Lec1HumanGeneTranscription Flashcards
1
Q
What is POU1F1?
A
a transcription activator (transactivator) for GH, PRL and TSHs in ant pituitary gland
2
Q
If POU1F1 is mutates, what occurs>
A
It leads to a decrease in GH, PRL, TSH (all hormones)
3
Q
In the article related to pituitary hormone deficiency, the young patient had a severe decrease on GH, PRL, and TSH due to
A
heterozygous mutations (2 separate mutations on POU gene)
4
Q
What are the heterozygous mutations that occurred for this pt?
A
- Deletion frameshift : deleted a base and it caused the reading frame to be different, so different amino acids) causing lacked DNA binding domain
- A missense mutation (diff protein) in the C-terminal
5
Q
True or False RNA synthesis is transcription
A
True
6
Q
What does every gene need for activation of transcription by RNA poly 2?
A
- every gene of ever cell has nonspecific proteins: to do PIC
- every gene of every cell has nonspecific elements: TATA seq,non specific DNA seq
nonspecific=every gene/cell has them
7
Q
How is transcription activated the right time and right place?
A
every cell has SPECIFIC proteins/elements that allow for specific genes to be transcribed.
ex: liver cells has specific elements that create protein for specific liver function
8
Q
_______ is the most efficient place to regulate
A
Transcription
9
Q
RNA poly 2 transcribes
A
all protein-coding genes
10
Q
RNA poly 1 transcribes
A
rRNA
11
Q
All RNA polymerase has their own ____
A
PIC
12
Q
RNA poly 2 has binding sites for ___ _____ which is why it is used for protein coding genes.
A
splicing factors
13
Q
What is similar between RNA poly 1,2,3?
A
They all have their own PIC
14
Q
TATA box is 4 NT. SSDBP recognizes 10 NT so we need to methylate H3K4. Why?
A
4NT is to small to recognizes to we methylate histone to create more binding sites to help recruit PIC
15
Q
The TATA is too small for SSDNP to recognize so what do we do?
A
H3K4 methylation to help recruit PIC
16
Q
What is TATA?
A
it is non specific and its present in almost all coding genes (10-20 bp upstream)
17
Q
What is TFIIH?
A
It is non specific and has helicase activity and phosphorylates carboxyl end of RNA poly 2 (CTD) (HELICASE AND KINASE )
18
Q
What is TFIID?
A
Contains a subunit that recognizes H3, K4 methlylation (post translational modification) AND has TBP to bind of TATA box (many subunit/polypeptide)
19
Q
We need _____ nucleotide
A
triphosphate
20
Q
What are some examples of non specific proteins, termed “general transcription factors” (GTFs)
A
TFIID, TFIIH, RNA poly 2
21
Q
What binds to DNA?
A
Transactivators and TFIID (TBP specifically)
22
Q
TF in TFIIX referes to
A
transciption factor
23
Q
II in TFIIX refers to
A
RNA poly2
24
Q
X in TFIIX refers to
A
any protein A-H
25
A kinase does what?
phosphorylates
26
What does TAF stand for?
TBP Associated Factors
27
The ____ subunit of TFIID recognizes _____ and binds the _____
TBP, H3K4, TATA
28
The ____ subunit of TFIID binds_____
TAF, other proteins
29
What represents the start of transcription?
TFIIH phosphorylates carboxy terminal domain of RNA poly2 (on serine 5)
30
What starts the PIC?
TFIID (TBP and TAF)
31
True or false TATA box is a specific DNA sequence at the start of every gene
FALSE (non specific DNA sequence) at the start of every gene
32
Most of the GTF's assemble by interacting with
each other, NOT by contacting DNA
33
Transcription factors are the same as transactivators which are
proteins that activate transcription
34
What are the decoys?
TFIIF, TFIIE
35
Which subunit of TFIID recognizes the TATA box?
TBP
36
Which subunit of TFIID recognizes the other DNA sequences near the transcription start point, regulates DNA binding by TBP
TAF
37
Unwinds DNA at the transcription start point, phosphorylates Ser5 of the RNA poly CTD, releases RNA poly from the promoter, initiating RNA synthesis
TFIIH
38
True or False TAFs DO NOT directly bind to DNA
true, its binding on to other proteins like transactivators
39
TAFs provide what for transactivators?
binding sites
40
What is so important about the interaction of transactivators with TAFs in TFIID?
Transactivators bind to TAF and stabilizes the weak interaction with DNA since TBP binds only the "TATA" seq
41
What does RNA poly 2 do?
synthesizes RNA
42
Regulation of eukaryotic (euk) transcription can be
developmental or inducible
43
What is developmental regulation of euk transcription?
transcription of different genes in different tissues or at different developmental stages
1. Globin switching: biochemical change
2. heart morphology: morphological change
44
What is inducible regulation of euk transcription?
Transcription of genes in response to a hormone. Specific pathways that activate transactivators and transcription occurs
1. TNF alpha
2. JAK/STAT
3.Hedgehog
4.RAS
5.FGF
45
Eating isoflavones they will bind to receptor and your cells go into apoptosis. What type of regulation of eukaryotic transcription is this?
inducible regulation
46
A person in infected with bacteria, and produce interferons. These binds to outside of lymphocytes and produce T cells and antibodies. What type of regulation of eukaryotic transcription is this?
