Regulation of Transcription and Translation Flashcards
what are the prokaryotic elongation factors?
EF-tu, EF-G
process of tRNA being linked to appropriate AA?
tRNA charging, resulting in aminoacyl-tRNA (because specific nucleotides in anticodon and AA-accepting arm allow correct tRNA to be recognized by synthetase enzyme
prokaryotic rRNA
smaller, contain 3 types of rRNA instead of 4
why is alpha amanitin so deadly?
it inhibits transcription in eukaryotes by binding to rna polymerase II
2nd step translation
carboxyl end of polypeptide chain is uncoupled from tRNA at P site and joined by a peptide bond to the free amino group of the amino acid linked to the tRNA at the A site
size of large and small subunits in eukaryotes?
large = 60S small = 40S
who does ricin inhibit translation?
causes eukaryotic ribosome inactivation: catalytic inactivation of 28S rRNA via N-glycosidase action on A.
can rRNA do anything by itself
no it must be bound to protein to be functional
what is alternative splicing?
mRNAs can be spliced different ways to produce different protein products from the SAME gene!
what are introns
long noncoding intervening sequences that need to be spliced by spliceosomes (snRNPs)
what are negative regulators (gene specific transcription factors)?
prevent recruitment of RNA polymerase
mechanisms of genetic switches
proteins recognize and bind to specific dna sequences by activating or repressing (activators enhance binding to promoter or opening DNA helix, repressors bind to sequences upstream from promoter and prevent binding to promoter)
when are the poly A tail and 5’ guanosine cap added to mRNA? (aka when is mRNA processing)
as the mRNA primary transcript is being produced from the RNA exit channel (the factors responsible for capping, splicing and polyadenylating are bound to the back of RNA polyII)
what is the weight of eukaryotic ribosomes?
80S
how does streptomycin inhibit prokaryotic translation?
prevents initiation by preventing formation of initiation complex, hinders elongation via codon misreading/insertion of improper AA in the A binding site
what are exons
expressed sequences encoding proteins
which are the translation initiation factors in eukaryotes?
eIF (eukaryotic initiation factors), eIF2, eIF3, eIF4A, eIF4E, eIF4G, eIF5B
how is translation terminated?
release factor (RF) binds to stop codon in A site (called RF in prokaryotes, eRF in eukaryotes)
why does tRNA have a cloverleaf shape?
it is single stranded so can fold upon self
what is the specific function of the CAAT box and GC box?
improves the efficiency of transcription
describe the prokaryotic promoter region
has two sequences, -10/Pribnow box TATAAT and -35 TTGACA
what are positive gene specific transcription factor regulators?
recruit transcription factors and RNA polymerase
what is rho independent transcription termination
the polymerase requires 2 sequences in the RNA (a GC rich hairpin and 8 uridines) in order to induce release of polymerase
where does translation occur?
cytoplasm
4th step translation
small subunit moves exactly 3 nucleotides along mRNA molecule, bringing it back to its original position relative to large subunit, resetting ribosome with empty A site for step 1
what does the aminoacyl site of ribosome do?
binds appropriate aminoacyl-tRNA determined by the codon-anticodon base pairing
MOA of rifampin
binds to beta subunit on bacterial rna (SPECIFICALLY prokaryotic) and prevents rna synthesis because RNA polymerase cannot initiate
what specific enzyme does tRNA require to function?
aminoacyl-tRNA synthetases, of which each amino acid has its own version
what do snRNPs do
they are small nuclear ribonucleoproteins starting with U’s (U1,U2,U4,U5,U6) that recognize beginnnig of intron and end of introns in mRNA
what is the general function of rRNA?
is not translated, acts as a structural molecule, forming subunit of ribosome when combined
what is the sequence of translation initiation in prokaryotes?
shine dalgarno sequence, 10 bases upstream from start codon, that base pairs with 16S rRNA on the 30S subunit
How many types of RNA polymerase?
3
what is the shine dalgarno sequence?
ribosome binding site within mRNA sequence in prokaryotes that is 10 bases upstream from start, it base pairs with 16S rRNA (30S) which allows to recognize RNA and sets up the ribosome in the right position to start translation
what happens when histone’s lysine tails are deaceytlated?
histones remain closely linked and dna transcription is repressed
what does the large subunit of ribosome do?
catalyzes the formation of peptide bonds that covalently link AA together into a polypeptide chain
what is the main function of DNA methylation?
covalent attachment of methyl group to cytosine bases (that are located 5’ to guanosine) in the promoter region of DNA represses genes
what does mRNA generally look like?
