gene expression regulation Flashcards
list the 7 cellular processes that can help regulate gene expression levels
transcription, mRNA processing, mRNA degradation, translation, post-translational modifications, protein targeting and transport, protein degradation
what are housekeeping genes
genes constitutively expressed at a constant level at all times in almost all cells of the organism
define regulated gene expression
gene expression that increases or decreases in response to molecular signals
define induction
when molecular signals increase expression of a gene
define repression
when molecular signals decrease expression of a gene
role of specificity factors + give an example
alter the specificity of RNA polymerase for a given promoter (ie sigma)
role of repressors
impede access of RNA pol to the promotor
role of activators
enhance pol-promotor interaction
where do repressors bind
to operators
where are operators located in regards to the promoter
downstream of promoter
repressor binding is regulated by small molecules/proteins called ____
effectors
where do activators bind
to activator binding sites
T or F: like repressors, activators are also regulated by effectors
true
which type regulation is more common in eukaryotes: positive or negative? explain
positive is more common in eukaryotes: without activators, genes will have little transcription because chromatin is more densely packed = inaccessible genes
other than activator binding sites, where can activators bind to in eukaryotes
enhancer sites
where are enhancer sites located in regards to the promoter
several thousand base pairs away from the promoter
since the enhancer site is so far from the promoter, how do we bring the two sites together
DNA looping occurs, which requires co-activators or architectural regulators as well
role of co-activators?
assists in DNA looping to bring the enhancer and promoter together
where is DNA binding in regulatory proteins more likely to occur; major groove or minor groove
major groove
describe why DNA binding to regulatory proteins occurs in the major groove
the exposed groups (ie H donors or acceptors or methyl groups) will differ in the major groove depending on the sequence (ie G-C vs C-G). This doesn’t occur in the minor groove. In the major groove, the protein is able to distinguish between G-C and C-G
define motif
a tiny collection of secondary structure
which is larger: motif or domain
domains are larger
structure of helix-turn-helix motif + how it binds to DNA
20 amino acids in 2 helical segments that are separated by a b-turn. One is the recognition helix and protrudes out the protein surface and binds to specific DNA sequences
example of a molecule that has a helix-turn-helix motif
Lac repressor has 4 of them
structure + function of the homeodomain
helix-loop-helix part of a larger 60 residue domain. Critical for embryonic body planning
structure of zinc finger motif + how it binds to DNA
30 aa in a loop held together by a Zn2+ ion bound to 2 H and 2 C residues. Zn stabilizes the structure, not binding with DNA.
describe the purpose of the RNA recognition motif
binds to noncoding RNA instead of DNA. However, both can fit, so DNA and RNA can compete with eachother to bind
why might a regulator need a protein binding domain
so it can bind to proteins like polymerases to regulate transcription
structure of leucine zipper motif
dimer of amphipathic a helices that interact through hydrophobic regions. The helices coil around each other. Leu repeats every 7th residue. There is a DNA binding domain with many + charged Lys or Arg residues to interact with - DNA backbone
structure of the basic helix-loop-helix motif
50 aa that allow for DNA binding and dimerization. The region forms two short amphipathic a helices linked by a loop. the motifs of two polypeptides can interact to form a dimer. Leu helps with dimerization. DNA binding is mediated by basic residues in the recognition helix
define operon
a cluster of bacterial genes that function together on a chromosome, along with a promoter and other regulatory elements
T or F: operons are transcribed together through a single promoter
true
list everything that the operon includes
activator binding site, promoter, operator (repressor binding site), and all the genes required to make amino acid
what genes does the Trp operon include
the 5 genes needed to convert chorismate to tryptophan
describe the structure of the Trp operon
has a repressor, which is a homodimer
what does the Trp repressor bind to
tryptophan
describe what happens to the Trp operon when tryptophan is present
the homodimer repressor binds to tryptophan and then binds to the operator. This blocks RNA pol from binding to the promoter, which prevents gene transcription
T or F: the Trp repressor is included in the Trp operon
false; it is not part of the operon
define transcription attenuation
when transcription starts but is halted before reaching the start codon
what type of sequence is involved in transcription attenuation
attenuation sequence
where is the attenuation sequence located (Trp operon)
in the leader region in the promoter
describe the 4 relevant parts of the leader region of the trp operon mRNA
has a sequence that encodes the leader peptide, and has 3 regions that can form secondary structures (denoted 2,3 and 4)
in the trp operon, which two sequences halt transcription when they pair
3:4
what is the name for the 3:4 pairing in the trp operon promoter sequence
3:4 pairing is called the attenuator sequence
when would you get 3:4 pairing in the promoter of the trp operon? explain
when trp is present. ribosome zooms through and covers sequence 2, forcing 3 and 4 to pair. Transcription stops because a hairpin is formed
when would you get 2:3` pairing in the promoter of the trp operon? explain
when trp is absent. The ribosome doesn’t cover sequence 2, so 2 and 3 can pair. No hairpin forms, so transcription continues
function of SOS genes?
