Transcription Pt. 1 Flashcards
What does a gene contain?
a transcribed segment of DNA and related regulatory elements (whatever those are)
What is a transcription unit?
a transcribed segment of DNA
What will a eukaryotic DNA segment usually contain?
the information for a single polypeptide
What will a eukaryotic DNA segment less commonly contain?
the information for a functional RNA
What is the first step of gene expression in all cells?
transcription of the information in the DNA nucleotide sequence into an RNA nucleotide sequence
What information does the transcribed RNA nucleotide sequence contain? Is this information the same or different than the gene it was transcribed from?
the same information for the polypeptide assembly as the gene it was transcribed from
What is the purpose of transcribing an RNA nucleotide sequence that is complimentary to the gene?
The gene (original copy) can be safely stored as a part of the DNA molecule while its information can be sent off into the cytoplasm in the RNA
T or F: there are not very many types of RNA molecules
False
there are 7 types
What type of RNA code for proteins?
Messenger RNA (mRNA)
If an RNA does not code for proteins, what are they called? What do they do?
All other proteins are called ‘non-coding’ and they all have distinct functions
What are the components of DNA?
A nitrogenous base
A sugar (deoxyribose)
A phosphate
What are the 4 nitrogenous bases in DNA?
Adenine
Guanine
Cytosine
Thymine
Which of the DNA nitrogenous bases pair together?
A-T
C-G
How many strands of DNA will be transcribed into RNA?
only 1
Describe a template DNA strand
one of the 2 double helices acts as a template for synthesis of the RNA molecule
it is the strand that is transcribed into RNA
How is the nucleotide sequence of the RNA transcript determined?
By the complimentary base pairing between the RNA transcript and the DNA template
Describe the structure of RNA
a linear polymer composed of 4 different types of nucleotides linked by phosphodiester bonds
In what ways are DNA and RNA similar?
they are both linear polymers made of four different types of nucleotides linked by phosphodiester bonds
List the differences between DNA and RNA
number of strands
type of sugar
type of nucleotide bases
RNA can fold into complex 3D shapes
What is the key distinguishing feature of RNA from DNA?
the sugar in RNA backbone is a ribose (at C2, there is an OH)
the sugar in DNA backbone is deoxyribose (at C2, there is an H)
What is another important distinguisher between RNA and DNA but not the main distinguisher?
RNA has uracil instead of thymine
DNA has thymine
T or F: the definitive feature of RNA that makes it different from DNA is the presence of uracil instead of thymine
False
It is the presence of a ribose sugar (has OH) instead of a deoxyribose (has H)
If the pentose sugar has four hydroxyl groups, it is ___
RNA
If the pentose sugar has 3 hydroxyl groups, it is ___
DNA
In RNA what does adenine pair with?
uracil
Describe how mRNA is transcribed and translated in a prokaryotic cell
mRNA produced by transcription is immediately translated and there’s no additional processing
How do transcription and translation of mRNA occur in a prokaryotic cell?
in the same place at the same time
there is no additional processing between transcription and translation
How do transcription and translation occur in a eukaryotic cell?
Transcription occurs separately in the nucleus
pre-mRNA (the original RNA transcript) is processed before leaving the nucleus
mRNA leaves the nucleus and is translated in the cytoplasm
Where is mRNA transcribed in a eukaryotic cell?
in the nucleus
Does processing of the RNA transcript occur in prokaryotic cells? eukaryotic cells?
No processing in prokaryotic cells
Processing in the nucleus of eukaryotic cells
Where is mRNA translated?
in the cytoplasm
What are 6 major differences between prokaryotes and eukaryotes regarding transcription?
- the presence of histones
- compartmentalization of the genetic material
- spatial and temporal differences between transcription and translation
- whether mRNA is processed
- whether an exportin is required for transcript transportation
- the presence of operons
Do prokaryotes have histones?
