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BIOL 2421 - Cellular Biochem > 6. Protein structure II > Flashcards

6. Protein structure II Flashcards

1
Q

what is tertiary structure

A

the overall 3D arrangement of all atoms in a polypeptide

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2
Q

describe residue interaction within tertiary structures

A

residues too far apart to interact in secondary structures may interact here

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3
Q

what holds tertiary structures together

A

non-covalent interactions: disulfide bonds, hydrogen bonds, ionic bonds

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4
Q

what is quaternary structure

A

arrangement of multiple polypeptides into a 3D dimensional shape to form a functional protein

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5
Q

T or F: monomers can have quaternary structure

A

false! only polymers can

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6
Q

define homodimer

A

polypeptide chains are identical

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7
Q

define heterodimer

A

polypeptide chains are not identical

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8
Q

what are the 3 key categories of proteins

A

globular, fibrous, and intrinsically disordered proteins

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9
Q

describe globular proteins

A
  • most enzymes are globular

- these proteins usually contain many secondary structures

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10
Q

describe fibrous proteins

A
  • many structural proteins are fibrous
  • contain long strands or sheets
  • examples: alpha keratin, collagen, silk fibroin
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11
Q

describe intrinsically disordered proteins

A

they have no secondary structure at all (either in a section or in the whole thing)

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12
Q

T or F: fibrous proteins have a high level of strength and flexibility

A

true

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13
Q

what properties allow fibrous proteins to be strong and flexible?

A
  • multiple polypeptides packed into long strands
  • insoluble in water (high levels of hydrophobic amino acids)
  • all consist of a repeating unit of one secondary structure
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14
Q

in fibrous proteins, why is tertiary structure not distinguishable from secondary structure

A

they’re fibrous, so folding isn’t really happening

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15
Q

what does a-keratin make up

A

almost the entire dry weight of hair, wool, nails, claws, quills, horns, and hooves

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16
Q

what type of filament is a-keratin

A

an intermediate filament

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17
Q

define intermediate filament

A

cytoskeleton component

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18
Q

T or F: a-keratin is only found in mammals

A

true

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19
Q

how many helices make up a-keratin

A

2

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20
Q

what direction are the helices that make up a-keratin

A

right handed

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21
Q

what do the two helices of a-keratin do

A

they coil around one another (left handedly) to form a coiled coil that’s strong like a rope

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22
Q

describe the surfaces where the helices of a-keratin touch

A

the surfaces where they touch are filled with hydrophobic amino acids, interlocking like a zipper

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23
Q

what strengthens the complex quaternary structure of a-keratin

A

disulfide bonds

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24
Q

what do the coiled-coils combine into

A

protofilaments

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25
Q

what do protofilaments combine into

A

protofibrils

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26
Q

how many strands of a-keratin are needed to bind together to make one intermediate filament

A

32

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27
Q

describe permanent hair treatments

A
  • reducing agents break disulfide bonds connecting the coiled coil
  • hair is heated and stretched into desired shape
  • oxidizing agent re-establishes the disulfide bonds
  • hair has a new shape
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28
Q

what does collagen make up (give examples)

A

connective tissue is filled with collagen. ie tendons, cartilage, parts of bone

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29
Q

describe the secondary structure of collagen

A

left handed helix with 3 residues per turn (=a tighter turn than an a-helix)

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30
Q

what amino acids usually make up the turns of collagen helices

A

glycine, proline, 4-hydroxyproline

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31
Q

what is the entire polypeptide of collagen called

A

an alpha chain

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32
Q

describe the structure when alpha chains twist around each other

A
  • forms a unique coiled coil
  • three left handed helices in the coil form a right handed twist
  • glycine projects inwards to the center where they all touch
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33
Q

how much of the protein in your body is collagen

A

roughly 1/4

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34
Q

what enzyme adds the hydroxyl group to proline to form 4-hydroxyproline

A

prolyl 3-hydroxylase

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35
Q

what does prolyl 3-hydroxylase require to function

A

ascorbic acid

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36
Q

what is ascorbic acid known as in humans

A

vitamin C

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37
Q

what happens when humans have no vitamin C

A

=no 4-hydroxyproline = improper collagen structure = scurvy

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38
Q

what are the symptoms of scurvy

A

swollen bleeding gums and teeth falling out, ruptured blood vessels, severe bruising, opening of previously healed scars, swelling and bleeding around joints, hair breakage, anemia

