Gene Regulation Flashcards
purpose of aminoacyl tRNA synthetase (ARS)
“recharge” “empty” tRNAs with the correct amino acid
how many ARS’s do we have?
one ARS for each amino acid; specific for one amino acid
enzymatic basis of the genetic code
aminoacyl tRNA synthetases
the redundancy in the genetic code arises because
some amino acids are coded for by multiple codons
where does transcription and translation happen in eukaryotes?
transcription happens in the nucleus; translation happens in the cytoplasm
where does transcription happen in prokaryotes?
prokaryotes have no nucleus, so transcription and translation can happen simultaneously in the cytoplasm
do prokaryotes do RNA processing?
prokaryotes don’t have introns and don’t process RNA transcripts (no splicing, caps, or tails)
why are genes differentially regulated?
every cell in our body has the same genome; however the body consists of trillions of cells and millions of distinct cell types
define differential gene expression (gene regulation)
results in different cell types expressing (transcribing and translating) different proteins
what is a cell’s structure and function defined by?
which genes it turns on and which genes it turns off
ARS genes are an example of what kind of genes
housekeeping genes
what allows cells and organisms to respond to their environment?
gene regulation
mechanism of insulin
high BG —> pancreatic B cells detect high BG —> B cells transcribe and translate more insulin —> insulin tells fat cells to take in glucose —> lower BG
how are alpha cells different from beta cells?
alpha cells always make glucagon and store it up until it is needed
where can gene expression be regulated?
transcription, pre-mRNA processing, mRNA degradation, translation, post-translational modifications to proteins, protein degradation
what is the main process controlling if a gene is turned on/off and at what level (how much protein is expressed)?
transcriptional regulation
where is the promoter located?
right next to the first exon
what are enhancers and where are they located?
transcription factors must bind enhancers in order to bind the promoter, but enhancers can be located far from the gene (before, after, or in the introns)
what are CIS-Regulatory Elements (CREs)?
DNA sequences on the same (cis) piece of DNA as a gene that regulate transcription of the gene
examples of CREs
enhancers and promoters
what must happen for transcription factors to bind enhancers and promoters at the same time?
the DNA between the enhancers and promoters bends
steps of transcription factors binding DNA
1) TFs bind enhancers
2) DNA bends via bending proteins so TFs can bind promoter
3) “pre-initiation complex” = enhancer + T.F. + promoter + RNA polymerase
describe the structure of enhancers
consist of many short DNA sequences (4-12 nucleotides) called transcription factor binding sites (TBSs) - transcription factors like particular sequences
how many TBSs does a transcription factor have?
several potential TBSs
where does the TF bind the enhancer?
several different places
how many transcription factors bind a certain enhancer? why is this important?
several kinds of TFs bind the enhancer, this is important because many TF molecules need to bind to each other to stabilize their binding to the enhancer (TFs + enhancer complex must be stable to bind to the promoter and activate transcription)
what is the threshold for enhancers?
they do not act in an all or nothing manner, as long as a minimum threshold of TFs bind stably, transcription will happen at some level (40, 75 or 100% max transcription)
do all your cells have the same enhancers and promoters?
yes, same genome so same enhancers and promoters
why are cells ultimately different from one another?
they have different transcription factors
what do specific levels of transcription depend on?
cell type and environment
how long does the “binding” between enhancers, TFs, and promoters last?
temporary, lasting only seconds or minutes usually
why can beta cells express insulin?
they have transcription factor PDX-1
how do the transcription factors present in different cells compare?
cells have some of the same TFs, but don’t ever have the exact same combo, cells are defined by the combo of TFs they have
how many TFs are there?
~2000
how can genes that aren’t being used be shut off semi-permanently?
via changes in chromatin structure
what sort of chemical modifications can be made to DNA to “shut them off”?
1) methylation of DNA
2) deacetylation of histones that wrap of DNA can cause regions of the genome to be blocked from transcription
how is RNA processing involved in gene regulation?
different exons of the same gene can be combined into different mRNAs and create different protein isoforms from the same gene (alternative splicing)
define splice factors
RNA-binding proteins expressed in different cell types that bind to pre-mRNA and direct the spliceosome to remove different exons and introns
how is mRNA transcript degradation regulated?
by tiny micro RNAs (miRNAs) transcribed from mi RNA genes
role of miRISCs
(miRNA + proteins) bind the 3’ UTRs and direct mRNA degradation
how many enhancers does one gene have?
may have several enhancers
where can enhancers be located?
5’ (upstream) or 3’ (downstream) of the promoter, or even in introns, not usually in protein coding exons
why do genes have multiple enhancers?
each enhancer typically controls transcription of the gene in a specific cell or tissue type, or at a specific time (i.e. each enhancer has different TBSs so it can be bound by the TFs present in them various cells and tissues (and times) where it is transcribed
what is it called when a gene is used in multiple cell and tissue types
pleiotropic gene (i.e. keratin)
how many protein coding genes are in the human genome?
20,000 protein-coding genes
how many cells are we made of?
30,000,000,000,000 (30 trillion)
how many of your protein coding genes are pleiotropic?
most if not all
what are most phenotypic differences within species and between species due to?
enhancer mutations
which proteins regulate splice factors expressed in which cell types?
transcription factors
miRISC
miRNA induced silencing complex
how might miRNAs inhibit translation?
by blocking ribosome binding (initiation) or elongation, usually by binding the 3’ UTR
how can protein activity be regulated?
post-translational modifications such as phosphorylation or methylation can turn proteins on or off
role of proteasomes
degrade proteins that are tagged for destruction with ubiquitins
