Week 9 Flashcards
Gene Regulation
at what levels can gene expression be regulated in prokaryotes
- transcription
- RNA processing
- RNA stability
- translation
- posttranslation
- protein function
what initiates transcription in prokaryotes
RNA polymerase recognizes the promoter
how is transcription controlled in prokaryotes
regulatory proteins bind to DNA
do regulatory proteins inhibit or enhance transcription
they can do both, depends on the individual protein
what is an example of negative regulation
lactose utilization in E. coli
what proteins get a 1000-fold increase what lactose is added
- β-galactosidase
- lac permease
- transacetylase
who studied E. coli lactose-utilization mutants (1950)
Monod and Jacob
what do lacZ, lacY, and lacA encode
- lacZ: β-galactosidase
- lacY: permease
- lacA: transacetylase
define: polycistronic mRNA
mRNA with 2 or more transcribed genes on it
define: operon
a unit of DNA composed of specific genes, plus a promoter and operator, which act in unison to regulate the response of structural genes to environmental changes
are all operons polycistronic
yes
are all polycistronic mRNA operons
no
what is the purpose of β-galactosidase
- cleaves lactose into glucose and galactose
- creates allolactose
what is the purpose of permease
transports lactose into the cell
what is the purpose of transacetylase
add an acetyl (CH3CO) group to lactose
define: constitutive mutants
mutants that result in protein synthesis, irrespective of environmental conditions
what does lacI encode
a negative regulator/repressor
what does the repressor bind to
operator
what does the repressor do
prevents transcription
define: derepression
when a gene that is usually repressed gets activated
what does a constitutive mutant of the operator imply
repressor cannot recognize and bind, lac enzymes are synthesized constitutively
what acts in cis and trans for gene regulation in prokaryotes
- trans: proteins
- cis: DNA sites (including promoters and operators)
define: meroploid
bacterial cells that are partially diploid
what type of meroploids did Jacob and Monod use
they combines plasmid operons with chromosomal operons
define: inducible regulation
gene control where transcription occurs only in the presence of an inducer; there is an environmental stimulator
what represses the diphtheria toxin
high iron concentrations
why do bacterial pathogens kill host cells with diphtheria toxin
to get iron as free iron is never found in high concentrations in the body
how does diphtheria toxin lead to cell death
inactivates eEF-2 which stops the transfer of the growing polypeptide chain from A site to P site of ribosome
why are polycistronic mRNA generally not present in eukaryotes
the 5’ cap is needed to start transcription
what is a cis-acting element of eukaryotic gene regulation
enhancer
where is the enhancer in eukaryotes located
varies; can be both upstream and downstream, can also be very far away
what is a trans-acting element of eukaryotic gene regulation
transcription factors
what does the core promoter contain in eukaryotes
- TATA box consisting of roughly seven nucleotides
- initiation site where transcription begins (+1)
define: basal factors
factors required for binding to the promoter and to maintain a basal level of transcription
what are the basal factors
- TATA box binding proteins (TBPs)
- TATA box binding protein associated factors (TAFs)
- RNA polymerase II
what types of genes are TBPs essential for
all class II genes with a TATA box
where do transcriptional activators bind in eukaryotes
enhancer sequences
what are the 2 important structural domains of transcriptional activators in eukaryotes
- DNA-binding domain
- transcription-activation domain
what do coactivators do in eukaryotic gene regulation
integrate signals from activators and perhaps repressors
what do most eukaryotic activators form to function
dimers
define: homomers
multimeric proteins composed of identical subunits
define: heteromers
multimeric proteins composed of nonidentical subunits
what is an example of a common motif that many transcription factors possess
zinc-finger
what type of transcription factor are steroids
coactivators
what do coactivators cause
transcription factor (activator) undergoes a conformational change to allow it to bind its enhancer element
define: allosteric proteins
proteins that undergo reversible changes in conformation when bound to another molecule
what is the structure of the glucocorticoid response element (enhancer element)
has inverted repeats
AGAACAnnnTGTTCT
TCTTGTnnnACAAGA
what must the activator protein do for a steroid hormone to turn gene transcription on
- bind to the hormone
- bind to a second copy of itself to form a homodimer
- be in the nucleus
- bind to its enhancer element
what are 2 ways transcriptional repressors can work to diminish transcriptional activity in eukaryotes
- competition
- quenching
how does competition of repressors work in eukaryotes
repressor binds to DNA directly, blocking activator
what are the 2 ways repressors quench in eukaryotes
- repressor binds to the DNA-binding region of the activator
- repressor binds to the activation domain of an activator
why is in vivo levels of basal levels of transcription so much lower than in vitro basal levels
DNA of eukaryotes is packages into chromatin by the wrapping of DNA around histone proteins to for nucleosomes, preventing transcription
how does methylation affect eukaryotic transcription
methylation -> tighter wrapping around histone proteins -> genes not accessible
why does acetylation expose the gene for transcription
acetyl groups reduce electrical attraction of negatively charged DNA to otherwise positively charged lysine in tails
how are Barr bodies formed
methylation of CpG dinucleotides in highly condensed heterochromatin
define: heterochromatin
tightly packed form of DNA
what determines methylation patterns
- inheritance from parents
- diet
how does methylation work with the Igf2 genes (produces insulin-like growth factor)
both copies are methylated and repressed in germ cells of females but not in males
why aren’t cloned copies of animals not identical
they have different epigenetic traits, different methylation patterns
