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CONJ 661 - Structure & Funct. of Bio Mol. > Test 1: Lect 4 Perona > Flashcards

Test 1: Lect 4 Perona Flashcards

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1
Q

What is the only form of RNA secondary structure found?

A

The A helix

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2
Q

In the A helix, which groove is more accessible?

Is this a problem?

A

In the A helix, which groove is more accessible?
Minor groove
Is this a problem?
Kind of. The major groove has more recognizable structure, so many proteins use it. G-U wobble pairs, bulges and other structures can still open it up (because its so tight it must open to allow these variants, allowing access to outer proteins were needed.

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3
Q

Internal Loop:

  • Why/when is one drawn?
  • What is an asymmetric internal loop?
  • What is a symmetric internal loop?
A
  • Why/when is one drawn?
    When their is no base pairing for a segment
  • What is an asymmetric internal loop?
    Unequal number of nucleotides on either side (say 4 on one side and two on the other.
  • What is a symmetric internal loop?
    Equal number of nucleotides on either side.
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4
Q

G-U pair:

  • Is also called:
  • Is what?
  • Does what for the RNA?
A 
- Is also called:
Wobble pair
- Is what?
G bonded in unusal formation to U
- Does what for the RNA?
The unusual pairing forces the tight major groove of RNA to open up, which provides access to the major groove to proteins.
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5
Q

Hairpins:

  • Size limitation?
  • Purpose?
  • Small RNA hairpins?
A
  • Size limitation?
    Never larger than 5 or 6, maybe 7 - 8 base pairs.
    If larger they interact with other portions of the structure.
  • Purpose?
    Change the direction of the RNA, allows it to double back, useful if you want a more globular and less linear structure.
  • Small RNA hairpins?
    Form very tight stable structure (2-4 bases)
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6
Q

What do nucleotides look like inside the internal loop?

A

Base stacking!! Non-canonical base pairing (reduced entropy loss by localizing hydrophobic forces), some irregular H-bonds may still occur.

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7
Q

What is the predominant force involved in RNA and DNA structure formations (Including helices and base pairing)?

A 
Base stacking (and the hydrophobic interactions between bases).
Hiding the bases from water, the bases stack in large part because they are hydrophobic
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8
Q

Bulge:

  • Is?
  • Does what?
A
  • Is?
    1, 2 or 3 nucleotides which have no matching base pair on side of folded RNA.
  • Does what?
    Causes a turn in the RNA. Exposes the major groove.
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9
Q

Do proteins have strong secondary structures or tertiary structures? Why?

A

Tertiary.
R groups have hydrophobic potential, so they will globe together. This hydrophobic force is very strong.
The secondary structure is weaker. It is held together between hydrogen bonding in N–C==C=O segments. These interactions are not as strong.

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10
Q

General details of protein structure:

A

Inside out of RNA

  • Stable hydrophobic core (reduced entropy loss by localizing hydrophobic forces)
  • Secondary structure elements pack well together
  • Tertiary fold is strong
  • Secondary structure is weak
  • 20mer generally adopts a random coil
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11
Q

Do RNA have strong secondary structures or tertiary structures? Why?

A

Secondary

  • Hydrophobic base stacking causes A-helices to form (reduced entropy loss by localizing hydrophobic forces)
  • Negatively charged phosphate backbones make tertiary interactions difficult (strands repel each other)
  • Weak tertiary structure
  • 20mer generally A helix with stem loop.
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12
Q

If phosphate backbones are negative how can you get them near each other?

A

Using divalent metals (essentially using strongly charged positive molecules as glue)

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13
Q

If an RNA is folding, starting from primary structure to a tertiary structure, what will be the general rate of this folding?
- Name one implication?

A

Very, Very fast primary to secondary (secondary strong in RNA) -> slower tertiary -> even slower tertiary
- Name one implication?
It is very hard to use heat to separate RNA strands, as it holds together so tightly.

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14
Q

Is a clover leaf a good way of drawing tRNA?

  • How should it be drawn?
  • What stacks with what?
A 
No
- How should it be drawn?
As an upside L
- What stacks with what?
D arm stacks with the T arm (these are loops stacking together)
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15
Q

Which nucleotides have hoogesteen faces?

A

Purines.

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16
Q

Triple pair:

- Name one application:

A

(hoogesteen pairing), a purine bound to one nucleotide normally, with another nucleotide binding in major groove.
- Name one application:
it is used to stabilize the more globular region were the tRNA has a 90 degree turn.

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17
Q

How many types of modified nucleotides in tRNA alone?

A

100s

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18
Q

Is the ribose 2’ OH used in RNA bonding?

A

Yes it is, as a hydrogen donar or acceptor to stabilize certain base pairings.

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19
Q

What make up do RNA tertiary structures normally have? Why?

A

Tend to be relatively flat and planar tertiary structures.
Coaxial stacking. It is better for RNA strand to run parallel to other motifs so that it can stack bases (put the hydrophobic stuff together). All of these strands trying to run parallel to each other, results in them all tending to be on the same axis, aka the same plane.

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20
Q

A protein binds as a ligand to an mRNA.

  • How did this happen?
  • What happens next?
A
  • How did this happen?
    The mRNA had a ligand binding site in its structure
  • What happens next?
    This is feedback inhibition.
    The protein is a product of the mRNA post translation. It binds to the site, facilitating self cleavage of the mRNA. If there is enough protein, there is breakdown of mRNAs which would make it, resulting in less.
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21
Q

What is the key problem in RNA design?

A

Contiguous RNA helices aside, it is very difficult to control/predict which RNA segments will stack with which (will it be some distal region in the RNA, or the one next door? How is it actually being arranged)
- in other words, tertiary structure is unpredictable

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22
Q

If a picture of an RNA structure has a long > 15 or so ssRNA stretch (an large asymmetrical internal loop, for example) what does this actually represent?

A

A failure of the methodology to determine the whole RNA structure. It means we don’t know what that segment is base stacking with, it is however, undoubtedly base stacking with something.

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23
Q

Steps of G1 intron splicing:

A 
A Guanine (no phosphates) base pairs with a nucleotide at the 3' end of the 5'exon. ->
Guanine attacks 5' phosphate of the intron, causing a break in the strand and a reverse pairing (the guanine is backwards) ->
CONFORMATIONAL SHIFT!!! ->
3' OH of the 5' exon attacks the 3' end of the splice site. Splicing the intron out, and rejoining the exons.
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24
Q

What did we learn from the P4 - P6 domain of the Tetrahymena group1 intron RNA structure?

A

Learned how RNAs handle to helices next to each other despite negative charges.

25
Q

Tetraloop:

A

Region where two RNA helices interact, forming connections between the two helices.

26
Q

Tetraloop receptor:

  • Define:
  • Example:
  • What is going on with A - A?
A
  • Define:
    Helices will be called left and right.
    Left has two A’s within a single strand, which bind to each other. This places 1 A out of the helix. There is a G below this A out of helix which base pairs to it, bending Left slightly.
    Right has three nucleotides (A’s in the example) which are flipped out of the helix, base pair with each other, and the A which is out of a Left. Their is a G opposite of the flipped out A’s in Right. They stabilize the A’s allowing them to stay flipped.
  • Example:
    GAAA tetraloop receptor found in tRNA
27
Q

Octahedral conformation:

  • Divalent or monovalent metals?
  • What does it look like?
A
  • Divalent or monovalent metals?
    Divalent metals adopt it.
  • What does it look like?
    It has six corners were an atom could be, two square based pyramids with the bases conjoined. Very structurally stable
28
Q

Metal ion core:

  • Define:
  • Use:
A
  • Define:
    Divalent metals, which interact with phosphate backbone to stabilize tertiary RNA structure.
  • Use:
    Their rigid octahedral structure allows them to act like glue to hold to RNA helices together.
29
Q

A platform (adenosine platform):

A

Two A’s in the same RNA strand base pair with each other. This places one RNA outside of the helix, allowing it to be stacked with another helix, nucleating a new tertiary structure.

30
Q

Nucleation:

A

The first step of a new structure or formation. An example being the first ice crystal forming in freezing water.

31
Q

Coaxial Stack:

A

when two RNA duplexes form a contiguous helix (they stack their bases together).

32
Q

Duplex:

A

a double-stranded polynucleotide molecule.

33
Q

Common elements which allow RNA tertiary structure:

A
  • Coaxial stacking
  • Tetraloop receptor
  • Metal ions (metal ion core)
34
Q

Common mechanism which facilitates catalysis in RNA:

A

2 metal ion mechanism.

35
Q

2 metal ion mechanism:

  • What does it do?
  • How does it do it?
A

Metal ion 1 (MI1) and 2 (MI2)
- What does it do?
MI1 will ligate (ionic interaction) with nucleophile (3’ O)
MI1 will ligate with non esterified O on phosphate (stabilizes position)
MI2 will ligate with non esterified O on phosphate (stabilizes position)
MI2 will ligate with leaving group (5’ oxygen and its strand)
MI2 will ligate with H20 holding it close to the leaving group so it can take the proton.
- How does it do it?
Allows one oxygen to attack the phosphate, phosphate give electrons to leaving group, leaving group take hydrogen from the nearby water.

36
Q

What does he want us to remember about the structure of the ribosome:

A

50S, 30S catalytic subunit is in the 50S.
The three tRNAs are in APE (A site, P site, E site).
A site and P site are close to each other
The codon to anticodon interactions are in the 30S

37
Q

A-minor motifs:

- Define:

A

1: Uses many hydrogen bonds.
2: Take advantage of the broad minor groove in A form RNA helix.
3: An adenosine interacts with both nucleic bases in the minor groove, AND the ribose sugars they bond to.

