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biochemistry Jonklaas > test 2: protein structure > Flashcards

test 2: protein structure Flashcards

1
Q

covalent bonds are present in what protein structure level

A

primary

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2
Q

what bonds do secondary protein structure have

A

covalent and hydrogen bonds

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3
Q

what bonds are more prevalent in tertiary and quaternary protein structuer

A

hydrophobic effect

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4
Q

what is significant about covalent bonds in protein strucutre

A
  • shows in amino acid sequence
  • location of s-s bonds
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5
Q

H bonds

A
  • interaction of amino acids close to each other
  • form specific patterns
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6
Q

hydrophobic effect level

A
  • 3d structure of polypeptide
    quat
  • arrangement of multiple folded molecules
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7
Q

what % of DB character does a peptide bond have

A

40

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8
Q

what are the characteristics of a peptide bond

A
  • planar
  • no rotation around peptide bond
  • cis/ trans isomerism
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9
Q

what isoermism are peptide bonds

A
  • nearly 90% are trans
  • 10% are cis
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10
Q

why is trans configuration better than cis

A

steric hinderance and interactions

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11
Q

in peptide bond where can rotation occur

A

around the alpha carbon but there is no rotation at all

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12
Q

what does a ramachandran plot show

A
  • sterically allowed alpha and beta angles for a polypeptide chain
  • limited amount of allowed configurations
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13
Q

2nd protein structure is found where

A
  • local segments of biopolymers
  • proteins and nucleic acids (DNA/ RNA)
  • local conformations
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14
Q

what is an example of a secondary protein structure

A
  • alpha helix
  • beta strnad
  • beta bend
  • collagen triple helix
  • loops and turns
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15
Q

what bonding is present in secondary

A
  • H bonding between backbone amide NH of one AAand the carbonyl of another
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16
Q

who proposed the alpha helix

A

linus pauling

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17
Q

what bonds are present in alpha helix

A
  • h bonds between n and n+4 residue
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18
Q

where do R groups poin on alpha helix

A

outward, perpendicular to the axis

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19
Q

what are some characteristics of alpha helix structure

A
  • h bonds are parallel
  • pitch = 5.4 angstrom
  • 3.6 residue/ turn
    1.5 Rise/AA
  • right hand
    -charged AA
  • dipole polarity
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20
Q

how is alpha helix dipole polarity

A
  • all c=O grpups point toward C and give dipole with + N, (-) C termini
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21
Q

how can you make a stable alpha helix

A
  • end C term with a charged AA to neutralize
22
Q

which protein has predominantly alpha helices

A

myoglobin

23
Q

what does proline do to alpha helix

A
  • detabilizes the alpha helix that why it is not found
24
Q

do alpha helices like bulky things

A

no

25
Q

what are the alpha helix detablilizers

A
  • proline
  • bulkiness
  • R groups to large( tryptophan and tyrosine)
  • too small (glycine)
26
Q

what is an amphipathic helics

A

hydrophonic residues on one side
- hydrophi8llic resides on opposite sides

27
Q

what is keratin

A

-key structural material in hair skin and nails
- coiled coil
- 2 amphipathic alpha helices

28
Q

what amino acid is kertatin rich in

A
  • cys to form s-s bonds
29
Q

what does a perm do

A
  • reduce s-s bonds–> 2RSH ; then reoxidize to s-s
30
Q

why is keratin important

A

used to detect heavy metal poisoning

31
Q

what are B strands

A

polypeptide chain almost fully extended found in B sheets

32
Q

what is a beta sheet

A

multiple b strands arranged side by side

33
Q

what are charactersitcs of B strands and B sheets

A
  • h bonds occur between aa on adjacent stands and perp to the strand direction
  • side chains R-gps alternate in pointing above and below plane perp to b bonds and stands
34
Q

do beta sheets like bulky

A

yes they do

35
Q

what is an antiparallel b sheet

A

stand runs in opposite direction

36
Q

parallel

A

run in the same N to C direction

37
Q

what is the beta sheet structure

A
  • zig zag
  • 6-12 residue
  • repeat 2AA
    distance 7A
  • may be amphipathic
38
Q

what is silk fibroin

A

antiparallel B sheets of Gly-ser-gly

39
Q

what does ala do in a silk fibroin

A

interlocksw/ ala from another sheett

40
Q

what is collagen

A
  • main sturctural protein in the extracellular matrix in connective tissues
  • most abundant protein in mamels
41
Q

where is collagen present

A
  • bone matrix
  • tendonds
    -cartilage
  • blood vessesl
42
Q

what is the repeating AA in collagen

A

G-P-P
proline helix

43
Q

where are the gly residues located in collagen

A
  • invariant
  • central axis of triple helix, other can’t fit
44
Q

does interchain H bonds occur in collagen

A

no

45
Q

what helps stabilize the helix

A
  • interchain H bonds w/ Hydroxypro
46
Q

what is osteogenesis imperfecta

A
  • mutation in a gene for collagen
  • gly is substituted for another AA
  • prevents normal production of collagen
  • leads to brittle bones
47
Q

to form hydroxypro what is required

A

O2 and ascorbic acid(vitamin c)

48
Q

what is scurvy

A

vitamin c deficiency
- lack of hydroxypro
- not enough interchain h bonding
- tweaking collagen

49
Q

how are collagen fibrils strengthened

A
  • interchain lysine-lysine
    interaction hydroxypyrindium covalent cross links
50
Q

increase in cross links =

A

less eslatic collagen= more brittle bones = sign of old age

51
Q

why are loops and turns important

A
  • allow chain reversal
  • found on the surface of globular protein
52
Q
A

biochemistry Jonklaas (17 decks)

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