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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
What does stable mean energetically?
Favourable
26
Does space have an influence on stability?
Yes, the less space the less stable If there eis not enough space for a group they interact
27
Why is antiparallel more stable? (beta-pleated sheets)
Bonds are stronger, more aligned
28
Are proteins assembled random?
No very orderly way because of the beta sheets and alpha helix
29
Which kind of alpha helix is most stable, right handed or left handed?
Right handed
30
Are the R groups closer in alpha helix or beta pleated?
Beta pleated sheet
31
What gives silk it's peculiar propert?
The long anti parallel beta sheets with simple amino acids
32
How many amino acids are involved in forming the beta-turn/hairpin loop?
4, typically small/simple amino acids
33
How many structures do proteins form?
Only 1 each
34
Which amino acids allow for beta turns?
Proline and glycine, other simple aa
35
What are random coils?
Longer connections between alpha helix and beta sheets
36
What are short connecting points called? 2 kinds
Loops and beta-turn
37
What are the longer connections called?
Random coil
38
What are ribbons diagrams useful for?
Studying interactions and protein structure
39
What differes in the insulin from humans and pigs? structure or amino acids?
Amino acids
40
Where does the arrow go when drawing beta pleated sheets
N->C
41
3 ways to classify proteins
Structure, composition and functions
42
3 structures of proteins
Fibrous Globular Intermediate
43
2 compositions of proteins
Simple Conjugated
44
3 functions of proteins
Structural (enzymes and hormones) Pigments, transport, contractile Storage, toxins
45
How is collagen classified? (structure)
Fibrous
46
What do fibrous protein look like?
Long intertwined alpha helix
47
What can rigidt proteins function as?
Structural elements in cytoskeleton or connective tissue
48
What are flexible proteins important for?
They can change formations when for example binding to oxygen (haemoglobin) The ability to respond with a conformational change
49
What does globular protein consist of?
Coiled and folded polypeptide chains forming spherical shape
50
Are fibrous proteins soluble in water?
No insoluable
51
Are globular proteins soluble in water?
Yes
52
Example of globular proteins
Enzymes and haemoglobin
53
Different name for fibrous protein
Scleroprotein
54
What is alpha keratin made up of?
Long alpha helix coiled together
55
Is kreatin able to go back to it's own structure after being denatured (by heat)?
Yes
56
Is collagen a rigid structure?
Yes
57
Which is the only amino acid where the R groups form a bond with the amino group?
Proline
58
What is hydroxyproline?
AA Proline with a hydroxyl group
59
What happens when your collagen lacks hydroxyproline?
Your collagen is weak
60
What can a vitamin C deficiency lead to?
Weak collagen (lack of hydroxyproline) -> scurvy
61
How many types of collagen?
3
62
Where is collagen 1 found?
Skin Bones Capsule of organs Tendons Cornea Fascia
63
Where is collagen II found?
Elastic cartilage
64
Where is collagen III found?
Skin Lungs Intestinal walls Walls of blood vessels
65
What is the dynamic structure of elastin called?
Beta spiral (loose held together by hydrophobic forces)
66
What is the overall shape which makes the polypeptide chain functional?
Tertiary structure
67
What interactions are in tertiary structures? (4)
Hydrophobic interactions Disulphide bridges Ionic bonds Hydrogen bonds
68
What kind of reaction forms disulphide bonds?
Oxidation
69
How many disulphide bonds in insulin makes the protein stable?
3
70
What does the hydrophobic effect help determine?
Protein structure
71
What is a protein domain?
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
Can a single protein have different domain?
Yes
73
What is a dimeric protein?
Has two different chains, subunits
74
Does a mutation always effect the structure of protein?
No depends on the location of the amino acid replaced
75
What determines the folding and function of proteins?
Tertiary structure
76
What dictates the characteristics of a protein?
Th linear amino acid sequence (primary structure)
77
What kind of hindrance do we have in cis form amino acids?
Teric hindrance
78
Which isomers are more stable?
Trans
79
Are all rotations allowed?
No
80
Which structure determines how proteins fold and interacts with other molecules?
Primary structure
81
What creates the secondary structure?
Regular repeating interactions between amino acids that are close in primary sequence
82
What bonds create the alpha helixes and beta sheets?
Hydrogen bonds Van der Waals forces
83
Between what does hydrogen bonds mainly occur?
H and O
84
Which bonding plays a big role in stabilising secondary structures?
Hydrogen bonding
85
Which Van der Walls control protein folding, repulsive or attractive?
Both
86
Van der Waals force are very weak, how do they are they still so significant?
Because there are so many of them
87
Can both parallel or anti-parallel beta sheets exist within the same protein?
Yes
88
What differentiates parallel and antiparallel beta sheets?
Different hydrogen bonding patterns
89
Where are random coil typically present?
At the end of the protein or in the middle of 2 alpha helices or beta structures
90
Are random coils conserved?
They can be but wast majority are not
91
What are loops?
Unstructured regions found between regular secondary structure elements
92
3 ways to classify proteins based on?
Structure Composition Function
93
What structure are fibrous proteins made by?
Secondary structure
94
What does fibrous protein consist of?
Long and parallel polypeptide chains forming helical structures or pleated sheets
95
What does globular protein consist of?
Coiled and folded polypeptide chains forming spherical shape
96
Are fibrous protein soluble in water?
No, insoluble
97
Are globular protein soluble in water?
Yes
98
Is the structure of fibrous protein stable or unstable?
Stable
99
Is the structure of globular protein stable or unstable?
Unstable
100
What does fibrous proteins play a big role in?
Mechanical and structural functions
101
What does globular proteins play a big role in?
Metabolite and chemical processes
102
2 examples of fibrous protein
Kreatin and collagen
103
2 examples of globular protein
Enzymes and haemoglobin
104
Are fibrous proteins strong or weak?
Strong
105
What is the characteristics of alpha helix?
Protective structures
106
What is the characteristics of beta sheets?
Soft and flexible filaments
107
What are fibrous proteins made up of?
elongated polypeptide chains of regular amino acid sequences that run parallel to one another
108
In what type of amino acids are there typically found many alpha helixes?
Hydrophobic amino acids
109
How much of the protein in your body is collagen?
About one quarter
110
111
Which is the only amino acid where the R group makes a bond with the amino group?
Proline
111
What does proline form when modified?
Hydroxylproline
112
What makes proline special?
The R group makes bond with the amino grojp
113
What does vitamin C deficiency do?
Slows the production of hydroxyproline and stops the construction of new collagen
114
What causes scurvey?
Vitamin C deficiency
115
Different name for vitamin C
Ascorbate
116
What is elastin?
Insoluble polymer which is rich in glycine. lysine and are hydroxyproline
117
What does elastin form when interacting with other proteins?
Reticulates
118
What kind of protein is elastin?
Fibrous (but very elastic)
119
What kind of protein is collagen?
Fibrous
120
How do membrane proteins fold in comparison to soluabl proteins?
Opposite way
121
What is the most important driving force for protein folding and assembly?
The hydrophobic effect
122
Can 2 different proteins have the same domain?
Yes

Biochemistry (28 decks)

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