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MFoM > 01a: Protein structure/function > Flashcards

01a: Protein structure/function Flashcards

1
Q

Medical professionals deal with proteins in what ways?

A
  1. Disease
  2. Diagnostic tests
  3. Therapy
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2
Q

How many AA have R groups?

A

19/20 (not Proline)

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3
Q

Proline’s R group is a(n) (X) group

A

X = secondary amino

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4
Q

T/F: There is rotation around the peptide bond.

A

False

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5
Q

T/F: There is no rotation around any bonds in polypeptide.

A

False - rotation can occur around alpha carbons

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6
Q

AA can be grouped by characteristics of (X). What are these categories?

A

X = side chain

  1. Nonpolar
  2. Polar uncharged
  3. Positively charged
  4. Negatively charged
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7
Q

Hydrophobic AA fall under which category?

A

Nonpolar

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8
Q

Hydrophilic AA fall under which category?

A

Polar

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9
Q

List the main characteristics of the Nonpolar AA.

A
  1. Hydrophobic
  2. Don’t accept/donate H+
  3. (R groups) Don’t participate in hydrogen or ionic bonds
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10
Q

AA especially known to reduce polypeptide flexibility.

A

Proline

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11
Q

Which AA are found high in serum levels in patient with Maple Syrup syndrome?

A

V, I, L

Branches chain AA

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12
Q

Which Nonpolar AA tend to cluster through hydrophobic interactions? This is (stabilizing/destabilizing) for proteins.

A

A, V, L, I

Stabilizing

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13
Q

Which uncharged polar AA have attachment site for phosphate? Which part of AA?

A

Ser, Thr, Tyr

Hydroxyl group on side chain

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14
Q

Which uncharged polar AA have attachment site for oligosaccharides? Which part of AA?

A

Asn (amide group of side chain)

Ser, Thr (hydroxyl group of side chain)

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15
Q

Which AA is important for enzyme active sites? Elaborate.

A

Cysteine (sulfhydryl group)

Sulfur atom coordinates with certain metal ions

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16
Q

Which AA is critical in Zn finger transcription factors?

A

Cys

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17
Q

(SH) group in the AA (X) can be oxidized to form:

A

X = cysteine

Forms dimer (cystine), covalent my linked through disulfide bond

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18
Q

Intrachain disulfide bond forms between (X).

A

X = two cysteine residues within SAME polypeptide

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19
Q

Interchain disulfide bond forms between (X).

A

X = two cys residues in different polypeptides

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20
Q

At physiological pH, acidic AA have net (X) charge.

A

X = negative

COO- on side chain

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21
Q

At physiological pH, His has (X) charge.

A

Varies!

Ionization depends on environment (can be uncharged or positive)

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22
Q

Which AA makes for a good buffer?

A

His

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23
Q

In first step of catabolism of branched chain AA, (X) is/are changed to (Y) by interacting with which enzyme?

A

X = Val, Leu, Ile

Y = alpha-keto acids

Enzyme: branched-chain aminotransferase

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24
Q

In second step of catabolism of branched chain AA, (X) is/are changed to (Y) by interacting with which enzyme?

A 
X = alpha-keto acids
Y = acetyl-coA derivatives

Enzyme: branched-chain alpha-keto acid dehydrogenase complex

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25
Q

In Maple Syrup urine disease, what’s the fundamental molecular issue?

A

Lack of proper function of branched-chain alpha-keto acid dehydrogenase complex (buildup of branched chain AA)

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26
Q

Which branched chain AA can be synthesized in the body?

A

None! All are essential AA

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27
Q

An infant diagnosed with Maple Syrup urine disease should be treated in which way(s)?

A

No breastfeeding! Restrict intake of nourishment that’s high in these AA

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28
Q

High levels of which protein can be indicative of CF?

A

IRT (Immunoreactive Trypsinogen)

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29
Q

IRT is produced by which organ?

A

Pancreas

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30
Q

Which key test is used to diagnose CF?

A

Sweat test

31
Q

How does CF occur?

A

Single mutation in CTFR gene

32
Q

CTFR gene encodes:

A

Cl channel protein that regulates anion movement across epithelial membranes of lungs, pancreas, and other organs

33
Q

Movement of which ion(s) is/are affected by CF?

