look less like the consensus sequence
A mutation within a gene sequence changes the start codon to a stop codon. How will this mutation affect the transcription of this gene?
A mutation within a gene sequence changes the start codon to a stop codon. How will this mutation affect the translation? of this gene?
It will prevent the synthesis polypeptide synthesis
Sigma factor can slide along the _______ groove of the DNA.
How is the sigma factor able to recognize base sequences that are exposed in the major groove of the DNA?
Sliding along the najor groove
What happens when a sigma factor encounters a promoter sequence?
hydrogen bonding between the bases and the sigma factor protein can promote a tight and specific interaction
hydrogen bonding between the ____ and the sigma factor protein can promote a tight and specific interaction.
hydrogen bonding between the bases and the _________ protein can promote a tight and specific interaction.
___________ between the bases and the sigma factor protein can promote a tight and specific interaction.
What is the sequence in Pribnow's box?
at the –10 region is 5ʹ–TATAAT–3ʹ