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bch again because you're fucking stupid > 4 > Flashcards

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1
Q

what types of interactions between functional groups hold a protein together

A

noncovalent and covalent interactions

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2
Q

quaternary structure

A

distinct chains assembled into multi-subunit structures

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3
Q

what bonds link amino acids

A

peptide bonds

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4
Q

what terminus is the start of the polypeptide chain

A

amino terminus

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5
Q

what is the backbone of the primary structure made of

A

peptide bonds and alpha carbon

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6
Q

how are the peptide bonds formed

A

condensation reaction, enzymatically

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7
Q

which bonds in amino acids are rigid and cannot rotate and why

A

peptide bonds, because they have resonance giving them characteristics of a double bond

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8
Q

which bonds in amino acids are not rigid

A

bonds linking amide (phi) and carbonyl (psi)

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9
Q

what angles can psi and phi angles be

A

-180 to 180, but not all are permitted.

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10
Q

alpha helix goes in what direction

A

right handed

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11
Q

alpha helix side chains go where

A

point out

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12
Q

where do h bonds form for alpha helix

A

intra-strand between backbone residues. i and i+4. C=O from the first and N-H from the second

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13
Q

how many residues per one turn in an alpha helix

A

3.6 residues

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14
Q

how many angstroms high is each residue in an alpha helix

A

1.5 angstroms

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15
Q

what types of alpha helix properties are there

A

polar, hydrophobic, amphipathic

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16
Q

what type of amino acids are common in alpha helices

A

smaller ones

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17
Q

what type of amino acids are common in beta pleated sheets

A

bigger ones, more extended and beta branched

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18
Q

what type of amino acids are common in reverse turns

A

proline, serine and aspartate (last two are because of a post translational modification). glycine common because small

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19
Q

how do r groups reduce steric hindrance in beta strands and sheets

A

alternate

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20
Q

h bonds in beta strands and sheets

A

betwee backbone carbonyl and amines of different strands

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21
Q

how do strands run in beta sheets

A

parallel or antiparallel, or mixed

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22
Q

hydrophobicity of beta pleated sheet

A

one sheet can be hydrophilic and vice versa

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23
Q

beta turn (reverse turn

A

4 residue segment, allows peptide chain to turn 180 degrees.

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24
Q

where are beta turns found

A

surface of globular proteins, connecting secondary structures (either helices or strands)

