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
Early events in prokaryotic transcription 
The sigma factor brings the polymerase into the promoter region
We see helicase activity and opening of the promoter region, the polymerase reads downstream of the promoter region
When promoter is clear, the DNA goes back to where it came from in the enzyme no longer needs factor and the sigma factor can find another polymerase
Eukaryotic promoters
Tatq box are boxes found in eukaryotic promoters for messenger RNA gene, very prominent, and highly conserved
Tata less genes housekeeping genes
CAAT box not as highly conserved
Please print motors and MRA and trna are all red by different promoters
TATA box describe it
Adina Cinco in eukaryotic promoters, crucial in forming the transcription initiation complex. It is a promoter for mrna genes
TATA less genes
It is a housekeeping, Jean always turned on and highly conservative every eukaryotic cell .
CAAT box
Essential, eukaryotic promoter sequence, that is not as highly conserved.
Prokaryotes bd eukaryotes
Prokaryotes have prinbow box
Eukaryotes have the TATA box
Tandem array
Our RNA genes are clustered in the nucleus which is moderately reiterated DNA sequence is found back to back, so ribosome RNA can have many copies
Polycistrinic vs monocystronic
Polycystronic is according pattern of prokaryotes, in which one mRNA can code for multiple proteins
Monocystronic is the coding pattern of eukaryotes in which one mRNA molecule codes for only one protein
Describe the Polymerase, one upstream court element
A specific DNA sequence relatively close to a core promoter that are polymerase one must buy near to start transcription
Transcription factors recognize it, and bring RNA poll one to read the gene if deleted RRNA gene will not be expressed
What are functional ribosomes commposed of
A large sub unit and small sub unit and each sub unit has its specific function
Prokaryotes have smaller ribosomes the new car is for sped. Unit is a unit of density talked about protein for purification
55s RNA
That is not a part of the tandem array, but it’s part of the eukaryotic ribosome. It is transcribed by rna polymerase 3 in eukaryotes.
Which 2 polymerases always need to be turned on
Polymerase 1 to make rRNA and polymerase 2 transcribes mRNA and the cell uses rRNA and tRNA
Basil expression and activator proteins
MRNa genes get turned on and off based on the sales needs these two things dictate whether mRNa is transcribed and the expression of genes .
What are enhancers
A segment of eukaryotic DNA containing multiple control elements acts upon to open up the promoter to begin transcription
What is basil expression?
This baseline expression always goes on in a gene example of a housekeeping gene
What is an activation? Property
An activator protein must have activation properties to charge a promoter region to open it up for polymerase
Domains that are acidic glen asp
Glutamine, rich domain, derivative of gin
Proline, rich domain heterocyclic
Describe DNA binding motifs
DNA has a sequence in enhancer region that is recognized by the DNA binding motives of the activator protein
Zinc fingers
Leucine zippers
And copper knuckles
Describe zinc, fingers, copper knuckles, and a leucine finger
Zinc fingers recognizes the region of DNA that is a promoter region and stabilizes the fold
Leucine zipper
Type of transcription factor in which repeating leucines four minute interaction domain in the middle of protein
Examples of transcriptional regulation
Tissue specific gene expression glucokonase is an enzyme only express in the liver and Is the first step of glycolysis can make glycogen.
Describe cell specific, gene expression
Erythrocytes are the only cell to express hemoglobin in a normal person
Describe stage specific, gene expression
Venus expresses gamma globin, but right at birth there’s a genetic switch that turns off gamma globin, and turns on globin
Cell specific, gene expression
Muscle cells can switch from myoblast, which is muscle building to fibroblast connective tissue activity to be structurally sound
Messenger RNA processing
The capping of the five end is May 1 and at risk of rnase h chewing it up and it must be cap. Extra bases are added, and then methylated later on.
Protein coating by hnRNP call the MRN after this cap for protection. These are highly concerned, basic proteins that interact with mRNA at very specific sequences called RNP boxes that protect the DNA from endonucleases
Splicing the spices zone takes out the electrons in the MRA many proteins, make up the spliceosome
Describe U1,U2,U4,U6,U5
U2 recognizes a lariat structure that is formed by the internal sequence
U1 recognizes five prime donor junction of the entrance, the Intron and extra on interphase
U4 and U6 bend the sequence over and over U5 is what links the 5 donor region with ten lariat structure
Variations and splicing
Beta thassemia means you’re not making beta globin properly due to alternate splicing premature stop codon or lcr deletion
GU to au point mutation
No longer recognizes splice site which causes U1 to recognize alternatives site alternative splicing
Describe polyadebylation
Pol 2 which is the consensesus sequence in AAUAAAG the signal to the polymerase
we are at the end of or reaching the primer end
Poly A polymerases adds poly a tail
ATP dependent
Polymerase a performs this task and is ago dependant it gets a from atp
Poly a binding protein is what the poly a tail wraps around .
Describe the steps in processing
Step one protein deposition proteins go in in the middle to be protected
Step two intro removal snorps target mRNA introns u3 u8 u13
Step three transport to cytoplasm because rRNA must be transported to the cytoplasm to be made into protein.
Ribosomes = rRNA molecules and a protein
Describe ribosomal rna processing
Tandem array structure
Highly conserved
rRNA genes are found in the nucleolus
Nuclear export mRNA processing
After the 3 end of mRNA is polyadenylated hmRNPs are exchanged for MrNps at the nuclear cytoplasmic interface
HmRNP protected in the inside they fall off and mRNPs take their place.
Describe the steps of mRNA processing
Step one capping of the five end
Step two protein coating by HnRNPs
Step three splicing of introns
Step 4 3 polyadenylatiob
Step 5 nuclear export
What is the lariat structure
A ring of intron segments that has been spliced out of a messenger ribonucleic acid molecule by enzymes
Describe alternative splicing
Post transitional RNA modification process in which some extrons are removed or joined in various combinations.
Describe transfer rna processing
Sequence outside anticodon loop are highly conserved
B= anticodon
Three introns in all tRNA genes ( 5 end of intron, 3 intron, anticodon intron)
Endonuclease cleaves the enzymes inside and exonuclease works from the outside and remove introns
