Lecture 14b Flashcards
In regards to posttranslation regulation, what is another way to do this besides feedback inhibition?
Covalent modification of protein structure.
Is covalent modification of protein structure reversible or irreversible?
Both
What is proteolytic processing? Is this reversible or irreversible?
Proteins can be cleaved to become either active or inactive.
This is irreversible.
What is covalent modifications? Is this reversible or irreversible?
Adding sugars, lipids, etc. to proteins.
This is irreversible.
What is methylation? Is this reversible or irreversible?
Adding a methyl group to proteins.
This is reversible.
What is acetylation? Is this reversible or irreversible?
Adding COCH3 to make the protein slightly more negatively charged. The protein will now run differently on a gel right now.
This is reversible.
What is phosphorylation?
Adding a PO4 to proteins making it more negatively charged. This was one of the first ways studied.
This is reversible.
What are transcription factors?
Proteins that influence the ability of RNA polymerase to transcribe a given gene.
What are the two types of transcription factors?
General transcription factors and regulatory transcription factors.
What are general transcription factors?
They are required for the binding of the RNA polymerase to the core promoter and its progression to the elongation stage.
What are general transcription factors necessary for?
Basal transcription.
What are examples of general transcription factors?
TFIID and TFIIH
What are regulatory transcription factors?
They serve to regulation the rate of transcription of target genes by enhancing or inhibiting gene expression.
What do regulatory transcription factors influence?
They influence the ability of RNA polymerase to begin transcription of a particular gene.
What percentage of human genes encode for regulatory transcription factors?
2-3% of human genes encode for regulatory transcription factors.
What is a structural feature of regulatory transcription factors?
Transcription factor proteins contain regions, called domains, that have specific functions. The domains can be a module or part of a module.
What can the domains in regulatory transcription factors be used for binding wise?
One domain could be for DNA-binding. Another could provide a binding site for effector molecules causing genes to be expressed or shut down.
What is a motif?
A domain or portion of a domain that has a very similar structure in many different proteins.
What are the two types of motifs we learned about?
Helix-turn-helix motif and helix-loop-helix motif.
What type of motif is seen in a lot of DNA-binding proteins?
Helix-turn-helix motifs.
Do most proteins bind to the major or minor groove?
Major groove
T/F: The second helix in a helix-loop-helix is binding to DNA.
False! It is not binding to the DNA.
What type of motif is this?
This is a helix-turn-helix.
What type of motif is this?
Helix-loop-helix motif.
In regards to motifs, what occurs at the DNA major groove?
Recognition helix will recognize and make contact with a base sequence along the major groove of DNA.
What is one way a transcription factor can bind to DNA?
Hydrogen bonding between an a-helix and nucleotide bases is one way.
What is a Zinc Finger motif composed of?
Composed of one a-helix and two b-sheets held together by a Zn2+ metal ion.
What does each Zinc Finger do?
Binds to 3 or 4 bases in the DNA using sequence-specific binding.
What are leucine zipper motifs used for?
Used for dimerizing proteins.
In leucine zipper motifs, how are proteins held together?
They are intertwined due to leucine motifs on the alpha helices which have hydrophobic interactions.
How do we get protein dimerization?
Alternating leucine residues in both proteins will interact and “zip up” resulting in protein dimerization.
What are Homodimers?
Formed by two identical transcription factors.
What are Heterodimers?
Formed by two different transcription factors.
What are transcriptional activators?
They bind enhancers to up-regulate transcription more than basal transcription.
How do transcriptional activators enhance transcription?
They help to recruit TFIID and activate its function.
What are co-activator proteins?
Some transcriptional activators require co-activator proteins to up-regulate transcription.
Does the co-activator protein bind to the DNA?
No!
What does an activator/coactivator complex do?
It recruits TFIID to the core promotor and activates its function, enhancing transcription.
What are transcriptional repressors?
They bind silencers to down-regulate transcription to stop gene expression.
How does a transcriptional repressor down-regulate transcription?
It inhibits the binding of TFIID to the TATA box or inhibits its function.
T/F: Most enhancers and silencers are located within a few hundred nucleotides upstream of the promoter.
If true, what are some exceptions?
True!
However, some are several thousand nucleotides away, some are upstream or downstream of the promoter, and some are even within introns.
What do mediators do?
They link enhancers and silencers to core promoters when they are far away.
For transcriptional enhancement, what stimulates the mediator?
Transcriptional activator stimulates the function of the mediator to recruit the RNA polymerase.
When the mediator recruits RNA polymerase, what happens as a result?
RNA polymerase forms a preiniation complex and proceeds to the elongation phase of transcription.
What inhibits the function of the mediator?
Transcriptional repressor inhibits the activator function of mediator.
Does the transcriptional repressor or the mediator repress transcription?
Transcription is repressed by the mediator.
