Transcription mechanisms Flashcards
what are the main characteristics of bacterial RNA polymerases
What are the roles of the different eukaryotic RNA polymerases
What are the Subcellular Distribution of Eukaryotic RNA Polymerases
Compare Bacterial Core RNAPs and Eukaryotic RNAPIIs
What is the key difference between bacterial RNA polymerases and eukaryotic RNA oil
Compare basic eukaryotic and prokaryotic transcription initiation
How are regulated levels of expression brought about in eukaryotic transcription
What are the sequence elements that define typical
eukaryotic promoters?
• How are the recognized?*
Core Promoter Elements (Near the Transcription Start Site, TSS):
TATA Box: Located about 25-35 base pairs upstream of the TSS, the sequence TATA(A/T)A(A/T) defines this region.
Recognition: Bound by the TATA-binding protein (TBP), a subunit of the transcription factor TFIID.
BRE (TFIIB Recognition Element): Found immediately upstream (BREu) or downstream (BREd) of the TATA box.
Recognition: Recognized by the transcription factor TFIIB.
DPE (Downstream Promoter Element): Located downstream of the TSS, common in TATA-less promoters.
Recognition: Interacts with TFIID subunits.
Distal Regulatory Elements (Enhancers, silencers, etc.
What is the TATA box and what is it recognised bt
What is meant by a strong promoter*
The TATA-Box And Other Moitfs are Specifically Recognized by TFIID
A strong promoter refers to a promoter sequence that drives high levels of transcription of its associated gene.
What is TFIID
What is the TATA binding protein and what does it do *
Binding induces a dramatic bending of the DNA (~80°), which helps to unwind the double helix and prepare the DNA for transcription.
TBP serves as a scaffold for assembling the pre-initiation complex (PIC) by recruiting other general transcription factors
What is the role of TFIIA and TFIIB*
By stabilising TBP binding (TBP is part of TFIID)
How are bases numerically labelled
Where does TFIIB bind
What Experimental Means of Detecting
Transcription Factor Complexes is used*
What other Promoter Elements exist
What are the roles of TFIIF, TFIIE and TFIIH
What is the CTD of RNA pol and what happens when it’s phosphorylated
How is promoter melting done
What are enhancers
What are proximal and distal enhancers
What are gene specific TF
What are repressors
What should gene specific TF be able to do
What is the general structure of Gene- Specific Transcription Factors
Where do gene specific TF bind
How can gene specific TF binding sites be mapped
By what interactions does DNA and proteins interact
What do electrostatic interactions between proteins and DNA do
How does sequence specificity of binding between proteins and DNA backbone arise (which reference to major and minor grooves of DNA)*
A particular sequence of base-pairs can be accessed either via the major or minor groove!
The sequence specificity of binding between proteins and the DNA backbone arises primarily from the interactions between amino acid residues in the protein and the chemical groups exposed in the major and minor grooves of DNA
The major groove of DNA is wider and provides a unique pattern of hydrogen bond donors, acceptors, and hydrophobic groups for each base pair (A-T, T-A, G-C, C-G).
Proteins can “read” the sequence of the DNA by recognizing this pattern without having to unwind the DNA.
What is the B form of DNA
How does base pair geometry work *
What are the ‘Standard’ DNA-Binding Domains
What are Helix-Turn-Helix Domains / Homeodomains
What is the structure of helix-turn-helix domains
Where else are Helix-Turn-Helix Domains expressed
What is the leucine zipper domain
What is c-jun/c-fos heterodimer
The DNA binding domain of the c-JUN (purple)/c-FOS (blue) heterodimer is formed by two long a-helices arranged in a Y- shape
The binding of c-jun/c-fos to DNA is stabilized by positively charged arginine and lysine side chains (purple)
What is a major characteristic of TF
What are helix loop helix domains (shape/ structure and what proteins their found in)
The binding of the Max homodimer to DNA is stabilized by positively charged arginine and lysine side chains (blue)
What are zinc finger domains
What is the structure on zinc finger motifs
How do zinc fingers work
The zinc finger domains follow the major groove and make a series of sequence-specific contacts
What is the role of p53
Where do TF bind on DNA
What is the role of activation domains
What are the characteristics of the genes GAL4, Sp1, NTF-1
What is MYC
Label the parts of MYC-MAX structure
Why is it important to know where activating domains (ADs) are
What is the first step of mapping activation domains
What is the second step of mapping activation domains
What is the third step of mapping activation domains
How can the location and presence of ADs be predicted
What is the first step of bioinformatic prediction of activation domains
What is the second step of bioinformatic prediction of activation domains
What kind of amino acids are usually found in ADs
What can ADpred be used for
How do activation domains work to activate transcription
What are coactivators
How does GCN4 interact with basal transcription machinery
What are the 3 conserved residues in GCN4 activation domains
What is the structure of a Nucleosomal Fibre and his can they be visualised
Digestion of purified nuclei with small amounts of micrococcal nuclease results in the generation of distinct DNA fragments containing one or more repeat units. These can be visualized by electrophoresis.
Mononucleosome
What are the nucleasome subunits (subunits that make up just one )
What is a histone fold
How do histone octamers assemble *
Histones H3 and H4 first form a heterodimer through strong interactions involving their histone folds
Two H3-H4 dimers associate to form a stable tetramer
Similarly, histones H2A and H2B form a dimer via their histone folds.
The (H3-H4)₂ tetramer serves as the core of the octamer.
Two H2A-H2B dimers associate with the tetramer to complete the histone octamer.
What is the evolutionary origin of histones
What are the different types of histone-DNA interactions to form the nucleosome
How does DNA bind to histones
What are linker histones
How are chromatin fibres formed
What is the solenoid*
The solenoid is a substructure within chromatin, specifically representing a higher-order folding stage. While chromatin is the overarching term for the organized complex of DNA and proteins, solenoids describe one way nucleosomes are compacted into a 30-nm fiber as part of chromatin’s structural hierarchy.
What is chromEMT and what is it used for
What are the conclusions of ChromEMT done to visualise nucleosome assembly
What is the role of the histone N termini
In addition to the conserved histone fold, histones contain additional sequences, mostly at the N-termini, that play an important role in controlling the gene-regulatory properties of nucleosomes
• These additional sequences are highly flexible (are intrinsically disordered) and therefore do not sLhoow uap din iXn-ragy c…rystal structures!
N termini can extend out and can be modified
How can chromatin be opened and closed
How can chromatin be opened locally
How can chromatin be closed locally
What is the effect of histone methylation
