Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

BIOC192 > Lecture 5: ELEMENTS OF PROTEIN STRUCTURE > Flashcards

Lecture 5: ELEMENTS OF PROTEIN STRUCTURE Flashcards

1
Q

What is each protein made of?

A

At least one protein (or polypeptide) chain

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

How many chains may proteins have?

A

Anywhere from one to several

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What is the most common variety of proteins?

A

Proteins with one chain

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Proteins are mostly…

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What is the structure of proteins primarily composed of?

A

Alpha helix, beta structure and turns

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

How many levels of protein structure are there?

A

4

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What is the primary structure?

A

Amino acid sequence of a protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What is the secondary structure?

A

Local three-dimensional (3D) arrangement of a protein chain over a short stretch of adjacent amino acid residues

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What is the tertiary structure?

A

Three-dimensional (3D) structure of a complete protein chain

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What is the quaternary structure?

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

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

A

Bonds which can rotate and are somewhat flexible

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What are the main chain atoms in a protein?

A

Nitrogen, alpha carbon and carbonyl carbon

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

How are the main chain atoms in a protein connected?

A

By single bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What is the bond between N and alpha carbon called?

A

Phi

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

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

A

Psi

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What is the range of values for phi and psi?

A

0 +/- 180 degrees

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

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

A

Omega

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What is the value of omega usually?

A

Very close to 180 degrees or 0 degrees

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Can phi bonds twist?

A

Yes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Can psi bonds twist?

A

Yes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Can omega bonds twist?

A

No

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

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

A

Because of steric hinderance

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What can phi rotation lead to?

A

O-O collision

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

What can psi rotation lead to?

A

NH-NH collisions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

What may their be steric hinderance between?

A

The hydrogen on the amide nitrogen and the carbonyl oxygen

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

What are most peptide bonds?

A

Trans

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

What does omega equal for a trans peptide bond?

A

About 180 degrees

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

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

A

On opposite sides of the peptide bond

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

What does omega equal for a cis peptide bond?

A

About 0 degrees

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

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

A

On the same side of the peptide bond

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

When is steric hinderance increased?

A

For cis peptide bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

Does the peptide bond angle usually rotate?

A

No, not very much

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

What amino acid tends to have a lot of cis bonds?

A

Proline

36
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

37
Q

What does a proteins 3D structure lead to?

A

The arrangement of all the side chains in the protein

38
Q

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

A

Its function

39
Q

What is secondary protein structure dominated by?

A

Two structures - alpha helices and beta strands/sheets

40
Q

What does the main chain do in an alpha helix?

A

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

41
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

42
Q

What symbol is the carbonyl oxygen given?

A

n

43
Q

What symbol is the nitrogen with hydrogen attached given?

A

n+4

44
Q

What is the O-N distance?

A

approximately 2.9 A

45
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

46
Q

How many residues/turn in alpha helices?

A

3.6

47
Q

What is the rise/turn in alpha helices?

A

5.4 A

48
Q

What is the d of one amino acid residue?

A

2.5. A

49
Q

Where are the side chains in alpha helices?

A

They point outwards to help stabilise the alpha helix

50
Q

What is phi in an alpha helix?

A

about -57 degrees

51
Q

What is psi in an alpha helix?

A

About - 47 degrees

52
Q

Which amino acid residues break the alpha helix pattern?

A

Glycine and proline

53
Q

What exists in the aloha helix?

A

A dipole, positive at the N terminus

54
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)

55
Q

What occurs between adjacent beta strands?

A

Hydrogen bonding

56
Q

What can adjacent beta strands form?

A

A beta sheet with two or more strands

57
Q

How many beta strands per beta Sheed?

A

Typically 2-10

58
Q

What is the average beta strand length?

A

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

59
Q

How many amino acid residues may each strand have?

A

Up to 15

60
Q

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

A

Parallel and antiparallel

61
Q

Describe parallel strutcure?

A

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

62
Q

Describe antiparallel strutcure?

A

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

63
Q

How is a beta sheet described?

A

Extended and pleated, planar with right handed twist

64
Q

Where are the side chains in beta sheets?

A

Above and below

65
Q

What will commonly form a beta strand?

A

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

66
Q

What are beta structures found in?

A

Silk

67
Q

What is the model beta sequence in silk?

A

Gly-Ser-Gly-Ala-Gly-Ala

68
Q

What do the Ala side chains do in silk?

A

Interlock with the Al side chain from another sheet

69
Q

Is beta sheets in silk parallel or antiparallel?

A

Antiparallel

70
Q

What do silks from different species have?

A

Different interlocking groups and differing physical properties

71
Q

What are turns needed for?

A

To form globules

72
Q

What are turns often like?

A

Short, hairpin like, involving 3 or 4 residues

73
Q

What amino acids are in high amounts in turns?

A

Gly (flexibility) and Pro (rigidity)

74
Q

What portion of residues are involve din turns?

A

Almost 30%

75
Q

What is common across turns?

A

Hydrogen bonds

76
Q

How many types of turns are there?

A

More than 16, which are given Roman numeral names

77
Q

What are the common types of turn?

A

Type I and Type II

78
Q

Where is the oxygen in Type I turns?

A

Up

79
Q

Where is the oxygen in Type II turns?

A

Down

80
Q

Why are protein structures challenging to display clearly?

A

There are lots of atoms, detailed internal cavities and complicated shapes

81
Q

What are all the elements of protein structure?

A

Alpha helix, beta strands, turns and loops (bigger turns)

82
Q

What are space filling models good for?

A

Overall shape but you can’t really see inside and the elements of structure

83
Q

How are helices shown in the consensus protein structural display?

A

As spirals (or cylinders)

84
Q

How are strands shown in the consensus protein structural display?

A

Arrows pointing from N terminus to C terminus

85
Q

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

A

As loops or rope-like structures

86
Q

What is a random coil?

A

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

87
Q

What are the advantages of the consensus protein structural display?

A
  • easily visualise the main chain path
  • identify elements of secondary structure
  • appreciation of proteins as 3D objects
  • allows comparison to other proteins

BIOC192 (38 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions