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BIOCH 320 > 3-3D structure, tertiary > Flashcards

3-3D structure, tertiary Flashcards

1
Q

what determines tertiary structure

A

amino acid sequence + environment where protein is

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2
Q

how do soluble proteins fold best

A

when in an aqueous environment

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3
Q

how do membrane proteins fold best

A

only fold properly in presence of membrane (or suitable replacements, like detergents)

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4
Q

what are the critical forces in determining tertiary structures

A

hydrophobic effect!!!
van der waals interactions
H-bonds
ionic interactions

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5
Q

why are van der waals important in determining 3ary structure even if they are weak

A

weak but many so they are significant

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6
Q

what is delta G for folding

A

-100kJ/mol

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7
Q

what energy state is the native conformation

A

low energy (folded)

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8
Q

can there be more than 1 native conformation

A

yes

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9
Q

why can there be more than one stable functional state (what are the other things that can make more)

A
  • ligand binding (allostery)
  • flexible portions of proteins (like a.a. that are not super useful/needed in that polypeptide)
  • “breathing”-kinetic motions of atoms in proteins
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10
Q

what are some methods to determine protein structure

A

circular dichroism
Xray crystallography
Protein NMR

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11
Q

what kind of techniques can be used to yield general characteristics of secondary structure

A

circular dichrois,

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12
Q

what kind of techniques can be used to yield detailed atomic information

A

X-ray crystallography

protein NMR

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13
Q

how does circular dichroism work

A

depends on differential absorption of left and right circularly polarized light

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14
Q

what is circular dichroism sensitive to (like what does it detect)

A

secondary structure

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15
Q

when is circular dichroism most useful in (what kind of experiments)

A

denaturation/ renaturation

transition from folded to unfolded

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16
Q

what kind of structures have characteristics circular dichroism spectra

A

alpha helices
beta sheets
random coil/irregular structures

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17
Q

how do you make the crystals in X-ray crystallography

A

protein preparations are used to grow crystals-must be very pure samples

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18
Q

what wavelength is exposed to the crystals

A

X-rays which are 1A

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19
Q

what kind of info does X-ray crystals give us - directly and indirectly
(aka what info is gotten from the experiment and how is it used)

A

makes a diffraction pattern which can be used to make an electron density map

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20
Q

is 6A or 1A better resolution

A

1A (smaller distance means easier to distinct between 2 points)

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21
Q

what do regions of high electron density mean in X-Ray diffraction

A

location of atomic nuclei

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22
Q

what are 3 pros for Xray

A

highly detailed
rapid solutions (sometimes, like drug companies wanna see quick before and after with drug)
useful for large proteins

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23
Q

what are 4 cons for Xray

A

requires crystal growth (difficult)
crystals must deffract (not all do)
structures are static (cant have dynamic action)
cannot see hydrogens!!! (usually-you see things with lots of electrons, so not H)

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24
Q

what are off diagonal peaks in 2D NMR

A

signals generated by close range interactions of protons

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25
Q

what can you do with a combination of off diagonal peaks

A

helps provide info on the 3D structure of protein

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26
Q

what does magnetic coupling provide information about

A

distances between atoms

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27
Q

what kind of information is protein NMR combined with

A

ideal geometry information (dont worry just one line)

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28
Q

does NMR give a single solution

A

gives a range of solution which reflects both dynamics/motions and error

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29
Q

what do the multiple lines on an NMR represent

A

a family of structures consistent with the distance constraints of NMR

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30
Q

what does it mean when there are areas that are less defined in protein NMR

A

they may be in motion or only have a few distances determined (not sure what is the exact conformation)

31
Q

what are 2 pros of protein NMR

A 
dynamic info (real time)
proteins are in solution (doesnt need to be a crystal which can be hard to deal with)
32
Q

what are 2 cons of protein NMR

A

difficult for large macromolecules

synthesis of peptides containing isotopes (13C and 15N) can be expensive and time consuming

33
Q

what amino acids are often found in alpha keratin

and why

A

alanine (alpha helix) and cysteine (crosslinks)

34
Q

what reinforces the alpha keratin structure

A

disulphides

35
Q

what does more disulphides in keratin cause

A

it becomes “harder”

36
Q

what does less disulphides in keratin cause

A

it becomes “softer”

37
Q

what direction is the individual alpha helix in alpha keratin

A

right handed

38
Q

how many chains are in alpha helix

A

2 (dimer)

39
Q

what happens to the 2 alpha helices in alpha keratin +RH or LH

A

they are twisted in a left handed superhelix

40
Q

what % of protein mass in mammals is made from collagen

A

25-35%

41
Q

what are the main forms of collagen in humans

A

extracellular matrix proteins like skin bones teeth

42
Q

what kind of structure is collagen

A

regular, helical

43
Q

how many residues per turn in collagen

A

3

44
Q

what direction are the individual chains in collagen

A

left handed

45
Q

how many chains are in collagen

A

3

46
Q

what direction do the 3 chains coil into in collagen

A

right handed (superhelix)

47
Q

where are the H bonds in collagen

A

interchain

48
Q

what characterizes the primary structure of collagen (which aa)

A

glycine proline hydroxyproline

49
Q

which 4 aa is collagen rich in

A

glycine
proline
4-hydroxyproline
5-hydroxylysine

50
Q

where do H bonds happen in the collagen helix

A

between strands, NOT WITHIN (like between the 3 chains, not within)

51
Q

what is 4-hydroxyproline

A

a post translational carbon with a hydroxyl group on carbon 4

52
Q

what is the point of 4-hydroxyproline

A

to ensure appropriate conformation in collagen helix

53
Q

when does hydroxylation happen of proline in collagen

A

after protein synthesis

54
Q

what does 4-hydroxyproline require to occur properly

A

vitamine c / ascorbic acid

55
Q

where does 5-hydroxylysine occur

A

at intervals in collagen polypeptides

56
Q

what is required in 5-hydroxylysine creation

A

modified lysine residues - requires vit C

57
Q

what causes cross-linking of peptides in collagen

A

lysine, hydroxylysine (and histidine) residues

58
Q

what are 4 similarities amongst soluble globular proteins

A
  • mix of 2ary structures( irregular + regular required)
  • hydrophobic core hydrophilic exterior
  • closely packed interiors
  • maximized H bonds in interior
59
Q

what are 3 differences between soluble globular proteins

A

secondary structure composition
prosthetic groups
presence of disulfides

60
Q

where are disulfides present/ allowed

A

extracellular proteins

61
Q

what are 3 rules for soluble globular proteins (3ary)

A

hydrophobic interactions are critical
extensive H-bonding occurs within 2ary structure (NOT between)
knots do not form

62
Q

what is required to form hydrophobic interactions

A

2 layers of secondary structure must come together (interior and exterior)

63
Q

where are non polar vs polar amino acids in globular proteins

A

non polar buried inside

polar aa on surface

64
Q

where do H bonds occur in globular proteins

A

within 2ary structure

65
Q

are elements closer in 1ary usually close in 3ary

A

yes

66
Q

are elements closer in 3ary usually close in 1ary

A

no not necessarily

67
Q

what directionality are connections between sequential beta strands in parallel beta sheets

A

usually Right handed

68
Q

is structure or sequence typically conserved better

A

structure

69
Q

what are 3 different classifications for tertiary structure

A

SCOP
CATH
Pfam

70
Q

what do SCOP CATH and Pfam do

A

attempt to describe the structure of a protein (in search of common features and relationships) - usually describe overall strucutre like alpha, beta, alpha/beta

71
Q

what are motifs/folds

A

recognizable combinations of 2ary structure that appear in a number of different proteins (can be a large or small part of the structure)

72
Q

what are domains

A

discrete, independently-folded compact units within a polypeptide (may be composed of or include motifs)

73
Q

can domains function if another part of the protein isnt working

A

likely yes, they can fold and function without other parts (if they have different functions)

74
Q

are there more intradomain interactions or interdomain interactions

A

more intradomain (more within that between)

BIOCH 320 (16 decks)

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