Transcription mechanisms

Question 1

what are the main characteristics of bacterial RNA polymerases

Answer 1

Question 2

What are the roles of the different eukaryotic RNA polymerases

Answer 2

Question 3

What are the Subcellular Distribution of Eukaryotic RNA Polymerases

Answer 3

Question 4

Compare Bacterial Core RNAPs and Eukaryotic RNAPIIs

Answer 4

Question 5

What is the key difference between bacterial RNA polymerases and eukaryotic RNA oil

Answer 5

Question 6

Compare basic eukaryotic and prokaryotic transcription initiation

Answer 6

Question 7

How are regulated levels of expression brought about in eukaryotic transcription

Answer 7

Question 8

What are the sequence elements that define typical
eukaryotic promoters?
• How are the recognized?*

Answer 8

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.

Question 9

What is the TATA box and what is it recognised bt
What is meant by a strong promoter*

Answer 9

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.

Question 10

What is TFIID

Answer 10

Question 11

What is the TATA binding protein and what does it do *

Answer 11

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

Question 12

What is the role of TFIIA and TFIIB*

Answer 12

By stabilising TBP binding (TBP is part of TFIID)

Question 13

How are bases numerically labelled
Where does TFIIB bind

Answer 13

Question 14

What Experimental Means of Detecting
Transcription Factor Complexes is used*

Answer 14

Question 15

What other Promoter Elements exist

Answer 15

Question 16

What are the roles of TFIIF, TFIIE and TFIIH

Answer 16

Question 17

What is the CTD of RNA pol and what happens when it’s phosphorylated

Answer 17

Question 18

How is promoter melting done

Answer 18

Question 19

What are enhancers

Answer 19

Question 20

What are proximal and distal enhancers

Answer 20

Question 21

What are gene specific TF
What are repressors

Answer 21

Question 22

What should gene specific TF be able to do

Answer 22

Question 23

What is the general structure of Gene- Specific Transcription Factors

Answer 23

Question 24

Where do gene specific TF bind

Answer 24

Question 25

How can gene specific TF binding sites be mapped

Answer 25

Question 26

By what interactions does DNA and proteins interact

Answer 26

Question 27

What do electrostatic interactions between proteins and DNA do

Answer 27

Question 28

How does sequence specificity of binding between proteins and DNA backbone arise (which reference to major and minor grooves of DNA)*

Answer 28

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.

Question 29

What is the B form of DNA

Answer 29

Question 30

How does base pair geometry work *

Answer 30

Question 31

What are the ‘Standard’ DNA-Binding Domains

Answer 31

Question 32

What are Helix-Turn-Helix Domains / Homeodomains

Answer 32

Question 33

What is the structure of helix-turn-helix domains

Answer 33

Question 34

Where else are Helix-Turn-Helix Domains expressed

Answer 34

Question 35

What is the leucine zipper domain What is c-jun/c-fos heterodimer

Answer 35

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)

Question 36

What is a major characteristic of TF

Answer 36

Question 37

What are helix loop helix domains (shape/ structure and what proteins their found in)

Answer 37

The binding of the Max homodimer to DNA is stabilized by positively charged arginine and lysine side chains (blue)

Question 38

What are zinc finger domains

Answer 38

Question 39

What is the structure on zinc finger motifs

Answer 39

Question 40

How do zinc fingers work

Answer 40

The zinc finger domains follow the major groove and make a series of sequence-specific contacts

Question 41

What is the role of p53

Answer 41

Question 42

Where do TF bind on DNA

Answer 42

Question 43

What is the role of activation domains

Answer 43

Question 44

What are the characteristics of the TFs GAL4, Sp1, NTF-1 sequences

Answer 44

Question 45

What is MYC

Answer 45

Question 46

Label the parts of MYC-MAX structure

Answer 46

Question 47

Why is it important to know where activating domains (ADs) are

Answer 47

Question 48

What is the first step of mapping activation domains

Answer 48

Question 49

What is the second step of mapping activation domains

Answer 49

Question 50

What is the third step of mapping activation domains

Answer 50

Question 51

How can the location and presence of ADs be predicted

Answer 51

Question 52

What is the first step of bioinformatic prediction of activation domains

Answer 52

Question 53

What is the second step of bioinformatic prediction of activation domains

Answer 53

Question 54

What kind of amino acids are usually found in ADs

Answer 54

Question 55

What can ADpred be used for

Answer 55

Question 56

How do activation domains work to activate transcription

Answer 56

Question 57

What are coactivators

Answer 57

Question 58

How does GCN4 interact with basal transcription machinery

Answer 58

Question 59

What are the 3 conserved residues in GCN4 activation domains

Answer 59

Question 60

What is the structure of a Nucleosomal Fibre and his can they be visualised

Answer 60

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

Question 61

What are the nucleasome subunits (subunits that make up just one )

Answer 61

Question 62

What is a histone fold

Answer 62

Question 63

How do histone octamers assemble *

Answer 63

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.

Question 64

What is the evolutionary origin of histones

Answer 64

Question 65

What are the different types of histone-DNA interactions to form the nucleosome

Answer 65

Question 66

How does DNA bind to histones

Answer 66

Question 67

What are linker histones

Answer 67

Question 68

How are chromatin fibres formed

Answer 68

Question 69

What is the solenoid*

Answer 69

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.

Question 70

What is chromEMT and what is it used for

Answer 70

Question 71

What are the conclusions of ChromEMT done to visualise nucleosome assembly

Answer 71

Question 72

What is the role of the histone N termini

Answer 72

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

Question 73

How can chromatin be opened and closed

Answer 73

Question 74

How can chromatin be opened locally

Answer 74

Question 75

How can chromatin be closed locally

Answer 75

Question 76

What is the effect of histone methylation

Answer 76