No
Though other proteins do pack the genetic material a bit
Do eukaryotes have histones? explain the effect of this
Yes
histones package DNA tightly and affect gene expression depending on their modifications
How is the genetic material stored in prokaryotic cells vs. eukaryotic cells?
prokaryotic: no nucleus/no compartments for genetic material
eukaryotic: nucleus is compartmentalized into different regions
How do transcription and translation occur in prokaryotic cells?
together, at the same time and in the same place
Are exportins required to transport the mRNA in prokaryotic cells?
No because there is no nucleus or separate compartments
Why are nuclear exportins required for transcription?
RNA is transcribed and processed in the nucleus and mRNA is translated in the cytoplasm
So the mRNA needs to move out of the nucleus
What are the functional units of proteins in a prokaryotic cell that can be transcribed together called?
operons
Do operons exist in eukaryotic cells? why/why not?
No because a transcription unit will encode for one protein or a functional RNA
T or F: the template strand for a given gene is always different each time transcription occurs
False
It will always be the same template strand
T or F: different genes may have different template strands
true
What is the template strand for gene b is not the same template strand for gene a
What direction is the template strand copied?
3’ –> 5’
What direction is the RNA transcript synthesized?
5’ –> 3’
Explain why the template DNA strand and the RNA transcript are complementary and antiparallel
Complimentary because RNA will be synthesized with RNA nucleotides (AUGC) that are complementary to the DNA strand (ATGC)
Antiparallel because the template strand is copied from 3’-5’ and the RNA transcript is made 5’-3’
T or F: different genes are transcribed with the same efficiencies
False
based on the cell’s needs, different genes are transcribed with different efficiencies
On an electron micrograph, how can you tell where transcription began and where it ended?
beginning: where the transcripts are very short
end: where the transcripts are very long
In eukaryotic transcription, what creates the transcript?
RNA polymerase II
Describe RNA polymerase II
an enzyme complex that creates the RNA transcript in eukaryotic cells
What are the 3 main steps of transcription?
initiation
elongation
termination
Describe the initiation process of transcription
transcription is initiated by transcription factor proteins recruiting and helping RNA polymerase
Describe the elongation process of transcription
As the RNA polymerase moves downstream, nucleotides are added one at a time to the growing transcript
Describe the termination process of transcription
When a specific the poly-A signal is reached, transcription will stop
What sequence triggers RNA polymerase to bind and start transcription?
the promoter sequence
How is the promoter sequence referred to in relation to the coding region?
upstream because it’s at the 5’ (before the coding region)
What sequence triggers RNA polymerase to fall off and end transcription?
the terminator sequence
How is the terminator sequence referred to in relation to the coding region?
downstream because it’s at the 3’ end (after the coding region)
What are the 3 RNA polymerase enzymes found in all eukaryotes?
RNA pol I
RNA pol II
RNA pol III
What is the function of RNA pol I in eukaryotic cells?
transcribes most rRNA
What is the function of RNA pol II in eukaryotic cells?
transcribes all protein-encoding genes
and snRNA and microRNA
What is the function of RNA pol III in eukaryotic cells?
transcribes tRNA and other small RNAs
What are the other two RNA polymerase enzymes found only in plants?
RNA pol IV
RNA pol V
What is eukaryotic RNA pol II similar in structure to?
bacterial RNA polymerase
Describe the function of RNA polymerases
they catalyze the formation of phosphodiester bonds that link nucleotides to form a linear chain
What is the substrate of RNA polymerases?
a nucleoside triphosphate
could be G,U,T,A,C
ex. guanine triphosphate
In what 2 ways are RNA polymerases similar to DNA polymerases?
they both catalyze the formation of phosphodiester bonds to link nucleotides
they both have nucleotide triphosphates as their substrate
In what 4 ways are RNA polymerases different to DNA polymerases?
