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Flashcards in PA20293 gene transcription and DNA Deck (149):
0

What is the difference between genetics and genomics?

Genomics is the study of all the genes in an organism, how genes and proteins work together and interact.
Genetics is the study of inheritance of genes, mutations and inherited diseases.

1

What determines expression rate?

How often genes get transcribed into proteins

2

Are all Polymorphisms harmful?

No, some are harmless, and are found in the non coding regions of genes (introns)
Polymorphisms are changes in gene sequence.

3

What does polygenic mean?

A disease caused by more than one gene being mutated.
These are very common
An example of a disease that isn't polygenic ie is caused by a single gene mutation: cystic fibrosis.

4

What is an autosomal disease?

The gene causing the disease is not present on the sex chromosome.
Ie not X linked (XX, XY)
Autosomal dominant and autosomal recessive

5

Two copies of each gene are inherited by a child, one maternal one paternal. If a mutation occurs, when will a disease show up in a child? Think about dominant and recessive genes...

If the allele is dominant, only one copy of the mutated gene needs to be inherited. The disease will show up if the child inherits one mutated copy from one parent and it's on a dominant gene.
If the child inherits two copies of a recessive mutated gene, one from each parent, the disease will show up. For a recessive linked disease to show up both copies need to be mutated.

6

What happens if a disease is X-linked, and in a male, there is a mutation on the X chromosome?

They will express the disease, males don't have another copy to back it up as their chromosome is XY unlike females which are XX.

7

What happens if a disease is X linked, and In a female a gene is mutated on one of her X chromosomes?

She won't express the disease as she has an back up healthy copy of the gene on her other X chromosome. She will be a carrier of the disease however. Females: XX

8

Does the sex of the child determine whether they inherit a disease or not with autosomal dominant/ recessive diseases?

No!
Only with X linked inheritance pathways

9

If a disease is autosomal recessive, and a child inherits one dominant copy and one mutated recessive copy from their parents, will they express the disease in their phenotype?

No,
They will be a carrier
For a recessive linked disease to show in the phenotype, 2 recessive genes must be present; homozygous recessive

10

Examples of diseases caused by X linked alleles?

Heamophilia and colour blindness
X linked diseases most often in males, most often X linked recessive

11

What are the three most common modes of inheritance?

Autosomal dominant, autosomal recessive, X linked recessive.
The 4th mode is X linked dominant but this is rare

12

What are molecular markers of disease?

Identifying molecular markers located along DNA which are inherited with disease, can help to locate the region of the gene causing the disease.
Molecular markers; map disease loci, they're based on Polymorphisms
Polymorphisms act as convenient markers for studying inheritance
If you've inherited a polymorphism it's likely you've inherited the genes around it

13

What are RFLP's and what are they used for?

Restriction fragment length Polymorphisms.
Changes in sequences of restriction site of enzymes
Enzymes won't cut at usual places,
Results in different sized fragments to usual
Inheritance of a polymorphism could indicate the likely presence of a linked allele for the inherited disease.

14

What are SSRs?

Simple sequence repeats
Repeat of 2-8 bases
Due to slippage of template
Can map disease loci, Map what's maternal and paternally inherited
These random repeated sequences make an individuals gene profile unique
You're looking for Polymorphisms and repeats when studying loci

15

Why do we want to map out/ locate genes that cause disease?

If we find out what the gene is we can target it for therapy, we can get an idea of what protein is involved, we can use the protein as a molecular target for treatment

16

What is gene mapping?

The process of determining the locus for a particular biological trait (phenotype) eg a disease.

Locus/ loci: the specific location of a gene / DNA sequence on a chromosome

Individuals get mapped at several different loci ie you're usually looking at about 14 different loci: and you're looking for different Polymorphisms and repeats.

17

Gene mapping:
Links are made between inheriting particular Polymorphisms and whether a disease is present or not.

You're looking for mutations in genes near to inherited markers, these markers may be Polymorphisms, SSRs, RFLPs

18

What's the problem with gene mapping?

It doesn't narrow the search for our gene down that much, only to about 10 genes. We need to use techniques such as northern blotting to search for our effected gene more thoroughly.
Also gene mapping has no success with polygenic diseases.

