Gene Regulation in Prokaryotes CP 36-42 Flashcards
when will RNA polymerase stop transcribing DNA?
RNA polymerase will keep transcribing DNA util it reaches a termination signal.
Rho-independent terminator (prokaryotic)
DEF: Transcriptional terminator that does not need Rho protein
TO KNOW: region of DNA with 2 inverted repeats six bases apart, followed by a stretch of A’s (forms a secondary structure) - Causes RNA polymerase to stutter and pause.
Rho- dependent terminator (prokaryotic)
DEF: Transcriptional terminator that depends on Rho protein
TO KNOW: region of DNA with 2 inverted repeats six bases apart, NOT followed by a string of As. Rho will unwind the DNA/RNA helix to stop the transcription process and release the RNA.
Rho protein (prokaryotic)
DEF: Protein factor needed for successful termination at certain transcriptional terminators
TO KNOW: a special helicase that unwinds the DNA/ RNA hybrid double helices
what are two difference in how prokaryotic and eukaryotic chromosomes are organized?
1) distance between prokaryotic genes is smaller -> eukaryotic genes are often deparated by large stretches of DNA that do not encode any protein
2) prokaryotic genes associated with one metabolic pathway are found next to each other
operon
DEF: A cluster of prokaryotic genes that are transcribed together to give a single mRNA
(i.e., polycistronic mRNA)
TO KNOW: clusters of genes that share the same promoter and are transcribed as a single large mRNA that contains multiple structural genes or cistrons
polycistronic mRNA
mRNA carrying multiple coding sequences (cistrons) that may be translated to give several different protein molecules; only found in prokaryotic (bacterial) cells
Phosphorelay system
Transfers one phosphate from one location to another to activate different proteins, ultimately regulating transcription of the genes
monocistronic mRNA (eukaryotes)
mRNA carrying the information of a single cistron that is a coding sequence for only a single protein
Two-component regulatory systems
A regulatory system consisting of two proteins: a sensor kinase and a DNA-binding regulator
how many open reading frames and metabolic pathways do bacterial mRNA transcripts have?
multiple open reading frames for the same metabolic pathways
how many open reading frames do eukaryotic mRNA transcripts have?
one open reading frame
is eukaryotic or prokaryotic transcription more complex?
eukaryotic
- occurs in the nucleus
- 3 different RNA polymerases
- more complex promoter sequence
Sensor kinase
A protein that phosphorylates itself when it senses a specific signal (often an environmental stimulus, but sometimes an internal signal)
RNA polymerase I
Eukaryotic RNA polymerase that transcribes the genes for the large
ribosomal RNAs - one long strand that becomes 18s and 28s rRNA
RNA polymerase II
Eukaryotic RNA polymerase that transcribes the genes encoding proteins
RNA polymerase III
Eukaryotic RNA polymerase that transcribes the genes for 5S ribosomal RNA and transfer RNA
autogenous regulation
When a DNA-binding protein regulates the expression of its own gene
what three regions does RNA polymerase II need?
1) initiator box
2) TATA box
3) upstream elements to bind transcription factors
initiator box
Sequence at the start of transcription of a eukaryotic gene
TATA box
Binding site for a transcription factor that guides RNA polymerase II to the promoter in eukaryotes
co-repressor
In prokaryotes: a small signal molecule is needed for some repressor proteins to bind to DNA
In eukaryotes: an accessory protein, often a histone deacetylase, involved in gene repression
Some repressors or activators rely on activation by these small molecules
general transcription factors
DEF: Proteins that work to enhance or repress gene expression for all genes
TO KNOW: required by RNA polymerase II to initiate transcription at all promoters
specific transcription factors
Regulatory proteins that exert their effect on a single gene or operon or on a very small number of related genes
Two forms of specific regulator proteins to activate RNA polymerase binding and transcription
- active (bind to DNA in promoter region)
2.nonactive (nonbinding)
TATA binding protein/TATA box protein (TBP)
DEF: Transcription factor that recognizes the TATA box
TO KNOW: TBP is found in protein complex TFIID for RNA polymerase II
aka TBP binds to the TATA box and is part of TFIID
inducer/signal molecules
Molecules that exert a regulatory effect by binding to a regulatory protein
What are the three structural genes the promoter region for the lac operation controls?
lacZ, lacY, lacA
does bacterial RNA polymerase need a promoter to have upstream elements/transcription factors?
NO!! only eukaryotic needs them.
how do activator and repressor proteins work in prokaryotes?
they bind to DNA in the promoter region and stimulate or block the action of bacterial RNA polymerase.
repressor proteins
Regulatory protein that prevents a gene from being transcribed
operator
binding site for the repressor protein
positive regulation
Control by an activator that promotes gene expression when it binds
AKA gene is expressed only when activator gives a positive signal - how activator proteins work
negative regulation
the gene is only expressed when the repressor is removed - how repressor proteins works
anti terminator protein
Protein that allows transcription to continue through a transcription terminator
CAP (catabolite activator protein)
activates the transcription of many different operons by using alternate sugar sources
what does the sigma subunit of prokaryotic RNA polymerase do?
recognizes the promoter and then binds the catalytic portion of the enzyme (core enzyme)
gratuitous inducer
A molecule (usually artificial) that induces a gene but is not metabolized
like the natural substrate
-the best known example: the induction of the lac operon by IPTG
chaperonins
Protein that mediates the refolding of misfolded or unfolded proteins
protease
An enzyme that degrades polypeptides by hydrolysis
what are the elements of an operon?
1) promoter
2) operator (repressor protein binding site)
3) regulatory gene (encodes repressor protein)
4) structural genes (encodes enzymes)
