transcription Flashcards
Enzyme that catalyzes the production of RNA on a DNA template
RNA polymerase
briefly explain the multisubunit structure in rna polymerase
core enzyme:
α (alpha): There are two of these.
β (beta): There is one of these.
β′ (beta prime): There is one of these.
ω (omega): There is one of these.
holoenzyme:
same as core and
σ (sigma): This one is special and helps the enzyme find where to start.
α, β, β′, ω - why are all these combine and which subunit is loosely bound
to make active site for polymerization [process where small units, called monomers, join together to form a larger, chain-like structure known as a polymer. ]
loosely bound - σ
template strand is also known as -
coding strand is also known as -
template strand is also known as - antisense or -ve strand
coding strand is also known as - sense or +ve or nontemplate strand
briefly explain the differences between template strand and coding strand
template strand:
template for rna synthesis
rna polymerase reads it from 3’ to 5’
= builds complementary rna strand in 5’ to 3’
coding strand:
same sequence as the rna that is produced (except for one difference, rna has uracil)
not used in the actual process of making rna but contains the information needed to determine what proteins will be made
In simple terms: the template strand is like the instructions for building RNA, while the coding strand is similar to the final product that shows what the RNA will look like.
what is the role of the σ subunit
recognize the promoter (signal start of rna and provide direction)
released after transcription begins
in which dna strand can the promoter be found
template strand
true or false:
In even the simplest organisms, there is a lot of DNA that doesn’t get turned into RNA. This means that not all parts of the DNA are used to make proteins.
true
what are some of the guidance that rna polymerase needs
- needs to known which strand of the dna is the template strand
- needs to know which parts of the dna to transcribe
- needs to find the exact spor where the transcription shld start
DNA sequences that provide direction for RNA polymerase
promoters
what are the sequence of representative promoters from E. coli
-35region:
35 bases awayy from the TSS, upstream
pribnow box:
10 bases awayy from TSS
transcription start site:
marked as +1
where the actual gene reading begins
‘upstream’ - 35 region and pribnow box (they are part of the promoters)
‘reference point’ - tss
explain promoters that are upstream
5’ to the side of the coding strand and ‘3 to the template strand
it is the % of occurrence of indicated bases
consensus bases
the base sequence of promoter regions has been determined to contain many bases in common
consensus bases
* promoter regions are rich in A-T than C-G
Part of transcription where RNA polymerase binds to DNA, the strands are separated, and the first nucleotide binds to its complement
chain initiation
chain initiation
closed complex:
open complex:
closed complex: (bind lang)
rna polymerase binds to the promoter and forms closed complex
complex that initially forms between rna polymerase and dna before transcription begins
rna polymerase able to distinguish coding and template strand
open complex:
form rna polymerase and dna that occurs during transcription
once the open complex is formed, rna polymerase can add the first nucleotide to the growing RNA strand
*a purine ribonucleoside triphosphate is the first base in RNA and binds to its complementary dna base at position +1(TSS)
chain initiation vs chain elongation in simple terms
Chain Initiation
1. Binding: The enzyme RNA polymerase attaches to a specific region of DNA called the promoter.
2. Opening: The DNA strands unwind and separate to form an open complex.
3.Starting RNA Production:
RNA polymerase adds the first nucleotide (the building block of RNA) to the growing RNA strand by pairing it with its complementary DNA base.
Chain Elongation
1. Adding Nucleotides: RNA polymerase continues to add nucleotides one by one to the growing RNA strand. Each new nucleotide matches with the DNA template strand.
2. Moving Along: As RNA polymerase moves along the DNA, the RNA strand gets longer, and the DNA strands re-anneal (come back together) behind it.
3. Completing the RNA Strand: This process continues until RNA polymerase reaches a termination signal, marking the end of the gene.
In summary, chain initiation is about starting the RNA copy, while chain elongation is about building that RNA strand by adding more nucleotides.
briefly explain chain elongation process
(refer to slides)
after dna has separated,
transcription bubble forms (at 17 base pairs wide) - this is whr rna is made
rna polymerase moves along the dna strand and adds nucleotides to the growing rna strand
- connects the ribonucleotides by forming phosphodiester bonds
after 10 ribonucleotides have been added, σ-subunit separates from the enzyme = recycled and used again
as rna polymeras move alon the dna, it twist and coils
negative supercoiling: (gg to 3’) in front of the transcription bubble
positive supercoiling: (gg to 5’)
twisting in the same direction
relax the supercoils in front of and behind the transcription bubble
Topoisomerases
briefly explain the 2 types of termination
- Intrinsic Termination
does not require any extra proteins (like rho) and is controlled by termination sites - Rho-Dependent Termination
require extra proteins, rho (ρ)
- ρ binds to the rna and chases the polymerase
Certain areas in the DNA which help end transcription.