RNA polymerase is:
- less accurate
- does not require a primer
- can unwind DNA themselves
- cannot dissociate from a transcript after initiation and before termination - the same enzyme has to complete the entire transcript
Why is it acceptable that the RNA polymerase is less accurate?
the original DNA is stored safely so it is okay if there are some errors in the RNA transcript
T or F: RNA polymerase, like DNA polymerase, can dissociate from a transcript at any point
False
the same RNA pol must complete the entire transcript
T or F: RNA polymerases can unwind DNA by themselves
True
What happens to the unwound DNA after the RNA polymerase has moved away?
it will rewind
If the template strand for the RNA polymerase is
3’ - AGGGCTGA - 5’
what is the mRNA sequence? explain
5’ - UCCCGACU - 3’
the mRNA sequence will run antiparallel to the template strand (3’-5’) and thymine will be replaced by uracil
If the (non-template) coding strand for the DNA polymerase is
5’ - AGGGCTGA - 3’
What is the mRNA sequence? explain
5’ - AGGGCUGA - 3’
the template strand will run antiparallel (3’-5’) to the non-template strand (5’-3’) and the mRNA sequence will run antiparallel to the template strand (5’-3’)
and thymine will be replaced by uracil
What is the substrate for RNA polymerase? give examples
A nucleoside triphosphate
ex. ATP, CTP, GTP, UTP
Why is RNA polymerase considered a ribozyme?
its function is catalytic (an enzyme)
What is the energy source for the reaction catalyzed by RNA polymerase?
RNA polymerase has a nucleoside triphosphate substrate
two phosphate groups are hydrolyzed which creates the energy
After two phosphate groups are hydrolyzed from the RNA polymerase substrate, what is incorporated into the growing RNA strand?
A nucleoside monophosphate
ex. AMP, CMP, GMP, UMP
whichever one was the triphosphate that was cleaved
What happens to the 2 cleaved phosphates from the RNA pol substrate?
the pyrophosphates leave
Describe transcription factors
proteins that encourage RNA polymerase to bind to the promoter region for initiation to begin
What process is a main transcription regulation point?
When transcription factors encourage the RNA polymerase to bind to the promoter region of DNA
How is transcription initiation a regulation point?
the efficiency of RNA pol can be increased or decreased by the presence of regulating transcription factors and their activity
What are the two types of transcription factors?
general
specific
Describe general transcription factors
proteins that encourage RNA polymerase to bind to almost all promoter regions
they are highly conserved
help form the initiation complex
Describe specific transcription factors?
proteins that encourage RNA polymerase to bind to promoters in specific instances (ex. specific cell types or in certain stages of development, after certain environmental changes)
What are the 3 general transcription factors looked at in this class?
TFIID
TFIIB
TFIIH
Describe the TATA box
A highly conserved section of the promoter region (just before transcription starts) made up of mostly adenine and thymine bases
Where is the TATA box located in relation to the start of transcription?
~25-30 base pairs upstream of the transcription start
What does TFIID bind to?
the TATA box region of the promoter
How does TFIID bind to the TATA box region?
through a TBP domain
TATA Binding Protein
What is a TBP domain?
TATA Binding Protein domain
What happens to the DNA when TBP binding occurs? What is the purpose of this?
when TBP binds to the DNA, it distorts the DNA so that other transcription factors can recognize the active promoter and bind to it
What does the TBP binding to the TATA box trigger?
TFIIB to binds just upstream of the TATA box
After TFIIB binds to the DNA, what happens?
Other transcription factors will bind (including TFIIH) and eventually RNA polymerase will bind
Where do all the transcription factors and RNA polymerase bind?
To the TATA box on the promoter region of the template DNA strand
What forms a complete transcription initiation complex?
