Chapter 16: Gene Expression Flashcards
What type of cell contains the full genome of an organism
Each somatic cell they have
How does regulation benefit organisms?
Regulation means efficiency, and because all genes do not need to go under gene expression it helps save energy, space, and time
prokaryotic gene regulation
What is an operon?
Proteins with similar function or in the same biochemical pathway are organized in blocks, which are called operons
Operons are regulated by three molecule types, what are the called?
Repressors, Activators, Inducers
What does a repressor do?
suppress transcription
What does an activator do?
increase transcription
What does an inducer do?
they may suppress or activate transcription based on the needs of the cell
What happens in a repressible operon (trp operon)
Binding of a specific repressor protein activated by a corepressor shuts off transcription (the repressor is innately inactive)
What happens in an inducible operon (lac operon)
Binding of an inducer molecule to an innately active repressor inactivates the repressor and allows transcription (repressor innately active)
In the trp Operon, when tryptophan is present, what happens?
The trp repressor binds to the operator, and RNA synthesis is blocked
Where do the two tryptophan molecules bind too?
They bind to the repressor protein at the operator sequence
What does the complex stop the RNA polymerase from doing?
It physically blocks the RNA polymerase from transcribing the tryptophan genes by binding to the operator
In the trp Operon, when there is an absence of tryptophan, what happens?
The repressor dissociates from the operator; and DNA synthesis proceeds
Now that the tryptophan is absent, what does the repressor protein do?
The repressor protein now cannot bind to the operator
There is no repressor protein on the operator so what does the RNA polymerase do?
The RNA polymerase can access the operator and the genes are transcribed
What are negative regulators?
Proteins that bind to the operator slience trp expression
In the lac operon, what happens in the absence of lactose?
The lac repressor binds the operator; transcription is blocked
In the lac operon, in the presence of lactose what happens?
The lac repressor is released from the operator, and transcription proceeds at a slow rate
in inducible operons, what is activation/repression based on?
It depends on the local environment and the needs of the cell
What is Catabolite Activator Protein (CAP)
An activator regulator
What does CAP do in the absence of cAMP?
CAP does not bind to the promoter, and transcription occurs at a slow rate
What does CAP do in the presence of cAMP
CAP binds to the promoterand increases RNA polymerase activity
What happens when glucose supplies become limited in the lac operon?
- cAMP levels increase
- cAMP binds to the CAP protein (a positive regulator)
- cAMP/CAP protein complex binds to an operator region upstream of the genes required to use other sugar sources
What are positive regulators?
Proteins that bind the promoter in order to activate gene expression
What does the cAMP-CAP protein complex do?
It stimulates RNA polymerase activity and increases RNA synthesis
When the repressor is bound to the operator is RNA synthesis still blocked?
Yes, even in the presence of cAMP-CAP protein complex.
What are the different eukaryotic gene regulation stages?
Epigenetic stage, Transcriptional stage, Post-Transcriptional stage, Translational stage, Post-Translational stage
What happens in the epigenetic stage?
Chemical modification during DNA processing
What happens in the transcriptional stage?
initation and rate regulation
What happens in the Post-Transcriptional stage?
alternative splicing
Translational stage
initiation regulation
What happens in the Post-Translational stage?
protein modification
Another way to describe what transcription factors are is?
Proteins that control the transcription of genetic information from DNA to RNA
Organzation of DNA and Proteins
DNA is folded around histone proteins to create nucleosome complexes
These nucleosomes control the access of proteins to the underlying DNA
Histone proteins and DNA nucleotides can be modified chemically, what do the modifications affect?
The modifications affect nucleosome spacing and gene expression
What does unwinding and opening of DNA allow?
It allows transcription factors to bind promoters and other upstream regions and initiate transcription
What happens when nucleosomes are closely together?
Transcription factors cannot bind and gene expression is turned off
What happens when nucleosomes are spaced far apart?
The DNA is exposed, which lets transcription factors bind to it, and further lets gene expression occur
What causes nucleosomes to be close to each other?
Methylation
What causes nucleosomes to be spaced far apart?
Histone Acetylation
Chemical tags are added to histones and DNA, what are these tags called?
Phosphate, methyl, and acetyl groups serve as these tags
What do these chemical tags do?
They act as signals to tell histones if region of chromosome should be opened or closed
Tags are not permenant, can be added or removed
Epigenetic regulation
“around genetics” temporary changes to nuclear proteins and DNA that do not alter nucleotide sequences but do alter gene expression
Describe a promoter
a region of DNA upstream of coding sequence (a few nucleotide to 100’s of nucleotides long)
Describe a TATA box
A series of thymine and adenine dinucleotides within the promoter just upstream of the transcriptional start site
What is distal CE?
Regulatory sequences of DNA that are found a great distance from the genes they help regulate
What is proximal CE?
Regulatory sequences of DNA that are found close to promoters of the genes they help regulate
Bind specific activator or repressor proteins to affect the rate of transcription
What is an enhancer?
Short regulatory sequence that promotes transcription by binding activator proteins
What is a sliencer?
short regulatory sequences of DNA that decreases transcription by binding to repressor proteins
What are enhancers made of?
They are made of short DNA sequences called distal control elements
What do the activators so with these distal control elements?
They bind with the distal control elements and interact with mediator proteins and transciption factors
What is something that enables differential gene expression?
Two different genes may have the same promoter, but different distal control elements, which enables differential gene expression
What do DNA bending protein change
it changes the shape of DNA and properly orients enhancer region
Before post-transcriptional modification what must RNA trancripts go through?
They must be processed into final form before translation can begin the post-transcriptional process
What are the ways could alternative splicing have evolved?
- Splicing requires proper identification of introns.
- Errors in this process could lead to splicing out of an intervening exon.
- Usually would be deleterious to organism…
- But it could produce a protein variant without loss of original protein.
- New variant might have had an adaptive advantage.
What does 5’ cap methylated guanosine triphosphate molecule (GTP) and Poly-A tail prevent?
It prevents degradation of transcript
RNA-binding proteins at these UTRs influences the RNA stability which..?
- can increase or decrease the length of time mRNA is present in the cytoplasm
- They can also regulate mRNA localization and protein translation
The protein coding region is flanked by?
5’ and 3’ untranslated regions (UTR)
What are microRNAs (miRNAs)?
They are short RNA molecules (21-24 nucleotides) that recognizes a specific sequence of mRNA
What do miRNAs associate with?
They associate with ribonucleoprotein complex called RNA-induced sliencing complex (RISC)
What do RISC/miRNA degrade?
They bind to the and degrade the mRNA
What is translation controlled by?
it is controlled by proteins that bind and initiate process (formation of initiation complex)
What is the first protein to bind and form complex?
Eukaryotic Initiation Factor-2(eIF-2)
What binds to eIF-2?
GTP binds and then this complex binds to 40S ribosomal subunit
What binds to this complex (eIF-2,GTP,40S)?
The methionine initiator tRNA brings mRNA to bind to this complex
Then, what is GTP converted to?
It is converted to GDP and energy is released
Lastly, what occurs when phosphate and eIF-2 are released and 60S binds?
Translation occurs
What happens when eIF-2 is phosphorylated?
Translation is blocked, no Translation
What happens when eIF-2 is not phosphorylated?
Translation occurs
Can proteins be chemically modified?
Yes!, chemical modifications affect protein activity.
What do the chemical changes regulate?
- Protein activity
- Length of time they exist in cell
What do the chemical changes alter?
- epigenetic accessibility
- transcription
- mRNA stability
- translation
all of these resulting in chnages in expression of various genes
