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biochem > Chapter 6: protein structure pt. 2 and 3 > Flashcards

Chapter 6: protein structure pt. 2 and 3 Flashcards

1
Q

Protein can be denatured by…

A
  1. heating
  2. Chaotropic agents
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2
Q

proteasome

A

proteolyzed or refolds misfolded proteins

*only some proteins can be refolded or renatured

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3
Q

chaotropic agents

A

disrupt interactions that stabilizes tertiary structure

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4
Q

Christian Anfinsen

A
  1. Used the correct folded state of RNase A
  2. denatured RNase A by using urea and beta-mercaptoethanol (reduced disulfide bonds)
  3. dialyzed out urea and most beta-mercaptoethanol to catalyze formation of correct disulfide bonds
  4. the RNase regained activity

-showed that primary structures determines tertiary structure
*-delta G=when its in its native state

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5
Q

Energetics of protein folding

A

the net delta G is negative=slightly favored

-delta G fold = -0.4 KJ/mol AA
-100 AA = -40 KJ/mol
*net energy of stabilization is small

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6
Q

Levinthal’s paradox

A

-proteins DONT sample all possible folding conformations
-fold by specific pathway

*most proteins fold in less than 10 secs

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7
Q

model of protein folding

A
  1. the polypeptide collapses in upon itself due to the hydrophobic effect
  2. secondary structure forms
    *molten globule state: lot of secondary structure and little tertiary structure
  3. tertiary structure begins to form
  4. then final native state forms

*takes less than 10 secs

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8
Q

Folding Funnel

A

energy landscape guides protein towards native structure

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9
Q

Folding in Vitro

A

-easy to fold
-folding by dilution in buffer

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10
Q

Folding in vivo

A

-difficult to fold
-the cellular environment is crowded so there is a high potential for misfolding and precipitation (aggregation)

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11
Q

Chaperons

A

-proteins that help other proteins fold in vivo
-also called Heat shock proteins (HSPs) bc they were discovered during HS

*most proteins can fold without chaperons

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12
Q

DnaJ and DnaK

A

-prevents precipitation/aggregation
-assists folding
-coats the unfolded protein and preventing denaturing/precipitation

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13
Q

GroEL and GroES: info

A

-also called Hsp60
-large chaperones called chaperonins
-actively fold proteins in prokaryotes, cytosol of eukaryotes, and mitochondria

-GroES: cap that seals unfolded protein from the outside
-GroEL: barrel

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14
Q

GroEL and GroES: mechanism

A
  1. protein in the barrel
  2. cap goes from one side to the other side of barrel?
  3. then it caps the end of the barrel that the protein went in
  4. completely folded protein comes out of the barrel

*requires energy from ATP hydrolysis

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15
Q

Protein disulfide isomerase

A

facilitates formation of correct disulfide bridges

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16
Q

peptidyl proline isomerase

A

catalyses cis-trans isomerisation of peptide bonds involving proline

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17
Q

How do protein folding diseases occur

A

-usually misfolded proteins get refolded immediately by a proteasome but sometimes they can accumulate as precipitates which can result in severe, chronic degenerative diseases that affect the brain and CNS

-Disease often occurs when protein with alpha-helix conformation misfolds into a precipitating beta-sheet conformation
*form a common cross-beta helical core filament structure

-leads to aggregation into amyloid fibrils masses which can form amyloid deposits (amyloid plaque) in brain
*can cause neuronal apoptosis

18
Q

Precipitated proteins are associated with what diseases?

A

1.Prions related illnesses
- like Transmissible Spongiform
Encephalopathies (TSE’s)
-Bovine Spongiform
Encephalopathy (BSE)/ mad cow’s
disease
- Creutzfeldt-Jakob disease (CJD,
human BSE)
2. Amyloid related illnesses
- Alzheimer’s,
-Parkinson’s
-ALS

19
Q

What is misfolding caused by

A

-genetics: through mutations
-transmission: Mad cow disease

20
Q

protein folding mechanism

A
  1. native monomer
  2. misfolding
  3. beta-sheet oligomers
  4. amyloid fibrillar aggregates
21
Q

prion def

A

proteinaceous Infectious particle

-infection involves a change of secondary structure and conformation in the protein
*converts from a alpha-helical to beta-sheet conformation

-PrP^C: protease-resistant protein, cellular = normal
-PrP^SC: protease-resistant protein, scrapie = bad prion
*can’t be broken down/ cant be destroyed by autoclave

22
Q

Kuru

A

Fore tribe of Papua New Guinea
-prions PrP^SC transmitted by eating dead love ones brain
-kuru stopped dying when cannibalism was stopped

23
Q

Stanley Pruiser

A

won nobel prize in medicine for discovering prions

-1st case of infectious agent being a protein ( was not a virus or bacteria)

24
Q

Chronic Traumatic encephalopathy (CTE)

A

butting heads caused Tau misfolding (precipitation of beta-sheets)

-Alzheimer’s requires the Tau neuron

25
Q

p53

A

tumor suppressor protein that sense damaged DNA sensor and stops them before they grow

-initiates apoptosis

26
Q

what happens when there is a mutation in p53?

A

causes misfolding in p53 which leads to unregulated cell growth = cancer

27
Q

LOOK AT CHAP 6 PT.3 SLIDES FOR STRUCTURES

A

OKAY

28
Q

Domains

A

-independent folding regions within a protein often associated with a certain function

-25-100 AA residues
-connected to each other by loops
-bound by weak interactions between side chains
-fundamental unit of TERTIARY STRUC
*has hydrophobic core

-made of folds???

*in multifunctional enzymes each catalytic activity can be on one of several domains

29
Q

Interfaces

A

btwn domains provide crevices, grooves, and pockets that make good binding or catalytic sites

30
Q

what are the 3 domains of a polypeptide chain?

A
  1. regulatory domain
  2. substrate binding domain
  3. nucleotide binding domain
31
Q

4 Protein Classes

A
  1. alpha
  2. beta
  3. alpha + beta
  4. alpha/beta: consists of 2 alpha+beta barrel
32
Q

folds

A

-combination of secondary structure that form the core of a domain

-made of motifs (supersecondary structure)

33
Q

EF-hand fold

A

-Structure: alpha helix; right hand like an L with fingers pointing towards you
*E helix = pointer finger
*F helix = thumb

-found in proteins that bind Ca^2+

34
Q

Calmodulin

A

*know structure
- has 4 EF-Hand folds

35
Q

Zinc Finger

A

-made with one alpha and one beta strand
-Zinc^2+ in the middle
-Zinc is bonded to cysteine and histidine

36
Q

Jelly/ Swiss-Barrel Roll Fold

A

squished antiparallel beta barrel

37
Q

TIM fold barrel

A
  • alpha/beta barrel
    -chicken muscle triose phosphate isomerase
38
Q

Rossman Fold

A

-also known as dinucleotide binding fold
-alpha/beta barrel
-can bind NAD+ and ATP

39
Q

Horseshoe Fold

A

-alpha/beta
-looks life a horseshoe
-Ribonuclease inhibitor

40
Q

Quaternary Structure

A
41
Q

rotational symmetry

A

-multisubunit protein display symmetry

-defined as Cn
*C: cyclical
*n: number of subunits

-higher order types: octahedral or tethrehedral etc..

42
Q

Dihedral symmetry N-fold

A

it intersects a two-fold rotational symmetry at right angles

biochem (13 decks)

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