Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

MCB2050 > f. LEC 3 + 4 > Flashcards

f. LEC 3 + 4 Flashcards

1
Q

What are the 7 GTFs associated w/ RNA pol II?

A

TFIIA, TFIIB, TFIID, TFIIE, TFIIH, TFIIF, TBP

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

T or F - all TATA-less promoters are CpG islands

A

F - There are some TATA-less promoters that are not rich in just Cs and Gs

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Name 3 features that make CpG islands special compared to most promoters

A
  1. place, where the TATA box would be, is instead rich in Cs and Gs
  2. transcription initiation is bidirectional
  3. they transcribe continuously and at a low rate
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

T or F - CpG islands initiate and elongate in both directions

A

F - they only initiate bidirectionally

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What is the significance of GTFs?

A

to help load the RNA pol II and help w/ transcription regulation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

a) What does the peak represent compared to the plateau
b) what type of promoter is being used
c) Is this bidirectional or uni-direction?
d) how many pol II’s are present?
e) What does the noise represent?
f) ChIP or RNAseq?

A

a) peak = initiation phase, plateau = elongation phase
b) TATA or TATA-less promoter
c) unidirectional
d) 1
e) the amount of RNA transcribed by the RNA pol II
f) RNAseq?

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

CpG islands continuously transcribe at a low rate. What feature allows it to do this?

A

less nucleosome = DNA is more open making it easier to transcribe continuously

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

T or F - CpG islands don’t have to initiate transcription at the start site

A

T - they can initiate at any position w/in its ‘island’

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

a) What does the peak represent compared to the plateau
b) what type of promoter is being used
c) Is this bidirectional or uni-direction?
d) how many pol II’s are present?
e) What does the noise represent?
f) ChIP or RNAseq?

A

a) peak = initiation phase + plateau = elongation phase
b) CpG islands
c) bidirectional
d) 2
e) the amount of RNA transcribed
f) RNAseq?

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Name + Describe the 2 types of graphs that are used as evidence of the bi-directionality of GpC islands.

A
  1. RNAseq = RNA synthesized over the region
  2. Chromatin immunoprecipitation (ChIP) = the binding of RNA pol II to the DNA using anti-RNApol II antibodies
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

a) What does the peak represent?
b) what type of promoter is being used
c) Is this bidirectional or uni-directional?
d) how many pol II’s are present?
e) ChIP or RNAseq?

A

a) initiation phase = the binding of a pol II
b) CpG islands
c) bidirectional
d) 2
e) ChIP

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

a) What does the peak represent?
b) what type of promoter is being used
c) Is this bidirectional or uni-directional?
d) how many pol II’s are present?
e) ChIP or RNAseq?

A

a) the binding of the Pol II
b) TATA or TATA-less
c) unidirectional
d) 1
e) ChIP

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What are the components that makeup TFIID?

A
  1. TBP = TATA-binding proteins
  2. TAFs = TBP associated factors
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What GTFs make up the core PIC? What is its purpose?

A

a) preinitiation complex = TFIID + TFIIA + TFIIB + TFIIF + TBP
b) loads the pol II onto the DNA at the right spot

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What GTFs make up the closed PIC? Which one is the most significant?

A
  1. Core PIC = TFIID + TFIIA + TFIIB + TFIIF
  2. closed = TFIIE + TFIIH (most)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

TFIIH is known as a multiprotein complex. What does this mean?

A

This means it has multiple domains;
1. Helicase DNA = unwinds the DNA so transcription can take place
2. kinase activity = phosphorylates the CTD to release the RNA pol II from the promoter sequence

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Why is the TFIIH GTF so important?

A

It facilitates the transition from the initiation phase to the elongation phase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What are the 2 elongation factors that pause elongation? Why do they do this?

A

a) NELF + DSIF
b) check to see if transcription is ready to begin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

After NELF + DSIF cause the attend of elongation what restarts the phase?

A

CDK9/CycT or PTEFb = a kinase that phosphorylates the CTD and the NELF causing the NELF to fall off which restarts elongation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What are the 7 steps to amplifying DNA using the massive parallel DNA sequencing technique?

