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Chem 521 - Biochemistry > Lecture 3 - Tertiary and quaternary protein structure > Flashcards

Lecture 3 - Tertiary and quaternary protein structure Flashcards

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1
Q

Tertiary structure refers to

A

the spatial arrangement of amino acid residues that are far apart in the sequence.

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2
Q

Tertiary structure is created by

A

the folding of the polypeptide into a compact, roughly spherical conformation.

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3
Q

Protein folding is driven by

A

the strong tendency of hydrophobic residues to be excluded from water.

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4
Q

When a polypeptide chain folds, the _______ side chains are buried inside, and the ______ chains are on the surface.

A

hydrophobic; polar

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5
Q

Amphipathic

A

Having a hydrophobic and polar side

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6
Q

______ and ______ are often amphipathic.

A

alpha helices; beta strands

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7
Q

Unpaired N-H and C=O groups prefer a(n) ______ environment

A

aqueous

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8
Q

Is the protein interior always hydrophobic and the exterior always polar?

A

No

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9
Q

An example of a protein with a hydrophobic exterior

A

Membrane proteins

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10
Q

Strength of van der Waals forces

A

0.4-4 kJ/mol

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11
Q

Strength of hydrogen bonds

A

12-30 kJ/mol

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12
Q

Strength of ionic bonds

A

20 kJ/mol

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13
Q

Strength of hydrophobic interactions

A

<40 kJ/mol

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14
Q

Motifs

A

Certain combinations of secondary structure present in the tertiary structure.

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15
Q

Motifs are known as

A

super secondary structures

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16
Q

Alpha-helix motifs

A
  1. Helix-turn-helix
  2. Helix-loop-helix
  3. EF hand
  4. Leucine zipper
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17
Q

Beta-sheet motifs

A
  1. Beta hairpins
  2. Greek key
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18
Q

Mixed motifs

A
  1. Beta-alpha-beta
  2. Rossmann fold
  3. Zinc finger
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19
Q

A helix-turn-helix motif is made up of

A

two alpha-helices connected by a turn.

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20
Q

Helix-turn-helix motifs are observed in

A

proteins capable of binding DNA.

21
Q

A helix-loop-helix motif is made up of

A

two alpha-helices connected by a loop

22
Q

Helix-loop-helix motifs characterize a family of

A

transcription factors

23
Q

EF hand motifs are made up of

A

two alpha-helices connected by a loop that contains residues to coordinate a calcium ion

24
Q

EF hand motifs are present in

A

calcium binding proteins

25
Q

A leucine zipper motif is made up of

A

two alpha-helices that form a coiled-coil structure at one end

26
Q

The two helices in a leucine zipper dimerize due to

A

the leucines present on each helix

27
Q

A beta-hairpin motif consists of

A

two antiparallel beta-strands connected by a hairpin turn

28
Q

A Greek key motif consists of

A

four adjacent beta strands with linking loops that fold upon themselves

29
Q

A beta-alpha-beta motif consists of

A

two parallel beta strands connected by an alpha-helix

30
Q

In a right handed beta-alpha-beta motif, the helix is ______ the plane

A

above

31
Q

In a left handed beta-alpha-beta motif, the helix is ______ the plane

A

below

32
Q

A Rossman fold consists of

A

two beta-alpha-beta motifs

33
Q

In a Rossman fold, the middle strand is often

A

shared between the two units

34
Q

A zinc finger motif consists of

A

an alpha-helix bound to a loop by a zinc ion

35
Q

In a zinc finger motif, the zinc ion is held in place by

A

two cysteines and two histidines

36
Q

Proteins with zinc fingers bind to

A

DNA

37
Q

Motifs can go together to form larger structures called

A

domains

38
Q

A helix bundle is made up of

A

two helix-turn-helices

39
Q

A beta barrel domain consists of

A

several beta-hairpins

40
Q

Quaternary structure describes

A

proteins with more than one polypeptide chain

41
Q

Subunit

A

Each folded three-dimensional polypeptide chain in the quaternary structure

42
Q

Dimer

A

A protein consisting of two subunits

43
Q

Trimer

A

A protein consisting of three subunits

44
Q

Homomeric

A

One type of subunit

45
Q

Heteromeric

A

More than one type of subunit

46
Q

Is hemoglobin a homotetramer or a heterotetramer?

A

heterotetramer

47
Q

Most oligomeric proteins are ______ arranged

A

symmetrically

48
Q

Proteins cannot have inversion or mirror symmetry because

A

that would require conversion of L to D chirality

49
Q

The simplest protein symmetry is

A

cyclic (C2, C3, etc.)

Chem 521 - Biochemistry (31 decks)

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