19

True or false: a loss of heterozygosity can lead to cancer

True
Polymorphic, heterozygous regions may be lost where it results in the loss of a functional tumour suppressor gene. If the person suffers a point mutation in the back up gene copy too a loss of heterozygosity has occurred.

20

What is the concept of heterozygosity of genes?

The fact we have "back up" copies of genes in case a mutation occurs
When genomic copies from each parent have different bases in polymorphic regions due to SNPs, the region is heterozygous
You loose heterozygosity if there is a mutation in both a gene and the back up

21

What is contact inhibition?

Receptors on a cell surface touch another cell surface ligand, which results in cell growth inhibition, ie this is a stop signal. This is lost in cancer cells

22

True or false: It only takes one mutated gene to cause cancer

False.
Multiple changes in DNA are needed to convert a normal cell into a cancer tumour cell.
usually at least 3 diff genes need to be mutated
Eg Loss of : apoptosis pathway, kinase pathway and repair mechanisms.

23

What do single base mutations and sequence mutations lead to?

Single base: one different amino acid; could lead to loss of protein function but not definate.
Sequence: deletions/ mutations may scramble encoded mRNA: leads to complete loss of function protein.

24

Cancer requires 3-7 hits on relevant genes for it to occur. What does this mean?

3-7 mutations need to occur on relevant genes which are those regulating cell growth and division, DNA repair, and cell death.

25

Proto oncogenes are the mutated, cancerous form of oncogenes. True or false?

False. Oncogenes are the mutated form of the normal cellular genes Proto-oncogenes
This mutation is usually dominant

26

Receptors on cell surfaces receive growth signals. What can increase numbers of receptors/ increase their activity?

If more receptors are made; due to gene number being amplified, or translocation of receptors gene to an area of high transcription rate.
Confrontational change in receptor; the receptor is always activated even without a Ligand
Constitutive dimerisation (dimerisation does not need a signalling molecule)

27

In breast cancer,what does the her 2 receptor suffer, and what does this lead to?

Oncogenic mutations
Results in neu oncoprotein
Ligand independent, therefore constitutively active

28

In cancer, what does the EGF receptor suffer and what does this lead to?

A deletion
Leads to the Erb B oncoprotein
This is a constitutively active protein tyrosine kinase
Ligand independent

29

What is Li Fraumeni syndrome?

Inherited mutation in p53 gene.
It results in many childhood tumours

30

A mutation in the ____ tumour suppressor gene leads to a retinoblastoma

pRB
Mutation in the second allele leads to retinoblastoma, a tumour in the eye

31

What are translocations?

Abnormal crossovers between chromosomes during cell division
They cause a split in a gene, and joining with another part of a gene
Can lead to genes normally regulated by one promoter being separated from this promoter region and instead being controlled by another promoter.

32

How do chronic myeloid Leukaemias occur?

Translocations: result In constituitively active c-abl tyrosine kinase,
by loss of the N-terminal regulatory domain (due to this translocation, lost part of gene therefore lost part of protein)
Leads to increased cell signalling and growth: forms tumour

33

Does each gene have the same upstream sequence?

NO
Each gene has a different upstream sequence
Different transcritpion factors therefore bind to different upstream elements, and specificity arises from these different transcription factors used. Different transcription factors switched on results in switching on of different genes.

34

Which Direction does RNA polymerase work in?

From 5' end to 3' end of DNA
Moves away from promoter region toward the downstream part of the gene
(but reads in 3' to 5' direction)

35

What assembles at the TATA box? What does this then recruit?

The initiation complex assembles here
This is where transcription factors come together an bind to the TATA box and then recruit RNA polymerase.

37

What does the position of the TATA box (~25 base pairs from start site) enable?

This is where RNA polymerase will bind, so the distance of the TATA box to the start of the gene will be correct in order to align the front of RNA polymerase enzyme up with the First base of the gene to be read!
The TATA box is CRITICAL in the positioning of RNA polymerase, and therefore where transcription starts from

38

What do RNA polymerase I, II & III translate DNA into?

