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BIO1332 - Biochemistry > Protein Structure > Flashcards

Protein Structure Flashcards

1
Q

Define primary structure of a protein:

A

sequence of amino acids

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2
Q

Define secondary structure of a protein:

A

simple, repetitive motifs that are found in almost all proteins

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3
Q

Define tertiary structure of a protein:

A

overall fold of the protein

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4
Q

Define quaternary structure of a protein:

A

when several proteins fold together

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5
Q

Does a peptide bond have a full or partial double bond character?

A

partial

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6
Q

Work out the peptide bond length (take into account a partial double bond):
C - N single bond = 1.49 A
C = N double bond = 1.27 A

A

Peptide bond = 1.32 A

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7
Q

How can a structure of an amino acid in polypeptide be adjusted?

A

Rotation about two pure single bonds

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8
Q

What are the types of angle of rotations that can determine the path of a polypeptide chain?

A

Phi and Psi

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9
Q

What is Phi?

A

The angle of rotation about the bond between the nitrogen and the a-carbon atom

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10
Q

What is Psi?

A

The angle of rotation about the carbonyl carbon atom and a-carbon atom

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11
Q

Are all combinations of Phi and Psi possible?

A

Many combination are forbidden due to steric collisions between atoms

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12
Q

Who recognised that not all combinations of phi and psi are possible?

A

Ramachandran et al in 1963

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13
Q

Psi and phi can be visualised on a two dimensional plot. What is it called?

A

Ramachandran Plot

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14
Q

Do highly flexible polymers with large number of possible conformations fold into unique structures?

A

No

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15
Q

What are 3 types of secondary structures of proteins?

A
  • Alpha helix
  • Beta Sheet
  • Turns and loops
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16
Q

The Ramachandran Plot is split into 4 squares on a graph. Where would you find an alpha helix?

A

Bottom right

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17
Q

The Ramachandran Plot is split into 4 squares on a graph. Where would you find a left handed alpha helix?

A

Top left

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18
Q

The Ramachandran Plot is split into 4 squares on a graph. Where would you find a parallel B-sheet?

A

Top right

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19
Q

The Ramachandran Plot is split into 4 squares on a graph. Where would you find an anti-parallel B-sheet?

A

Top right

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20
Q

Which is more common the right handed or left handed alpha helix?

A

The right handed alpha helix

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21
Q

What is a hydrogen bond?

A

Partially electrostatic attraction between a hydrogen and a more electronegative atom which bears a lone pair of electrons

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22
Q

Alpha Helix: What is the number of residues?

A

3.6

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23
Q

Alpha Helix: what os the pitch (distance the helix rises along its
axis/turn)?

A

5.4A

24
Q

Alpha Helix: What is causing the shape?

A

Hydrogen bonding capacity of the backbone NH and CO groups

25
Q

Alpha Helix: Are the side chains facing inwards or outwards?

A

Outwards

26
Q

Alpha Helix: How is the hydrogen bonded formed?

A

CO group of residue n forms a hydrogen bond with the NH group of residue n +4

27
Q

What example is made of 75% of a-helices?

A

Ferritin

28
Q

What type of storage protein is ferritin?

A

Iron

29
Q

What is a B-sheet?

A

Made of at least two polypeptide chains which can be parallel or anti-parallel or both

30
Q

What do B-sheets look like?

A

ripples or pleated appearance

31
Q

B-sheets: Which is the successive side chain group?

A

2 residue repeats of 7.0A

32
Q

B-sheets: Where is the hydrogen binding occurring?

A

Between C=O of one chain to N-H of another

33
Q

B-sheets: How many residues long is it in a globular protein?

A

15

34
Q

B-sheets: How are they normally shown in a diagram?

A

Broad arrows pointing in the direction of the carboxyl-terminal end

35
Q

What is another name for B-turn?

A

hairpin turn

36
Q

What is another name for hairpin turn?

A

B-turn

37
Q

What is another name for both B-turn and hairpin?

A

Reverse turn

38
Q

Reverse Turn: How is the hydrogen bond occurring?

A

CO of residue i of polypeptide is hydrogen bonded to NH group of residue i + 3

39
Q

Reverse turn: what does the hydrogen bond do?

A

Stablises abrupt changes in direction of the polypeptide chain

40
Q

What is different about the structure of loops compared to a-helices and b-strands?

A

No regular periodic structure in loops

41
Q

Loops: What is the structure like?

A

Rigid and well defined

42
Q

Where do you find loops and turns in a protein?

A

On the surface

43
Q

What are mini-domains?

A

elements of secondary structure link together into combinations

44
Q

What is a myoglobin made out of?

A

100% a-helix protein

45
Q

How many amino acids are there in a single polypeptide chain of myoglobin?

A

153

46
Q

What is the structure of a myoglobin molecule?

A

70% of main chain is folded into 8 a-helices and the rest forms turns and loops

47
Q

What is concanavalin A made of?

A

100% B-sheet protein

48
Q

How many b-strands are there in a concanavalin A?

A

14 beta-strands

49
Q

What is a lectin?

A

carbohydrates-binding protein

50
Q

What is the purpose of a concanavalin A?

A

A lectin

51
Q

What is meant by domains in chemistry when talking about proteins?

A

Many proteins have several sections that could fold independently

52
Q

What do we call a quaternary structure that is made out of the same protein?

A

Homomultimers

53
Q

What do we call a quaternary structure that is made out of different protein?

A

Heteromultimers

54
Q

Relating to human haemoglobin what structure does it have?

A

a2b2 tetramer

55
Q

How many heme groups does the human haemoglobin have?

A

4

BIO1332 - Biochemistry (19 decks)

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