A
  1. Fragmentation: fragment DNA
  2. Primers: ligate linkers (primers onto DNA) onto each side of the fragment
  3. Fix to plate: denature and anneal one of the linkers to a complimentary link that is stuck on a plastic plate
  4. Get target DNA: Synthesize the fragment (including the other linker that is not annealed)
  5. Get rid of original DNA: denature and wash away the old fragment of DNA (the synthesized strand contains the target DNA)
  6. Horseshoe: Form a horseshoe shape w/ the Fragment by annealing the other linker to a complimentary primer that is fixed to the plastic plate
  7. PCR: Synthesize and amplify the DNA using PCR
21
Q

Describe the 6 steps associated w/ the dNTP fluorescent part of Massive parallel DNA sequencing

A
  1. Cut, denature and wash away one DNA strand from the horseshoe
  2. anneal a new primer onto the end of the DNA that is not fixed to the plastic plate.
  3. Then Wash fluorescently labeled dNTPs (each labeled using a differ colour) to see if it binds (if it’s complimentary to the DNA strand)
  4. once the dNTP is bound use fluorescent imaging to determine the type of dNTP
  5. Remove the fluorophore
  6. repeat steps 3 to 5 until who genome is sequenced
22
Q

What are the 2 types of libraries involved in putting all the dNTPs in the correct sequence wrt massive parallel sequencing? Which one is easier?

A
  1. aligned sequencing = where you chop up the fragments at the beginning and keep them in the same order. So by the end, all you need to do is put them together to get the sequence
  2. random sequencing = Fragmentation is random for this usually causing some overlap due to there being multiple genomes in the sample. This overlap allows for a computer to sequence the DNA. (easier)
23
Q

We know many ways to sequence DNA but how is RNA sequenced?

A

Due to RNA being so unstable compared to DNA, we convert the RNA to DNA using an RNA-Dependent-DNA Polymerase. This allows us to sequence RNA no differently then DNA.

24
Q

Why is massive Parallel sequencing named the way it is?

A
  1. massive = generates billions of reads for a genome within a short period of time
  2. parallel = the Genome a fixed parallelly to the plastic plate during the amplification phase and it organized parallelly during the sequencing phase
25
Q

What does cDNA stand for?

A

complimentary DNA

26
Q

Describe the chromatin immunoprecipitation (ChIP) technique. How does this differ from the Gel-Mobiliity shift?

A

a) it is a multi-step technique used to detect the binding of a specific protein to a specific DNA element
b) its the same but it looks at DNA in vitro (outside the body) instead of Vivo (inside the body)

27
Q

What are the 4 steps of ChIP using an anti-RNApol II antibodies?

A
  1. cross-link Pol II to DNA that it binds to
  2. fragment the DNA + add anti-RNApol II antibodies
  3. isolate the fragments of DNA that contain the pol II cross-linked via immunoprecipitation
  4. reverse cross-link the DNA (separate DNA from pol II + antibody) + sequence DNA via massive parallel
28
Q

Wrt TFIIH
a) What is the name of the domain that does helicase activity?
b) How does the helicase domain open the DNA?
c) Where does the DNA get opened?

A

a) SsI2
b) melts the H-bonds (denaturation)
c) at the initiation site

29
Q

Describe Xeroderma pigmenotsum
a) What is it?
b) What does it cause?
c) This is a mutation of which GTF?
d) What does this tell us wrt that GTF?

A

a) a skin cancer
b) it inhibits DNA repair
c) TFIIH
d) shows evidence that TFIIH is involved in transcription-coupled DNA repair

30
Q

Fill in the blanks; HIV has a mechanism that suppresses ________ activity by encoding the protein _______. This causes the RNA Pol II to pause at the ________ (before initiation is complete). Due to this stress the ______ releases the ________ and the polymerase transcribes the virus.

A

CDK9/CycT (or PTEFb), TAT. promoter, TAT, CDK9/Cyct (or PTEFb).

31
Q

What are the 2 elongations factors that cause the pausing of the polymerase after initiation. Which one remains after the conformational change of the Pol II (phosphorylation).

