topic 8 (oops)

housekeeping genes

proteins in all cells

specialized proteins

responsible for a cells distinctive properties

which 2 regions are recognition sites for RNA polymerase

promoter and transcription initiation site

where does a transcription regulator bind in the DNA

into the grooves of DNA 

what are operons

cluster of genes all transcribed at the same time

describe the trp operon

transcribes 5 genes that code for trp manufacture, high trp turns off, low trp turns on

the operator (the thing the transcription regulator binds to in the promoter) is bound by the trp repressor when the gene is off to prevent RNA polymerase from binding. it is an allosteric protein controlled by feedback inhibition (only binds to DNA if also bound by trp)

when do transcriptional activator proteins come in

when the promoter can’t tightly bind the RNA polymerase by itself, often need more molecules to come help (ex. catabolite activator protein (CAP) in bacteria needs cAMP to bind too)

describe the lac operon

controls break down, a repressor binds when there is no lactose and when there is lactose, transcription is on and repressor comes off. also controlled by glucose, when glucose is not there, lots of cAMP which binds to CAP which acts as an activator, but when glucose is there, the gene is repressed. so any situation other than there is no glucose and lots of lactose, the gene is off 

enhancer

region where eukaryotic activators bind, work at a distance up or downstream from start site. a loop of DNA brings the activator to a mediator which connects everything together and helps form the transcription initiation complex

what is the transcription initiation complex made of

activator, mediator, RNA polymerase, and other transcription regulators

how can nucleosomes inhibit transcription and how do we get around it

if the position of the promoter is blocked by the nucleosome physically. activators bind and attract histone modifying things to do histone acetylation

what do you do if you want large amounts of heterochromatin of some genes but not others

histone deacetylase works gene by gene

how to loops control enhancers

gives it close proximity to what it needs to affect so it doesn’t accidentally affect another gene

what happens if a loop is formed wrong

can lead to something being expressed at the wrong time which can lead to cancer or other inherited diseases

what is combination control

when multiple transcription regulators all help control, all need to be there to work

can form bimolecular condensates which help assemble committees (proteins in the protein scaffold)

what do bacteria use to control the expression of many genes vs eukaryotes

bacteria use operons

we use many transcription regulators that are already in place, waiting for that one left to activate everything (ex. cortisol increases expression in the liver for starvation or prolonged stress)

what do we call embryonic stem cells

pluripotent

what is weird about embryonic stem cells relative to our normal cells

they have a small number of regulators that act in different combination to control cell types 

what is a master transcription regulator + example

produces a cascade of regulator reactions that make an organ

ex. fruit fly eye is made from 1 TR called ey, mutations causes no eye at all, and it is so powerful, if randomly activated, an eye can grow somewhere else

what are terminally differentiated cells

so specific they can’t divide

describe cell memory and connect it to + feedback loop

remembers patterns through cell division, positive feedback loop is when master TR causes its own transcription and is passed down to daughter cells 

describe DNA methylation

modifies C and turns off the gene by attracting proteins that like the methylated C, works like epigenetic inheritance

describe miRNA, and connect to RNAi

base pairs with mRNA, then dicer cuts dsmiRNA into siRNA which is then taken up by RISC. Risc discards one of the strands and uses the other to complimentary pair to mRNA to see where to cut. OR RITS uses a single strand of siRNA to find the comp. mRNA and attract histone modifiers and make it heterochromatin

what is RNAi used for naturally

cell defence, eliminated foreign RNA 

describe how CRISPR is used in bacteria

short cuts of attacker DNA is put into the genome at specific spots and CRISPR remembers it. then it us made into short RNAs called crRNA which is put into Cas so it looks for complimentary pair and cuts its

3 examples of long noncoding RNAs

forms part of telomerase, Xist (coats one of the X chromosomes in heterochromatin to deactivate it since we only use 1), scaffold molecules