5’ guanosine cap, untranslated region (UTR), start codon AUG, coding region , stop codon, and the trailer aka polyA tail
what is different about the prokaryotic genome?
is organized in a polycistronic way, meaning many of their genes are found in operons in which multiple genes are encoded by one transcriptional unit
what if microRNA is not an exact match to mRNA?
mRNA is stored and eventually degraded
what is the function of the 5’ cap?
7-methyl guanosine seals 5’ end and decreases the rate of degradation and serves as recognition site for the binding of the mature mRNA to a ribosome at protein synthesis initiation
which drugs are translation inhibitors?
streptomycin, tetracycline, clindamycin, erythromycin, ricin
what are the eukaryotic elongation factors?
eEF-1, eEF-2
what if the microRNA is an exact match to the mRNA?
if complementary to mRNA, then the mRNA is degraded and RISC is released
what is rho dependent transcription termination?
the rho protein binds a cytosine rich region in new mRNA, travels in a 5-3’ direction so when rho comes into contact with the rna polymerase it physically knocks off the rna polymerase
main difference between prokaryotic and eukaryotic gene structure?
prokaryotic genes have operons and polycystonic genes
what are the prokaryotic initiation factors?
IF-1, IF-3, IF-2
how many eIF?
12 +
size of large and small subunits in prokaryotes>
large = 50S small = 30S
general mechanism of ribosome?
bring tRNA and mRNA together and coordinates translation
3rd step translation
shift of large subunit relative to small subunit moves the 2 tRNAs into the E and P sites of the large subunit
biggest differences between eukaryotic and prokaryotic translation?
- binding of mRNA to small ribosomal subunit
- first AA
- initiation factors
- ribosome size
what enzymes regulate gene transcription through histone modification?
histone acetyltransferase (HAT) histone deacetyltransferase (HDAC)
what happens when histone’s lysine tails are acetylated?
chromatin is relaxed and loosely associated with histone, DNA is available for transcription
what occurs when iron is low in cells?
iron response protein binds to IRE in transferrin mRNA and stabilizes it to allow for translation (on 3’ end) to increase expression of transferrin; it also binds to the IRE on the 5’ end of ferritin mRNA to shut down expression of ferritin
what are microRNAs?
short, noncoding RNAs that bind mRNA in 3’ UTR, they are transcribed from the genome in a large form that requires cleavage and binding to RISC to be active
general mechanism of tRNA?
links mRNA sequence to corresponding amino acid -physical link between nucleotide sequence of RNA and amino acid sequence of proteins
MOA of interchangable RNA polymerase subunits in gene regulation
the RNA polymerase associates with different versions of sigma subunit which gives specificity to specific gene promoters
what does the small subunit of ribosome do?
matches tRNA to codons of mRNA
describe the prokaryotic RNA polymerase
the functional unit consists of the 5 subunit core enzyme and a sigma factor (sigma 70)
tRNA processing occurs where?
in nucleus, transcribed by RNApolymerase III with introns first, then spliced, then CCA added to 3’ end
what type of RNA polymerase transcribes mRNA or protein coding genes?
RNA polymerase II
what causes binding of mRNA to small ribosomal subunit in prokaryotes?
the shine delgarno sequence upstream of AUG binds to complementary sequnce in 16S rRNA
what does the ejection site do?
binds free tRNA (AA free) before it leaves the ribosome
where is rRNA synthesis and processing occur? and how?
nucleolous by rna pol I, 45S transcript made which is then cleaved into 3 mature rRNA (5.8S, 18S, 28S) then 5S is transcribed by rna polIII
how many IF?
3
2 translation factors?
translation initiation factors and translation elongation factors
how does diptheria toxin inhibit translation?
inactivates eukaryotic eEF-2 through ADP-ribosylation
what do the TFII’s do in transcription?
form the pre-initiation complex for RNA polymerase II during eukaryotic transcription, help bind, recruit, helicase, bridge
binding sites for tRNA on ribosome?
aminoacyl site (A), peptidyl site (P), ejection site (E)
how does clindamycin inhibit prokaryotic translation?
binds to 50S subunit, overlapping A and P sites to block peptidyl transferase activity (peptide bond formation)
2 means of gene regulation in prokaryotes?
