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Biochemistry > Protein structures > Flashcards

Protein structures Flashcards

1
Q

Functions of proteins (9)

A

Structured mechanics
Enzymes
Hormones
Signalling molecules
Antibodies
Fluid balance
Acid-base balance
Channels and pumps
Transport function

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2
Q

What is the definition of secondary structure?

A

Regular repeating interactions between amino acids that are close in primary sequence
Alpha-helix
Beta-pleated sheet

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3
Q

Are there proteins that contain only secondary structure?

A

Yes

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4
Q

Example of protein that only have secondary structure

A

Collagen

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5
Q

Definition of tertiary structure

A

Amino acids interaction that are far from each other in the cell
Globular and fibrous structures

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6
Q

Definition of quaternary structure

A

Interaction between two different sub units

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7
Q

Can you have both alpha-helix and beta-pleated sheet in the same protein structure?

A

Yes, complex protein typically have both

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8
Q

Can proline exist in the cis-configuration in peptides?

A

Yes

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9
Q

What is the rotation around the N-C bond called?

A

Phi

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10
Q

What is the rotation around the C-C’ bond called?

A

Psi

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11
Q

Why is rotation limited? and only few angles allowed when the amino acid is stable

A

The R groups. If they rotate more the two R groups will interact

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12
Q

What does the blank space on the Ramachan plot represent?

A

The angles where the amino acid isn’t stable

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13
Q

Does protein structure influence it’s function?

A

Yes very much so

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14
Q

What is the secondary structure due to? (1 type of bonding and 1 type of forces)

A

Hydrogen bonding and Van der Waals forces

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15
Q

What happens if you disrupt the structure of the protein?

A

It becomes inactive, denatured

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16
Q

Are the van der Waals attractions attractive or repulsive?

A

Both

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17
Q

What is residues/turn?

A

Same as amino acids per turn

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18
Q

Do aa/turn change in an alpha helix depending on the R group?

A

No, almost always 3.6 aa/turn

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19
Q

What model is used to study secondary structures?

A

Ribbon model

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20
Q

Which way does the R group point in the alpha- helix? inwards or outwards

A

Outwards

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21
Q

Are there more interactions between amino acids in the alpha helix or the beta pleated sheets

A

Not a big difference, if anything then more in the beta structures because multiple sheets can be close and cause additional interactions

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22
Q

Are the amino acids in beta-pleated sheets typically parallel or anti parallel?

A

Anti parallel, but can be both
It’s more stable typically

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23
Q

What decides wether it’s parallel or anti parallel? (beta-pleated sheets)

A

The space available

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24
Q

What makes the parallel beta pleated sheets less stable?

A

Longer hydrogen bonds and R groups close together

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25
Q

What does stable mean energetically?

A

Favourable

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26
Q

Does space have an influence on stability?

A

Yes, the less space the less stable
If there eis not enough space for a group they interact

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27
Q

Why is antiparallel more stable? (beta-pleated sheets)

A

Bonds are stronger, more aligned

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28
Q

Are proteins assembled random?

A

No very orderly way because of the beta sheets and alpha helix

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29
Q

Which kind of alpha helix is most stable, right handed or left handed?

A

Right handed

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30
Q

Are the R groups closer in alpha helix or beta pleated?

A

Beta pleated sheet

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31
Q

What gives silk it’s peculiar propert?

A

The long anti parallel beta sheets with simple amino acids

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32
Q

How many amino acids are involved in forming the beta-turn/hairpin loop?

A

4, typically small/simple amino acids

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33
Q

How many structures do proteins form?

A

Only 1 each

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34
Q

Which amino acids allow for beta turns?

A

Proline and glycine, other simple aa

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35
Q

What are random coils?

A

Longer connections between alpha helix and beta sheets

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36
Q

What are short connecting points called? 2 kinds

A

Loops and beta-turn

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37
Q

What are the longer connections called?

A

Random coil

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38
Q

What are ribbons diagrams useful for?

A

Studying interactions and protein structure

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39
Q

What differes in the insulin from humans and pigs? structure or amino acids?

A

Amino acids

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40
Q

Where does the arrow go when drawing beta pleated sheets

A

N->C

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41
Q

3 ways to classify proteins

A

Structure, composition and functions

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42
Q

3 structures of proteins

A

Fibrous
Globular
Intermediate

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43
Q

2 compositions of proteins

A

Simple
Conjugated

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44
Q

3 functions of proteins

A

Structural (enzymes and hormones)
Pigments, transport, contractile
Storage, toxins

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45
Q

How is collagen classified? (structure)

A

Fibrous

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46
Q

What do fibrous protein look like?

A

Long intertwined alpha helix

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47
Q

What can rigidt proteins function as?

A

Structural elements in cytoskeleton or connective tissue

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48
Q

What are flexible proteins important for?

A

They can change formations when for example binding to oxygen (haemoglobin)
The ability to respond with a conformational change

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49
Q

What does globular protein consist of?

A

Coiled and folded polypeptide chains forming spherical shape

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50
Q

Are fibrous proteins soluble in water?

A

No insoluable

51
Q

Are globular proteins soluble in water?

A

Yes

52
Q

Example of globular proteins

A

Enzymes and haemoglobin

53
Q

Different name for fibrous protein

A

Scleroprotein

54
Q

What is alpha keratin made up of?

A

Long alpha helix coiled together

55
Q

Is kreatin able to go back to it’s own structure after being denatured (by heat)?

A

Yes

56
Q

Is collagen a rigid structure?

A

Yes

57
Q

Which is the only amino acid where the R groups form a bond with the amino group?

A

Proline

58
Q

What is hydroxyproline?

A

AA Proline with a hydroxyl group

59
Q

What happens when your collagen lacks hydroxyproline?

A

Your collagen is weak

60
Q

What can a vitamin C deficiency lead to?

A

Weak collagen (lack of hydroxyproline) -> scurvy

61
Q

How many types of collagen?

A

3

62
Q

Where is collagen 1 found?

A

Skin
Bones
Capsule of organs
Tendons
Cornea
Fascia

63
Q

Where is collagen II found?

A

Elastic cartilage

64
Q

Where is collagen III found?

A

Skin
Lungs
Intestinal walls
Walls of blood vessels

65
Q

What is the dynamic structure of elastin called?

A

Beta spiral (loose held together by hydrophobic forces)

66
Q

What is the overall shape which makes the polypeptide chain functional?

A

Tertiary structure

67
Q

What interactions are in tertiary structures? (4)

A

Hydrophobic interactions
Disulphide bridges
Ionic bonds
Hydrogen bonds

68
Q

What kind of reaction forms disulphide bonds?

A

Oxidation

69
Q

How many disulphide bonds in insulin makes the protein stable?

A

3

70
Q

What does the hydrophobic effect help determine?

A

Protein structure

71
Q

What is a protein domain?

A

Region of the protein’s polypeptide chain that is self-stabalizing and that fold independently from the rest
Repetitive structure that can allow the protein to move

72
Q

Can a single protein have different domain?

A

Yes

73
Q

What is a dimeric protein?

A

Has two different chains, subunits

74
Q

Does a mutation always effect the structure of protein?

A

No depends on the location of the amino acid replaced

75
Q

What determines the folding and function of proteins?

A

Tertiary structure

76
Q

What dictates the characteristics of a protein?

A

Th linear amino acid sequence (primary structure)

77
Q

What kind of hindrance do we have in cis form amino acids?

A

Teric hindrance

78
Q

Which isomers are more stable?

A

Trans

79
Q

Are all rotations allowed?

A

No

80
Q

Which structure determines how proteins fold and interacts with other molecules?

A

Primary structure

81
Q

What creates the secondary structure?

A

Regular repeating interactions between amino acids that are close in primary sequence

82
Q

What bonds create the alpha helixes and beta sheets?

A

Hydrogen bonds
Van der Waals forces

83
Q

Between what does hydrogen bonds mainly occur?

A

H and O

84
Q

Which bonding plays a big role in stabilising secondary structures?

A

Hydrogen bonding

85
Q

Which Van der Walls control protein folding, repulsive or attractive?

A

Both

86
Q

Van der Waals force are very weak, how do they are they still so significant?

A

Because there are so many of them

87
Q

Can both parallel or anti-parallel beta sheets exist within the same protein?

A

Yes

88
Q

What differentiates parallel and antiparallel beta sheets?

A

Different hydrogen bonding patterns

89
Q

Where are random coil typically present?

A

At the end of the protein or in the middle of 2 alpha helices or beta structures

90
Q

Are random coils conserved?

A

They can be but wast majority are not

91
Q

What are loops?

A

Unstructured regions found between regular secondary structure elements

92
Q

3 ways to classify proteins based on?

A

Structure
Composition
Function

93
Q

What structure are fibrous proteins made by?

A

Secondary structure

94
Q

What does fibrous protein consist of?

A

Long and parallel polypeptide chains forming helical structures or pleated sheets

95
Q

What does globular protein consist of?

A

Coiled and folded polypeptide chains forming spherical shape

96
Q

Are fibrous protein soluble in water?

A

No, insoluble

97
Q

Are globular protein soluble in water?

A

Yes

98
Q

Is the structure of fibrous protein stable or unstable?

A

Stable

99
Q

Is the structure of globular protein stable or unstable?

A

Unstable

100
Q

What does fibrous proteins play a big role in?

A

Mechanical and structural functions

101
Q

What does globular proteins play a big role in?

A

Metabolite and chemical processes

102
Q

2 examples of fibrous protein

A

Kreatin and collagen

103
Q

2 examples of globular protein

A

Enzymes and haemoglobin

104
Q

Are fibrous proteins strong or weak?

A

Strong

105
Q

What is the characteristics of alpha helix?

A

Protective structures

106
Q

What is the characteristics of beta sheets?

A

Soft and flexible filaments

107
Q

What are fibrous proteins made up of?

A

elongated polypeptide chains of regular amino acid sequences that run parallel to one another

108
Q

In what type of amino acids are there typically found many alpha helixes?

A

Hydrophobic amino acids

109
Q

How much of the protein in your body is collagen?

A

About one quarter

110
Q
A
111
Q

Which is the only amino acid where the R group makes a bond with the amino group?

A

Proline

111
Q

What does proline form when modified?

A

Hydroxylproline

112
Q

What makes proline special?

A

The R group makes bond with the amino grojp

113
Q

What does vitamin C deficiency do?

A

Slows the production of hydroxyproline and stops the construction of new collagen

114
Q

What causes scurvey?

A

Vitamin C deficiency

115
Q

Different name for vitamin C

A

Ascorbate

116
Q

What is elastin?

A

Insoluble polymer which is rich in glycine. lysine and are hydroxyproline

117
Q

What does elastin form when interacting with other proteins?

A

Reticulates

118
Q

What kind of protein is elastin?

A

Fibrous (but very elastic)

119
Q

What kind of protein is collagen?

A

Fibrous

120
Q

How do membrane proteins fold in comparison to soluabl proteins?

A

Opposite way

121
Q

What is the most important driving force for protein folding and assembly?

A

The hydrophobic effect

122
Q

Can 2 different proteins have the same domain?

A

Yes

Biochemistry (28 decks)

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