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Cell and Molecular Biology > Contol of gene transcription > Flashcards

Contol of gene transcription Flashcards

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1
Q

Changes in gene expression underlie what?

A

The diversity of cell types in the body

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2
Q

All cells have the same … but different sets of …

A

Genes

Proteins

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3
Q

What can affect which genes are expressed?

A

Responses to signals and other cues in the enviroment

Cells also change gene expression in some disease states

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4
Q

What affects the level of translation?

A

The level of transcription in a cell

High levels of transcription can mean more RNA is produced so more protein is made

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5
Q

What is the charge of DNA binding proteins?

A

They are positive

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6
Q

What is the target of DNA binding proteins?

A

The major groove

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7
Q

What is the charge of the phosphate backbone?

A

Negative

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8
Q

Unlike proteins, DNA has a limited what?

A

Topology

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9
Q

Regulatory proteins must recognise what on the DNA?

A

A specific nucleotide sequence

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10
Q

Why does the outisde of the helix contain information?

A

So that the double helix does not have to open

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11
Q

The edge of each pair is exposed at the surface, presenting a distinctive pattern of what?

A

H-bond acceptors
H- bond donors
Hydrogen atoms
Methyl groups

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12
Q

Which groove is marked differently for each pair?

A

The major groove

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13
Q

Give the pattern of the major groove for:
G-> C
A- > T
Know this to know the reverse

A

G to C
H bond acceptor, H bond acceptor, H bond donor, Hydrogen atom

A to T
H bond acceptor, H bond donor, H bond acceptor Methyl group

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14
Q

Molecular recognition usually relies on what?

A

Exact fit between the two surfaces of a molecule

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15
Q

How do gene regulatory proteins recognise a specific DNA sequence?

A

The surface of the protein is complementary to the features of the double helix in that region

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16
Q

Proteins make a series of contacts using which 3 interactions?

A

Hydrogen bonds
Ionic bonds
Hydrophobic interactions

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17
Q

How are interactions between the proteins and DNA strong?

A

Even though each contact is weak, there are about 20 contacts making them hard to break

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18
Q

Where does ROX1 bind?

A

Known to bind to eight sites in three yeast genes

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19
Q

Do all the DNA binding sites have the same affinity for the ROX1 protein?

A

No

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20
Q

Describe the structure of a helix-turn-helix DNA binding motif

A

2 Alpha helices connected by a short constitute of amino acids
The 2 alpha helixes are held at a fixed angle
The more C terminal is called the recognition helix as it fits in to the major groove of DNA, making specific contacts

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21
Q

Helix-turn-helix proteins tend to bind as dimers to what?

A

Two consecutive major grooves

22
Q

The DNA recognition site for Helix-turn-helix DNA binding motif is what?

A

Palindromic

23
Q

Describe the structure of the zinc finger binding domain?

A

Four amino acids which hold the zinc atom
Held by cis-cis-his-his
Has three fingers

24
Q

The alpha helix of the zinc finger can recognise how many bases?

A

Two

25
Q

Describe the structure of a leucine zipper DNA binding motif

A

The alpha helical monomers are held together by a hydrophobic amino acid eg leucine
Forms a Y shaped structure allowing the side chains to contact the major groove of DNA

26
Q

What do homodimers and herterodimers bind?

A 
Homo = symetrical sequences
Hetero = Non identical sequences
27
Q

What is the purpose of heterodimerisation?

A

It expands the repetoire of DNA sequences that gene regulatory proteins can bind to

28
Q

The helix-loop helix is related to what?

A

The leucine zipper

29
Q

What is the effect of DNA binding proteins binding as dimers?

A

It increases their strength - also known as syngergy

30
Q

What are the domains of a transcription factor?

A

DNA binding domain
Protein binding domain
Regulatory domain
Activation domain

31
Q

How can DNA binding proteins be identified?

A

DNAse I footprinting

32
Q

List the steps in DNAse footprinting

A

1) Radioactively label one end of the DNA
2) Mix DNA with cell extract
3) Add DNAse to partially digest the DNA
4) Heat the sample to destroy DNAse and release the binding proteins
5) Run samples by gel electrophoresis
This shows regions DNA protected from digestion due to protein binding

33
Q

DNAse I footprinting can also be used to identify what?

A

Where a protein binds on a sequence of DNA

34
Q

What is EMSA?

A

Electrophoretic mobility shoft assay

35
Q

What is EMSA used for?

A

Identify DNA binding proteins

36
Q

Give the steps in EMSA

A

1) Radioactively label one end of the DNA
2) Mix with the cell extract (or purified protein)
3) Run samples by gel electrophoresis
Lanes with a protein bound will move through the gel slower

37
Q

What are the three forms of transcription factors?

A

Permissive
Specific
Regulatory

38
Q

What are permissive transcription factors?

A

General - neccessary for all transcription

Bind at the promoter

39
Q

How do regulatory transcription factors function?

A

Interactions with the RNA polymerase complex
Altering acetylation of the DNA
Binding to other transcription factors

40
Q

Where do regulatory transcription factors bind?

A

Anywhere around the gene - it can be far away

Or they dont bind DNA directly and bind to a regulatory complex

41
Q

What does DNA looping play an important role in?

A

Forming DNA/protein complexes

42
Q

Because chromatin does not bend easily it is thought that what is needed for two proteins to interact?

A

They need to bind directly to neighbouring DNA sequences

OR to two sites that are >500 base pairs apart

43
Q

What is the role of insulators and barriers?

A

They block regulatory sequences from affecting neighbouring genes

44
Q

Which inputs can alter gene expression by integrating?

A

Activating proteins

Inhibition proteins

45
Q

Genetic switches respond to what

A

Extrinsic or intrinsic regulation

46
Q

What is tryptophan repressor protein?

A

A repressor protein which represses genes required for tryptophan synthesis

47
Q

List ways that a transcription factor could be regulated

A

a) Protein synthesis
b) Ligand binding
c) Covalent modification
d) Addition of a second subunit
e) Unmasking
f) Stimulation of nuclear entry via removal of an inhibitory protein allowing it to enter the nucleus
g) Release from membrane

48
Q

Transcription factors can interact in what way with each other on the DNA?
Give an example

A

They act syngergistically
eg just A = 1 unit of transcription
Just B = 1 unit of transcription
A + B = 100 units of transcription

49
Q

Binding of transcription factors on the DNA helps to prevent what and also helps with what?

A

Prevents them falling off the DNA

Helps as binding of one may enable another to bind

50
Q

What are the ways in which transcription factors can regulate the transcription of transcription factors?

A

Positive feedback = more made
Negative feedback = less made
Flip flop device - two inhibit each other
Feedforward loop

Cell and Molecular Biology (17 decks)

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