termination sites
-by generating hairpin loops and a zone of weak binding between dna and rna (between A & U bases)
true or false:
rho-dependent termination sequences cause a hairpin loop to form
true
Ways to Control Transcription in Prokaryotes
Alternative σ factors
Enhancers
Operons
Transcription attenuation
Viruses and bacteria exert control over which genes are expressed by producing different σ-subunits that direct the RNA polymerase to different genes
(example)
Alternative σ Factors
example:
σ32 > σ70 @ higher T
[E. coli (a type of bacteria) is exposed to high temperatures (heat shock), it switches from using a regular σ factor (σ70) to a different one (σ32). This new σ factor helps activate genes that help the bacteria cope with the stress of heat, ensuring they survive the harsh conditions.]
DNA sequences that bind to a transcription factor and increase the rate of transcription
enhancers
- they are DNA sequences that increase transcription rates by binding transcription factors, which then help RNA polymerase do its job more effectively
what are transcription factors
Proteins or other complexes that bind to DNA sequences and alter the basal level of transcription (makes them )
RNA polymerase does not bind directly to enhancers, these enhancers interact with transcription factors. When a transcription factor binds to an enhancer, it helps recruit RNA polymerase to the promoter (the starting point for transcription), boosting the transcription of nearby genes.
what are the three upstream sites of E. coli genes
they are called Fis sites
- binding sites for the protein called Fis
enhancers vs promoters
(refer to slides)
enhancers:
fis sites
bind to transcription factors
increase rate of transcription
promoters:
pribnow box (core promoter)
-35 (core promoter)
UP element (-60 to -40)
bind to RNA polymerase
does not enhance TSS
determine TSS
Group of operator, promoter, and structural genes
operon
- physically adjacent to the
structural gene in the dna (located next to each other on the DNA and are usually transcribed together) - not transcribes all the time
Directs the synthesis of a protein under the control of some regulatory gene
structural gene
Triggering of the production of an enzyme by the presence of a specific inducer
induction
is a set of genes in E. coli that helps the bacteria digest lactose, a sugar found in milk
lac operon
Molecule that turns on the transcription of a gene
inducer
For example, if a bacterium needs to break down a sugar, the presence of that sugar can act as an inducer to turn on the operon responsible for making the necessary enzymes.
lac operon consists of
lacZ: Codes for β-galactosidase, an enzyme that breaks down lactose.
lacY: Codes for lactose permease, a protein that helps transport lactose into the cell.
lacA: Codes for transacetylase, an enzyme involved in lactose metabolism.
this gene produces a repressor protein that can block transcription of the structural genes. The repressor can be located some distance away from the operon.
lacI
When the lacI gene is expressed, it produces a repressor protein that can form a complex (tetramer) and binds to the operator (O) region of the lac operon.
repressor protein
This is a specific DNA sequence where the repressor attaches, blocking RNA polymerase from binding to the promoter (the starting point for transcription).
operator
The operator and promoter together help control whether the lac operon genes are turned on or off.
control sites
Repression of the synthesis of lac proteins by glucose
catabolite repression
binds to cAMP and then attaches to the promoter, enhancing the binding of RNA polymerase to the promoter. This promotes the transcription of the lac operon when lactose is available.
Catabolite Activator Protein (CAP)
Type of transcription control in which the transcription is controlled after it has begun via pausing and early release of incomplete RNA sequences
Transcription Attenuation
Transcription Attenuation possible hairpin loops
Pause Structures:
1·2 Pause Structure: When the RNA polymerase encounters this structure, it causes a pause in transcription. If this happens, transcription can terminate prematurely, stopping the production of the RNA.
Terminators:
3·4 Terminator: This structure can cause the RNA polymerase to release the RNA transcript early, preventing the full RNA molecule from being made.