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25
what atoms form all hydrogen bonds for secondary structure
for alpha helices, beta strands, and beta turns, all three are carbonyl oxygen and amine hydrogen
26
which residues form h bonds in beta turns
i and i+3
27
where is proline common in beta turns
position turns
28
linker segments
parts that link secondary structures to form 3D tertiary
29
motifs or domains
common structures in tertiary structures with specific functional rules
30
what forces form tertiary structure
noncovalent interactions, cofactors, disulfide bonds
31
aside from tertiary, what other structures do disulfide bonds play a role in
quaternary structures
32
are disulfide bonds covalent
yes
33
zinc finger motif
found in dna binding proteins and have zinc ions that coordinate distant side chains, stabilizing domains
34
how can you predict domains present in a protein
similar function may have similar domains, predict functional domain based on other domains known
35
heterodimer
nonidentical polypeptides quaternary
36
covalent or noncovalent forces in quaternary structure
both are possible
37
what might cause different subunits in quaternary structure
multiple genes or post translational cleavage of precursor
38
other reasons for forming of quaternary structure
interactions between polypeptide chains
39
how to differentiate between different antibodies
primary sequence. it dictates noncovalent interactions between antibodies and protein it binds to.
40
why is it hard to differentiate antibodies
quaternary is very similar
41
how does x ray crystallography work (physically)
light (x ray beam) hits a sample, which hits a detector for computer analysis
42
what do you need for the protein sample in x ray crystallography, how is this acquired
ordered crystals. you need varying conditions to form it like pH, or high salt.
43
how does an x ray diffractometer work
produces diffraction patterns that can be interpreted in terms of atomic positions (x,y,z).
44
what does x ray crystallography tell you
3D structures at high resolution, including backbone and side chains
45
where is info regarding x ray crystallography put for proteins
protein data bank
46
lower resolution number means what for x ray crystallography
higher resolution (like you can differentiate between two very close things)
47
NMR is done on proteins in what state
proteins in solution(buffer)
48
what type of proteins can you do NMR on
small (<25 kDa), but now can be done on larger
49
how is NMR better than x ray crystallography
can measure conformational changes (e.g. binding to something else), protein folding
50
how does NMR work chemically
nuclear spin of certain nuclei, measured in a strong, static magnetic field
51
what does absorption of electromag radiation tell you
environment of the nucleus, tells you protein's structure
52
2D NMR spectra of protein, a dot represents
the PPM of N and H (two different peaks). it is labelled with the amino acid and the number
53
different colors in 2D NMR of protein
red can represent changes observed upon binding or conformational change
54
cryo electron microscopy pros
larger complexes can be visualized (greater than 100 kDa)
55
how do you prepare the sample for cryo electron microscopy
thin layer of protein solution prepared on fine grid, frozen very fast to trap molecules in different orientations
56
what do you do after the sample is prepared in cryo?
high powered microscropes measure a beam of electrons that go through the protein. diffraction of beam used to measure structure.
57
how is the 3d structure concluded in cryo microscopy
averaging multiple structures
58
AI in predicting protein structures and molecular interactions
alphafold
59
cons of AI for protein structure
limited size and processing power
60
protein chromaphores are
molecules with conjugated double bonds that absorb UV and/or visible light at specific wavelengths
61
important chromaphore groups in proteins
aromatic rings and amide carbonyls
62
what do chromaphores tell you about protein structure
structure of protein influences accessibility of chromophore to light absorption
63
fluorophore
absorb AND emit light, used for cellular localization
64
tryptophan fluorescence, what frequency and how
indole ring allows Trp to absorb and emit light when excited with UV light. absorbs 270-295, emits 310-355. exact wavelength depends on polarity of environment in protein
65
polar environment does what to tryptophan fluorescecne
red shifting. longer wavelengths and less intense fluorescence
66
buried tryptophan fluorescence
blue shifted (shorter wavelengths and more intense)
67
what forces hold secondary structures together
hydrogen bonding
68
what forces hold tertiary and quaternary structure together
noncovalent (H bond, ionic, Van der Waal), and disulfide (covalent) bonds
69
primary driving force in protein folding
hydrophobic effect
70
random coils
not actually random. may be stable. nonrepetitive secondary structure with structure, but without repeating dihedral angles of beta strands or helices.
71
chaperone proteins
prevent aggregation of newly synthesized and unfolded proteins by binding exposed hydrophobic regions. so hydrophobic parts can come together without water interaction
72
denaturation
disruption of weak forces holding protein structure together using heat or chemicals, causing loss of structure and function. only noncovalent bonds are broken!
73
how to prevent denaturing in lab
keep on ice to prevent H bond breaking
74
wild type prion is
PrPc. alpha coil
75
scrapie form of prion
PrPSC, beta sheet.
76
similarities between wild type and scrapie prion
same primary sequence, stability about the same
77
can proteins have many conformations during their function
yes, it can be stable or have a variety of conformations
78
what does knowing structure (1/2/3/4) tell you
how to design molecules that interact and inhibit a protein's function
79
inhibitors for proteins
mimic substrate but prevent reaction. antagonist
80
aside from inhibitors, how can drugs prevent activity
block and prevent binding interactions between proteins for signalling, or block ownstream event. modify amino acids to change protein structure, block noncovalent interactions for structure.
81
chelators of metal binding do what
block noncovalent interactions needed for structure
82
computational approach for protein folding
analyze backbone and side chain interactions to find most stable structure

bch again because you're fucking stupid (7 decks)

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