RNA pol I: into rRNA, in nucleolus
RNA pol II: into mRNA, in nucleoplasm
RNA pol III: into tRNA, in nucleoplasm

39

What must all amino acid sequences start with to make a functional protein?

Must start with the start codon, methionine (Met)

40

How is the mRNA strand positioned when it attaches to the ribosome?

mRNA is sandwiched between the two subunits of the ribosome (the large and small subunit)
tRNA molecules bring in amino acids that match the sequence on the mRNA strand

41

What's the regulatory region of DNA called?

The promoter region
Contains enhancer region, upstream elements, TATA box where RNA polymerase binds and start site.
These are several highly conserved regions bound to by regulatory proteins.

42

What is gene transcription mediated by?

A transcription complex which includes RNA polymerase II, this is the initiation transcription complex that assembles at the TATA box and then proceeds to move along the gene

43

What position is the start site of a gene? What is everything to the left (upstream ) of this?

Start site is position +1
Everything to the left upstream of This is negative numbers, everything to the right downstream is positive numbers

44

What do the enhancer region and upstream elements bind?

These bind constitutuive and inducible transcription factors

45

What are constitutive transcription factors?

There all the time, present in all cells all the time!

46

What are the inducible transcription factors? When are they activated?

These are regulated downstream of receptors and will only get activated when the receptor is activated and therefore the signal pathway is activated.
These TFs aren't present all the time!!

47

What are upstream elements also called?

Promoter-proximal elements
(these are any regulatory sequence located within ~200 BP upstream of the start site

48

Where is the enhancer located? Upstream or downstream? Is it one enhancer per gene?

It can be located upstream or downstream of the gene
One enhancer can oversea several related genes, it's not just one enhancer per one gene

49

Are transcription factors part of RNA polymerase?

No, RNA pol is a separate enzyme, the only thing they have to do with RNA pol is that basal/ general TFs associate and then recruit RNA pol to form the transcription initiation complex, which allows transcription to occur.
General/ basal TFs are coassociated with RNA Polymerase

50

What are the TF-11 family coassociated with?

RNA pol II

51

During the formation of the preinitiation transcription complex, where do the TFs first bind?

To the TATA box
Eg in preinitiation complex involved RNA Pol II, TF11D first binds to the TATA box with its TBP (TATA binding protein).

52

During the transcription initiation complex (preinitiation complex) formation, what distorts the structure of DNA?

TBP binds to the major groove of the TATA box of DNA.
TBP is a protein, if you stick a protein onto coiled DNA it will bend it and distort it. TBP binding results in considerable bending of the DNA. ☡

53

Overall, what does the formation of the transcription Initiation complex involve?

It's a slow build up of associated proteins (transcription factors)
Emphasis that this is a STEPWISE assembly of TFs coming together.
The transcription initiation complex comprises associated general transcription factors and RNA Pol II

54

Which transcription factor activates the whole transcription initiation complex at the end?

TFIIH, it's the final protein to bind.
It has helicase activity, so can unwind the DNA strand for the gene we need.
It also has kinase activity, and phosphorylates the carboxyl terminal domain of RNA Pol II

55

Once the RNA polymerase starts moving downstream, all the basal/ general TFs dissociate and are released, all except from ___?

TBP
TBP, TATA binding protein, stays bound

56

When the transcription initiation complex is first formed, where does the active site of RNA pol II lie?

Above the start site of the gene, the TATA box is located in a position so that it is the correct distance away to allow the front of RNA pol to be aligned with the start of the gene!

57

What kind of histones does euchromatin contain?

Acetylated histones
Relaxed DNA binding around chromosomes, actively transcribed DNA

59

What is a nucleosome?

A basic structural unit, DNA is wound around a protein called a histone.
Nucleosomes are the core OCTOMER of histone proteins
146 BPs of DNA wound round each histone core, 2 histones in each OCTOMER
DNA is very tightly packed (wrapped) around these histones

60

What's the name of the structure whereby DNA is coiled really tightly so it's tightly packed? Diameter?

DNA coiled into SOLENOID structure
30 nm diameter

61

We need another set of proteins to the general TFs to unwind DNA so that it's more accessible by general TFs and RNA Pol.
These work by activating a set of ____ that activate ____ _____

Activate a set of enzymes, that activate histone acetylation.

