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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?

A

3.5Ang

2

24
Q

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

A

Gly required

Pro preferred

25
Q

What interactions stabilize a reverse beta turn?

A

H-bonds

26
Q

Where are reverse beta turns found?

A

end of one sheet to form the next

27
Q

What kind of residues usually comprise loops/random coils?

A

hydrophilic

28
Q

What is the alpha-turn-helix?

A

motif - txn factor

29
Q

What is the difference between a domain and a motif?

A

motif - small - cut out of protein –> don’t have that function
domain - large, subjective

30
Q

What is the antennapedia homeodomain?

A

txn factor

has alpha turn helix motif

31
Q

in the antennapedia homeodomain, where does the alpha turn helix bind?

A

major groove

32
Q

What is the zinc finger?

A

motif - txn factor

33
Q

What is the primary composition of zinc fingers?

A

His, Cys repeats

34
Q

What does Zn2+ do in a zinc finger?

A

holds structure together

35
Q

What is the coil coil? How is it characterized?

A

domain - heptad repeat

36
Q

What is a heptad repeat and where is it found?

A

coiled coil
a,d are hydrophobic
e,g have opposite charges

37
Q

how are helices of a coiled coil held together?

A

H-bonds and van der Waals

38
Q

what is the DNA binding domain of GCN2 txn factor?

A

coiled coil

39
Q

What is the charge on the N-terminal of the GCN2 txn factor?

A

Very +

40
Q

How is the C-terminal of the GCN2 txn factor characterized?

A

heptad repeat leucine zipper

41
Q

How does the GCN2 txn factor demonstrate characteristics of an intrinsically disordered protein domain?

A

N-terminus is only structured as a helix when it is bound to DNA
(folds only when it binds its target ligand)

42
Q

What are four roles of coiled coil domains?

A

*bind DNA
protein-protein recognition
mechanical force transduction (ex. myosin tails)
viral penetration

43
Q

What designates a coiled coil?

A

at least 3-4 heptad repeats –> hydrophobic region

44
Q

what domain differentiates flu strains?

A

influenza haemagglutinin

45
Q

What allows fusion of the influenza virus to the host cell membrane, resulting in release of viral mRNA into the cell and infection?

A

fusogenic peptide - very hydrophobic

46
Q

How does the flu virus enter a host cell?

A

endocytosis

47
Q

what is the structure of the influenza haemagglutinin?

A

triple stranded coiled coil

48
Q

Many viruses use a _______ method to gain entry to cells

A

harpooning

49
Q

In viral entry of the flu and HIV, the mechanism of action involves ________ mediated by the _______

A

membrane distortion

harpooning protein

50
Q

What step in viral entry of the flu and HIV have been targeted by small molecule inhibitors?

A

entry to host cell

51
Q

What is a key difference between trigger mechanisms during harpooning in flu vs HIV?

A

flu induced pH change within cell

HIV induces receptor binding

52
Q

What are the roles of gp120 and gp41 in HIV?

A

gp120 binds CD4 and CXCR4/CCR5 co-receptors; induces conformational chance in gp41
gp41 has fusogenic peptide

53
Q

What happens after HIV’s fusogenic peptide is trust into cell?

A

form prehairpin intermediate

N-trimer and C-peptide region of gp41 come together to form six-helix bundle

54
Q

What structure of HIV is vulnerable to inhibition and why?

A

prehairpin intermediate - long lifetime

55
Q

What is the problem with targeting the HIV prehairpin intermediate? What is an example of a drug which is not successful?

A

drugs often degraded by protease

Fuzeon

56
Q

What concept was used to create a drug which has more advantageous properties than does fuzeon?

A

mirror-image peptide inhibitor

D conformation binds to L conformation of gp41 tightly

MCP Unit 2 (17 decks)

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