A
  1. Cl transport impaired

2. Na absorption enhanced (net increase in water absorption)

34
Q

W1282X mutation means:

A

Stop codon inserted at expense of Tryptophan

35
Q

G551D mutation means:

A

Glutamate replaced by Aspartate

36
Q

R117H mutation has what effect on polypeptide charge?

A

No effect - His and Arg both positive

37
Q

Proteins tend to fold in configuration with lowest (X) and most (Y).

A 
X = E
Y = hydrogen bonds
38
Q

T/F: All proteins require chaperones told properly.

39
Q

Most important stabilizing influence in protein structure:

A

AA sequence

40
Q

Primary structure includes (X) bonds.

A

X = peptide and disulfide (all covalent bonds)

41
Q

Protein structure always written from (X) terminus to (Y) terminus.

A 
X = N
Y = C
42
Q

How many AA per turn of alpha helix?

43
Q

Peptide bonds are (perpendicular/parallel) to alpha helix.

44
Q

Each peptide bond forms (X) bond with peptide bond (Y) residues above it.

A 
X = hydrogen
Y = 4
45
Q

Which AA favor formation of alpha helix?

A

Met, Ala, Leu

46
Q

Which AA destabilize structure of alpha helix?

A
  1. Pro
  2. Gly
  3. Large numbers of charged AA
47
Q

Beta pleated sheets can form between how many polypeptide chains?

A

Within same polypeptide or between multiple different polypeptide chains

48
Q

Which portion of AA involved in hydrogen bonding in secondary structure of protein?

A

Peptide bonds

49
Q

Parallel beta pleated sheets can be distinguished from anti-parallel by:

A

Two amino terminals near each other (same orientation) in parallel sheet structure

50
Q

Turns, loops, coils are examples of (primary/secondary/tertiary/quaternary) structure.

51
Q

Which type of bonding primarily stabilizes secondary structure?

A

Hydrogen bonding

52
Q

Which type of bonding primarily stabilizes tertiary structure?

A

Many weak interactions and disulfide bonds

53
Q

Motifs occur primarily in (primary/secondary/tertiary/quaternary) structure.

A

Tertiary and quaternary

54
Q

Regions of polypeptide chains that can fold stably/independently wrt entire protein.

55
Q

Proteins fall into which two major categories?

A
  1. Fibrous

2. Globular

56
Q

(Fibrous/Globular) proteins provide structural support.

57
Q

(Fibrous/Globular) proteins have simple tertiary structure.

58
Q

(Fibrous/Globular) proteins are high in hydrophobic amino acids.

59
Q

Most proteins are (Fibrous/Globular).

60
Q

Give example of a disordered protein

A

p53 tumor suppressor (unstructured C-terminus that can bind to >4 proteins and has different conformation in each case)

61
Q

Dornase Alfa is:

A

DNase that thins the thick, sticky CF mucus

62
Q

Ivacaftor is:

A

CFTR potentiator that improves Cl transport (binds channels directly) in CF

63
Q

Ivacaftor useful in (X) patients with which mutation?

A

X = CF

G551D

64
Q

Most common CF mutation:

A

(Delta)F508

65
Q

Patients with most common CF mutation should likely take which drug?

66
Q

Lumacaftor is found in which drug? What’s its function?

A

Orkambi

Improves conformational stability of CFTR protein

67
Q

Ka signifies:

A

Tendency for acid to lose proton and form conjugate base

68
Q

Stronger acid will have (lower/higher) pKa than a weaker acid.

69
Q

Which point on titration curve is indicative of pKa?

A

The pH when molecule is 50% acid and 50% base form.

70
Q

At isoelectric point (pI), the molecule is electrically (positive/negative).

71
Q

When is the pH most resistant to change?

A

When close to pKa value

72
Q

T/F: essentially all misfolded proteins in cytoplasm are targeted to same intracellular location.

A

False - targeted to specific intracellular inclusions

73
Q

Proteins in JUNQ are:

A
  1. Degraded

2. Mobile

74
Q

Proteins in IPOD are:

A
  1. Persisting

2. Trapped

MFoM (20 decks)

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