62

Why are histones and DNA so tightly attached normally?

Positive charge on histones (from basic amino acids, such as Lysine, NH4+)
Interacts with the negatively charged backbone of DNA

63

How does acetylation loosen the interaction of DNA and histones?

Acetylation results in positive charges on the histone proteins amino acids being masked, loosening the interaction with the negatively charged DNA.

64

Is heterochromatin actively transcribed? Why?

No
Densely packed nucleosomes that are condensed.
Not easily accessible.
Contains deacetylated histones

65

Do upstream elements influence the initiation complex at all?

Yes they increase it's efficiency, by binding to transcription factors the rate of Assembly is influenced and therefore rate of formation of the initiation complex.
Remember the upstream elements increase the efficiency of the transcription initiation complex.

66

What are reporter assays?

Reporter genes which can be used to assay for the expression of the gene of interest.
The reporter directly attaches to the gene of interest by gene fusion.
An example of a reporter assay is the Luciferase assay

67

What happens in the Luciferase assay?

Its a reporter assay
Luciferase is an enzyme
Luciferase + luciferin (substrate) = light flash
Used to determine if we have activated transcription factors that bind to the gene region of interest, as this would mean we have stimulated Luciferase production.
Can be used to see the effects of shortening the promoter region. Ie we loose activity when we remove the enhancer region and when we remove the upstream elements!
Activity monitored by light flash 

68

Where is the enhancer region located?

It can be 1000 BPs away from the start site
It can be 50-200 BPs in length.
It can be upstream or downstream from the start site
One enhancer region can oversee and control several different genes

69

Where is the CAAT box located?

~75 BPs upstream from the start site

70

Upstream TFs that will bind to CAAT sites?

C/EBP and NF1

71

What's special about the CAAT box? (3 things?!)

This sequence can function in either orientation (so can be bound to in any orientation)
This box increases promoter STRENGTH rather than specificity
Can have more than one CAAT box present on a gene

72

Where is the GC box located?

Around 90 BPs upstream from the start site position -90

73

What transcription factor binds to the GC box?

SP1

74

How many copies of the GC box are present on a gene?

Can have more than 1 copy, usually multiple copies of this sequence present in a gene promoter region

75

TATA box, GC box, CAAT box, which ones are basal elements and which upstream?

TATA box is a basal element
GC and CAAT box are upstream elements

76

What do basal elements such as the TATA box determine in contrast to the upstream elements?

Basal determine LOCATION, ie where RNA polymerase should bind to
Upstream elements determine FREQUENCY; ie how often transcription factors bind and activate transcription.
Upstream and basal sites interact, basal site in turn interacts with RNA polymerase  basal and upstream factors integrate together

77

Where are enhancers usually located? How many BPs in length are they?

Usually located 1000s of BPs upstream or downstream from the start site (a long way away!)
They're usually around 50-200 BP long

78

The binding of transcription factors to the consensus sequences in the enhancer region is often ______. What does this mean?

Often cooperative
This is where the binding of one transcription factor will increase the likelihood of another one binding, ie first to bind is quite slow, second to bind is faster etc.....
This happens with all TFs coming together, not just in the enhancer region!

79

What is the net effect of enhancers?

Increase initiation of transcription.
Often responsible for tissue specific gene expression.

80

How many genes can enhancers activate?

One enhancer can activate several genes
Wherever the enhancer is, it will activate the genes in the vicinity of that region.
Remember enhancers can increase gene expression up to 200-fold!

81

How do TFs bound to the enhancer region interact with the basal initiation complex, when the enhancer region is so far away?!

By looping and bending of DNA, which brings sites together.
Also by co-activators, which are bridging proteins, which will link DNA binding Transcription factors to basal apparatus

82

What does coactivators speed up the assembly of? How?

They'll bind to transcription factors, eg the starter subunits TF11D, TF11A, and then bring them into the TATA box region, therefore coactivators help to speed up the rate of assembly of the transcription initiation complex, and therefore increase efficiency of transcription!!!!

