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BIOC192 2024 Melia > Lecture 5 - Elements of Protein Structure > Flashcards

Lecture 5 - Elements of Protein Structure Flashcards

1
Q

Amino acids are joined by?

A

Peptide bonds

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2
Q

How are the amino acid residues in a polypeptide chain numbered?

A

Starting from the amino terminus to the carboxyl terminus (N-terminus to C-terminus)

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3
Q

What is each protein made of?

A

At least one protein (or polypeptide) chain

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4
Q

How many chains may proteins have?

A

Anywhere from one to several

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5
Q

What is the most common variety of proteins?

A

Proteins with one chain

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6
Q

Proteins are mostly…

A

Globular so the main chain has to double back and form a more compact shape

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7
Q

What is the structure of proteins primarily composed of?

A

Alpha helix, beta structure and turns

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8
Q

What are the levels of protein structures?

A

Primary, Secondary, Tertiary, Quaternary

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9
Q

Primary:

A

amino acid sequence of a protein

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10
Q

Secondary:

A

Local 3D arrangement of a protein chain over a short stretch of adjacent amino acid residue

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11
Q

Tertiary:

A

3D structure of a complete protein chain

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12
Q

Quaternary:

A

Interchain packing and structure for a protein that contains multiple protein chains

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13
Q

What do the protein main chain and side chain atoms have?

A

Bonds which can rotate and are somewhat flexible

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14
Q

What are the main chain atoms in a protein?

A

Nitrogen, alpha carbon and carbonyl carbon

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15
Q

How are the main chain atoms in a protein connected?

A

By single covalent bonds

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16
Q

What is the bond between N and alpha carbon called?

A

Phi

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17
Q

What is the bond between alpha carbon and carbonyl carbon called?

A

Psi

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18
Q

What is the range of values for phi and psi?

A

0 +/- 180 degrees

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19
Q

What is the bond angle between the carbonyl carbon and N (peptide bond) called?

A

Omega

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20
Q

What is the angle value of omega usually?

A

very close to 180 degrees or 0

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21
Q

What is one way a 3D structure can be described?

A

By listing the rotation angles found around the bonds of each residue of the protein chain

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22
Q

What bonds can twist

A

Phi and Psi

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23
Q

What bond cannot twist

A

Omega

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24
Q

Why do phi and psi angles have restrictions in their values?

A

Due to steric hindrance

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25
Q

What can phi rotation lead to?

A

O-O collision

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26
Q

What can psi rotation lead to?

A

NH-NH collisions

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27
Q

What may their be steric hinderance between?

A

The hydrogen on the amide nitrogen and the carbonyl oxygen

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28
Q

What are most peptide bonds?

A

Trans

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29
Q

What does omega equal for a trans peptide bond?

A

About 180 degrees

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30
Q

Where are the alpha carbon atoms found in a trans peptide bond?

A

On opposite sides of the peptide bond

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31
Q

What does omega equal for a cis peptide bond?

A

About 0 degrees

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32
Q

Where are the alpha carbon atoms found in a cis peptide bond?

A

On the same side of the peptide bond

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33
Q

When is steric hinderance increased?

A

For cis peptide bonds

34
Q

which bond is shorter:
C-N bond or Ca - N bond.

A

C-N bond.

35
Q

What does the combination of all the rotations and twists around all the bonds in a protein lead to?

A

Its overall 3D structure

36
Q

What does a proteins 3D structure lead to?

A

The arrangement of all the side chains in the protein

37
Q

What does the arrangement of all the side chains in the protein lead to?

A

Its function

38
Q

What is secondary protein structure dominated by?

A

Two structures - alpha helices and beta strands/sheets

39
Q

What does the main chain do in an alpha helix?

A

Spirals around the central axis like a spiral axis - right handed spiral

40
Q

What type of interaction is there in alpha helices?

A

A non-covalent interaction called a hydrogen bond between the carbonyl oxygen which is partially negatively charged and the hydrogen attached to the N which is slightly positively charged

41
Q

What symbol is the carbonyl oxygen given?

A

n

42
Q

What symbol is the nitrogen with hydrogen attached given?

A

n+4

43
Q

What is the O-N distance?

A

approximately 2.9 A

44
Q

What do hydrogen bonds do in alpha helices?

A

Help stabilise the structure, (adding 3-7 cal/mol or 12-28kJ/mol of stability)

45
Q

How many residues/turn in alpha helices?

A

3.6

46
Q

What is the rise/turn in alpha helices?

A

5.4 A

47
Q

What is the d of one amino acid residue?

A

1.5 A / residue

48
Q

Where are the side chains in alpha helices?

A

They point outwards to help stabilise the alpha helix

49
Q

What is phi in an alpha helix?

A

about -57 degrees

50
Q

What is psi in an alpha helix?

A

About - 47 degrees

51
Q

Which amino acid residues break the alpha helix pattern?

A

Glycine and proline

52
Q

What exists in the alpha helix?

A

A helix dipole, positive at the N terminus

53
Q

What is the beta structure comprised of?

A

Peptide chains with a more extended structure than the alpha helix. Each is called a beta strand (not stable on own)

54
Q

What occurs between adjacent beta strands?

A

Hydrogen Bonding

55
Q

What can adjacent beta strands form?

A

A beta sheet (with two or more strands)

56
Q

How many beta strands per beta Sheet?

A

typically 2-10

57
Q

What is the average beta strand length?

A

About 6 amino acid residues which is typically shorter than alpha helices

58
Q

How many amino acid residues may each strand have?

A

Up to 15

59
Q

What are the two types of hydrogen bonding interactions between beta sheets?

A

Parallel and antiparallel

60
Q

Describe parallel strutcure?

A

The two strands run in the same direction but the hydrogen bonds aren’t parallel

61
Q

Describe antiparallel strutcure?

A

The two strands run in the opposite direction and the hydrogen bonds are parallel

62
Q

How is a beta sheet described?

A

Extended and pleated, not planar with right handed twist

63
Q

Where are the side chains in beta sheets?

A

Above and below

64
Q

What will commonly form a beta strand?

A

Any NP-P-NP-P stretch of amino acid residues

65
Q

What is the model beta sequence in silk?

A

Gly-Ser-Gly-Ala-Gly-Ala

66
Q

What do the Ala side chains do in silk?

A

Interlock with the Ala side chain from another sheet

67
Q

Is beta sheets in silk parallel or antiparallel?

A

Antiparallel

68
Q

What are turns needed for?

A

To form globules

69
Q

What are turns often like?

A

Short, hairpin like, involving 3 or 4 residues

70
Q

What amino acids are in high amounts in turns?

A

Gly (flexibility) and Pro (rigidity)

71
Q

What portion of residues are involved in turns?

A

Almost 30%

72
Q

What is common across turns?

A

Hydrogen Bonding

73
Q

How many types of turns are there?

A

More than 16, which are given Roman numeral names

74
Q

What are the common types of turn?

A

Type I and Type II

75
Q

Where is the oxygen in Type I turns?

A

Up

76
Q

Where is the oxygen in Type II turns?

A

Down

77
Q

How are helices shown in the consensus protein structural display?

A

As spirals (or cylinders)

78
Q

How are strands shown in the consensus protein structural display?

A

Arrows pointing from N terminus to C terminus

79
Q

How are turns and random coils shown in the consensus protein structural display?

A

As loops or rope-like structures

80
Q

What is a random coil?

A

A section of protein structure that does not fit into any of the standard groups

BIOC192 2024 Melia (36 decks)

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