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BIOC192 > Lecture 6 - Protein Folding > Flashcards

Lecture 6 - Protein Folding Flashcards

1
Q

What is Supersecondary structures?

A

Elements of secondary strucutre i.e helices and strands are connected by turns or regions of less ordered strucutre called loops or coils to make up Supersecondary structure

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2
Q

Common motifs of Supersecondary strucutre

A
  • helix - turn - helix
  • beta hairpin
  • Greek key
  • strand-helix strand
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3
Q

What is a helix-turn-helix

A
  • Supersecondary structure
  • two helix connected by a turn (polypeptide sequence that causes a change in direction - 4 residues)
    E.G: found in:
  • DNA binding protiens
  • Calcium binding proteins
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4
Q

EF-hand proteins

A
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5
Q

B-hairpin

A
  • common
  • antiparralel
  • length varies

Two examples:
- bovine pancreatic trypsin inhibitor
- snake venom toxin

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6
Q

Greek key

A
  • 4 antiparalalel strands
  • 4 beta strand connected by loops and turns
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7
Q

The Greek key as one long, bent hairpin

A
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8
Q

Strand, helix, strand

A
  • alpha helix sits just below or just above the beta strands
  • parallel beta strands - hydrogen bonds
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9
Q

Protien domains

A
  • Supersecondary structure elements combine to form domains
  • independently folded regions that often possess a specific function within the protien
  • hydrophobic core (very important for protein stability)
  • hydrophobic parts are arranged on the surface in contact or near solvent
  • small protiens contain usually one domain, larger protiens may have multiple domains
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10
Q

Tertiary structure families

A

a domain family
a/B family
Antiparralel B family

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11
Q

How to form a protien domain

A
  • Supersecondary stucture elements combine
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12
Q

Structure of protein domains

A
  • independently folded regions that often possesses a specific function within the protein
  • hydrophobic core (very important for protein stability)
  • hydrophilic parts are arranged on the surface in contact or neat solvent
  • small protiens contain usually one domain
  • larger proteins contain multiple domains
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13
Q

A-domain family is mainly___

A

Helical

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14
Q

a-domain family - four helix bundle

A
  • amphipathic helices with side-chains packed closely together within a hydrophobic core
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15
Q

a-domai family - globin fold

A
  • amphiathic helices with side-chains packed closely together within a hydrophobic core
  • packing can occur between no adjacent helices
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16
Q

What is a/B family a mix of

A

A mix of a and B strucutre

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17
Q

a/B barrel

A
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18
Q

a/B family - horseshoe fold

A

16 stand - helix motif repeats

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19
Q

Anti-parallel B family consists of..

A

Mostly antiparallel B strucutre

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20
Q

Anti-parallel B family

A
  • anti-parallel B barrel - retinol binding protein
  • hydrophobic inside of barrel
21
Q

Many more families of protien strucutre exist

A

Yep

22
Q

In _____ common _____ ______ are repeated and ______ to make different types of ______

A

In nature common structural domains are repeated and combined to make different types of proteins

23
Q

_____ are often ‘_____’ by nature and combined with other domains to make proteins with different _____

A

Domains are often ‘reused; by nature and combines with other domains to make proteins with different functions

24
Q

Common protein domains

A
25
Q

Proteins are…

A

… synthethsised as linear polymers that must fold into a 3D functional structure

26
Q

Where are proteins made and what happens after they are made

A
  • protein is made at the ribosome
  • and then generally they fold into their active shape spontaneously
27
Q

Where are the instructions needed for protien folding

A

The only “instructions” needed are embedded in the amino acid sequence

28
Q

The Anfinsen experiment in a nutshell

A

In absence of everything apart from a string of amino acids - it reforms itself

29
Q

Protein folding directed largely by…

A

…its internal hydrophobic residues, which form an internal hydrophobic core, while hydrophobic residues are solvent exposed

30
Q

Likely folding pathway sequence

A
  1. Formation of short secondary strucutre segments
  2. Subdomains form
  3. Subdomains come together to form a partly folded domain; a “molten globule” that can rearrange, (tertiary strucutre still partly disordered)
  4. Final domain strucutre emerges, small conformational adjustments to give final compact native structure
31
Q

Stabilisation of protein folding

A
  • non-covalent interactions - individually weak in proteins, collectively make a significant contribution to protein conformational stablility
  • in some proteins additional covalent bonds (e.g disulfide binds) may be present that contribute to conformation stability
  • the hydrophobic core is likely the most important non covalent contributor to protein stability in aqueous soluation
32
Q

3 ways it can fold

A
  1. Chaperone-independent
  2. Chaperone-depended e.g Hsp70
  3. Chaperoning-dependent e.g GroEL-GroES
33
Q

Unfolding proteins occurs if the non-covalent bonds break due to…

A
  • change in pH
  • heating (kinetic energy)
  • more
34
Q

If you change the side chains - not going to face the same properties - heat cause bonds to vibrate breaking hydrogen bonds

A

If you change the side chains - not going to face the same properties - heat cause bonds to vibrate breaking hydrogen bonds

35
Q

Can protiens in living orgasnisms that are folded normally sometimes change their shape and become misfolded?

A

Yes

36
Q

Some misfolded proteins can ______ other _____ to change their _____ as well, sometimes with ________ ___________

A

Some misfolded proteins can cause other proteins to change their shape as well, sometimes with disastrous consequences

37
Q

How do prion diseases form

A
  • prp changes its shape and form aggregates that cause Brian damage
38
Q

Prion diseases include

A
  • Bovine spongiform encephalopathy (BSE)
  • Creutzfeldt-Jacob disease
  • Kuru
39
Q

What is a prion

A
  • the protiens that cause the problem are called prions for “protiens infections agent”
40
Q

The abnormal form of a prion protein induces the normal form of this protein to become misfolded

A

The abnormal form of a prion protien induces the normal form of this protien to become misfolded

41
Q

What transformation does prion disease induce

A

A —-> B transformation

42
Q

Treatment for prion diseases

A
  • no treatment available
  • always fatal
43
Q

Model for prion conformation

A
44
Q

Diseases which protein misfolding or aggregation is THOUGHT to contribute to

A
  • alzheimers disease
  • type two diabetes
    • prions are not involved in these ailments
    • abnormally folded protien called amyloid is thought to contribute
45
Q

All the _____ required for a protein to ___ is in the ____ _____ of _____ _______

A

All the requires information requires for a protein to fold is in the primary sequence of amino acids

46
Q

A domain is….

A

An independently folded region of a protien, often with a specific role, and usually with a hydrophobic core

47
Q

The tertiary strucutre of a protein is largely stabilised by…

A

…non-covalent interactions

48
Q

Protien misfiling can lead to..

A

Disease

BIOC192 (38 decks)

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