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DNA-Protein Interactions 1

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Sequence Specific & Antiviral Innate Immunity
gina_evans0312
Quiz by gina_evans0312, updated more than 1 year ago
gina_evans0312
Created by gina_evans0312 over 10 years ago
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Question 1

Question
What is required for the protein surface to bind to the DNA surface?
Answer
  • For the protein surface to be complimentary to the DNA surface
  • For the protein surface to be positive (DNA backbone's are negative)
  • For the protein surface to contain hydrophobic residues

Question 2

Question
In which groove can the order of base pairs be differentiated?
Answer
  • Major groove
  • Minor groove

Question 3

Question
The major groove is 15A wide
Answer
  • True
  • False

Question 4

Question
Which is smaller?
Answer
  • Major groove
  • Minor groove

Question 5

Question
Proteins that bind in the major groove must be more specific than those that bind in the minor groove
Answer
  • True
  • False

Question 6

Question
Why is Arg such a useful residue?
Answer
  • It has 2 H acceptors, so it can bind to guanine
  • It has 2 H donors, so it can bind to guanine
  • It has 2 H acceptors, so it can bind to cytosine

Question 7

Question
Which of the following can bind to both G & A
Answer
  • Glu
  • Val
  • Asn
  • Tyr

Question 8

Question
What is base stacking?
Answer
  • Where hydrophobic bases stack to avoid water
  • Where hydrophobic bases pull the DNA inwards to avoid water
  • Where hydrophobic bases twist the DNA to avoid water

Question 9

Question
What is required for a protein to take advantage of base stacking?
Answer
  • Residues with delocalised electrons
  • Hydrophobic residues
  • Hydrphillic residues
  • For it to make a gap between bases

Question 10

Question
10bp covers a distance of 34 A
Answer
  • True
  • False

Question 11

Question
Describe DNA
Answer
  • Long, repetitious and thin
  • Long, non-repetitious and thick
  • Short, repetitious and thin
  • Long, repetitious and thick
  • Short, non-repetitious and thin

Question 12

Question
DNA can bend 180 dgrees over how long a stretch?
Answer
  • 40
  • 30
  • 20

Question 13

Question
What does Phage Lamda Repressor bind to?
Answer
  • Phage DNA
  • Bacterial DNA

Question 14

Question
What is being shown here?
Image:
Half_Sites (image/png)
Answer
  • A half site
  • A palindromic sequence
  • A restriction site

Question 15

Question
How does Phage Lambda Repressor Work?
Answer
  • Binds to bacterial DNA at the lambda cro gene
  • Binds to phage DNA at the Lambda cro gene
  • And blocking RNA polymerase binding

Question 16

Question
Phage Lambda Repressor binds to only one target sequence
Answer
  • True
  • False

Question 17

Question
The Phage Lambda repressor binds as a _
Answer
  • Monomer
  • Dimer
  • Tetramer

Question 18

Question
Each subunit attaches to the DNA using a _ and binds to the other subunits using a _
Answer
  • Alpha helix, alpha helix
  • Alpha helix, nothing- it's a monomer
  • Beta sheet, beta sheet
  • Beta sheet, nothing- it's a monomer

Question 19

Question
Phage Lambda Repressor has multiple subunits because ...
Answer
  • It binds to a sequence long enough that the protein cannot be removed
  • It binds to a sequence long enough that the sequence becomes unique int the DNA
  • It binds more exactly - so it only has a single target sequence

Question 20

Question
Where does Phage Lambda Suppressor bind?
Answer
  • 2 adjacent major grooves
  • 2 adjactent minor grooves
  • An adjactent major & minor groove
  • 32A apart
  • 34A apart
  • 36A apart

Question 21

Question
A non-specific interaction doesn't involve bonding with any particular base
Answer
  • True
  • False

Question 22

Question
List some specific interactions between Phage Lambda Repressor and DNA
Answer
  • Ser - G, and Gly - T,
  • Gly- T and Ser-G
  • Gly- C- and Ser-T

Question 23

Question
The DNA sequence is all read from the same DNA strand
Answer
  • True
  • False

Question 24

Question
A helix-turn-helix motif is often used for reading DNA
Answer
  • True
  • False

Question 25

Question
Different alpha helices (of the helix-turn-helix) motif perform specific and non-specific interactions
Answer
  • True
  • False

Question 26

Question
Proteins don't have to land on the DNA in exactly the right spot, they only need to...
Answer
  • Bind to the phosphate backbone
  • Bind to the bases
  • And then roll freely along the DNA

Question 27

Question
Methionine repressor...
Answer
  • prevents methionine production
  • prevents binding of methionine to tRNA
  • prevents methionine being added to the amino acid chain

Question 28

Question
The Methionine Repressor binding site is...
Answer
  • Palindromic
  • Almost palindromic
  • 8bp
  • 16bp

Question 29

Question
The binding site of most helix-turn-helix proteins are 16-18bp long
Answer
  • True
  • False

Question 30

Question
How does the Methionine repressor bind to the DNA?
Answer
  • Uses 2 alpha helices
  • Uses 2 beta sheets
  • One from each monomer
  • One from each end of the monomer
  • Into one major groove
  • Into two major grooves

Question 31

Question
Two beta strands have the same diameter as an alpha helix
Answer
  • True
  • False

Question 32

Question
Specific interactions in the methionine repressor happen between Lysine, Threonine, A & G
Answer
  • True
  • False

Question 33

Question
Restrictions enzymes are part of the bacterial immunity... how?
Answer
  • Recognises and destroys non-self DNA
  • Cuts around viral DNA that has infected the genome
  • Proteases break down the viral coat

Question 34

Question
Restriction enzymes and transferases come in pairs, with the restriction enzyme made first
Answer
  • True
  • False

Question 35

Question
How does EcoRI bind?
Answer
  • Phosphate backbone reactions in the minor groove
  • Phosphate backbone reactions in the major groove
  • Specific interactions in the minor groove
  • Specific interactions in the major groover

Question 36

Question
EcoRI looks for 2 G-C on top of each other because they're more bendable
Answer
  • True
  • False

Question 37

Question
Where in the GAATTC sequence does EcoR1 cut?
Answer
  • After the C, before the C
  • After the A & T
  • In the middle

Question 38

Question
Eco RI needs an Fe iron to bind
Answer
  • True
  • False

Question 39

Question
Where are the distortions of the DNA caused by EcoRI?
Answer
  • In the centre of GAATTC
  • G/AATT/C
  • GA/AT/TC

Question 40

Question
Hydrophobic interactions in ECORI-DNA ineractions recognise what?
Answer
  • AA atacking
  • AT stacking
  • TT stacking

Question 41

Question
ECORI uses water mediated interactions to assist DNA recognition
Answer
  • True
  • False

Question 42

Question
What is strange about the EcoRV restriction enzyme?
Answer
  • It has an abnormally large binding site
  • It leaves blunt ends
  • It binds to 2 different sequences

Question 43

Question
EcoRV forms a dimer
Answer
  • True
  • False

Question 44

Question
ECORV creates major distortions where?
Answer
  • In the middle
  • At the ends
  • One residue in

Question 45

Question
ECORV binds to the backbone in the minor groove and wraps 'arms' around into the major groove
Answer
  • True
  • False

Question 46

Question
The recognition loops in the major groove cause...
Answer
  • H bonding between stacks
  • H bonding between A-G
  • H bonding between T-C

Question 47

Question
ECORV looks for ATAT bases
Answer
  • True
  • False

Question 48

Question
Where in the GCGC sequence does M.Hal methylate?
Answer
  • The first G
  • The first C
  • The second G
  • The last C

Question 49

Question
Methylation prevents the restriction enzyme from recognizing a sequence, so it cannot be cot
Answer
  • True
  • False

Question 50

Question
Describe the actions of methylases
Answer
  • Methylate both strands at once
  • Methylate one strand at a time
  • Are monomers
  • Are dimers

Question 51

Question
Interactions 'pull out' one of the bases to gain chemical access
Answer
  • True
  • False

Question 52

Question
What is the donor for methylation?
Answer
  • S-adenosyl-methionine
  • Methanol
  • Methide

Question 53

Question
How the methylation interaction studied?
Answer
  • The cystine had the 5th H replaced with an F
  • Trapping it in the active site
  • The cystine had the 3rd H replaced with an F

Question 54

Question
Once in the active site, a thiol bond forms between the cystine and the cytosine so the methyl can be added
Answer
  • True
  • False

Question 55

Question
What is inserted to bind with the widowed G?
Answer
  • Glu
  • Arg
  • Cys

Question 56

Question
The inserted bases fill up the space left by the flipped out cytosine
Answer
  • True
  • False
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