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BIOC192 > Lecture 6: FOLDING A PROTEIN > Flashcards

Lecture 6: FOLDING A PROTEIN Flashcards

1
Q

What is super secondary structure?

A

Elements of secondary structure - helices and strands are connected by turns or by regions of less ordered structure called loops to coils

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2
Q

What are common motifs of supersecondary structure?

A

helix-turn-helix, beta hairpin, greek key ad strand-helix-strand

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3
Q

What are examples of helix-turn-helix?

A

DNA binding proteins and calcium binding proteins

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4
Q

What helix-turn-helix protein has a more complicated turn?

A

Calcium binding proteins

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5
Q

Are beta hairpins common?

A

Yes

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6
Q

What is the structure of the beta hairpin?

A

Antiparallel

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7
Q

What varies in beta hairpins?

A

Length and number

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8
Q

What happens in a beta hairpin?

A

A single strand has nothing to bond with but the other strand in the hairpin coming back is able to bond

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9
Q

What are examples of beta hairpins?

A

Bovine pancreatic trypsin inhibitor and snake venom toxin

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10
Q

What does snake venom toxin have?

A

2 beta hairpins and one other strand

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11
Q

What is involved in a greek key?

A

4 antiparallel strands

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12
Q

Is strand-helix-strand common?

A

Yes

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13
Q

Where are the helix and strands in stran-helix-strand found?

A

In different planes

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14
Q

How are the strands stabilised in strand-helix-strand?

A

By the side chains of the helix and other strand

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15
Q

What do super secondary structure elements combine to form?

A

Domains

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16
Q

What are domains?

A

Independently folded regions that often possess a specific function within a protein

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17
Q

What does a protein domain typically have?

A

A hydrophobic core and the hydrophilic parts of the protein are arranged on the surface in contact or near solvent

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18
Q

What is very important for protein stability?

A

Hydrophobic core

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19
Q

What do small proteins contain?

A

Usually one domain

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20
Q

What do larger proteins (>250 residues) contain?

A

May have multiple domains

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21
Q

What are protein families based on?

A

Structure

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22
Q

What are the protein families?

A

Alpha domain family, alpha/beta family and antiparallel beta family

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23
Q

What is the structure of the alpha domain family?

A

Mostly helical

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24
Q

What does the alpha domain family include?

A

4 helix bundles

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25
Q

How are 4 helix bundles arranged?

A

Slightly tilted to allow side chains to fit tight. The hydrophobic residues are found on the interior and hydrophilic on the exterior causing a hydrophobic core to form

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26
Q

What is amphipathic?

A

When something is partly hydrophobic and partly hydrophilic

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27
Q

What does the alpha domain also include?

A

Globin fold

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28
Q

What does the global fold have?

A

Amphipathic helices wth side chains packed closely together within a hydrophobic core. Packing occurs between non-adjacent helices

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29
Q

What is the alpha/beta family?

A

Mix of alpha and beta structure including strand-helix-strand repeated many times

30
Q

What does the barrel structure have?

A

Bottom and middle internal layers of side chains hydrophobic and pointing out is he hydrophilic side chains which commonly form the active site

31
Q

What is the horseshoe fold?

A

A 16 strand helix motif repeat where all of the strands are parallel

32
Q

What is antiparallel beta family?

A

Mostly anti-parallel beta structure with no helices, just turns

33
Q

What is an example of antiparallel beta family?

A

Retinal binding protein

34
Q

What is the structure of retinal binding protein?

A

It has a hydrophobic inside of a barrel with the strands wrapping around a molecular held inside. The end of the tip of retinol is a hydrophilic hydroxyl group which sticks outside the barrel slightly

35
Q

What does nature do with domain?

A

Common structural domains are repeated and combined to make different types of proteins

36
Q

What are common protein domains?

A

EGF, chymotrypsin, kringle domain and calcium-binding domain

37
Q

How are proteins synthesised?

A

As linear, non-branching polymers that have to fold into a 3 dimensional functional structure

38
Q

Where are proteins made?

A

At the ribosome and then generally they fold into their active shape spontaneously

39
Q

Where are the instructions needed for protein folding found?

A

Embedded in the amino acid sequence

40
Q

Who proved that the instructions for protein folding were in the amino acid sequence?

A

Christian Afinsen, in a series of experiments that lead to a Nobel prize

41
Q

What did Afinsen first do?

A

Took native ribonuclease and reduced the disulphide bonds causing the protein to denature

42
Q

What did Afinsen observe?

A

The denatured protein was able to refold itself into native ribonucleas

43
Q

What is protein folding directed largely by?

A

Its internal hydrophobic residues which form an internal core while hydrophobic residues are solvent exopsed

44
Q

How his the sequence of protein folding described?

A

Not random

45
Q

What is the first step in protein folding?

A

Formation of short secondary structure segments

46
Q

What happens after formation of short secondary structure segments?

A

Nuclei or subdomains form

47
Q

What happens after nuclei or subdomains form?

A

Subdomains come together to form a partly folded domain; a “molten globule” that can rearrange (tertiary structure still partly disordered)

48
Q

What happens after a molten globule forms?

A

Final domain emerges small conformational adjustments to give final compact native structure

49
Q

How are non covalent bonds individually?

A

Weak but in proteins, collectively they make a significant contribution to protein conformational stability

50
Q

What do some proteins have?

A

Additional covalent bonds (disulphide bonds) which contribute to conformational stability

51
Q

What is most likely the most important non covalent contributor to protein stability in aqueous solution?

A

Hydrophobic core

52
Q

How do some proteins get assistance in folding?

A

By chaperones

53
Q

What are the types of protein folding?

A

Chaperone independent, chaperone dependent and chaperonin dependent

54
Q

What is an example of a chaperone?

A

Hsp70

55
Q

What is an example of chaperonin?

A

GroEL-GroES

56
Q

What % of proteins fold chaperone independent and dependent?

A

85%

57
Q

What % of proteins fold chaperonin dependent?

A

15%

58
Q

What can weakening of non covalent interactions do?

A

Lead to unfolding and loss of biological function (denaturation)

59
Q

What may denaturation result from?

A

Change in pH, heating, detergents, organic solvents, urea and guanidium HCL

60
Q

What forms of denaturation are irreversible?

A

Change in pH and heating

61
Q

What forms of denaturation are reversible?

A

Urea and guanidium HCL

62
Q

What can proteins in living organisms that are folded normally do?

A

Sometimes change their shape and become misfolded

63
Q

What can some misfiled proteins do?

A

Can cause other proteins to change their shape as well, sometimes with disastrous consequences

64
Q

What has been identified in the brain?

A

Three conditions due to a protein, PrP,that changes its shape and then form aggregates that cause brain damage: bovine spongiform encephalopathy (BSE), creutzfeld-jacob disease (CJD) and Kuru

65
Q

What are the proteins that cause the brain disease called?

A

Prions or “proteins infectious agent”

66
Q

What does the abnormal form of a prion protein, PrP do?

A

Induces the normal form of this protein to become misfolded

67
Q

What transformation occurs due to prions?

A

alpha to beta

68
Q

Is there treatment for the brain diseases?

A

No, they are always fatal

69
Q

What other diseases are thought to be caused by protein misfiling or aggregation?

A

Alzheimers and Type 2 diabetes

70
Q

What is involved in alzheimers an type 2 diabetes?

A

Not prions, an abnormally folded protein called amyloid is thought to contribute

BIOC192 (38 decks)

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