Chapter 6: Gene Expression Flashcards
This is a consensus promoter sequence that usually occurs ~25 bps upstream from the gene it primes
TATA box
before transcription, the RNA polymerase binds – generally – to this region
promoter region
what is the combined error rate of DNA polymerase and exonuclease activity?
1 x 10^7
What is the combined error rate of RNA polymerase activity?
1 x 10^4 (1 in 10,000)
What are 3 reasons why RNA polymerase has a higher error rate than DNA polymerase?
- energy conservation
- RNA mutations are non-hereditary
- much faster
What is the name of the TBP transcription-associated protein?
TATA-binding protein
this transcription-associated protein identifies and binds to the TATA box sequence with high affinity
TBP (TATA-binding protein)
What is the function of TIID protein?
distorts DNA @ the TATA box which allows for further transcription factor assembly
What is the function of the TFIIH protein?
has both helicase and kinase activity
Why are there so many transcription factors required for RNA transcription initiation?
prevents nonsense transcriptions from hyperexpression/overproduction of non-functional protein
what are promoter regions (enhancers)?
a region of DNA (upstream) that binds activator proteins that can then bind to corresponding mediator
What is the function of promoter regions (enhancers)?
method of regulating RNA pol activity
What are the two binding fates of activator protein binding to promoter regions?
- activator binds to mediator
- addition of histone-modifying and chromatin-remodelling proteins
What are the two outcomes of activator protein binding to promoter regions?
- activator binds to mediator
- addition of histone-modifying and chromatin-remodeling proteins
what is the function of mediators and activators?
allows for various methods of RNA transcription/gene expression control; can increase/decrease transcription speed
what is an advantage of splicing?
allows for the usage of a single DNA regions for the production of multiple different proteins
whats the name of snRNP?
small nuclear ribonuclear protein
what is the function of snRNPs?
bind and replace DNA regions to splice out introns
where does snRNP activity occur?
in the nucleus
what happens to mRNA after splicing
- new 5’ end is capped
- new 3’ end is polyadenylated
why must capping and adenylation occur after splicing?
ensures that immature mRNA sequences can’t be translated before exiting the nucleus
in what organisms does capping and adenylation not occur?
prokaryotes
what are 3 functions of the nucleolus?
- stable environment for rRNA and subunit synth
- recycling and modifying rRNA proteins
- rRNA transcription location
what are the 2 ribosomal subunits in eukaryotes?
40S and 60S
what region of the DNA are the ribosomal subunits sourced from?
45S precursor rRNA
how many nucleotides are in the 45S precursor rRNA?
13,000
what are the two ribosomal subunits found in prokaryotes?
30 and 50S
what is the start codon?
AUG
What are the stop codons?
- UAA
- UAG
- UGA
What is the function of tRNA synthase (tRNA ligase)?
pairs each tRNA complex with its corresponding amino acid for each codon
What is the error rate of tRNA synthase?
1 in 40,000 AAs
what is the rate of translation?
2 AA per second
what are the 3 ribosomal sites (and their functions)?
- A –> tRNA and AA binding site
- P –> peptide bond formation
- E –> ejection site
how many proteins are needed for 60S synthesis? 40S synthesis?
~49; 33
this is an estimate of a protein’s density and molecular weight as is settles in sucrose
sedimentary coefficient
what two translation factors are associated/binded with the 5’ cap of mRNA
elF4E and elF4G
what transcription factor is associated with initiator tRNA when binding to the P site of the small subunit?
elF2 protein
what are 7 steps of translation initiation?
- initiator tRNA binds to P site with elF2 protein
- 5’ cap of mRNA binds to elF4E and elF4G
- initiator tRNA runs along mRNA for AUG
- elF2 and other factors dissociate
- large subunit binds
- new aminoacyl tRNA attaches to A site
- P region forms peptide bond between AAs
about what percentage of proteins will be misfolded and dysfunctional?
~33%
about what percentage of proteins will be misfolded in general
~66%
what are the 3 methods of protein folding?
- cotranslational protein folding
- chaperone-assisted protein folding
- chaperonin rescue
what is cotranslational protein folding?
protein folding that beings spontaneously right after release from ribosome
what proteins utilize chaperone-assisted folding?
proteins with sensitive R-groups that may react easily
what machinery is required for chaperone-assisted protein folding?
hsp70 machienery and ATP
what is the function of hsp70 macheinery?
protects sensitive R-groups (using ATP) until necessary to fold them
how do hsp70 proteins respond to heat and stress?
concentrations increase to counteract unideal protein folding environment
how does ATP help hsp70 proteins?
remove Pi from bound ATP
what method of protein folding uses hsp60 proteins?
chaperonin rescue of misfolding
what are the stages of chaperonin rescue?
- incorrect protein binds to hydrophobic sites
- GroES cap contains protein in hsp60
- ideal environment for refolding is created
- correctly folded protein is released
these are misfolded proteins that stick together in large, stable complexes
protein aggregates
what is the purpose of polyubiquitin?
acts as a death/digestion tag for unwanted proteins; sends to proteosome
this is the portion of a proteosome that chops up the peptide bonds between proteins
protease
this is a portion of a proteosome that interact’s the a target protein’s polyubiquitin tag
unfoldase
this is a type of protein aggregate that is the result of highly abnormal protein misfolding
prion
why are prions so dangerous?
the collect correctly folded proteins to convert them to the stable aggregate form with no function; clogs up nervous systems
this is structure is formed when a normal protein interacts with its abnormal prion form
heterodimer
this structure results when a normal protein is converted to an abnormal prion form
homodimer