- interchangable rna polymerase subunits
2. genetic switches
what causes the binding of mRNA to the small ribosomal subunit in eukaryotes?
the cap at the 5’ end binds the eIF’s and the 40S subunit containing the tRNA at the start codon
what is the difference between pre-mrna and mature mrna?
pre- has introns and exons, no cap or tail
1st step translation
tRNA carrying next amino acid in chain binds to the vacant A site on the ribosome by forming base pair with the codon that is exposed there
what are the 4 functional units of RNA polymerase?
- Jaws - to clamp around DNA template and hold into place
- ribonucleoside triphosphate tunnel - to allow free ribonucleoside triphosphates into the active site
- active site - enzymatic activity adding nucleotides to 3’ end
- RNA exit channel - point of exit for newly formed mRNA
is tRNA translated?
no, but is an important part of mRNA translation, 20 different tRNAs one for each AA
how does tetracycline inhibit prokaryotic translation?
inhibits aminoacyl-tRNA binding at A site during elongation
weight of prokaryotic ribosomes?
70S
first AA in eukaryotes?
Met
what happens if cytosine is methylated?
gene is not transcribed
example of gene specific transcription factors?
myo-D in myogenesis, binds to promoter region that are important to myogenic process
what does the peptidyl site of ribosome do?
binds to peptidyl-tRNA (tRNA bound to the peptide being syntheized)
what 4 things are needed for translation?
processed mRNA molecule, tRNA, ribosomes, translation factors
what are the 3 general components of a eukaryotic gene?
promoter, regulatory sequences, coding region
what occurs if the anticodon and amino acid accepting arm both allow correct tRNA to be recognized by synthetase?
an aminoacyl-tRNA is formed
3 types of RNA?
mRNA = messenger rna, encodes a protein rRNA = ribosomal rna, component of the ribosome tRNA = tranfer rna, translates the information encoded on mRNA into AA sequence
eukaryotic rRNA
contain 4 types of rRNA = 18S, 28S, 5S and 5.8S,
what is the function of the polyA tail?
prevents degradation of mRNA until it is translated
what is the specific function of TFIID?
the TATA binding protein
what occurs when iron is high in cells?
iron binds to IRP (iron response protein) and releases it from the transferrin receptor in mRNA and causes it to degrade to decrease cellular uptake of iron, iron also binds to IRP of ferritin mRNA and allows for its translation to increase iron storage
7 steps of prokaryote transcription
- holoenzyme binds to promotor site
- rna polymerase unwinds dna
- transcription starts
- after first 10 bases, sigma factor is released
- rna polymerase changes form slightly and continues
- rna polymerase reaches termination sequence
- hairpin structure disrupts polymerase and dissociates with DNA
function of polyribosomes
more protein molecules made in a given amt of time due to a large cytoplasmic assembly of several ribosomes spaced apart along a single mRNA molecule
3 types of eukaryotic regulation of transcription
OVERALL: promotion or prevention of transcription initiation complex assembly
- histone modification
- DNA methylation
- gene specific transcription factors
what is the function of sigma70 in RNA polymerase?
has a high affinity for DNA and binds specifically to the -35 and -10 sequences of the promoter - important to recruit core enzyme for initiating transcription
what is the first step of transcription in eukaryotes?
TFIID binds to the TATA box
TFIID recruits TFIIB
then TFIIE, TFIIF, TFIIH and the associated RNA polymerase bind to TFIID/B complex and begin
what is the promoter region in eukaryotes comprised of?
TATA box at -25, CAAT box and GC box at -40 to -110
what is the unique characteristic of prokaryotic gene replication?
transcription and translation can occur simultaneously because prokaryotes do not have a nuclear envelope or have to ship their DNA to the cytoplasm
how do mRNA molecules leave the nucleus?
the exon junction complex (EJC) associates with mRNA, associates with nuclear pore complex and escorts it out of the nuclear pore
How does release factor work for termination?
peptidyl transferase adds water molecule to peptidyl-tRNA instead of an amino acid which frees the carboxyl end of the polypeptide chain from its attachment to tRNA molecule
what is the weight of mitochondrial ribosomes?
55S
2 functional domains on tRNA
1anticodon region = recognizes speciifc codon in mRNA
2 amino acid attachment site on opposite side
what is the first amino acid in prokaryotes?
formyl-methionine
what happens if cytosine/promoter is demethylated?
gene is transcribed
