Lecture 10 Flashcards Preview

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Flashcards in Lecture 10 Deck (34)
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1

How do specific or regulatory transcription factors differ from permissive transcription factors

Specific or regulatory transcription factors bind to specific genes are play a regulatory role in transcription. They can be transcriptional activators or transcriptional repressors and bind anywhere in the gene, sometimes quite far away.

2

What is meant by the term transcription factor synergy

Transcription factors cooperate in order to influence gene transcription. Binding of one transcription factor to another may help prevent them from falling off the DNA. Instead of one interaction, each protein would need to lose two interactions to fall off the DNA. Similarly, binding of one transcription factor to DNA may enable another transcription factor to bind to that sequence also

3

Rox1 is a DNA binding protein found in yeast, how many different sites does it bind to

8 sites in three different yeast genes

4

Transcription factors recognise short stretches of DNA through interactions with individual base pairs, T or F

T

5

Which groove of the DNA do protein interact with and why

DNA binding proteins interact with the major groove of the DNA because the minor groove is too narrow

6

What is significant and unusual about DNA binding proteins that allows them to bind to DNA

DNA binding proteins have a positive charge due to high positively charged amino acids contained within them. This allows the protein to interact and remain bound to the negatively charge phosphate backbone

7

Usually the consensus sequence is the sequence with the highest affinity for the DNA binding protein, T or F

F – often it isn’t

8

What is meant by DNA looping

Chromatin is quite stiff and so does not bend easily. It is thus thought that for two proteins to interact with the DNA they need to bind directly to neighbouring DNA sequences. These binding sequences for regulatory transcription factors need to be over 500 base pairs apart, this leads to DNA looping

9

Give an example of a permissive transcription factor

TATA binding protein (TBP)

10

What is meant by the probability of transcription

There are usually many inputs that alter gene expression, referred to as genetic switches. Each switch responds to intrinsic or extrinsic regulation. The combination of enhancers, repressors, silencers and activators is what determines the probability of transcription.

11

Explain how electrophoretic mobility shift assays can be used to identify DNA binding proteins

EMSA involves the radioactive labelling of a known sequence of DNA that contains the binding site to which you want to identify interacting proteins for. This labelled DNA in then mixed with purified proteins or cell extracts. Instead of adding DNAse and heating, the mixture is then immediately run by gel electrophoresis. If a protein has bound to the labelled sequence, then it won’t move as far though the gel as the unbound DNA and would be represented by an additional band in the gel

12

What is meant by the term permissive transcription factors

Permissive transcription factors are general transcription factors necessary for all transcription and are non-regulatory. These bind at the promoter sequence of the gene and are ubiquitously expressed. Binding of permissive transcription factors to the promoter helps the polymerase machinery to find the start site

13

The Rox1 gene contains a binding site for the Rox1 protein itself, what is the significance of this

Rox1 regulates its own transcription

14

Binding sites for the same DNA binding protein all usually show a similar frequency of bases at the same location in binding site genes, T or F

T

15

Describe the structure and interaction of leucine zipper domains with DNA

Leucine zippers consist of 2 ? helices that form a dimer held together by hydrophobic amino acids such as leucine. These domains straddle the DNA binding to symmetrical sequences in the case of homodimers, or non-identical sequences if the two helices are a heterodimer

16

Recall the four hypothesised mechanisms of regulating transcription factors

Protein synthesis of inhibitors etc. Ligand binding, protein phosphorylation and addition of subunits

17

What is meant by a sequence logo

A sequence logo is a size representation of the bases within a DNA sequence where the size of the letters represents the frequency of bases within the sequence

18

How do regulatory transcription factors function

They interact with the RNA polymerase complex and either alter acetylation of the DNA (which effects chromatin structure), bind to other transcription factors or act upstream of permissive/general transcription factors

19

What is the role of insulators and barriers in the control of gene expression

Insulators and barriers block regulatory sequences from affecting neighbouring genes and prevent enhancers from activating the wrong genes

20

What type of bonding holds DNA binding proteins in place at the major groove of the DNA

hydrogen bonds

21

What do Y, H and N represent in the consensus sequences

Y represents either a C or a T. H represents and A, C or T. N refers to any base

22

Cells often express different genes in a diseased state, T or F

T

23

Specific/regulatory transcription factors don’t have to bind directly to the gene which they regulate, T or F

T – they can exert their regulation of transcription by binding to a regulatory complex

24

What is meant by the consensus sequence

The consensus sequence shows the generally conserved sequence common to all binding sites for a DNA binding protein. This can be used to identify other binding sites with the same consensus sequence and that may bind to a DNA binding protein of interest.

25

What is the name given to the sequence in the DNA to which transcriptional repressors bind

Silencers

26

Describe the structure and interaction of zinc finger domains with the DNA

Zinc finger domains consist of an ?-helix and B-sheet. The ?-helix interacts with the major groove of the DNA by interactions of arginine and histidine residues with bases in the DNA sequence. These domains require the presence of a Zn2+ ion to stabilise the structure and hold the domain in place. These domains are usually found in combination with several other zinc fingers

27

DNA binding proteins form stable interactions with the DNA sequence to which they bind, T or F

F – the interactions between DNA and DNA binding proteins are not stable

28

Which sequence is perfectly conserved across all Rox1 binding sites

GTT

29

What attribute of enhancer sequences results in the need of insulators and barriers

Enhancers are binding sites for transcriptional activators. These sequences are usually promiscuous and activate transcription of any adjacent genes. Insulators and barriers are required

30

Give an example of a simple genetic switch

The tryptophan repressor protein represses genes required for tryptophan synthesis and storage. When levels of tryptophan are high then it turns off genes required for tryptophan synthesis