Antiterminators:
2·3 Antiterminator: When this structure forms, it allows transcription to continue instead of stopping. This means the complete RNA sequence is produced.
true or false:
transcription in prokaryotes, single rna polymerase does all the work
true
-can switch sigma factor to interact w different promoters
true or false:
transcription in eukaryotes,
3 primary RNA polymerases with
different activities and recognize a same set of promoters
false - recognize a different set
of promoters
what are the 3 RNA polymerase (location)
- function
RNA polymerase I (nucleolus):
- synthesis precursors of most but not all
- ribosomal RNAs
RNA polymerase II (nucleoplasm):
- synthesis mRNA precursors
RNA polymerase III (nucleoplasm):
- synthesis tRNA
- precursors of 5S ribosomal RNA and a variety of other small RNA molecules involved in mRNA processing and protein transport
RNA Polymerase I synthesizes ribosomal RNA (rRNA)
RNA Polymerase II produces messenger RNA (mRNA) for protein coding
RNA Polymerase III generates transfer RNA (tRNA) and other small RNAs.
what are the pol II promoters
eukaryotic promoters:
they bind to transcription factors
1) upstream elements
- GC box (-40)
- CAAT box (extending -100)
2) TATAA box (25 base upstream)
3) initiator element - loosely conserved
4) downstream regulator - rare
genes that do not have TATA boxes
TATA-less promoters
why is TATA box necessary for transcription
as it orients the RNA polymerase correctly
it eliminated the TATA box in these genes causes transcription at random starting points
briefly explain the initiation of transcription
forms PIC, preinitiation complex, whr control of transcription occurs
PIC: RNA pol + GTFs, general transcription factors
GTFs: 6 transcription factors that bind to DNA
order of events of transcription
index card
what is the eukaryotic consensus sequence for termination
AAUAAA
Giant protein complex that bridges the promoter and general transcription factors with remote silencers and enhancers
Mediator
a structure where the eukaryotic DNA is supercoiled
chromatin
- tightly packed state, RNA polymerase II has no access to the promoter regions and transcription cannot occur
chromatin structure depends on what for the relied of repression
chromatin remodeling complexes:
uses ATP to change the structure of nucleosomes
= dna more open and accessible
histone-modifying enzymes:
make chemical changes to histones of dna
= rna polymerase access for transcription
to activate transcription, cells need to open up tightly packed dna using chromatin remodeling and histones modifications
acetylation vs deacetylation in the modifications of histones
acetylation:
HATs histone acetyltransferases adds acetyl groups to the histones
removes + charge
reduces the attraction to -ve charged dna
= less tightly bound n more open, allow transcription
deacetylation:
reversed by HDAC histone deacetylase
restores the charges on histones
= tightly packed, stops transcription
true or false:
98% of transcriptional output of human genomes comprises noncoding RNAs
true
these are small double-stranded RNA (dsRNA) that are involved in control of gene expression via several related mechanisms
noncoding RNAs, NcRNAs
what are the 2 types of noncoding RNAs
miRNA, micro:
endogenous (naturally produced inside the cell)
22 nucleotides long
- affects gene expression
- growth and development
siRNA, small:
exogenous (come from outside the cell)
21-25 nucleotides long
- control gene expression
- selective suppression of genes
help both regulate how genes are turned on and off
what are the different types of binding domains
dna-binding domains: part of a transcription factor that binds to the dna
- helix-turn-helix HTH
alpha helix tht fits into the major grooves
20 aa - zinc finger
transcription factor of rna polymerase III, TFIIIA
9 repeating structures of 30 aa
2 cys & 2 hid spaced after 12 aa - basic region leucine zipper bZIP
residues of lys, arg and his
what are the modification in tRNA and rRNA
tRNA:
methylation
subs of sulfur for oxygen
rRNA:
methylation in prokaryotes and eukaryotes
what are the modifications in mRNA
- capping 5’ end
guanylate residue - methylated at N-7 position
to form a protective cap from exonuclease degradation - polyadenylating 3’ end
100 - 200 (A) nucleotides long = poly-A tail
protects the mRNA being degraded by nucleases and phosphates
help mRNA exits - splicing of coding sequences
exons - expressed
introns - not expressed
hence removal of introns and join the exons tgt = fully functional
splicing - guided by small proteins and snRPS, small nuclear ribonuclear proteins
different forms of a protein produced by alternative splicing reactions
what are the 2 possible differences
isoforms
- 2 forms of the mRNA in the same cell
- 1 form in one tissue but a diff from in another tissue
it catalyze their own self-splicing
ribozymes
what are the 2 types of ribozymes
group I ribozymes:
require external nucleotide, Guanosine
group II ribozymes:
do not require external nucleotide
display a lariat mechanism