83

Examples of coactivators ?

p300/ CBP (Creb binding protein)
PCAF

84

How can coactivators make DNA less tightly compact?

They have histone acetyl transferase activity
Acetylating histones makes them bind less tightly to DNA.

85

Do coactivators bind to DNA?

No! They do not bind to DNA!!
They'll bind to proteins, they act as bridges between proteins (TFs) that need to come together during transcription initiation.
They bind to transcription factors and help them bind to basal proteins

86

Proteins such as TFs bind to DNA. Where do they make contact with on DNA? What part of the protein makes contact with the DNA?

Proteins often make contact with the major groove of DNA
Often alpha helical regions of proteins make contact/ insert into the DNA

87

If a protein has a _____ ______, it's likely to be a transcritpion factor (hint: examples are Cys2 and His2)

ZINC FINGER! 

88

True or false: zinc fingers are the same in every protein?

True
Zinc fingers have a common structure, protein consensus (ie same proteins/ same amino acids in every one)

89

What does the zinc finger bind to?

The zinc finger or a protein is the domain that comes into contact with DNA ☡☡☡

90

How many amino acid residues are homeodomains?

A sequence of around 60 amino acid residues

91

What are homeodomains?

Helix-turn-helix domains
Three regions of alpha helices
It contains a 6 amino acid minor groove which determines specificity, it is sequence specific

92

How many amino acid residues are in helix LOOP helix domains??

40-50 amino acids

93

How many helices do helix turn helix domains have? How many do helix loop helix domains have?

Helix turn helix have three ALPHA helices (joined by 3 turns)
Helix loop helix have two Amphipathic helices (joined by a loop)

94

What are Amphipathic helices?

Helices which contain both hydrophobic and Hydrophillic regions

95

Dimers allow us to have more variation and specificity.
How do helix-loop-helix domains forms Dimers?!

Helix loop helixes have Amphipathic helices, containing Hydrophillic and hydrophobic regions
The HYDROPHOBIC residues on the faces of the helices can interact, forming Dimers/ dimerisation.

96

In leucine zippers, how often do leucines occur?

Every 7th amino acid

97

Why is it called a leucine zipper?

Two helices come together, and leucines on face of each helix have hydrophobic interactions with eachother, this cross-linking of the leucines looks like a zip! It is a protein dimerisation motif

98

What are leucine zippers?

Perfect summary:
Consist of multiple leucine residues at approx 7-residue intervals, which form an Amphipathic alpha helix, with a Hydrophobic region along one side
The hydrophobic region provides an area for dimerisation, allowing the motifs to "zip together"
This leucine rich region is required for DNA binding and regulating gene expression, as these DNA binding motifs are often found in transcription factors!

99

Is it the leucines on leucine zippers that bind to DNA then?

No! Adjacent to the regions of leucine repeats are highly basic regions with a positive charge, these basic regions of leucine zipper motives can bind to the negatively charged DNA ☺

100

2 examples of leucine zippers?

C/EBP (binds to the CAAT box)
AP-1

101

When are response elements switched on?

They're switched on due to changes and responses to the environment

102

What kind of transcription factors bind to response elements?

Inducible transcription factors

103

Response elements are short sequences of DNA. Where are they located?

Within gene promoter regions

104

Response elements are just consensus sequences in the promoter region that bind to inducible transcription factors.

They regulate gene transcription
They ensure genes only get expressed when we receive a CERTAIN STIMULUS! Remember they bind inducible transcritpion factors and inducible transcription factors are only made when the cell needs something!

105

What do inducible transcritpion factors bind to?

Bind to response elements, theyll only bind to them due to extracellular stimuli that tell them to switch on these response elements due to responses to the environment

106

Inducible transcription factors arent present all the time. When are inducible made?

Only made when the cell wants something in response something. They're made and then can bind to response elements of the promoter region to initiate transcription of the certain proteins the cell has decided it needs! 

107

As a steroid an inducible transcription factor on its own?

