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CHEM 350 > Lecture 8 - Protein Structure from primary to quaternary > Flashcards

Lecture 8 - Protein Structure from primary to quaternary Flashcards

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1
Q

what is the primary structure of a protein?

A

-amino acid sequence in a polypeptide chain

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2
Q

what is the secondary structure of a protein?

A

-helix

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3
Q

what is the tertiary structure of a protein?

A
  • one complete protein chain

- beta chain of hemoglobin

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4
Q

what is the quaternary structure of a protein?

A

-the four separate chains of hemoglobin assembled into a oligomeric protein

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5
Q

what is the second level of protein structure dictated by?

A

hydrogen bonds between nearby residues

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6
Q

what are protein folds made up of?

A

secondary structural motifs interrupted by loops

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7
Q

how can secondary motifs be identified?

A

from backbone torsion angle distributions

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8
Q

What do backbone torsion angles describe?

A

-the twisting of the protein peptide backbone

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9
Q

Why is the — angle almost always 180?

A

peptide bond has special resonance structure

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10
Q

What does a Ramachandran plot show?

A

(..,..) angle distribution in a protein

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11
Q

what are alpha helices?

A

right-handed coils

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12
Q

how many residues per turn in an alpha helix?

A

average 3.6 residues per turn

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13
Q

What is the average alpha helix lenght?

A

12 residues, ~3 turns

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14
Q

are beta sheets parallel or antiparallel?

A
  • can be both

- anti parallel sheets occur more frequently

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15
Q

What is a quality of an antiparallel sheet?

A

-pleated with repeated distance averaging 7.0

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16
Q

What do helices and sheets form?

A

-a continuum

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17
Q

which amino acids favor alpha helices?

A 
ala
cys
leu
met
glu
gln
his
lys
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18
Q

which amino acids favor beta sheets?

A 
val
ile
phe
tyr
trp
thr
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19
Q

which amino acids favor turns?

A 
gly
ser
asp
asn
pro
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20
Q

What is the difference between fibrous and globular proteins?

A

globular proteins: compact + tightly folded

fibrous proteins: elongated, dominated by helices

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21
Q

what do fibrous proteins serve mostly as?

A

structural elements

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22
Q

what is alpha keratin?

A

coiled coil

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23
Q

what is keratin?

A

-principal component of hair, horn, nail + feathers in birds/animals

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24
Q

what is keratincomposed of?

A

-long alpha helix

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25
Q

what do two keratins form?

A
  • hydrophobic interactions to form a coiled coil

- keratin dimer coiled coil

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26
Q

what is collagen?

A

triple helix

27
Q

collagen is the most _______ in ____

A
  • abundant protein

- vertebrates

28
Q

What is collagen the main component of?

A

bone, teeth, cartilage, tendon, skin, blood vessels

29
Q

how is hydroxyproline made?

A
  • by modifying prolines after the collagen fiber is assembled
  • requires vitamin C
30
Q

what are 2 methods used to determine tertiary structures?

A
  1. X-ray

2. NMR

31
Q

what is X-ray?

A

-differaction method

32
Q

What does X-ray require?

A

crystal of the protein

33
Q

what does X-ray reveal?

A

-electron density contours of the molecule

34
Q

what is the structure of a protein in solution identical to?

A

-largely identical to its crystal structure

35
Q

what is NMR?

A
  • nuclear magnetic resonance

- solution-based method

36
Q

What does NMR measure?

A

distances between H atoms on the protein

37
Q

what does NMR usually contain?

A

-ensemble of structures

38
Q

what is the key determinant of side chain locations?

A

-hydrophobicity

39
Q

AA with nonpolar side chains

A 
val
ile
leu
met
phe 
(occur mostly on inside)
40
Q

AA with charged side chains

A 
arg
lys
his
asp
glu
(mostly occur on outside)
41
Q

AA with polar side chains

A 
ser
thr
asn
gln
(usually on surface, can be see on inside)
42
Q

what do tertiary structures contain?

A

-combinations fo secondary motifs

43
Q

larger proteins have ______

A

multiple domains

44
Q

what is a quality of multiple domains in larger proteins?

A

-each domain folds like a separate unit and has a distinct function

45
Q

are domains the same as subunits?

A

NO
-domains: on same chain

-subunits: on different chains

46
Q

what do quaternary structures describe?

A

how subunits are packed

47
Q

how are subunits assembled?

A

by van der Waals interactions

48
Q

for identical or near-identical subunits there is often _____

A

an overall symmetry

49
Q

what are 4 factors involved in the stability of protein folds?

A
  1. hydrophobicity
  2. disulfide bonds
  3. metal atoms
  4. electrostatic interactions
50
Q

Proteins can undergo ____ and _____

A

denaturation and renaturation

51
Q

what are 2 common denaturants?

A
  1. Guanidinium ion

2. urea

52
Q

what are the 5 steps of denuration?

A

1.

53
Q

what are conformations?

A

-the different geometries the protein can fold into

54
Q

when does the protein have highest conformational entropy?

A

in its unfolded state

55
Q

What is the entropy of a protein when it is in its unfolded state?

A

-the protein has highest conformational entropy

56
Q

what is the folding funnel?

A

-hierarchical pattern of folding

57
Q

what does the folding funnel say about structure and entropy?

A

…

58
Q

what happens to proteins as they are being synthesized in the ribosome?

A

they fold

59
Q

what accelerates S-S interchanges?

A

disulfilde isomerase

60
Q

what does disulfide isomerase do?

A

accelerates S-S interchanges

61
Q

what is the GroEL-GroES chaperonin complex?

A

an ATPase motor protein

62
Q

what do chaperone proteins do?

A

help correct misfolding

63
Q

what are the 4 steps of a chaperone protein?

A

1.

CHEM 350 (22 decks)

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