Inducible regulation
47
True or False Transactivators are just upstream
FALSE, transactivators can be up or down stream
48
A basic element for SPECIFIC developmental and inducible regulation of transcription is that "genes" (can be subset or 1) contain __________ , which are short, specific sequences of DNA
regulatory (or response) elements (not present in other genes)
49
A basic element for SPECIFIC developmental and inducible regulation of transcription is that the specific proteins that are able to bind _________ can activate or repress transcription. The proteins that activate transcription are referred to as ____
regulatory elements, transcriptional activators/transactivators
50
A basic element for SPECIFIC developmental and inducible regulation of transcription is that the response elements are generally located _____ base pairs upstream or downstream of the TATA box
100-300
51
A basic element for SPECIFIC developmental and inducible regulation of transcription is that a set of ______ contain similar response elements
genes regulated in concert
52
Upon binding a sequence specific transactivator to the response elements it activates genes with
same or similar response element (does not need to be 100% identical)
53
What is a polypeptide
specific exons spliced together, a transactivator
54
True or False, transactivator binds to DNA + TFIID (specifically TAF protein) to help stabilize PIC
true
55
What does this picture represent?
transactivator
56
What are the structures of sequence specific transactivator?
amino terminal, c terminal, transactivation domain, DNA binding domain
57
True or false, DNA binding domain is a regulatory element of DNA and binds specific DNA sequence
True
58
The DNA binding domain can come _______ the transactivation domain in terms of which is on the N terminal or C terminal end
before or after (they can switch)
59
Contacts other proteins especially TAFs and help TFIID be stable
Transactivation domain
60
In consensus sequence___ DNA sequences are needed for response to interferon (it can vary). But certain nucleotides cannot vary if a particular transactivator is to bind a specific sequence
Similar
61
True or false, transactivators have many binding sites which can be present at the same time (or not)
TRUE
62
What does this picture represent?
Specific DNA sequences representing the binding sites for transactivators
In this photo we are looking for specific seq but it DOES NOT have to have a EXACT match, in b/w the specific seq it can be different
63
The more transactivators you have the
greater the chance of transcription
64
These wrap over and interact with general transcription factors and PIC to stabilize and help transcribe
co-activators and transcription regulators
65
What do co-activators interact with and what do they recruit?
DNA binding proteins, HATs or contact the PIC
66
Co-activators have the same role as transactivators but they dont bind a_______, but rather bind to a _____ that binds to the ____
DNA sequence, DNA protein, DNA sequence
(this is because it lacks a DNA binding domain that transactivators have)
67
Co-repressors interact with what and mostly recruit what?
DNA binding proteins, HDAC
68
Co-repressors do not bind
DNA
69
What is an example of a classical co-repressor?
RB
70
Transactivators typically bind where?
relatively close to the transcription start site
71
Transactivators bind to which side of the transcription start site?
either side
72
MYC and E2F1 E2F4 are example of what?
Transactivator
73
What is MYC
human oncoprotein that increase proliferation
74
Transactivators bind to their ____ regions, located among the regulatory elements of genes after being activated by a certain inducer or at a certain stage in tissue development
regulatory
75
_______ recruit the TAFs of TFIID leading to the binding of the TFIID complex to the TATA box and brings RNA Poly 2 along.
Transactivators
76
TFIID binding to the TATA box leads to the formation of the complete PIC and_______
transcription
77
What three factors stabilize the PIC
Transactivator----TAF interaction
TATA----TBP binding
Histone post-translation modification (methylation of histone 3)
78
What are 6 biochemical mechanisms that make transactivators available (activate transactivators)?
1. Activate protein synthesis of transactivators
2. Covalent modification: phosphorylate transactivators and activate it
3. Add 2 subunits (EACH 4-5 BP) and combine them to activate
4. Remove inhibitor on transactivator and now activate
5. Stimulation of nuclear entry
6. Release transactivator from membrane now its active
79
In the reading about melanoma, many oncogens in melanoma effect the
RAF/MEK/ERK (MAPK) pathway
80
Most melanomas have activating mutations in _____ that exerts an oncogenic effect by activating ____ pathway increasing proliferation and survival (aka cancer)
BRAF (V600 E mutation that turns valine into glutamate), MAPK
81
____ have worked for melanoma treatment but there's resistance
BRAF inhibitors
82
MAPK signaling axis
Extracellular (Growth factor)
RAS
MAP3K (MAPK kinase kinase) --->RAF
MAP2K (kinase)--->MEK
MAPK--->ERK
Phosphorylate Transcription factors
83
The ERK pathway is constantly active in up to ___% of melanomas, and increase with early to advanced stages
90%
84
N-RAS mutation observed _____% of melanomas (which activates ERK)
15/30%
85
What is the name of PLX4032 and what does it do?
VEMURAFENIB: this is a potent/selective BRAF inhibitor
10x more selective for v600E
no activity with other kinases
86
What is the mechanism of resistance of VEMURAFENIB?
1. upregulate proteins to incr ERK
2. platelet derived growth factor receptor B mediates activation of alternative survival pathway
3. no gate keeper mutation (prevents binding to target site)
87
True or False Transactivators only bind upstream to the transcription start site
a. True
b. False
false
88
Which of the following proteins below has both helicase and kinase activity?
a. TFIIA
b. TFIIE
c. TFIID
d. TFIIH
d
89
Explain the need for Histone methylation to initiate transcription
a. The TATA box only has 6 base pairs and SSDBP’s can only recognize 15 base pairs
therefore histone methylation is needed
b. The TATA sequence is significant enough for transactivators to recognize and histone
methylation is not needed
c. The TATA sequence only has 4 base pairs, and 10 base pairs are required for SSDBP’s
to recognize the sequence
d. The TATA sequence is located at the transcriptional start site therefore histone
c
90
What is indicated in the arrow below ? (black arrow, bottom right corner)
A) Transactivator
B) Histone
C) Specific transcription factor
D) Co activator
b
91
Which of the following can directly bind to DNA?
a. Co activators
b. Co repressors
c. Transactivators
d. TFIID
e. C and D
e
