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Flashcards in Protein Structure. Deck (139):
1

How many levels of structure are there to a protein?

There are 4 levels of protein structure.

However, most proteins only use 3 levels of protein structure.

2

What is the primary structure of a protein?

It is the sequence of amino acids that make up the polypeptide.

3

How are the amino acids attached to each other within the polypeptide?

By peptide bonds.

4

What is the secondary structure of a protein.

It is the localised 3D arrangement of a polypeptide within space.

5

What is the tertiary structure?

It is how the secondary structure can be manipulated to give a certain structure.

6

What is the tertiary structure also known as?

The native structure.

7

Why is the tertiary structure also known as the native structure?

Because this is the shape that the protein takes up inside the cell.

8

What is the quaternary structure of a protein?

It is the shape that is taken up when multiple tertiary structures come together.

9

Why is the primary structure of proteins so important?

Because, if 1 wrong amino acid is inserted into the primary structure, it can lead to an alteration in the overall protein structure.

10

What is a point mutation?

When 1 wrong amino acid is inserted into the primary structure.

Sickle cell disease arises from point mutations.

11

Give an example of the primary structure of a protein?

Val-Arg-Leu.

12

The primary structure has how many amino groups and how many carboxyl groups?

1 amino group.

1 carboxyl group.

13

Which amino acid can form disulphide bonds?

Cysteine.

14

When 2 cysteine molecules form a disulphide bridge, what is the resulting molecule called?

Cystine.

15

Will disulphide bridges be formed between cysteine molecules within the same polypeptide or can they be formed between cysteine molecules within different polypeptides?

Disulphide bridges can be formed between cysteine molecules on the same polypeptide.

Disulphide bridges can be formed between cysteine molecules on different polypeptides.

16

When a bond is formed between molecules within the same polypeptide, what is the bond referred to as?

An intramolecular bond.

17

When a bond is formed between molecules within different polypeptides, what is the bond referred to as?

An intermolecular bond.

18

Can a protein have both inter and intra molecular bonds?

Yes, insulin is made up of 2 polypeptides and has 3 disulphide bonds.

2 intermolecular and 1 intramolecular.

19

Are peptide bonds covalent or non-covalent bonds?

They are covalent bonds.

20

What kind of reaction leads to the formation of a peptide bond?

A dehydration or condensation reaction.

21

What is the name for 2 amino acids joined by a peptide bond?

A dipeptide.

22

What is a polypeptide?

A polypeptide is made up of many monomers which are the individual amino acid residues.

23

If the amino acids valine, glycine and alanine are joined together, what is the name of the molecule?

Valyl-glycyl-leucine.

24

How do you name amino acids in a dipeptide?

The name of the amino acid at the amino terminus is altered, adding the suffix yl to where the ine was.

E.g. valyl instead of valine.

The carboxyl terminus remains unaltered.

If valine and alanine join together, the molecule will be called valylanaline.

25

How do you name amino acids in a polypeptide?

The middle amino acids will also adopt the yl suffix,

e.g. valine, alanine and leucine will become valylleucylalanine.

26

Are peptide bonds strong or weak?

Peptide bonds are very strong.

27

What is required to break a peptide bond?

Acid and heat.

28

Can rotation occur around a peptide bond?

No.

29

Why is there no rotation around the peptide bond?

Because the bond has double bond characteristics.

30

Why does a peptide bond have double bond characteristics?

Because of a resonance of electrons between the double bond to oxygen and the nitrogen.

31

Describe the resonance of electrons in a peptide bond?

At any point in time the double bond could be between the carbon and the oxygen.

Or between the carbon and the nitrogen resulting in a positive charge on the N and a negative charge on the O.

32

Do peptide bonds have a net charge?

No.

But, they do have a partial charge.

33

Describe the partial charge on a peptide bond?

The partial charge arises due to the slight positive charge on the nitrogen and the slight negative charge on the oxygen.

34

Can peptide bonds be involved in non covalent interactions.

Yes, thanks to their partial charge.

35

Which components of a polypeptide are able to rotate?

The R groups and the ketone.

36

Are the R groups within a polypeptide able to take up a cis or trans position?

They can take up both.

37

In what conformation do polypeptides prefer to have their R groups?

In the trans conformation.

38

Why do polypeptides prefer to have their R groups in the trans conformation?

So they can minimise steric hindrance and electrostatic repulsion between R groups.

39

What are the 3 ways to determine the amino acid composition of an unknown protein?

Acid hydrolysis.

Amino acid sequencing from the amino terminus.

DNA sequencing.

40

How does the acid hydrolysis method of determining protein structure work?

The unknown polypeptide is subjected to concentrated acid at a heat of 100 degrees C for 24 hours.

This will break the peptide bonds within the polypeptide. and the remaining amino acids can be analysed.

41

Which amino acids are destroyed by the acid hydrolysis technique?

Glutamine.

Glutamate.

Asparagine.

Aspartate.

Tryptophan.

42

Do the amino acids that remain after acid hydrolysis carry a charge?

Yes.

They carry a positive charge.

43

How are the positively charged amino acids separated after acid hydrolysis has occurred?

By cation exchange chromatography.

44

How does cation exchange chromatography work?

The positive amino acids are placed in an ion exchange column.

The pH is slowly changed allowing amino acids to be released from the ion exchange column.

As amino acids are released, they react with ninhydrin and a colour change occurs which is recorded by a photometer.

The photometer will tell you the amino acid composition.

45

Will acid hydrolysis tell you the exact order of amino acids within the polypeptide?

No.

It only tells you the amino acid composition, not the order.

46

How does amino acid sequencing work?

It involves using Edmans reagent under alkaline conditions to label and break off the amino terminus.

This single amino acid can then be analysed and identified.

The 2nd amino acid in the chain will now become the new amino terminus.

47

What is Edmans reagent also known as?

(Phenylisothiocyanate).

48

Where does amino acid sequencing take place?

In a sequenator.

49

Does amino acid sequencing give you the exact amino acid sequence?

Yes.

50

How many amino acids within a polypeptide does amino acid sequencing work for?

100 or fewer.

51

How does DNA sequencing of amino acids work?

If you know the DNA sequence, then you can work out the gene that encodes for the polypeptide.

52

What is the secondary structure of a protein?

The localised 3D shape that segments of the polypeptide takes up within space.

53

What is the most common type of bond within the secondary structure?

Hydrogen bonds.

54

How do hydrogen bonds occur?

When a hydrogen has a slight positive charge due to being bound to a more electronegative atom.

The slightly positive hydrogen is capable of forming a weak non-covalent bond with an oxygen atom due to the slight difference in charge.

55

Are hydrogen bonds covalent or non-covalent?

Non-covalent.

56

Hydrogen bonds allow the secondary structure to do what?

To keep their primary structure and shape.

57

What are 2 types of secondary structure?

Alpha helix.

Beta pleated sheet.

58

An alpha helix structure looks like what?

A spiral staircase.

59

Do alpha helix structures spiralise to the left or the right?

They can spiralise in both directions.

60

How does hydrogen bonding work in an alpha helix structure?

Every peptide bond within the polypeptide forms a hydrogen bond with another peptide bond that is 4 residues away.

61

Which atoms within the peptide bonds bind together?

The O on the carbonyl group of one bond will hydrogen bond with an H-N on the amino group of bond.

62

Are hydrogen bonds covalent or non covalent bonds?

Non covalent.

63

Are hydrogen bonds weak or strong?

Weak.

64

How can weak hydrogen bonds keep an alpha helix structure together?

Lone hydrogen bonds are very weak.

Many hydrogen bonds together are strong.

65

If the hydrogen bonds in an alpha helix structure fail, what will happen?

The structure will collapse and revert back to a primary structure.

66

What happens to the R groups of amino acids within an alpha helix?

The R groups stick out of alpha helix structure.

67

If the R groups that stick out from an amino acid are polar, will the structure be water soluble or insoluble?

If the R groups are polar, then the amino acid will be soluble in water.

68

What 2 amino acids will disrupt an alpha helix structure?

Proline.

Glycine.

69

Why will proline or glycine break the alpha helix structure?

Because glycine cannot form hydrogen bonds.

Proline is too bulky.

70

Can an alpha helix structure contain many charged amino acids?

No.

Because the similar or unlike charges will repel or attract each other if they are close by.

71

Are amino acids with bulky R groups likely to be found in an alpha helix structure?

Some can fit in, but too many will break the alpha helix.

72

What is the basis for a beta structure?

Beta structures occur when the polypeptide is stretched out and bonds form between at least 2 polypeptide segments.

73

Can a beta sheet be formed with 1 polypeptide segment?

No.

You need at least 2 polypeptide segments to form a beta sheet.

74

Can a beta sheet be formed from 1 polypeptide?

Yes.

A beta sheet can be formed by aligning 2 polypeptide segments from the same polypeptide.

75

Can a beta sheet be formed from different polypeptides?

Yes.

If 2 polypeptides are arranged correctly, they can form a beta sheet.

76

What usually represents a beta sheet in a drawing of a polypeptide?

An arrow.

77

How does an arrow represent a beta sheet?

The tail represents the amino terminus and the head represents the carboxyl terminus.

Each undulation represents one of the pleats.

78

What are the 2 forms that a beta sheet can exist in?

The arrows can be arranged pointing in the same direction or in opposite directions.

Therefore all of the carboxyl groups can be at the same end or they can be alternating with the amino groups.

79

If all the carboxyl ends of a beta sheet are at the same end, what is the name of the sheet?

If the arrows all go in the same direction then it is a parallel pleated sheet.

80

If the carboxyl and amino ends alternate on a beta sheet, what is the name of the sheet?

If the arrows go in different directions, then it is an antiparallel pleated sheet.

81

What bonds hold a beta sheet together?

Hydrogen bonds.

82

Where are the hydrogen bonds within a beta sheet formed?

Every peptide bond forms a hydrogen bond to the peptide bond that is closest to it.

83

How many amino acids make up a beta bend?

4 amino acids.

84

What amino acids are always in a beta bend?

Proline or a glycine.

85

Beta bends often contain charged or uncharged amino acids?

Charged amino acids.

86

What kind of bonds stabilise a beta bend?

Hydrogen and ionic bonds.

87

What is the job of a beta bend?

They will reverse the direction of the polypeptide.

88

Are beta bends found in antiparallel or parallel sheets?

Both.

89

Give an example of some supersecondary structures?

Beta barrels or a twisted beta sheet.

90

What is a random coil chain structure?

There is no way to define the pattern and it is said to be random.

91

Are tertiary protein structures spontaneous?

Yes.

The objective is to create the most stable structure.

92

The most stable structures usually maximise what, within the polypeptide?

The non covalent interactions.

93

If the tertiary structure is a proteins final structure, what is the structure also known as?

Its native structure.

94

How is the tertiary structure formed?

By folding the secondary structure into a 3D shape.

95

Globular proteins are usually what shape?

Spherical.

96

Is there a particular secondary structure that is found in globular proteins?

No.

There can be a variety of secondary structures within globular proteins.

97

What kind of amino acids usually make up the exterior of globular proteins?

Polar amino acids as globular proteins are hydrophyllic.

98

What kind of amino acids usually make up the interior of globular proteins?

Non polar amino acids.

99

Do globular proteins usually have a function?

Yes.

They are often transport proteins or enzymes.

100

What shape are fibrous proteins?

Long thin rods.

101

Are fibrous proteins usually soluble in water?

No.

102

Are fibrous proteins made up of a variety of secondary structures?

No.

They usually have 1 dominant secondary structure.

103

What are fibrous proteins usually used for?

Structural components of cells such as collagen and keratin.

104

What are the 4 types of bonds that stabilise the tertiary structure?

Hydrogen bonds.

Disulphide bonds.

Hydrophobic Interactions.

Electrostatic interactions (ionic and polar interactions).

105

What are the 4 types of hydrogen bonds that can be formed within a tertiary structure?

N-H~~~N-.

-N-H~~~O-.

-O-H~~~N-.

-O-H~~~O-.

106

Are hydrogen bonds covalent or non covalent?

Non covalent.

107

Hydrogen bonds are usually formed between the R groups of which amino acids?

Polar amino acids.

108

How do hydrogen bonds form?

When a slightly positive hydrogen forms a weak electrostatic interaction with a slightly negative atom e.g. oxygen or nitrogen.

109

Which R groups can form H bonds with water?

Serine and glutamine.

110

How do disulphide bridges form?

Between 2 cysteine molecules.

Each cysteine loses a hydrogen and the 2 sulphurs form a bond.

111

What is a cystine molecule?

It is formed when 2 cysteine molecules form a disulphide bridge.

112

Are disulphide bridges covalent or non covalent interactions?

Covalent.

So they are strong bonds.

113

Do the 2 cysteine residues need to be very close to form a disulphide bridge?

No.

They can be very close or far apart.

114

Are disulphide bridges inter or intra molecular bonds?

Both.

115

Disulphide bridges can be broken down by what?

Reducing agents.

116

Hydrophobic interactions involve what kind of amino acids?

Non polar amino acids.

117

How do hydrophobic interactions occur?

When polar molecules surround non polar molecules and force the non polar molecules together.

The non polar molecules form hydrophobic interactions.

118

Hydrophobic interactions usually occur in what area of a protein?

In the interior of a protein.

119

Electrostatic interactions occur between which R groups?

Between R groups with opposite charges.

120

What are electrostatic interactions also referred to as?

Salt bridges.

Ionic interactions.

121

What is a domain?

A small pocket that folds independently within a globular protein.

122

Domains are often found within what kind of protein?

A globular protein.

123

Domains are made up of how many amino acids?

At least 200.

124

What are the characteristics of a domain?

Each domain has the characteristics of a small compact globular protein.

Therefore, each one has its own specialised function.

125

What allows amino acids from different parts of the polypeptide to form bonds with each other?

Protein folding.

126

What kind of proteins help the tertiary structure to fold correctly?

Chaperone proteins.

127

What is the denaturation of a protein?

The destruction of a protein until all that is left is its primary structure.

128

Why does denaturation destroy a protein?

Because all the bonds except the peptide bonds are destroyed.

129

Give some examples of denaturing agents?

Heat.

Heavy metals.

Detergents.

130

Is denaturation always permanent?

Sometimes denaturation can be reversed.

131

Will any of the protein remain after denaturation has occurred?

Yes.

The primary structure will remain.

132

What 2 ways can cause a protein to be misfolded?

Either spontaneously or via a genetic mutation.

133

The proteolytic cleavage of the amyloid beta protein is associated with what disease?

Alzheimers disease.

134

How are amyloid plaques formed?

The amyloid protein is part of the cell membrane and extends into the extracellular matrix.

Sometimes the part that sticks out is cut off from.

Once removed, the extracellular potion will start to form plaques.

135

What is the quaternary structure of a protein?

When at least 2 polypeptides in their native state come together to form the final, functional protein.

136

Do the polypeptides that form the quaternary structure have to be identical?

No.

They can be the same or they can be different.

137

The polypeptides that make up a quaternary structure can also be referred to as what?

Subunits.

138

What type of bonds hold the quaternary structure together?

Non covalent-bonds.

139

What kind of non-covalent bonds hold the quaternary structure together?

Hydrogen bonds.

Electrostatic interactions, (ionic bonds).

Van Der Waals forces.