38
Q

A-minor motifs:

  • Functions:
  • Examples:
A
  • Functions:
    1: Can be purely structural.
    2: Can investigate the groove to determine if the base pair bonding is canonical.
  • Examples:
    The methods below ensure the fidelity of translation.
    These occur at the A site (the site of entry)
    1: The 16S rRNA of the 30S ribosome checks if anticodon codon base pairing is correct
    2: The 16S can also bind with two molecules to investigate.
39
Q

How does the wobble position differ from the other positions in how it is monitored?

A

The A-minor motif/interaction is less specific in this site.

40
Q

Direct Readout:

- Define:

A

Determining A nucleotides identity by direct interaction with the bases functional groups.

41
Q

Direct Readout:

- Major vs Minor groove:

A

The minor groove has less functional groups which are distinct between bases. This makes direct readout from the minor groove inherently more weak than from the major groove.

42
Q

Which groove in A form RNA does an alpha helix fit? What is the significance of this?

A

The major groove! It makes this an even better system for direct readout.

43
Q

What makes thymine easy to recognize?

A

Steric hinderance.
It has a 5-methyl group. Steric hinderance is a strong form of differentiation. It is very easy to say “oh, there’s something occupying that space, I can’t go in, must be thymine.”

44
Q

How does side chain rotation effect direct readout?

A

It could rotate to no longer be able to bond. Though the side chain will likely rotate to the more stable configuration.

45
Q

What is the exception to the statement “there is no simple recognition code”

A

Zinc fingers.

46
Q

Affinity:

  • Define:
  • Units:
  • What does the units mean?
  • What is a common affinity?
A
  • Define:
    How strongly the molecules bind to each other
  • Units:
    molarity
  • What does the units mean?
    What concentration do you need for binding to occur. So a uM affinity binds better than a mM affinity
  • What is a common affinity?
    usually around 50 - 100 uMolar (around the affinity of proteins and fluids around the cell), so that the binding will be tempory
47
Q

Specify:

  • Define:
  • Units:
  • How is it calculated:
A
  • Define:
    How specific is it for one molecule over another?
  • Units:
    unitless
  • How is it calculated:
    10^6 Km (1st interaction) / 10^3 Km (2nd interaction) the reaction is 1000 more specific to the 1st interaction than the 2nd.
48
Q

Km:

A

The substrate concentration at 1/2 the maximum velocity. Lower substrate concentrations mean very little substrate is needed to start the reaction, it is very favored/stable.

49
Q

What indicates whether the specificity is good for Direct Readout?

A

Ask yourself what can rotate where, and what groups would be there if I switched to a different base at that location.

50
Q

What are some good amino acids for direct readout?

Why?

A

Arganine. Glutamine, Asparagine etc.
Any with groups which form polar bonds and don’t rotate into very strange configuration (asparagine for example has double bond in amide which lowers rotation)

51
Q

Which nucleotides are the hardest to tell apart from the minor groove?

A

G - C vs C - G in minor groove has no possible differentiation.
A - U vs U - A is also hard to tell apart in minor groove

52
Q

Water-mediated sequence specific-recognition:

- How does it work?

A
  • How does it work?
    Two hydrogen acceptors exist on nucleotide chain. Water binds to the two H acceptors, we can then see if donors bind to the other end (your elaborately checking if H donors are a water molecule away.
53
Q

How many donors and acceptors does water have?

A

2 donors

2 acceptors

54
Q

Water-mediated sequence-specific recognition:

- Issues:

A
  • Issues:
    1: amino molecules can rotate
    2: entropic cost associated with trapping the water
55
Q

Indirect readout:

  • How is it done?
  • What is another way?
A
  • How is it done?
    Measure differences in how the sugar - phosphate positioning based on differences in how nucleotides interact with each other.
  • What is another way?
    It could be water mediated
56
Q

Define a base pair step.

A

one 5’ - 3’ step on a single strand.

for 5’ ACG 3’ the first base pair step is A C.

57
Q

Order the preferences of different base pair steps.

A

GC > CG > GG > GA ~ GT ~ CA > CT > AA > AT > TA
Lower affinity are easier to distort
This is why we have TA TA boxes, not GC GC boxes. TA TA are less stable, easier to open.

58
Q

Align X as the direction the nucleotides bond G - C, and Y as perpendicular to this.
Name types of shifts between two stacked basepairs.

A

Shift (movement in the Y axis):
Slide (movement in the X axis) (like a sled)
Rise (longer distance between base pair above and themselves)
Tilt (opening up along the X axis)
Roll (opening up along the Y axis)
Twist (rotating one nucleotide relative to the other)

59
Q

Draw the different structures of base pair stacking:

What are these differences based on?

A

The sequence of the RNA.

CONJ 661 - Structure & Funct. of Bio Mol. (8 decks)

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