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Biochemistry > 3D structure of proteins > Flashcards

3D structure of proteins Flashcards

1
Q

what is primary structure?

A

the linear arrangement of amino acid residues. They are linked via peptide bonds, and sequences are written N terminus to C terminus.

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2
Q

What is secondary structure?

A

the coiling or pleating of peptide/protein chains; includes alpah helices, beta pleated sheets and beta turns.

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3
Q

What is an antiparallel beta sheet?

A

A sheet with hydrogen bonds to one amino acid. They look parallel.

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4
Q

What is a parallel beta sheet?

A

A sheet with hydrogen bonds to two amino acids. They look crooked.

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5
Q

What is the tertiary structure?

A

A specific 3D conformation of a particular peptide chain. Most proteins are in globular or spherical conformation.

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6
Q

What kinds of bonds make up tertiary structure?

A

hydrophobic interactions, disulfide bonds, metal ions and hydrogen bonding.

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7
Q

What are two purposes of tertiary structure?

A

structural and functional

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8
Q

What is quarternary structure?

A

Protein structure into which subunits are arranged in a complex. the subunits are held together by noncovalent associations (e.g. H bonds, salt bridges, hydrophobic interactions and van der waals forces).

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9
Q

What is the sequence of collagen?

A

A repeated triplet sequence of Gly-X-Y-Gly

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10
Q

What is the structure of collagen?

A

A triple helix

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11
Q

What amino acid in collagen creates a “kink” in the structure?

A

proline

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12
Q

What needs to occur to proline to allow collagen to function?

A

it has to be hydroxylated.

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13
Q

Where are hydrophobic residues on a protein usually located?

A

the inside of the protein.

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14
Q

Where are hydrophilic residues on a protein usually located?

A

the outside of the protein

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15
Q

What interactions govern protein folding stability?

A

non-covalent interactions and hydrophobic interacitons.

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16
Q

What does beta-mercaptoethanol do?

A

eliminates sulfate bridges

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17
Q

What is protein folding driven by?

A

the hydrophobic effect.

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18
Q

What is the hydrophobic effect

A

The tendency of hydrophobic residues to aggregate and avoid water.

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19
Q

What determines the possibilities of protein folding?

A

the amount of free energy.

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20
Q

What is the molten globule state

A

An intermediate conformational state between the native and fully unfolded states of a globular protein; no semi-folded proteins are present, and the protein is in the process of finding a thermodynamically stableproduct.

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21
Q

What structure is the molten state usually in?

A

secondary

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22
Q

What structure lacks in the molten globule?

A

tertiary

23
Q

What is at the core of the molten globule?

A

loosely packed hydrophobic residues; there are still pockets of hydrophobic nature that increase the surface area of the solvent.

24
Q

What is the molten globule state stabilized by?

A

nonspecific hydrophobic interactions.

25
Q

What is a molten globule?

A

a compact globule with a “molten” side-chain structure that is primarily stabilized by nonspecific hydrophobic interactions.

26
Q

What are motifs?

A

combinations of secondary structure in proteins that exhibit similar structures; they also help with the stability of the structure.

27
Q

Can the same peptide sequence exhibit different conformational states?

A

yes

28
Q

protein folding is a highly __ process

A

cooperative

29
Q

What does it mean when protein folding is “all or none?”

A

partial loss of folding in one part of the protein destabilizes the rest of the structure.

30
Q

Where is in the information needed to specify the catalytically active structure of enzymes?

A

AA sequence

31
Q

What binds are broken during denaturation?

A

weak bonds in the tertiary structure.

32
Q

What conditions can cause protein denaturation?

A

heat, pH, agitation and chemicals

33
Q

What are accessory proteins?

A

proteins that help molecules to position inthe proper place (and thermodynamically favorable)

34
Q

What is an example of an accessory protein?

A

chaperonin

35
Q

What do chaperones do?

A

prevent misfolding of proteins.

36
Q

Where are incorrectly folded proteins detected?

A

the ER

37
Q

What causes the accumulation of misfolded proteins?

A

an overwhelmingly working proteasome system or a malfunctioning check system.

38
Q

What do normal proteins mostly contain (structurally)?

A

alpha; chemicals, external factors, etc, cause alpha to beta conversion

39
Q

What do beta strands often form?

A

aggregates or amyloid forms

40
Q

How do amyloids progress to amyloid plaques?

A

seeding (nucleation), fibril formation, or deposit.

41
Q

What can soluble proteins be conformed into?

A

insoluble amyloid fibrils.

42
Q

What is an amyloid fibril?

A

a corss beta structure with beta strands perpindicular to the backbone structure. It is derived from amyloid precursor proteins.

43
Q

What initiates amyloid fibrillation?

A

seeded polymeriztaion (seeding of growing proteins), and covalent modification of proteins (oxidative modification, phosphorylation, etc).

44
Q

How do aggregates lead to the death of cells that harbor them?

A

by smaller proteins that cause the cell membrane to be damaged, and therefore the integrity is compromised.

45
Q

What are common metals needed for protein folding?

A

zinc, calcium, iron and copper

46
Q

What do metallochaperones do?

A

insert the correct metal ion into metal-containing proteins.

47
Q

What are infectious proteins?

A

proteins that are transmitted cell to cell and cause infection. They are aggregates of specific proteins, resistant to dissolving, and derived from a cellular protein.

48
Q

What are characteristics of infectious proteins?

A

Are aggregates of specific proteins
Resistant to dissolving
Derived from a cellular protein

49
Q

What are examples of infectious proteins (plaques)?

A

prions, amyloid plaques

50
Q

What do amyloid fibrils have in common?

A

The same core structure

51
Q

What is the core structure enriched in?

A

beta sheets

52
Q

What do the insoluble fibrils form?

A

aggregates

53
Q

Are amyloid fibrils disease specific and transmissible?

A

yes

Biochemistry (6 decks)

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