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39
Q

what protein is silk comprised of

A

fibroin

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40
Q

describe the structure of fibroin

A

it has extended antiparallel beta sheets with lots of glycine and alanine for tight packing of multiple strands

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41
Q

what stabilizes the beta sheets of silk

A

extensive hydrogen bonds and optimal van der waals forces

42
Q

T or F: silk is stretchy

A

false

43
Q

T or F: silk is flexible

A

true; due to many weak interactions

44
Q

describe the shape/structure of globular proteins

A
  • globs

- much more compact than fibrous proteins b/c they fold back on themselves many times

45
Q

describe the common characteristics of globular proteins

A

tightly packed and compact, hydrophobic core, asymmetrical, water soluble

46
Q

what varied tertiary structures do globular proteins have (2)

A

motifs and domains

47
Q

what is another name for a motif

A

fold or supersecondary structure

48
Q

what is a motif

A

a recognizable folding pattern involving two or more elements of secondary structure and the connections between them

49
Q

what are 2 examples of motifs

A

beta-alpha-beta loops, beta barrels

50
Q

T or F: motifs are always independently stable

A

false; they may or may not be stable

51
Q

T or F: small motifs can combine into larger motifs

A

true

52
Q

give an example of small motifs forming a larger one

A

the beta strands of multiple b-a-b loops have joined together to form a a-b barrel (in pyruvate kinase)

53
Q

what is a domain

A

a part of a polypeptide chain that’s independently stable or could undergo movements as a single entity

54
Q

up to how many amino acids can a domain be

A

roughly 400

55
Q

does each domain have the same function

A

no, each domain may have a different function

56
Q

T or F: domains denature when protease cleaves them away from the rest of the protein

A

false; when this happens, they usually retain their 3D structure

57
Q

T or F: domains are always isolated from the rest of the protein

A

false; they may be isolated (forming distinct lobes), but other times there are lots of interdomain interactions

58
Q

what are helices and strands in a protein often connected by

A

connected by loops

59
Q

do the loops that connect helices/strands to the rest of the protein adopt a regular backbone conformation

A

no, they do not adopt a regular backbone conformation, and they often protrude on the surface of proteins

60
Q

describe intrinsically disordered proteins

A

these are protein segments or even entire proteins that lack an ordered structure in solution

61
Q

why don’t intrinsically disordered proteins have a structure

A

they lack the large number of hydrophobic residues to drive folding, and are high in proline residues which disrupt possible secondary structures

62
Q

describe how intrinsically disordered proteins have flexibility that is key to their function

A
  • they tend to have many binding partners
  • they can wrap around dif. enzymes to inhibit them
  • they can serve as linkers between ordered segments
63
Q

describe how P53 is disordered

A

it has a structured central core, but has disordered N and C termini

64
Q

when does p53 fold, what part folds, and describe what this looks like

A

the C termini folds when it binds to a ligand. There are 4 possible ligands, and the folded shape is different depending on which ligand is bound

65
Q

describe quaternary structure, as well as the structure of each protein involved

A

a protein with more than one polypeptide

each polypeptide within this protein has its own tertiary structure

66
Q

how are polypeptides in proteins held together

A

non-covalent interactions

67
Q

what’s another name for proteins with quaternary structure

A

multisubunit proteins or multimers

68
Q

describe the structure of multimers

A

most of them have identical subunits or repeating groups of non-identical subunits (repeating unit called a protomer)

