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MCP Unit 2 > Lecture 11: Forces and Structures > Flashcards

Lecture 11: Forces and Structures Flashcards

1
Q

What is approximated by the Lennard-Jones potential?

A

distance dependence of van der Waals forces

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2
Q

What is the principle “glue” that holds proteins together?

A

hydrophobic effect

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3
Q

Which amino acid is the most hydrophilic? Which is most hydrophobic?

A

Ala - hydrophilic

Leu - hydrophobic

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4
Q

What is the origin of the hydrophobic effect?

A

water forms calthrates in a hydrophobic environment

energetically unfavorable, but best

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5
Q

Why is the formation of clathrates ultimately favorable?

A

reduces area of water exposed to hydrophobic environment

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6
Q

What are protein secondary structures?

A

alpha helix
beta sheet
beta turn

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7
Q

____ degrees of rotation around the _____ bond will remove carbonyl-side chain clash

A

60 degrees

phi

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8
Q

What is the rise (z-axis) of an alpha helix? How many resides per turn? This makes every ____ amino acid close in space

A

1.5 angstrum
3.6 residues/turn
4th

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9
Q

How do backbone-backbone interactions stabilize alpha helices?

A

NH and CO H-bonds (4 residues apart, along helix axis)

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10
Q

What forms the macrodipole in backbone-side chain interactions of alpha helices?

A

excess +/- charge on N- and C- termini, respectively

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11
Q

What feature in an alpha helix allows side chain-side chain interactions to occur?

A

3.6 residue repeat

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12
Q

what residues are strong helix breakers and why?

A

Pro - no NH –> can’t H-bond

Gly- flexible

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13
Q

What residue is a helix former and why?

A

Ala - lacks side chain, loses no rotational freedom

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14
Q

what residues are medium helix breakers and why?

A

Val, Thr, Trp, Phe

beta-branched or bulky - lose rotational freedom in helix

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15
Q

what residues are helix indifferent and why?

A

Arg, Lys, Glu
long straight chains
don’t lose as much rotational freedom

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16
Q

How can you tell if a peptide membrane-bound?

A

hydrophobic region corresponding to 6-7 turns of a helix

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17
Q

What is an example of an amphipathic helix?

A

Myoglobin

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18
Q

Why are parallel beta sheets less frequently observed than are antiparallel sheets?

A

H-bonds are slightly bent in parallel sheets

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19
Q

What holds alpha helcices and beta sheets together?

A

H-bonds

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20
Q

Are beta sheets flat?

A

No - pleated

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21
Q

What type of beta structure forms between adjacent strands in denaturing conditions?

A

Amyloid

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22
Q

What is the psi-phi angle of a beta sheet?

A

140 degrees

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23
Q

What are the rise and periodicity of beta sheets?

24
Q

What residue is required for a reverse beta turn? Which is preferred?

A

Gly required

Pro preferred

25
What interactions stabilize a reverse beta turn?
H-bonds
26
Where are reverse beta turns found?
end of one sheet to form the next
27
What kind of residues usually comprise loops/random coils?
hydrophilic
28
What is the alpha-turn-helix?
motif - txn factor
29
What is the difference between a domain and a motif?
motif - small - cut out of protein --> don't have that function domain - large, subjective
30
What is the antennapedia homeodomain?
txn factor | has alpha turn helix motif
31
in the antennapedia homeodomain, where does the alpha turn helix bind?
major groove
32
What is the zinc finger?
motif - txn factor
33
What is the primary composition of zinc fingers?
His, Cys repeats
34
What does Zn2+ do in a zinc finger?
holds structure together
35
What is the coil coil? How is it characterized?
domain - heptad repeat
36
What is a heptad repeat and where is it found?
coiled coil a,d are hydrophobic e,g have opposite charges
37
how are helices of a coiled coil held together?
H-bonds and van der Waals
38
what is the DNA binding domain of GCN2 txn factor?
coiled coil
39
What is the charge on the N-terminal of the GCN2 txn factor?
Very +
40
How is the C-terminal of the GCN2 txn factor characterized?
heptad repeat leucine zipper
41
How does the GCN2 txn factor demonstrate characteristics of an intrinsically disordered protein domain?
N-terminus is only structured as a helix when it is bound to DNA (folds only when it binds its target ligand)
42
What are four roles of coiled coil domains?
*bind DNA protein-protein recognition mechanical force transduction (ex. myosin tails) viral penetration
43
What designates a coiled coil?
at least 3-4 heptad repeats --> hydrophobic region
44
what domain differentiates flu strains?
influenza haemagglutinin
45
What allows fusion of the influenza virus to the host cell membrane, resulting in release of viral mRNA into the cell and infection?
fusogenic peptide - very hydrophobic
46
How does the flu virus enter a host cell?
endocytosis
47
what is the structure of the influenza haemagglutinin?
triple stranded coiled coil
48
Many viruses use a _______ method to gain entry to cells
harpooning
49
In viral entry of the flu and HIV, the mechanism of action involves ________ mediated by the _______
membrane distortion | harpooning protein
50
What step in viral entry of the flu and HIV have been targeted by small molecule inhibitors?
entry to host cell
51
What is a key difference between trigger mechanisms during harpooning in flu vs HIV?
flu induced pH change within cell | HIV induces receptor binding
52
What are the roles of gp120 and gp41 in HIV?
gp120 binds CD4 and CXCR4/CCR5 co-receptors; induces conformational chance in gp41 gp41 has fusogenic peptide
53
What happens after HIV's fusogenic peptide is trust into cell?
form prehairpin intermediate | N-trimer and C-peptide region of gp41 come together to form six-helix bundle
54
What structure of HIV is vulnerable to inhibition and why?
prehairpin intermediate - long lifetime
55
What is the problem with targeting the HIV prehairpin intermediate? What is an example of a drug which is not successful?
drugs often degraded by protease | Fuzeon
56
What concept was used to create a drug which has more advantageous properties than does fuzeon?
mirror-image peptide inhibitor | D conformation binds to L conformation of gp41 tightly

MCP Unit 2 (17 decks)

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