Chapter 8 Control Gene expression

Does every cell have the same genome

yes

Why does a cell change it’s gene expression

in response external signals

What is the main way to regulate the central dogma

Transcription control, in other words making RNA in the first place

Whats a cool fun fact about portein

most proteins need post-translational modifications to be fully active 

If the 3’ end carries an OH group what does the 5’ end carry

a Phosphate group

How does is there regulation from RNA to mRNA

Splicing

How is exporting of mRNA regulated

where it’s moved from different cell via the 3’ UTR and weather it’s degraded or not

What is the formation of most regulator proteins

alpha heliceis

Why are most regulator proteins alpha helicies

Because it allows the protein to fit into major grooves of DNA and form tight associations with it’s base pairs

Where do regulator proteins/homeodomains interact

major grooves but can be minor grooves to

How do regulator proteins detect the specific sequence of DNA it wants to target

it uses it’s amino acid’s hydrogen bond (ionic bond and hydrophobic interactions) to ‘feel’ the dna sequence it wants to target

When homeodomains and regulators hydrogen bond with the DNA does it disrupt the base pair hydrogen bond interaction

No

What is a homeodomain

When a regulator protein interacts with DNA

What is translational control on mRNA

we can control when mRNA is translated

(it can exist outside of the nucleus but untranslated just sitting there waiting for it to be translated)

What is example of protein activity control

phosphorylation of protein to turn it on or off

How many different types of controls of protein activity/making is there

roughly 7

In Logo Diagrams what does each letter represent

The nucleotide frequency that a protein regonizes in a specific sequence of ONE STRAND

Where does transcription regulator bind too

regulatory sequences

What does transcription regulators dimer do

it increases strength of protein DNA interaction

What must happen for transcription regulators to be dimer

the sequence that the monomer binded to must be repreated

How is DNA regulated

either it can be tightly coiled by nucleosomes/histomes or very loose and accessible

What is chromsome

DNA in it’s most packed state nothing can bind to DNA

What two proteins recognize a transcription regulator and binds to it to unwinding chromatin fibers

histone acetyltransferases and ATP-dependent chromatin-remodeling complex

How does ATP-Dependent chromatin remolding complex work

Binds to transcription regulator that sits on top of chromatin fiber and starts to unwind the chromatin fiber near by

How does histone acetyltransferase work

adds acetyl groups to histone so proteins can bind to it and start transcription

Is there long distance interaction with enhancers and transcription factor

Yes

What does an Enhancers do

They increase probability of transcription working and rate, but they can be found thousands of base pairs away

How do enhancers reach promoter region

2 ways either a clamping technique or just attracting the general transcription factors

What binds to enhancer region

an activator protein

What does an activator protein do

stabilize overall sequence that promotes transcription by binding to a mediator complex

What does a mediator complex do

acts as a mediator between activator protein and transcription factors to stabilize and start RNA polymerase

How is the clamp between enhancer and promoter region created

by chromosome loop-forming clamp proteins (2 is needed)

What is the more formal name for the loop the chromosome loop forming clamp proteins create

topological associated domains

What is the difference between transcription regulator and transcription factor

Transcription regulators are not found at promotor regions while transcription factors are found there

True or False: A single transcription regulator can help express many different genes

True

How do some cells turn on transcription due to external stimuli

They have an activator protein that binds to a transcriptional regulator to turn on transcription

What 3 regulation factor make a cell act like a stem cell

Klf4, Sox2, Oct4

How does a cell get locked into their fate

Some times a gene makes a protein, that protein circles back increase transcription of that gene this allows cells to keep their identity even after dividing as the same process will occur

Is there memory from cell dividing

yes, because once you make a protein it can feedback and increase transcription (have to be an activator)

Why can’t you have a memory as a repressor

because it turns the “gene” off

Can transcription regulators activate/repress different genes

yes because they will bind different transcription factors

What does miRNA do

they fold on themselves and a portion of it is broken down on each other than the RISC protein comes and unwinds it to make it single stranded

What does the miRNA and RISC complex do

if it all the bases pairs on miRNA and mRNA match then RISC + miRNA complex degrades the mRNA via nuclease found in RISC

if some of the base pairs from mRNA and miRNA align then mRNA gets either degraded or stuck so it can’t go through translation where nuclases can destroy it

What is RNA interference 

a defense mechanism with double stranded RNA is cleavage by dicer protein, and the small pieces pair with RISC to target viral RNA that initially hit

What is LncRNA

long non coding RNA it’s used to bind to protein to the bind to DNA