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Z OLD Molecules, Genes and Disease > Protein Folding and Function > Flashcards

Protein Folding and Function Flashcards

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Organic Chemistry 101 flashcards
1
Q

What is protein structure?

A

The string of amino acids folded into a unique 3D shape

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2
Q

What does protein shape depend on?

A

Amino acid sequence

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3
Q

What does sequence determine?

A

Function

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4
Q

What is the primary structure of a protein?

A

The linear amino acid sequence of a polypeptide chain

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5
Q

What is the secondary structure of a protein?

A

The local spatial arrangement of the polypeptide backbone

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6
Q

What are we looking at when considering secondary structure?

A

Localised folding, not the whole molecule

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7
Q

What does secondary structure looking at the backbone mean?

A

We are not looking at side groups

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8
Q

What is the tertiary structure of a protein?

A

The 3D arrangement of all atoms in a polypeptide

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9
Q

What is the quaternary structure of a protein?

A

The 3D arrangement of 2+ protein sub-units

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10
Q

What can you often determine from the 3D structure of a protein?

A

How it works

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11
Q

When is knowing the 3D structure of a protein useful?

A

When making new drugs

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12
Q

Why is knowing the 3D structure of a protein useful when making new drugs?

A

Can use it to find active site shape, and therefore make inhibitor of protein, for example if its overexpressed in a disease

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13
Q

What holds together the primary structure

A

Covalent peptide bonds

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14
Q

Can the bonds in a polypeptide rotate?

A

The C-N bond cannot, but other bonds can

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15
Q

What does the bond angle determine?

A

The conformation of the peptide backbone, and therefore the ‘fold’ of the protein

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16
Q

Why does the bond angle of the backbone determine the fold of a protein?

A

Not all bond angles are allowed, for example if there are bulky side chains the bond angles may be limited

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17
Q

What do certain bond angles promote?

A

The formation of folding patterns

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18
Q

How many amino acids are there in one turn of an α-helix?

A

3.6

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19
Q

What is the pitch of anα-helix?

A

0.54nm

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20
Q

What is meant by pitch of theα-helix?

A

How far it is for it to go one complete turn

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21
Q

What kind of helix is theα-helix?

A

Right-handed

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22
Q

Is theα-helix structure compact or loose?

A

Compact

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23
Q

How is theα-helix held together?

A

H bonds

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24
Q

Where are the H bonds between in anα-helix?

A

The backbone -C=O group of one residue is H-bonded to the -NH group 4 amino acids away

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25
Q

Where are the R groups in aα-helix?

A

Sit on the outside

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26
Q

Are the R groups involved in the formation of anα-helix?

A

No

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27
Q

Do all polypeptides form anα-helix helix structure?

A

No

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28
Q

What residues are strongα-helix formers?

A

Small, hydrophobic ones, e.g. Ala, Leu

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29
Q

What residues acts as helix breakers?

A

NAME?

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30
Q

Why does Pro act as a helix breaker?

A

Rotation around the N-C α bond impossible

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31
Q

Why does Gly act as a helix breaker?

A

Has a tiny R group, so is too flexible- supports other confirmations

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32
Q

Is the ß-strand compact or extended?

A

Fully extended

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33
Q

How far is there between amino acids on the ß-strand?

A

0.35nm

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34
Q

How are the R groups positioned on the ß-strand?

A

Between opp sides of the chain

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35
Q

What doß-strand’s form?

A

An antiparallel ß-sheet

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36
Q

How areß-strands arranged in the antiparallel ß-sheet?

A

Running in opposite directions

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37
Q

What holds theß-strands together in the ß-sheet?

A

Multiple interstrand H-bonds stabilise the structure

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38
Q

How does a parallel ß-sheet differ from an antiparallel one?

A

The H bonds are at more of an angle

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39
Q

What can secondary structures contain?

A

Both α-helixes and ß-strands

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40
Q

What is the tertiary structure?

A

The spatial arrangement of amino acids far apart in the protein sequence

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41
Q

What are the two main types of proteins?

A
  • Globular

- Fibrous

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42
Q

What is the role of fibrous proteins?

A

NAME?

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43
Q

What is the structure of fibrous proteins?

A

Long strands or sheets

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44
Q

What kind of secondary structure do fibrous proteins have?

A

Single type of repeating secondary structure

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45
Q

Give an example of a fibrous protein?

A

Collagen

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46
Q

How are collagen chains arranged?

A

In a triple helical arrangement

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47
Q

Why are collagen molecules not α-helixes?

A

Because the strands are elongated collagen α-chains that form a helical structure, not one amino acid chain forming helical structure

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48
Q

What is the primary structure of collagen molecules?

A

Gly-X-Y repeating sequence

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49
Q

What stabilises interactions between collagen chains?

A

Hydrogen bonds

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50
Q

What happens to collagen in extracellular form?

A

The molecules line up together, forming collagen fibrils from covalently cross linked collagen molecules

51
Q

What is collagen important for?

A

Structural stability in skin, bones and tendons

52
Q

What is the role of globular proteins?

A
  • Catalysis

- Regulation

53
Q

What kind of shape do globular proteins have?

A

Compact

54
Q

Do all globular proteins have the same type of secondary structure?

A

No, variety of types

55
Q

What features do globular proteins’ tertiary structure have?

A
  • Motifs

- Domains

56
Q

What are motifs?

A

Folding patterns containing 1 or more elements of secondary structure

57
Q

Give two examples of motifs

A
  • ß-α-ß loop

- ß-barrel

58
Q

What are domains?

A

Part of a polypeptide chain that folds into a distinct shape

59
Q

What do domains often have?

A

A specific functional role

60
Q

What may a single protein have?

A

Lots of different domains

61
Q

What do domains define?

