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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
In Maple Syrup urine disease, what's the fundamental molecular issue?
Lack of proper function of branched-chain alpha-keto acid dehydrogenase complex (buildup of branched chain AA)
26
Which branched chain AA can be synthesized in the body?
None! All are essential AA
27
An infant diagnosed with Maple Syrup urine disease should be treated in which way(s)?
No breastfeeding! Restrict intake of nourishment that's high in these AA
28
High levels of which protein can be indicative of CF?
IRT (Immunoreactive Trypsinogen)
29
IRT is produced by which organ?
Pancreas
30
Which key test is used to diagnose CF?
Sweat test
31
How does CF occur?
Single mutation in CTFR gene
32
CTFR gene encodes:
Cl channel protein that regulates anion movement across epithelial membranes of lungs, pancreas, and other organs
33
Movement of which ion(s) is/are affected by CF?
1. Cl transport impaired | 2. Na absorption enhanced (net increase in water absorption)
34
W1282X mutation means:
Stop codon inserted at expense of Tryptophan
35
G551D mutation means:
Glutamate replaced by Aspartate
36
R117H mutation has what effect on polypeptide charge?
No effect - His and Arg both positive
37
Proteins tend to fold in configuration with lowest (X) and most (Y).
``` X = E Y = hydrogen bonds ```
38
T/F: All proteins require chaperones told properly.
False
39
Most important stabilizing influence in protein structure:
AA sequence
40
Primary structure includes (X) bonds.
X = peptide and disulfide (all covalent bonds)
41
Protein structure always written from (X) terminus to (Y) terminus.
``` X = N Y = C ```
42
How many AA per turn of alpha helix?
3.6
43
Peptide bonds are (perpendicular/parallel) to alpha helix.
Parallel
44
Each peptide bond forms (X) bond with peptide bond (Y) residues above it.
``` X = hydrogen Y = 4 ```
45
Which AA favor formation of alpha helix?
Met, Ala, Leu
46
Which AA destabilize structure of alpha helix?
1. Pro 2. Gly 3. Large numbers of charged AA
47
Beta pleated sheets can form between how many polypeptide chains?
Within same polypeptide or between multiple different polypeptide chains
48
Which portion of AA involved in hydrogen bonding in secondary structure of protein?
Peptide bonds
49
Parallel beta pleated sheets can be distinguished from anti-parallel by:
Two amino terminals near each other (same orientation) in parallel sheet structure
50
Turns, loops, coils are examples of (primary/secondary/tertiary/quaternary) structure.
Secondary
51
Which type of bonding primarily stabilizes secondary structure?
Hydrogen bonding
52
Which type of bonding primarily stabilizes tertiary structure?
Many weak interactions and disulfide bonds
53
Motifs occur primarily in (primary/secondary/tertiary/quaternary) structure.
Tertiary and quaternary
54
Regions of polypeptide chains that can fold stably/independently wrt entire protein.
Domains
55
Proteins fall into which two major categories?
1. Fibrous | 2. Globular
56
(Fibrous/Globular) proteins provide structural support.
Fibrous
57
(Fibrous/Globular) proteins have simple tertiary structure.
Fibrous
58
(Fibrous/Globular) proteins are high in hydrophobic amino acids.
Fibrous
59
Most proteins are (Fibrous/Globular).
Globular
60
Give example of a disordered protein
p53 tumor suppressor (unstructured C-terminus that can bind to >4 proteins and has different conformation in each case)
61
Dornase Alfa is:
DNase that thins the thick, sticky CF mucus
62
Ivacaftor is:
CFTR potentiator that improves Cl transport (binds channels directly) in CF
63
Ivacaftor useful in (X) patients with which mutation?
X = CF G551D
64
Most common CF mutation:
(Delta)F508
65
Patients with most common CF mutation should likely take which drug?
Orkambi
66
Lumacaftor is found in which drug? What's its function?
Orkambi Improves conformational stability of CFTR protein
67
Ka signifies:
Tendency for acid to lose proton and form conjugate base
68
Stronger acid will have (lower/higher) pKa than a weaker acid.
Lower
69
Which point on titration curve is indicative of pKa?
The pH when molecule is 50% acid and 50% base form.
70
At isoelectric point (pI), the molecule is electrically (positive/negative).
Neutral
71
When is the pH most resistant to change?
When close to pKa value
72
T/F: essentially all misfolded proteins in cytoplasm are targeted to same intracellular location.
False - targeted to specific intracellular inclusions
73
Proteins in JUNQ are:
1. Degraded | 2. Mobile
74
Proteins in IPOD are:
1. Persisting | 2. Trapped

MFoM (20 decks)

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