No, steroids in blood have to pass in to cells, and its when they bind to their receptor that it's a transcription factor that can bind to DNA.
Steroid receptor/ steroid hormone complex travels into nucleus and binds to steroid response elements in the promoter region of DNA, thereby acting as a transcritpion factor

108

What are the effects of steroid inducible transcription factors (ie steroid/steroid receptor complex)

Increase gene transcritpion, therefore alter protein levels in the cell.
Also bind to mRNA and stabilise it, mRNA usually unstable, stabilised mRNA so you get more protein produced
Athletes use steroids to build up protein mass 

109

Where must a steroid hormone/ steroid receptor complex translocate from and too to switch on transcritpion?

Steroid hormone binds to steroid receptor in the cytoplasm of the cell,
Then must translocate to the nucleus where it can bind to the promoter region of DNA, binds to the steroid response element.

110

The steroid hormone/ steroid receptor complex binds to DNA in the promoter region. What is present in the complex that allows it to bind to DNA?

In the steroid receptor there is a DNA binding region consisting of two Zinc fingers!!!

111

How do steroids give an anti inflammatory response?

Glucocorticoids (a type of steroid) bind to the GR receptor.
Dampens down T cell and macrophage activation
This isn't about stimulation of transcription it's about repression! We are trying to reduce cell numbers so dampen down transcription! Anti inflammatory response. 

112

What are most steroid response elements regulated by?

GR receptors
These bind glucocorticoids, remember this has a repression effect on transcritpion!

113

Where are steroid response elements located?

In enhancer region
Can therefore activate several promoter regions of genes near this enhancer region!

114

The steroid response elements have two ___ ___ repeats. These these repeats are sequences known as ______

2 Half site repeats
These are 0-4 BPs apart, space apart determines specificity of the response element

These repeats are sequences known as palindromes. These are inverted repeats so each repeat reads the same as the other one backwards!

115

What are the 5 steroid receptors forming HOMOdimers?

GR, MR, AR, ER, PR (remember Gramp, and add R on each!)

116

Steroid receptors can be homoDimers, where each unit of the dimer is the SAME and binds to the steroid response element. What does each unit bind to in this response element?

Each subunit of the dimer binds to one of the half site repeats, remember the steroid response elements consist of two half site repeats!

117

How are steroid receptors kept in their inactive state when steroid hormones aren't bound to them?

An inhibitor molecule is bound to them
Gets displaced when steroid hormone binds

118

Steroid receptors can also form heterodimers. This is where the two units forming the steroid receptor are different. what is an example of this?

RXR receptor forms a heterodimer with Vitamin D receptor.

119

A spacing of ___ base pairs between half sites of the steroid response element is recognised by VDR. (Vit D receptor)

3 BPs

120

What does NFkB switch on?

Switches on production (transcription) of the light chain of antibodies in B cells
Therefore it is key in regulating immune response to infection!
Switches on all the genes we need for inflammation during an immune response (genes for cytokines, gene for complement)

121

What kind of transcription factor is NFkB?

An INDUCIBLE transcription factor!!

123

Where is NFkB found?

In lots of cells, not just B cells (even though it turns on transcription of the light chain of antibodies in B cells)

124

What's the most common NFkB in the family of 5 dimeric transcription factors?

p65
p stands for protein
65 is the size

125

NFkBs are transcription factors. They are DIMERS.
What domain do they all have that allows two subunits to come together and form these Dimers? What else does this domain get involved in?!

They have a REL HOMOLOGY DOMAIN (RHD)
Allows dimerisation of NFkB subunits to form NFkB Dimers
Also involved in binding to DNA
This RHD domain also allows interaction with IkB proteins (inhibitors of NFkBs!)

126

What do different NFkB Dimers recognise? What does this result in?

Different dimers recognise different NFkB response elements
This results in specificity, as genes have different NFkB response elements in their promoter regions

127

NFkB contain conserved regions (300 amino acids)

Their inhibitor molecules, IkBs also contain conserved regions (called ankyrin repeats) (30 amino acids)

128

How do NFkB and IkB (inhibitors) interact? Hint: it's a domain in NFkB and a 'repeat' in IkB!

RHD domains in NFkB interact with Ankyrin repeats of IkBs

IkBs inhibit NFkBs by binding to them and holding them in cytoplasm, so that they can't translocate into the nucleus and have their effects on transcription!

