transcription Flashcards
(64 cards)
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.]
