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BIOC 212 > PROTEIN FOLDING > Flashcards

PROTEIN FOLDING Flashcards

1
Q

Name all nonpolar amino acids

A

Alanine, glycine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan, cysteine

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2
Q

Name all acidic amino acids

A

Aspartic acid (aspartate), glutamic acid (glutamate)

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3
Q

Name all basic amino acids

A

Arginine, lysine, histidine

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4
Q

Name all uncharged polar amino acids

A

Asparagine, glutamine, serine, threonine, tyrosine

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5
Q

Why is histidine only partly positive at neutral pH

A

Cause the N have a weak affinity for the H, it is therefore only partly + (protonated).

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6
Q

What’s the characteristic of hydrophobic amino acids and why

A

Methyl group: cause it doesn’t have the ability to form H bonds with another molecule.

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7
Q

How do hydrophobic amino acids interact?

A

They interact through the hydrophobic interactions (exclusion of water molecules)

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8
Q

Why is proline special?

A

Cause it’s the only amino acid that has a side chain locking with the alpha-carbon, making it unable to interact with H2O.

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9
Q

Why is cysteine special?

A

Cause it has an SH group, which when oxidized allows for the formation of a disulfide bond (covalnet bond btw 2 SH groups)

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10
Q

Why is glycine special?

A

Cause it is so small and even tho it is hydrophobic, can be found everywhere (throughout the polypeptide)

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11
Q

Name all nonpolar amino acids (1 letter)

A

A, G, V, L, I, P, F, M, W, C

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12
Q

Name all acidic amino acids (1 letter)

A

D, E

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13
Q

Name all basic amino acids (1 letter)

A

R, K, H,

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14
Q

Name all uncharged polar amino acids (1 letter)

A

N, Q, S, T, Y

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15
Q

Name all nonpolar amino acids (3 letter)

A

ala, gly, val, leu, ile, pro, phe, met, trp, cys

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16
Q

Name all acidic amino acids (3 letter)

A

Asp, glu

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17
Q

Name all basic amino acids (3 letter)

A

arg, lys, his

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18
Q

Name all uncharged polar amino acids (3 letter)

A

asn,gln, ser, thr, tyr

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19
Q

Name all uncharged polar amino acids (3 letter)

A

asn, gln, ser, thr, tyr

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20
Q

Out of S, T, F, which ones can make H-bonds and why?

A

S&Y cause they have OH groups that can share the H with other molecules

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21
Q

Out of S, T, F, which ones can make hydrophobic interactions

A

Y&F cause they have an aromatic ring that is hydrophobic and cause allow hydrophobic interactions

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22
Q

Out of S,T F, which ones can have ionic bonds and why?

A

None because ionic bonds need charged molecules, so acidic and basic amino acids

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23
Q

In an alpha helix, what kind of bonds can be found and which groups are partaking in them

A

H-bonds: btw the carboxyl group and amino group every 4 peptide bonds

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24
Q

Which way do the side chains point in an alpha-helix

A

Outwards

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25
Distance between each coil in an alpha-helix
3.6 amino acids, 0.54nm distance
26
What are B-sheets/strands
Neighbouring segments of the polypeptide backbone
27
In an B-sheet, what kind of bonds can be found and which groups are partaking in them
H-bonds btw the backbones of the strands btw the carboxyl and amino groups
28
Which way do the side chains point in a B-sheet
They alternate sides
29
What kind of interactions can be found in tertiary structure? (2)
Hydrophobic interactions btw secondary elements and long-range interactions btw residues that are far apart in primary sequences
30
Describe a loop's structure and character
loops have no regular secondary structure and can be flexible
31
What do ribbon diagrams show
secondary structures: "skeleton" where the blank spaces btw are not empty in reality
32
What do space-filling diagrams show
All the atoms involved in the protein structure
33
What's a domain
domain is an independently folded unit within a protein
34
What kind of interactions do domains have with other molecules
reversible, specific, non-covalent
35
What other molecules can domains interact with
other proteins, lipids, carbs, RNA, DNA, other cofactors
36
Average length of a domain
50-200 amino acids long
37
Define thermal motion
thermal motion means all molecules are constantly moving and tumbling, and colliding
38
What does it mean to have a specific interaction and provide an example
only certain molecular surfaces are bound | Ex: “lock and key”
39
Name an amino acid that's chemically similar to N
Q (glutamine)
40
Name an amino acid that's chemically similar to S
T (threonine)
41
Name an amino acid that's chemically similar to R
K (lysine)
42
Name an amino acid that's chemically similar to E
D (aspartic acid)
43
Name an amino acid that's chemically similar to F
W (tryptophan)
44
What's one way to measure evolutionary conservation btw organisms?
We can check their sequence similarity (homology)
45
What are divergent polypeptides
Polypeptides that do not have any sequence similarity
46
What's a protein family
a set of proteins or domains which have homologous sequences and structures, and often have related functions
47
Why can Y and C form hydrophobic interactions
It's cause they have the aromatic ring that's hydrophobic
48
Why can W make hydrogen bonds?
Cause it has an H at the end of it's R group that's willing to be shared with another molecule
49
Name the 3 different types (classes) of modifications that can happen to proteins
1. cleavage into smaller proteins by peptidases 2. covalent modification of N-terminus (co-translational) 3. covalent modification of side chains: Introduce functional groups to proteins
50
What can side chain modifications result in
- can change surface or conformation of protein - can create or block a binding site for other proteins - gain or loss of protein function
51
Main types of post-translational modifications
- Phosphorylation - Methylation - Acetylation - Glycosylation, Sumoylation, Ubiquitination
52
What is the consequence of adding a phosphate
change of charge and size
53
What do kinases do
transfer phosphates from ATP
54
What do phosphatases do
remove phosphate
55
What do you call it when you need an amino acid to be phosphorylated to be able to bind
Phosphopeptide binding
56
What are the consequence of acetylation of Lys amine?
changes its polarity from + to neutral, and increases its size
57
What kind of bond do we see in the acetylation of Lys amine
isopeptide bond
58
What are the consequences of methylation
change in size only
59
Which amino acids are usually methylated
Lysine (K) and arginine (R)
60
What is methylation
addition of 1/2 methyl groups to the guanidino group
61
What do phosphorylation, acetylation and methylation do in common?
they provide new binding sites for proteins and can possibly change the protein's function
62
Folded structure of a protein depends on:
hydrophobic interactions in the interior of the structure
63
What's the Native State
The Native State is the completely folded conformation of a protein, it is the most stable conformation of a protein
64
When do side chain modifications happen
Side chain modifications usually take place after folding is complete
65
Organize these from strongest to weakest: hydrophobic, van der waals, disulfide bonds, hydrogen bonds, ionic bonds
Disulfide (both super strong), Ionic and hydrophobic (strong), hydrogen bonds (moderate), van der waals (weak)
66
Which bonds stabilize secondary structures
hydrogen bonds cause they involve the peptide bond
67
Which bonds form the tertiary structure
Hydrophobic interactions between secondary structures form the tertiary structures cause they Involve the side chains
68
What are the 3 conclusions that Anfinsen came to at the end of his experiment
1) Native structure is determined by the primary sequence of AA 2) Native structure is the state of minimal energy: Folding is thermodynamically favoured (negative ΔG free energy) 3) Folding can be spontaneous in principle, but assisted by different biological mechanisms
69
Describe the folding process
it's complex and proceeds through intermediated that have increasing structure, to the native state
70
Do unfolded domains have secondary or tertiary structure
No
71
Why is there a risk of aggregation when proteins are trying to fold
cause hydrophobic regions prefer to stick together and different proteins' hydrophobic regions can come into contact and aggregate and become insoluble
72
What can cause protein misfolding
- if the required ligand isn't found - if there's a genetic mutation - if there's harmful environmental conditions - with aging our protein quality control mechanisms lose efficiency
73
What are some genetic mutations that cause changes in polypeptides
amino acid substitutions, insertion/deletions, premature stops
74
What's proteostasis
an extensive network of components that acts to maintain proteins in the correct concentration, conformation, and subcellular location, to cooperatively achieve the stability and functional features of the proteome
75
What do chaperones do
-assist folding and prevent aggregation, without being part of the native state -recognize exposed hydrophobic regions of folding intermediates: this means there's a misfolding
76
Heat shock response is:
cytosolic and nuclear proteins that protect against cell death
77
Unfolded protein response is:
endoplasmic reticulum proteins that promote cell death if stress is too severe
78
Main concept of stress response in cells:
Cells Tailor the expression of chaperones (HSPs) to the level of unfolded and misfolded proteins
79
Example of inducible chaperones
heat shock proteins (heat induces the expression of these proteins by allowing the activation of the transcription of these proteins)
80
What are constitutive chaperones
Proteins that facilitate the folding of others by stabilizing hydrophobic residues and assisting in the folding
81
Stress response is triggered by: (3)
- heat stress - oxidative damage - proteasome inhibition
82
Which protein mediates the heat shock response
HSF1
83
HSF1 has: (3)
DNA binding domain, regulatory domain, transcription activation domain
84
Which version of HSF1 is monomeric and which is trimeric
monomeric: inactive, trimeric: active
85
Heat shock elements are recognized by:
active HSF1
86
Steps to regulation of HSF
1. Monomeric HSF1 is folded, but mimics unfolded protein and is bound by Hsp90 2. After heat shock, unfolded proteins compete with HSF1 for Hsp90 binding 3. Free HSF1 trimerizes and activates transcription 4. Chaperones including Hsp90 are expressed and help fold or degrade unfolded proteins 5. HSF1 is down-regulated by binding of excess Hsp90 to the monomer form
87
Substrate binding and release are regulated by:
ATPase cycles
88
What do ATP-independent chaperones do?
prevent aggregation and can catalyze some | folding steps

BIOC 212 (1 decks)

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