129

What triggers IkB to let go of NFkB so it can translocate to the nucleus and activate transcription?

An immune response: Bacteria, viruses, cytokines Il-1 and TNFa.
Triggers IkB kinases to phosphorylate IkB causing it to detach from NFkB- known as UBIQUITINATION

130

What act as both a stimuli for NFkB translocation, and are something NFkB activates transcription of?!

The cytokines such as IL-1 and TNFa

131

What diseases could result from over-activation of NFkB?

Arthritis, septic shock, autoimmune diseases such as diabetes
These are all in some way linked to too much inflammation
NfKB results in inflammation!

132

NFkB (TF) ⇒ Cox (protein) ⇒ inflammatory responses
What can you think of that inhibits NFkB?
What about cox?!

NFkb: glucocorticosteroids, omega3, antioxidants
Cox: NSAIDS

133

What kind of transcription factor is Creb and what is it regulated by?

An inducible transcription factor
Regulated by Serine phosphorylation

134

What is the name of the coactivator CREB binds to? What does this go on to Interact with to further initiate transcription?

CREB binds to coactivator CBP/ p300
This interacts with basal transcriptional machinery (basal transcription factors: involved in formation of transcription initiation complex)

135

What kind of transcription factor is AP-1?

An inducible transcription factor

136

AP-1 Is a Dimeric TF, what families are each subunit of the dimer a member of?

One member of the fos family, one member of the jun family
Eg c-fos and c-jun
They dimerise together to form the active transcription factor AP-1

137

What is the inactive form of c-jun of the AP-1 dimer Transcription factor?

In its inactive form, c-jun is phosphorylated at the C terminal, which prevents DNA binding.
Certain stimuli will lead to the dephosphorylation, which allows DNA to bind and activate C-jun

138

How is c-jun then activated?

C terminal dephosphorylated
JNK phosphorylates c-jun on the N terminus.
Serines 63+ 73 are targets for phosphorylation by JNK

139

Does c fos of AP-1 need activating?

No just it's expression needs increasing

Activators of AP-1 need to increase c-fos expression, and activate c-jun!!!

Cfos is an example of a TF that only gets synthesised when needed!

140

What are AP1 and NFkB both activated by? What do they therefore have opposite effects to?

Both activated by inflammatory signals to trigger inflammation, therefore have opposite effect to glucorticosteroids which dampen down inflammatory response

141

Creb and AP-1 are both regulated by____ ______

Serine phosphorylation!
If you don't understand this, see Educreations video AP1

142

What are STATS regulated by? Hint; not the same as AP-1 and Creb!

Tyrosine phosphorylation!

143

What does STATS stand for?

Signal transducers and activators of transcription
These transcription factors are only activated in cells of the immune system

144

Which one of the STATs family is a tumour suppressor TF?

STAT 1
A mutation in stat1 would lead to a loss of ability to apoptose things, could lead to cancer.
Linked with IFNy, which generally promotes apoptosis in cells infected with viruses/ bacteria

145

Which STAT protein negatively regulates apoptosis? Ie promotes proliferation and cell cycle progression?

Stat 5
Too much of stat 5 could lead to a tumour

146

What is STAT 3 needed for?

Needed in EMBRYOS
If its absent, could be lethal to lil baba
Stat 3 is activated in many tumours however!

147

What do CREB Activators promote? CREB repressors?

CREB activators promote Long term memory
Repressors ERASE memory

148

Linking them together: which inducible TF regulates levels of CREB mRNA?

AP-1 regulates levels of Creb mRNA
Ap-1 synergies with Creb in long term memory function

149

What kind of steroids inhibit ap-1 and NFkB transcription?

Glucocorticoids
AP-1 and NFkB both involved with inflammation
Glucocorticoids are antiinflammatory

150

Many inducible TFs are regulated by phosphorylation. This phosphorylation can be direct as with _____, or indirect as with ______

Direct: CREB, STAT, AP-1 (phosphorylated at c-jun N terminal)
Indirect: NFkB: IkB attached to NFkB is phosphorylated, releasing it.

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What are the five inducible TFs, that are only active when required?

CREB, NFkB, steroids, AP-1, STATs

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