lecture 27 Flashcards
regulation of gene expression
what determines a cell’s function?
gene expression
what do prokaryotic organisms lack?
defined nucleus
how is dna stored in a prokaryotic cell?
it is free floating and circular
in what order to transcription, translation, and protein formation occur in a prokaryotic cell?
simultaneously
what happens to transcription when the protein is no longer needed in a prokaryotic cell?
it stops
what is the primary method of controlling gene expression in prokaryotic cells?
controlling transcription
what are the two major protein classes that regulate chromatin remodeling?
ATP-dependent protein remodeling complexes and histone modifying complexes
what is the name of the complex that regulates expression by moving, ejecting, or restructuring nucleosomes?
ATP-dependent protein remodeling complex
what happens to the chromatin structure once the ATP-dependent chromatin remodeling complex binds to DNA around the nucleosome?
it is loosened which allows for the histone core octomer to move
if a histone is acetylated, what happens to the gene?
it is expressed
if a histone is de-acetylated, what happens to the gene?
it is silenced
what is the name of the complex that enzymatically modifies N-terminal histone tails?
histone/DNA modifying complex
if DNA is methylated, what happens to the gene?
it is silenced
if DNA is de-methylated, what happens to the gene?
it is expressed
what is the histone code hypothesis?
transcription of DNA is regulated, in part, by specific chemical modifications to histone proteins.
acetylases, methylases, and phosphorylases are involved in what type of histone modification?
writing (uses HAT, HMT, and kinases)
deacetylases, demthylases, and phosphatases are involved in what type of histone modification?
erasing (uses HDAT, HDM, and phosphotase)
brodomain(Ac-K), chromodomain(Meth-K), PHD finger(H3K4me3), and WD40 repeat(scaffold) are involved in what type of histone modification?
reading (protein-protein interactions)
what does modifying the histone proteins themselves do?
it recruits other proteins to the modified histone
what are the SIX things that must happen for a gene to be expressed(turned on)?
- initiating signal
- signaling pathway cascade
- activation of transcription factor
- recruits other member of transcription complex
- transcriptional complex recruits rna polymerase ii
- promotor site initiates transcription
what is a molecule that is produced in one cellular location but its effects are seen in another?
hormone
what does a hormone require in a target cell?
receptors specific to that hormone
how do transcription factors control the rate of gene transcription?
they help or hinder RNA polymerase II binding to DNA, interact with other proteins to build a transcription complex, contain binding domains, multiple binding sites for distinct transcription factors
what structural level do transcription factors contain DNA binding domains?
tertiary
what do DNA binding domains do?
attach to specific DNA sequences
what does multiple binding sites for distinct transcription factors signify?
multiple transcription factors can affect expression of a single gene
what type of transcriptional regulation is found in the DNA itself?
cis-activating factor
what type of transcriptional regulation acts on the DNA?
trans-activating factor
where is the TATA box found?
promotor region
where do transcription factor complex proteins bind?
TATA box
what region of DNA initiates transcription?
promotor
where is the promotor located?
upstream but near the transcription start site of a particular gene
what region of DNA binds to activator proteins to activate the transcription process?
enhancer
what region of DNA binds to repressor proteins to prevent binding of RNA polymerase II to the promotor?
repressor
what region of DNA prevents the interaction of enhancers with promotors?
insulator
what is responsible for basal level of expression and is the site of basal factor binding?
core promotor region
what is responsible for the induced/repressed level of expression and is the site of activator protein binding?
promotor-proximal elements
where do tissue specific transcription factors bind?
promotor-proximal elements
what can lie far away from the gene of interest and can retain its function even when it’s reversed?
promotor-proximal elements
what allows promotor-proximal elements, specifically enhancer, to work?
looping of DNA - it brings transcription factors and trans-activating factors together
what leads to higher efficiency transcription of gene of interest?
enhancer
what is the primary role of insulators?
prevent transcription of NON-TARGET genes
what are the FIVE steps of RNA processing?
- 5’ capping
- 3’ tail poly-adenylation
- RNA splicing
- RNA transport
- miRNA
what does the 5’ guanine cap do?
it protects the RNA chain from degradation by nucleases
when does 5’ capping occur?
it happens co-transcriptionally, once the RNA chain is ~30 nucleotides long
what is the poly A signal?
AAUAAA
is the poly A signal conserved or unconserved?
conserved
what is the name of the enzyme that cleaves nascent RNA DOWNSTREAM of the AAUAAA site?
ribonuclease
what is the name of the enzyme that adds adenine ribonucleotides to the 3’ end?
poly(A) polymerase
what are the two major functions of 3’ polyadenylation?
- enhances stability of RNA molecule
- regulates transport to the cytoplasm
what are INtervening sequences of RNA NOT expressed in proteins?
introns
what is the mechanism by which introns are removed?
splicing
what are sequences of RNA that are RETAINED in mRNA and ARE expressed in proteins?
exons
what is the protein/RNA complex that directs and ensures proper RNA splicing?
spliceosome
what is the process that exports mature mRNA from the nucleus into the cytoplasm?
RNA transport
what protein controls RNA transport?
messenger ribonucleo-proteins
through what is mRNA transported?
large multi-protein pore complexes
what is a class of naturally occurring, small non-coding RNA molecules whose main function is to down-regulate gene expression?
miRNA (mature micro RNA)
what structure does miRNA have?
stem-loop, hairpin structure
how does miRNA down-regulate gene expression?
it blocks translation by the ribosome and speeds up deadenylation(breakdown of the poly-A tail)
during which stage does most translational regulation occur?
initiation
ribosomal subunit proteins and initiation proteins for a complex to recognize what part of mRNA?
5’ guanine cap
the complex scans down the RNA sequences until it finds what?
the start codon (AUG)
to which large subunit(60S) part is the initiation codon lined up with by the initiation complex?
P site
what are the subunits of a ribosome and what do they make when combined?
40S, 60S, 80S
what is the process wherein ribosomes are stacked on an mRNA molecule?
ribosomal pausing
what are the effects of ribosomal pausing?
the ribosome can release and the incomplete polypeptide may prematurely degrade
what happens once the ribosome reaches a STOP codon?
release factors bind to the ribosome
by what process is the protein released from the ribosome?
hydrolysis
what are the TWO types of structural post-translational modifications?
- disulfide bonds
- proteolytic cleavage
between what do disulfide bonds form?
cysteine residues
what does proteolytic cleavage cleave and what does it result in?
it cleaves a pre-protein, resulting in a mature, functional protein
what are the TWO functional groups of post-translational modification?
myristolation and phosphorylation
what type of functional group is characterized by the attachment of lipid chains resulting in membrane localization of a protein?
myristolation
what type of functional group is characterized by the attachment of phosphate group to specific amino acids resulting in regulation of enzymatic activity?
phosphorylation
what is added to a protein in myristolation?
lipid chains
what is added to a specific amino acids in phosphorylation?
phosphate group
what is the result of myristolation?
membrane localization of a protein
what is the result of phosphorylation?
regulation of enzymatic activity