DNA repair
when is the SOS response activated
when there’s extensive DNA damage
what are the two main SOS response players
LexA repressor and RecA
role of LexA repressor?
inhibits expression of DNA repair genes
role of RecA?
repairs double stranded DNA breaks
describe the structure of a chromosome that will need the SOS response (ie where are LexA repressor and RecA located on the chromosome)
normally the LexA repressor will be repressing the transcription of DNA repair genes and preventing the SOS response. It has an operator sequence right before each repair gene
RecA is one of the genes that is beside the LexA repressor’s operator. It’s transcription is only partly blocked by LexA
describe the activities of the SOS response
extensive DNA damage creates single stranded DNA. The small amount of RecA present in the cell will bind to the ssDNA, and can now act like a protease. RecA induces LexA to self-cleave into two parts, causing LexA to be inactive. With an inactive repressor, all the DNA repair genes (including more RecA) can now be transcribed
how much of the eukaryotic genome is heterochromatin
10%
how much of the eukaryotic genome is euchromatin
90%
which is always transcriptionally inactive: heterochromatin or euchromatin
heterochromatin
T or F: euchromatin can be either transcriptionally active or inactive
true
when does chromosome remodelling occur
when a chromatin region becomes transcriptionally active
list 2 examples of chromosome remodelling
change in nucleosome position, changes in covalent modifications of the nucleosome
which family of proteins can separate histones from DNA near transcription start sites
SWI/SNF complex
role of SWI/SNF complex?
separate histones from DNA near transcription start sites
describe the issues solved by combinatorial control
in bigger eukaryotic genomes, there’s a higher chance that a DNA binding sequence for a regulatory protein will appear elsewhere in the genome. Also, you would need so many regulatory proteins to separately regulate tens of thousands of eukaryotic genes
describe the basics of combinatorial control
you have only a few regulatory proteins, but they bind in different combinations to regulatory sequences. Also you require multiple regulatory sites per gene, lowering the chance that all regulatory sequences will randomly appear elsewhere together
describe all the steps of eukaryotic gene regulation, starting with activators and coactivators binding to enhancers
after binding to enhancers, activators recruit a large co-activator complex, the Mediator. They also recruit chromatin remodelling complexes to help adjust nucleosomes. They also recruit architectural regulators to loop DNA (ie a family called HMG). Mediator facilitates recruitment of TATA binding protein (TBP) and TFIIB. TFIIB then recruits pol II + other TFs. When pol II arrives, mediator binds to the CTD, and helps stabilize the entire initiation complex
in regards to steroid hormones, what does NR stand for
nuclear receptor
how many nuclear receptor types do steroid hormones have
2
give 2 examples of type 1 steroid hormone NR
estrogen + glucocorticoids
give an example of type 2 steroid hormone NR
thyroid hormones
what do nuclear receptors bind to
DNA sequences called hormone response elements
what motif do NRs have
zinc-finger DNA binding motifs
describe type 1 NR in eukaryotic signalling
these ones are monomeric and found in the cytosol. They are complexed with heat shock protein (HSP70). Steroid binding to NR causes HSP dissociation, receptor dimerization which exposes a nuclear localization sequence, and migration to the nucleus
describe type 2 NR in eukaryotic signalling
these are dimers and always found in the nucleus. They’re bound to HRE but also a co-repressor. Steroid binding causes a conformational change in the dimer that leads to co-repressor dissociation
what are translational repressors + what do they do
proteins that bind to RNA transcripts, usually in the 3’ UTR before the polyA tail. They interact with translation IFs or with the small ribosomal subunit. they impede translation initiation + save time by making the transcript a circle
what does miRNA stand for
micro RNA
what do miRNAs do
they interact with mRNA to inhibit translation
describe the structure of miRNA
25 nt long, have hairpin-like secondary structures, they bind to the 3’ UTR of the mRNA
describe briefly how miRNA production and processing occurs
they’re initially transcribed as much longer RNA molecules but then are cleaved/shortened by nuclear endonucleases
how do miRNA get to the cytosol (out of the nucleus)
through nuclear pores via Exportin
what occurs to miRNA once it gets to the cytosol
it’s released from exportin and picked up by Dicer
what two activites does Dicer have
endonuclease and helicase
describe what dicer does to miRNA
cuts miRNA even smaller and unwinds any complimentary sequences that form hairpins
what is miRNA called after interacting with Dicer
mature miRNA
what does mature miRNA do in the cytosol
binds to RISC
what does RISC stand for
RNA-induced silencing complex
what does RISC do after miRNA binds to it
binds to a target mRNA
describe what occurs when miRNA-RISC-mRNA interact
if there is complementarity between miRNA and mRNA, RISC can trigger mRNA cleavage