69
Q

what symbols are used to refer to non-identical repeating subunits

A

greek letters

70
Q

describe the subunits of hemoglobin

A

has 4 subunits

- alpha subunit and beta subunit form a pair, and there are 2 symmetrical pairs

71
Q

T or F: protein folding occurs randomly

A

FALSE; it would take way too long to find the native state this way

72
Q

describe folding shortcuts

A

small sections of secondary structures find their final folded form first, which then form localized motifs and then finally longer range interactions

73
Q

what is proteostasis

A

it includes all the processes to maintain an active set of properly folded proteins in a cell

74
Q

what are chaperones

A

specialized protein complexes that help fold or refold proteins

75
Q

what happens if a protein is irreversibly misfolded

A

the cell will have extensive pathways to recycle or degrade it

76
Q

what is denaturation

A

the disruption of the native conformation of a protein, leading to loss of function

77
Q

does denaturation always lead to complete loss of function

A

no, it can be mild, leading to a partially folded state, or complete unfolding and return to only the primary structure

78
Q

what causes denaturation

A

changes in the environment (ie temperature, pH, chemical treatments)

79
Q

T or F: unfolding of a protein is gradual

A

false; proteins remain intact until a sudden loss of structure and function. The loss of structure in one part helps destabilize other protein parts

80
Q

T or F: denaturation is sometimes reversible

A

true; some proteins will regain completely their native structure and function when the offending condition is removed

81
Q

describe protein aggregates and how they occur

A

misfolded proteins will have exposed hydrophobic residues on their surface, and will therefore aggregate and clump together

82
Q

describe how amyloid fibers are formed

A

when a protein that is normally secreted from the cell is secreted in it’s misfolded state, and converts into an insoluble amyloid fiber

83
Q

T or F: amyloid fibers are harmless

A

FALSE! they’re connected to many diseases ie parkinson’s and alzheimer’s

84
Q

what are amyloid-caused diseases called

A

amyloidoses

85
Q

how do amyloids typically arise? explain their structure

A

arise from proteins that have some beta sheets when properly folded. Before proper folding is complete, beta sheet regions from one polypeptide associate with sheets from another, and these aggregate into a fibril core with other regions of the protein misfolding around it

86
Q

what type of residues stabilize the amyloid fibril

A

aromatic hydrophobic residues

87
Q

in regards to aromatic residues, what can promote fibril formation

A

when mutations occur in specific proteins that introduce aromatic residues

88
Q

is amyloid formation fast or slow

A

slow; the age on onset is typically 65+

89
Q

what is PrP

A

a normal constituent of brain tissue in mammals (role=unknown)

90
Q

what is the structure of normal PrP (denoted PrPC)

A

3 alpha helices

91
Q

what is the second conformation of prp

A

PrPSc

92
Q

what is the structure of prpsc

A

amyloid-like beta sheets

93
Q

describe the interaction between the two conformations of prp

A

prpsc converts prpc into prpsc (=domino effect)

94
Q

how is prpsc damaging

A

it causes brain degeneration, holes in the brain, and death (=mad cow disease)

95
Q

what is a prion

A

proteinaceous infectious particle

96
Q

describe the early process of viewing atomic structure via xray

A
  • proteins are purified and crystallized
  • X ray is pointed at the crystal, the beam diffracts onto a photographic film
  • the diffraction patterns lead to an electron density map
97
Q

what does the electron density map allow us to see

A

allows the determination of the position of each nucleus in the crystal. We can then use computers to generate 3D structures

98
Q

what was the purpose of crystallizing the protein for viewing

A

hopefully each individual protein is fixed in the same orientation

99
Q

describe cryo-electron microscopy

A

used to determine protein structure

- protein was frozen and purified, and then observed under the EM

100
Q

why is cryo-EM better than xray crystallography

A

cryo-EM can visualize large and dynamic proteins, while the other cannot

BIOL 2421 - Cellular Biochem (21 decks)

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