chapter 2 and 5 Flashcards
Why are transcription and gene expression are coupled?
In prokaryotes, mRNAs are translated while they are transcribed.
what does transcription require ?
Transcription requires a template to take the DNA from RNA.
In summary, RNA polymerase is required for transcription because it is the enzyme that catalyzes the formation of the RNA strand from the DNA template.
During transcription, RNA polymerase uses nucleotide triphosphates (NTPs) to synthesize a complementary RNA strand in the 5’ to 3’ direction on the template strand 1. NTPs are the building blocks of RNA, and they are required for the formation of the phosphodiester bonds between the nucleotides of the RNA strand .
why are promoters always upstream from the starting site ?
promoters are always upstream because they provide an enzyme binding site for RNA polymerase, which must attach to DNA near a gene for transcription to occur
What is the importance of the sigma factor ?
The importance of the sigma factor essential for the initiation of transcription in prokaryotes. It enables specific binding of RNA polymerase and is responsible for promoter recognition and allows the enzyme to find the promoter region.
what is the rho factor ?
in summary, Rho factor is a bacterial protein that functions as an ATP-dependent helicase to terminate transcription by dissociating the newly synthesized mRNA transcript
what is rho independent pathways?
rho independent pathway is a process in which transcription is terminated without the involvement of Rho factor. GC rich palindrome procedees a uracil rich stretch and is facilitated by the formation of a hairpin loop that stablizes the prokaryotic mRNA but destablizes the interaction between RNA polymerase and DNA template leading to the release of the newly synthesized mrNa transcript.
why does the GC rich stem in mRNA correspond to the the gc in dna.
In summary, the GC-rich stem in mRNA corresponds to the GC-rich region in DNA because of the complementary base pairing between G and C
describe rho dependant pathways.
Rho dependent pathways
Rho = hexameric protein possessing RNA-dep ATP-ase activity
termination sequence that features regularly spaced C residues
RNA wraps around Rho while ATP hydrolysis provides energy for the dissociation of mRNA into DNA.
prokaryotes vs eukaryotes
prokaryotes have no histones but have superhelices or other high other proteins that package DNA.
prokaryotes have one polymerase and eukaryotes have polymerase for each type of RNA.
Prokaryotes lack introns only one compartment.
Prokaryotes genes are clustered into operons and polycistronic there are more proteins that are coded for the single messenger RNA.
operons linked to one promoter.
eukaryotes histone packaging, several rna polymerases, and compartmentalization where nucleus takes place.
transcription contains introns and each gene has a unique promoter.
eukaryotic polymerases : pol 1
transcribe ribsomal rna genes and are never translated
genes clustered in a nuclelous tandem array
specific sequences in promoters clalled upstream core elements
eukaryotic polymers: polymerase 2
transcribes mrNa and viral
requires class 2 transcription factors and uses tata and caat boxes in promoters
eukaryotic polymerases : polymerase 3
Pol III
Transcribes tRNA & 5S rRNA
A & B boxes HIGHLY conserved
TFIIIA needed to recognize the 5S rRNA promoter
what dictates the gene expression
basal expression always means baseline
activator proteins are proteins that bind to the dna and open the promoter and regulate and activate the promoter .
explain activation properties
acidic domains
gln rich domains
pro rich domains
explain dna binding motifs. dna has a sequence in the enhacerr region that is recognized by the dna binding motif of the activator protein.
zinc fingers
leu zipper
copper knuckle
exaples of transitional regulation
tissue specific regulation
glucokinase is only found in the liver and in enzyme that is expressed
cell specific regulation erythrocytes only enzyme to express hemoglobin in a normal person.
Developmental stage specific gene expression
EX: fetus, gamma globin
Cell cycle specific gene expression
EX: muscle cell, myoblast to fibroblast activity
describe hmRNA,hmRNP,snRNA,and snorp,and poly A, and snrp
hnRNA = heterogenous nuclear RNA is the rna found in the nucleus that will be messenger RNA after it is matured,
hnRNP = heterogenous nuclear ribonucleoprotein (ubiquitous) coats the hRNA making sure the RNA which is single stranded don’t get broken down as quicly as it is made and are bound everywhere.
snRNA = small nuclear RNA
snRNP = snRNA + protein (mRNA processssing) molecules involved in messenger RNA processing
snORP = snRNA + protein (rRNA processing) dont process out introns from messenger rna rather ribosomal rna
polyA RNA = “mature” mRNA by the time make it to cytoplasm talking about messenger RNA found in cytoplasm.
RNA vs DNA
RNA is ingle-stranded nucleic acid that contains the sugar ribose. Has a 2’ OH. Is made up of nucleotides.
-base content: U replaces T
-single stranded nature makes it more dynamic, but less stable than DNA
describe a northern southern and western blot
western blot screens for proteins. It uses antibodies to tag the substrate.
southern blot This type of blog looks for DNA. It screens for the sequence using probes.
Northern Blot
This blotting technique involves a radioactive probe binding to sample RNA . The test looks for mRNA (very short lived so radioactivity must be involved).
-benefit: you can se if a cell is making more of a specific mRNA. You can see how cells are regulating gene expression
Specifics about the promoter
Promoters are not enhancers they allow dreams to be read, but can be affected by enhancers
Initiation requires a promoter to open up, replication.
The promoter sequence determines the transcription will proceed, and only One Direction.
Prinbow box
The sequence that I conserved is the TATAAT sequence and spacing between she was highly preserved, and that is how the sigma factor recognizes where the polymerase needs to bind
