Brainscape's Knowledge GenomeTM

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


See full index

Structure, Function And Analysis Of Proteins > SFP18: Protein DNA Interactions And RNA Complexes > Flashcards

SFP18: Protein DNA Interactions And RNA Complexes Flashcards

1
Q

Do repressors and activators bind to selected DNA regions with high or low specificity?

A

high specificity

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

What is eukaryotic transcription regulated usually by?

A

Multi protein complexes

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

What can initial binding of transcription factor to the promoter region be followed by?

A
  • Secondary TF protein binding to the initial promoter regulator
  • Secondary TF binding to DNA adjacent to the promoter regulator
  • Secondary TF binding to DNA away from the promoter region, followed by DNA binding and protein-protein complex formation
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

How do protein interact with DNA?

Five ways

A
  • TATA-box binding proteins
  • helix-turn-helix motif (prokaryotes)
  • zinc fingers (eukaryotes)
  • leucine zippers
  • Homeodomains
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What does RNA polymerase II require?

A

Transcription factor II (TFII)

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

Where does TFII target promoter site?

A

At -10 position (TFII contains a TPB component (~30kDa protein))

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

What is the summary of the TATA-box binding proteins?

A
  • Recognition of TATA by TBP
  • TBPs bend and partially unwind the DNA
  • Binding of other proteins follows
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What is TPB?

A

Thyroxine-binding protein

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

What region of TFII is highly conserved?

A

C-terminal region

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

Does TBP target the minor or major grooves?

A

TBP targets the minor grooves

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Why does TBP leave the major grooves available?

A

The major grooves remain available for targeting by interaction partners (e.g. RNA polymerase II)

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

What does bending of the DNA cause?

A

Bases to be splayed and hydrogen bonds to be broken

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

What is a lysogenic state?

A

Spread of viral DNA occurs through usual prokaryotic reproduction

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What is a lytic state?

A

Is more immediate in that it results in many copies of the virus being created very quickly and the cell is destroyed

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

How does bacteriophage lambda-repressor regulate its own synthesis?

A
  • high levels of repressor prevent onset of lytic state
  • lysogeny is terminated by proteolysis of the lambda-repressor and synthesis of Cro
  • Cro suppresses synthesis of lambda repressor
  • low levels of repressor induce lysis
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What are the HTH motifs usually stabilised by?

A

By non-polar interactions between the helices

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

How does an alpha-helix interact with the DNA?

A

The major groove of DNA is 12A wide and 7A deep
A protein alpha-helix has a diameter of approx. 12A
Alpha helix can insert into the major groove and serve as a recognition helix

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

How is the helix and DNA specific?

A

SPECIFICITY: hydrogen bonding between side chains from residues on the helix and the exposed portions of the base pairs in the major groove

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

Can loops of beta-sheet elements may also serve as recognition elements?

A

Yes

20
Q

What is Cro?

A

The lambda repressor antagonist

21
Q

How are lambda repressor genes and Cro genes related?

A

They are close together but read in opposite directions… operator regions 1-3 are shared

22
Q

Which operator region does Cro have highest affinity for?

A

OR3

23
Q

Which operator region does lambda-repressor have highest affinity for?

A

OR1

24
Q

What does lambda-repressor suppress?

A

Lambda-repressor suppresses lysis and maintains lysogeny

25
Q

What does Cro suppress?

A

Cro suppresses lysogeny ( and lambda-repressor transcription) and triggers lysis

26
Q

How do tandem zinc fingers regulate gene expression?

A

By binding to extended DNA sequences

27
Q

What does transcriptional control of 5S ribosomal RNA genes rely on?

A

Transcription factor IIIA (TFIIIA) a 40kDa protein

28
Q

What amino acids do zinc fingers contain?

A

Two cys and two his residues, coordinated by a Zn2+ ion

29
Q

What is zinc finger structure?

A

Alpha helices insert into DNA major groove
Loop and beta-sheet are structurally connected to alpha-helix by a Zn2+ ion connecting 2xCys and 2xHis
The domain fold is stabilised by the Zn2+ ion

30
Q

What part of leucine zippers play in regulation of transcription?

A

Leucine zipper motifs are common in transcription regulators
In yeast (transcription activation), amino acid starvation leads to expression of GCN4, a leucine zipper protein
GCN4 activates more than 40 genes that encode bio synthetic enzymes
When bound to the DNA, GCN4 interacts with TFIID at the TATA box to initiate transcription

31
Q

What is the structure of leucine zippers?

A

An alpha-helical coiled coil - heptad organisation

A pair of DNA binding domains

32
Q

How often is leucine present over 35 residue stretch?

A

Leucine is present at n, n+7 …

33
Q

How does leucine zipper DNA recognition work?

A

Two reading heads engage the DNA
Arg and Lys secure binding to the DNA sugar phosphate backbone
Arg and Glen form hydrogen bonds with bases in the major groove
Phe engages bases via ring-ring and hydrophobic interactions

34
Q

How do leucine zipper proteins mediate the effect of cAMP on transcription/

A
  • G-protein cascade activates protein kinase A via cAMP production
  • cAMP-controlled genes contain a cAMP response (CRE), a palindromic 8bp sequence
  • a 43kDa protein (CREB) CRE binding protein)) binds the target DNA sequence and dimerises through a leucine zipper
  • phosphorylation of CREB increases transcriptional efficiency
  • CREB is a Ca2+/ calmodulin activated kinase II
35
Q

What does the sequence of homeo box genes correspond to?

A

They correspond precisely to their order of action along the anterior-poster axis of the embryo

36
Q

How do Homeodomains bind?

A

Homeodomains bind as monomers or specific sites on DNA

Consist of three helices

37
Q

How do the helices 1,2 and 3 line up

A

helices 1 and 2 are antiparallel, helix 3 is perpendicular to both

38
Q

Where does helix 3 of homeodomain insert?

A

Helix 3 inserts into the major groove, while the N-terminal arm fits into the minor groove

39
Q

The ribosome consists of small and large subunits…

What are the links?

A

Prokaryotic: 50S and 30S -> 70s - tRNA met
Eukaryotic: 60S and 40S -> 80S - tRNA met

40
Q

Which direction does protein synthesis occur in?

A

From 5’->3’ direction

41
Q

stages of protein synthesis?

A

Initiation
Elongation
Termination

42
Q

Name 3 methods for studying protein RNA interactions?

A
  • Co-precipitation of RNA with specific RNA-binding proteins
  • Polyadenylated RNA-binding proteins
  • Orthogonal organic phase separation
43
Q

What is co-precipitation of RNA with specific RNA-binding proteins (RBP)…
With regards to studying protein RNA interactions?

A
  • Immunoprecipitation of protein with RNA cargo

- Analysis of cargo

44
Q

What is Polyadenylated RNA-binding proteins…

With regards to studying protein RNA interactions

A
  • UV cross linking
  • Oligo (dT) with magnetic bead
  • Analysis of bound proteins
45
Q

What os orthogonal organic phase separation… with regards to studying protein RNA interactions?

A 
-Polar/appolar separation:
> protein partition in the organic phase
> RNA partitions in the aqueous phase
> RNA/RBP complexes remain at the interface
- RNA sequencing

Structure, Function And Analysis Of Proteins (18 decks)

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