RNA polymerase and the transcription factors (TFIID, TFIIB, TFIIH) bound to the TATA box on the promoter sequence of DNA
What happens after the transcription initiation complex is formed?i
the 2 DNA strands must be separated
conformational changes in the initiation complex need to occur for RNA polymerase to leave the complex and enter the elongation phase
Why do the DNA strands need to be separated?
in order for RNA polymerase to be able to access the template strand
Describe TFIIH
A large, multi-subunit protein complex that has 2 enzymatic activities:
helicase activity
kinase activity
What are the two activities of TFIIH?
helicase activity
kinase activity
Describe helicase activity - which transcription factor has this function?
TFIIH separates the DNA strands by cleaving the hydrogen bonds between nitrogenous bases using the energy from ATP hydrolysis
What separates the DNA strands in transcription initiation?
TFIIH can unwind the DNA (helicase activity) by breaking the hydrogen bonds between nitrogenous bases and use the energy from the ATP hydrolysis
What powers the process of unwinding the DNA in transcription iniation?
the energy released from ATP hydrolysis when TFIIH cleaves the hydrogen between the nitrogenous bases (helicase activity)
Describe kinase activity - what transcription factor has this function?
TFIIH phosphorylates RNA polymerase to induce conformational changes and allow it to leave the complex
How is RNA polymerase released from the transcription initiation complex?
the kinase activity of TFIIH phosphorylates the RNA polymerase which causes conformation changes
What is RNA polymerase II phosphorylated on? How does this happen?
TFIIH phosphorylates RNA pol II on a C-terminal domain (CTD) by kinase activity
Describe a C-terminal Domain (CTD)
a small tail trailing behind the enzyme that is very exposed
Where RNA Polymerase II is phosphorylated
When does initiation end?
when the first 2 RNA triphosphates are brought in to form a phosphodiester linkage
What remains when the RNA polymerase is released toward the coding region? why?
TFIID and TFIIB remain behind to initiate more transcription for the next incoming RNA polymerase
Besides transcription factors, what are the other 4 protein types required for transcription initiation?
transcription activators
mediator protein
chromatin remodeling enzymes
histone modifying enzymes
Describe transcription activators
proteins involved in transcription initiation that bind 100s - 1000s of base pairs away from the promoter at enhancer sites
Where do transcription activators bind?
at enhancer sites (100s-1000s of base pairs away from the promoter)
Describe the mediator protein
a large co-activator protein complex involved in transcription initiation
it allows transcription activators to bind to the general transcription factors at the promoter and RNA pol
Describe chromatin remodeling enzymes
proteins that are involved in transcription initiation that increase access to the DNA in chromatin (DNA bends or curves)
Describe histone modifying enzymes
proteins involved in transcription initiation that temporarily adjust histones so that the coiled DNA can be transcribed
What phase begins after the initiation complex is cleared?
elongation
How does elongation occur?
RNAPII move along the DNA template strand in the 3’-5’ to create a 5’-3’ RNA transcript
Which direction does RNAPII move along the DNA template?
3’-5’
What direction is an RNA transcript made?
5’-3’
How is the DNA helix unwound in elongation?
by RNAPII helicase activity
What forms temporarily in elongation?
an RNA-DNA hybrid
What happens to the unwound DNA after the RNAPII passes?
it is rewound
T or F: the new RNA strand is complementary to the DNA template
True
when does elongation end?
when RNAPII reaches the termination signal
What is the termination signal?
AAUUAAA sequence at the end of the coding region
What binds to the end of the coding region when RNAPII reaches the terminal sequence?
a poly-adenlyation complex
What does a poly-adenylation complex do?
cleave the RNA strand 10-35 nucleotides down so that RNA can leave
Add ~250 adenosine bases
What 3 proteins are involved in eukaryotic termination?
cleavage factors
an endonuclease
A polyadenylate polymerase
What are cleavage factors?
Proteins that are originally bound to the RNAPII CTD but transfer to the AAUAAA signal when it is transcribed
What is the function of the endonuclease in termination?
it cuts in the middle of a nucleic acid polymer
What is the function of polyadenylate polymerase in termination?
it adds ~250 adenine bases one at a time without a template