A

a) NELF
b) DSIF - remains

32
Q

What does the following stand for? What are they associated w/?
a) TAR
b) TAT

A

a) Transactivation RNA element
b) transactivation of transcription
- HIV hijacking the PIC in order to transcribe its own DNA

33
Q

Describe the features of the following;
a) promoters - 3
b) promoter-proximal elements and enhancers - 1
c) transcription activators and repressors - 2

A

a) they directly bind RNA Pol II to DNA, determines the initiation site of transcription, and influences the frequency of transcription initiation
b) they are cell-type specific
c) they are modulator proteins that contain a DNA-binding domain + one or more activation/repression domains

34
Q

What are the 3 types of regulatory sequences/proteins that regulate transcription. Indicate which ones are sequences (DNA) vs proteins

A
  1. promoters - sequence
  2. promoter-proximal elements + enhancers - sequence
  3. transcription activators/repressors - proteins
35
Q

Describe promoter-proximal elements

A

they are DNA sequences that can be either upstream or downstream of a promoter. They are used to regulate the transcription of a gene by acting as a binding site for activators or repressors

36
Q

What is the difference b/w a silencer and an enhancer sequence?

A

a) silencer turns genes on or off
b) enhancers speed up or slow down transcription of a gene

37
Q

T or F - enhancers only enhance transcription

A

F - they can enhance or repress transcription dep on the type of protein/GTF (activator/repressor) that binds to it

38
Q

Name 4 things that distinguish promoters from enhancers

A
39
Q

We know that enhancers can regulate transcription from distal positions how it this possible?

A

enhancers communicate w/ the promoters by bending the DNA which brings them close

40
Q

How many domains does a transcriptonal activator/repressor have? Describe each?

A
  1. DNA-binding domain - domain on the protein that binds to the DNA (enhancer sequence)
  2. effector domain - the domain that interacts w/ the promoter to either INC (activation domain) or DEC (repression domain) transcription
41
Q

How does one identify the DNA-binding domain and effector domains of a transcriptional activator/repressor?

A

deletion analysis - by mutating certain segments of DNA an recording the difference in mRNA produced.

42
Q

Fill in the blanks; Transcriptional activators and repressors each have multiple _______ and each of them have conserved _______ that each have their own fxn w/in the ________

A

domains, motifs, protein

43
Q

If the top activity is from the wild-type protein describe which ones show a mutation in the following
a) DNA-binding Domain
b) activation domain
c) repressor domain

[FIX]

A

a) 2nd + 7th + 8th = no transcription can take place due to there being no part of the protein that can bind to the DNA
b) 5th, 6th, + last = due to there being transcription however less of it
c) none = there is no sign of more activity thus there is no repressor domain present w/in this protein

44
Q

Describe the following;
a) a domain
b) a motif

A

a) a part of a protein
b) a part of a domain that dictates that domains fxn

45
Q

Describe 4 types of motifs; What do they all have in common?

A
  • they are all unique to DNA-binding proteins
    1. Zn finger = contains Cys + His interact w/ Zn + other nonpolar AAs interact with a specific sequence
    2. Leu Zipper = rich in leucines that interact w/ eachother
46
Q

Describe 4 types of motifs; Indicate for each whether they are involved in DNA-protein or Protein-protein interactions

A
  1. Zn finger = contains Cys + His interact w/ Zn + other nonpolar AAs interact with a specific sequence (DNA-Protein)
  2. Leu Zipper = rich in leucines that interact w/ each other (Protein-Protein)
  3. Helix-turn-Helix = a monomer (DNA-Protein)
  4. helix-loop-helix = a dimer that has many AAs that interact w/ each other (Protein-Protein)
47
Q

How does protein dimerization INC the complexity of DNA-binding specificity?

A

The random combining of monomers to form dimers where each have their own DNA-binding domains that are sequence specific and may or may not be effected by an inhibitory factor.

48
Q

Describe the 2 types of dimers. Which one causes more variation?

A
  1. homodimers = two identical monomers dimerizing
  2. heterodimer = two distinct monomers dimerizing (more)

MCB2050 (18 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions