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Bio chem > Lecture 6 - Protein Structure & Protein Folding > Flashcards

Lecture 6 - Protein Structure & Protein Folding Flashcards

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1
Q

Building up Protein Tertiary Structure

A
  • Secondary structure
  • Supersecondary structure
  • Protein domains
  • Complete protein structures
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2
Q

Supersecondary structure

A

helices
strands

connected by turns or by loops or coil

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3
Q

Common motifs of supersecondary structure

A
  • Helix - turn – helix
  • b hairpin
  • Greek key
  • Strand-helix-strand
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4
Q

Helix-turn-helix

A

2 helices together joined by a loop or turn

Common supersecondary structure

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5
Q

Helix - turn - Helix examples

A

DNA binding proteins

Calcium binding protein (longer turn) - hand

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6
Q

β hairpin

A

Strands antiparallel
Length varies

β strand goes up has a turn and back down

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7
Q

β hairpin examples

A

Bovine pancreatic trypsin inhibitor

Snake venom toxin

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8
Q

Greek key

A

4 antiparallel strands

Connected starting in centre

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9
Q

Strand, Helix, Strand

A

Strands Interact with H bonds

Helices above or below

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10
Q

Supersecondary structure elements combine to form

A

Domains or motifs

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11
Q

Domains or motifs

A

Independently folded region in a protein that sets apart from other regions

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12
Q

Small protein

A

1 domain

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13
Q

Long big protein

A

Multiple domains packed together

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14
Q

Domain size

A

150 - 200 amino acids stretch

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15
Q

Protein domain has

A

Hydrophobic core

Hydrophilic parts on surface

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16
Q

Glyceraldehyde 3 phosphate dehydrogenase

A 
2 domains (1 binds NAD cofactor helps coenzyme work)
1 protein chain
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17
Q

Proteins can be grouped into families based on tertiary structure 3 examples

A

α domain family (helices)

α / β family (Strand helix strand)

Antiparallel β family

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18
Q

α domain family

A

4 helix bundle

Eg myoglobin

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19
Q

4 helix bundle

A

Hydrophobic sidechains in middle (up to vanderwaal radius - max energy)

Hydrophilic sidechains outside
Good for stabilisation

Tilted helices (20 degrees) stabilize sidechains & can nestle next to each other

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20
Q

Myoglobin

A

Globin fold

Wraps around heme group

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21
Q

α / β family

A

Mix of α and β structure
Strand helix strand

α / β barrel
α / β open twisted sheet

22
Q

α / β barrel

A

8 strands 8 helices
Barrel of strands in middle helices on outside
H bond to each other

Hydrophobic interior
Hydrophilic outside (asp, lys, glu)
23
Q

α / β open twisted sheet

A

a helices and b strands alternating

Sequence determines pathway

24
Q

Antiparallel β family

A

Antiparallel β barrel
Hydrophobic interior of barallel
Eg retinal binding protein

25
Q

Retinal binding protein

A

Hydrophobic Retinal inside barrel
b strands nestles retinal
Retinal nose hydroxide sticking out
Carries retinal around body

Surround retinal with hydrophobic sidechains, OH sticks out

26
Q

In nature common structural motifs and domains are repeated and combined to make

A

different types of proteins

27
Q

Domains are often reused by nature and combined with other domains to make

A

proteins with different functions.

28
Q

Common Protein Domains

A

EGF (Hexagon)
Chymotrypsin (Oval)
Kringle Protein (K) - held by disulfide bridges
Ca bind protein (Triangle)

29
Q

Urokinase

A

3 domains together

EGF, K, Chymotrypsin

30
Q

Factor IX

A

4 domains

1 Ca bind protein, Chymotrypsin, 2 EGF

31
Q

Plasminogen

A

6 domains

5 K, 1 Chymotrypsin

32
Q

Proteins are synthesized as

A

linear polymers that have

to fold into a 3D functional structure

33
Q

Protein are made at the

A

ribosome,

fold into active shape spontaneously

34
Q

Where are the instructions that proteins need?

A

embedded in amino acid sequence

sequence contains the instructions

35
Q

Afinsen experiment

in nutshell

A

Unfold ribonuclease A structure by Urea and b mercaptoethanol

Remove urea and b merca

Amino acids fold themselves up
Made correct disulfide bonds, and tertiary structure, became active

36
Q

Proteins contain

A

information that leads to own structure in their sequence

37
Q

Collectively what makes a significant contribution to protein conformational stability?

A

Non-covalent interactions, while individually weak in proteins, collectively

covalent bonds (eg. disulfide bonds)

38
Q

what’s the most important noncovalent contributor

to protein stability in aqueous solution?

A

hydrophobic core

39
Q

Protein folding is directed by

A

internal hydrophobic residues,

hydrophilic residues are solvent exposed.

40
Q

is protein folding a random process?

A

Yes

41
Q

Folding pathways events

A

(i) Formation of short secondary structure segments
(ii) Nuclei come together, growing cooperatively to form a domain
(iii) Domains come together (but tertiary structure still partly disordered)
(iv) Small conformational adjustments to give compact native structure

42
Q

Some protein folding is

assisted by

A

chaperones

43
Q

Chaperones

A

(a) ‘chaperone’-independent
(b) Chaperone-dependent eg Hsp70
(c) Chaperonin-dependent eg GroEL-GroES

44
Q

What can lead to unfolding

and loss of biological function (denaturation)?

A

Weakening of non-covalent interactions

45
Q

Unfolding of proteins may result from…

A 
Change pH
Heating
Detergents
Organic solvents
Urea
Guandium HCL
46
Q

Proteins in living organisms that are folded normally can

sometimes

A

change their shape and become misfolded

47
Q

Some misfolded proteins can cause

A

other proteins to change
their shape

sometimes with disastrous consequences

48
Q

In the brain three conditions have been identified as being due to a protein,

A

PrP changes shape and forms aggregates that cause brain damage

BSE bovine spongiform
encephalopathy

CSD Creutzfeld-Jacob Disease

49
Q

PrP

A

abnormal form of prion protein

induces the normal form of this protein to become misfolded

a → b transformation

No treatment, fatal

50
Q

Kuru The proteins that cause the problem are called

A

prions for

“proteins infectious agent”

51
Q

Other diseases in which protein misfolding or

aggregation is thought to contribute:

A
  • Alzheimer’s Disease
  • Type 2 Diabetes

amyloid (abnormally folded protein)

Prions not involved

Bio chem (36 decks)

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