A

The function of a protein

62
Q

What tends to happen when different proteins have the same domain?

A

They do the same thing

63
Q

How do water soluble proteins fold?

A

Fold so that hydrophobic side chains are buried, and polar and charged amino acids are on the surface

64
Q

Why do water soluble fold in the way they do?

A

Because don’t want hydrophobic amino acids exposed to water

65
Q

What is the folding of water soluble proteins an example of?

A

The characteristics of amino acids driving the 3D structure of protein

66
Q

What do membrane proteins often show?

A

‘Inside out’ distribution of amino acids

67
Q

Why is there an ‘inside out’ distribution of amino acids?

A

So hydrophobic amino acids can interact with the hydrophobic tails of phospholipids, and the hydrophilic exterior can form a water filled channel

68
Q

What happens in quaternary structure?

A

Individually folded polypeptide chains interact with other polypeptide chains

69
Q

What forces maintain primary structure?

A

Covalent

70
Q

What forces maintain secondary structure?

A

H-bond

71
Q

What forces maintain tertiary structure?

A

NAME?

72
Q

What forces maintain quaternary structure?

A

NAME?

73
Q

Where are disulphide bonds formed?

A

Between Cys residues

74
Q

What is being bought together in disulphide bonds?

A

Sulfhydryl groups

75
Q

What kind of reaction is the formation of disulphide bonds?

A

Oxidation

76
Q

Why is the formation of disulphide bonds an oxidation reaction?

A

Because you loose H’s

77
Q

How can disulphide bonds be broken?

A

Using reducing agents

78
Q

What is the fate of most proteins containing disulphide bonds?

A

Secretion

79
Q

Why do secreted proteins need disulphide bonds?

A

They need to be strong, as the environment can’t be controlled

80
Q

What do secreted proteins need to be able to withstand?

A

Differences in pH, osmotic potential and concentration of various metabolites

81
Q

Where are electrostatic interactions formed?

A

Between charged groups

82
Q

Where are hydrogen bonds formed?

A

Between electronegative atom and a hydrogen bound to another electronegative atom

83
Q

Are hydrophobic interactions bonds?

A

Not as such

84
Q

Where does the hydrophobic effect occur?

A

Between hydrophobic side chains

85
Q

What is the hydrophobic effect due to?

A

Displacement of water

86
Q

How is water excluded from hydrophobic residues?

A

They pack together

87
Q

Why is the exclusion of water from hydrophobic residues thermodynamically favourable?

A

Because if water is excluded, the entropy increases

88
Q

What are van der Waals forces?

A

Dipole-dipole interactions

89
Q

Where are van der Waals forces very important?

A
  • In large proteins

- When surface of two large molecules come together

90
Q

Are proteins stable?

A

Not very

91
Q

What is disruption of protein structure known as?

A

Denaturation

92
Q

What is the denaturation of proteins due to?

A

Breaking forces that hold proteins together

93
Q

Can denaturation break proteins down into individual amino acids?

A

No

94
Q

What happens once a protein has been denatured?

A

It cannot do what it typically does in its native shpae

95
Q

What factors can cause denaturing of proteins?

A

NAME?

96
Q

Why can heat denature proteins?

A

Because of the increased vibrational energy

97
Q

Why can pH denature proteins?

A

Because it alters the ionisation states of amino acids

98
Q

How does pH alter the ionisation states of amino acids?

A

It changes the [H + ], which changes interactions between charged molecules.

99
Q

What happens to originally deprotonated groups when the pH changes?

A

They become protonated

100
Q

What bonds are affected by changes in pH?

A

NAME?

101
Q

Why can detergents/organic solvents cause denaturation?

A

Disrupt hydrophobic interactions

102
Q

Where is the information proteins require to fold?

A

In the primary structure

103
Q

Is protein folding a random process?

A

No

104
Q

How does protein folding proceed?

A

Through local folding

105
Q

What do some proteins need to assist in folding?

A

Chaperones

106
Q

What is the purpose of chaperones?

A

To stop a protein misfolding

107
Q

How do chaperones work?

A

Hold on to a protein as its folding

108
Q

What can protein misfolding cause?

A

Disease

109
Q

What diseases are caused by protein misfolding?

A

Transmissible spongiform encephalopathies

110
Q

Give 3 examples of transmissible spongiform encephalopathies

A

NAME?

111
Q

What has happened in transmissible spongiform encephalopathies?

A

Altered confirmation of normal human protein promotes the conversion of existing proteins to the diseased state

112
Q

What are amyloidoses?

A

Clusters of misfolded proteins that come together

113
Q

Give an example of a disease caused by misfolded proteins?

A

Alzheimers

114
Q

How do misfolded proteins cause Alzheimers?

A

The proteins form plaques, which cause lesions in neuronal cells

115
Q

What are amyloid fibres?

A

Misfolded, insoluble forms of a normally soluble protein

116
Q

What is the problem with amyloid fibres?

A

They are highly ordered, so once formed, they are not broken down

117
Q

What do amyloid fibres have a high degree of?

A

ß-sheet

118
Q

Why are amyloid fibres so stable?

A

Because they have one sheet on top of another with lots of hydrophobic side chains between sheets

119
Q

What part of the amyloid fibre forms first?

A

The core ß-sheet

120
Q

Do amyloid fibres form quickly or slowly?

A

Slowly

121
Q

What is the result of the slow formation of the amyloid fibres?

A

The diseases are usually late onset

122
Q

How do amyloid fibres usually develop?

A

Starts with 1 misfolded molecule, which triggers the formation of more, which accumulate

123
Q

How is the interchain assembly of amyloid fibres stabilised?

A

By hydrophobic interactions between aromatic amino acids

Z OLD Molecules, Genes and Disease (14 decks)

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