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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
Q

Distance between each coil in an alpha-helix

A

3.6 amino acids, 0.54nm distance

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26
Q

What are B-sheets/strands

A

Neighbouring segments of the polypeptide backbone

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27
Q

In an B-sheet, what kind of bonds can be found and which groups are partaking in them

A

H-bonds btw the backbones of the strands btw the carboxyl and amino groups

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28
Q

Which way do the side chains point in a B-sheet

A

They alternate sides

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29
Q

What kind of interactions can be found in tertiary structure? (2)

A

Hydrophobic interactions btw secondary elements and long-range interactions btw residues that are far apart in primary sequences

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30
Q

Describe a loop’s structure and character

A

loops have no regular secondary structure and can be flexible

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31
Q

What do ribbon diagrams show

A

secondary structures: “skeleton” where the blank spaces btw are not empty in reality

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32
Q

What do space-filling diagrams show

A

All the atoms involved in the protein structure

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33
Q

What’s a domain

A

domain is an independently folded unit within a protein

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34
Q

What kind of interactions do domains have with other molecules

A

reversible, specific, non-covalent

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35
Q

What other molecules can domains interact with

A

other proteins, lipids, carbs, RNA, DNA, other cofactors

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36
Q

Average length of a domain

A

50-200 amino acids long

37
Q

Define thermal motion

A

thermal motion means all molecules are constantly moving and tumbling, and colliding

38
Q

What does it mean to have a specific interaction and provide an example

A

only certain molecular surfaces are bound

Ex: “lock and key”

39
Q

Name an amino acid that’s chemically similar to N

A

Q (glutamine)

40
Q

Name an amino acid that’s chemically similar to S

A

T (threonine)

41
Q

Name an amino acid that’s chemically similar to R

A

K (lysine)

42
Q

Name an amino acid that’s chemically similar to E

A

D (aspartic acid)

43
Q

Name an amino acid that’s chemically similar to F

A

W (tryptophan)

44
Q

What’s one way to measure evolutionary conservation btw organisms?

A

We can check their sequence similarity (homology)

45
Q

What are divergent polypeptides

A

Polypeptides that do not have any sequence similarity

46
Q

What’s a protein family

A

a set of proteins or domains which have homologous sequences and structures, and often have related functions

47
Q

Why can Y and C form hydrophobic interactions

A

It’s cause they have the aromatic ring that’s hydrophobic

48
Q

Why can W make hydrogen bonds?

A

Cause it has an H at the end of it’s R group that’s willing to be shared with another molecule

49
Q

Name the 3 different types (classes) of modifications that can happen to proteins

A
  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
Q

What can side chain modifications result in

A
  • can change surface or conformation of protein
  • can create or block a binding site for other proteins
  • gain or loss of protein function
51
Q

Main types of post-translational modifications

A
  • Phosphorylation
  • Methylation
  • Acetylation
  • Glycosylation, Sumoylation, Ubiquitination
52
Q

What is the consequence of adding a phosphate

A

change of charge and size

53
Q

What do kinases do

A

transfer phosphates from ATP

54
Q

What do phosphatases do

A

remove phosphate

55
Q

What do you call it when you need an amino acid to be phosphorylated to be able to bind

A

Phosphopeptide binding

56
Q

What are the consequence of acetylation of Lys amine?

A

changes its polarity from + to neutral, and increases its size

57
Q

What kind of bond do we see in the acetylation of Lys amine

A

isopeptide bond

58
Q

What are the consequences of methylation

A

change in size only

59
Q

Which amino acids are usually methylated

A

Lysine (K) and arginine (R)

60
Q

What is methylation

A

addition of 1/2 methyl groups to the guanidino group

61
Q

What do phosphorylation, acetylation and methylation do in common?

A

they provide new binding sites for proteins and can possibly change the protein’s function

62
Q

Folded structure of a protein depends on:

A

hydrophobic interactions in the interior of the structure

63
Q

What’s the Native State

A

The Native State is the completely folded conformation of a protein, it is the most stable conformation of a protein

64
Q

When do side chain modifications happen

A

Side chain modifications usually take place after folding is complete

65
Q

Organize these from strongest to weakest: hydrophobic, van der waals, disulfide bonds, hydrogen bonds, ionic bonds

A

Disulfide (both super strong), Ionic and hydrophobic (strong), hydrogen bonds (moderate), van der waals (weak)

66
Q

Which bonds stabilize secondary structures

A

hydrogen bonds cause they involve the peptide bond

67
Q

Which bonds form the tertiary structure

A

Hydrophobic interactions between secondary structures form the tertiary structures cause they Involve the side chains

68
Q

What are the 3 conclusions that Anfinsen came to at the end of his experiment

A

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
Q

Describe the folding process

A

it’s complex and proceeds through intermediated that have increasing structure, to the native state

70
Q

Do unfolded domains have secondary or tertiary structure

A

No

71
Q

Why is there a risk of aggregation when proteins are trying to fold

A

cause hydrophobic regions prefer to stick together and different proteins’ hydrophobic regions can come into contact and aggregate and become insoluble

72
Q

What can cause protein misfolding

A
  • 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
Q

What are some genetic mutations that cause changes in polypeptides

A

amino acid substitutions, insertion/deletions, premature stops

74
Q

What’s proteostasis

A

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
Q

What do chaperones do

A

-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
Q

Heat shock response is:

A

cytosolic and nuclear proteins that protect against cell death

77
Q

Unfolded protein response is:

A

endoplasmic reticulum proteins that promote cell death if stress is too severe

78
Q

Main concept of stress response in cells:

A

Cells Tailor the expression of chaperones (HSPs) to the level of unfolded and misfolded proteins

79
Q

Example of inducible chaperones

A

heat shock proteins (heat induces the expression of these proteins by allowing the activation of the transcription of these proteins)

80
Q

What are constitutive chaperones

A

Proteins that facilitate the folding of others by stabilizing hydrophobic residues and assisting in the folding

81
Q

Stress response is triggered by: (3)

A
  • heat stress
  • oxidative damage
  • proteasome inhibition
82
Q

Which protein mediates the heat shock response

A

HSF1

83
Q

HSF1 has: (3)

A

DNA binding domain, regulatory domain, transcription activation domain

84
Q

Which version of HSF1 is monomeric and which is trimeric

A

monomeric: inactive, trimeric: active

85
Q

Heat shock elements are recognized by:

A

active HSF1

86
Q

Steps to regulation of HSF

A
  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
Q

Substrate binding and release are regulated by:

A

ATPase cycles

88
Q

What do ATP-independent chaperones do?

A

prevent aggregation and can catalyze some

folding steps

BIOC 212 (1 decks)

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