3D structure of proteins

Question 1

what is primary structure?

Answer 1

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

Question 2

What is secondary structure?

Answer 2

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

Question 3

What is an antiparallel beta sheet?

Answer 3

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

Question 4

What is a parallel beta sheet?

Answer 4

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

Question 5

What is the tertiary structure?

Answer 5

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

Question 6

What kinds of bonds make up tertiary structure?

Answer 6

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

Question 7

What are two purposes of tertiary structure?

Answer 7

structural and functional

Question 8

What is quarternary structure?

Answer 8

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).

Question 9

What is the sequence of collagen?

Answer 9

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

Question 10

What is the structure of collagen?

Answer 10

A triple helix

Question 11

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

Answer 11

proline

Question 12

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

Answer 12

it has to be hydroxylated.

Question 13

Where are hydrophobic residues on a protein usually located?

Answer 13

the inside of the protein.

Question 14

Where are hydrophilic residues on a protein usually located?

Answer 14

the outside of the protein

Question 15

What interactions govern protein folding stability?

Answer 15

non-covalent interactions and hydrophobic interacitons.

Question 16

What does beta-mercaptoethanol do?

Answer 16

eliminates sulfate bridges

Question 17

What is protein folding driven by?

Answer 17

the hydrophobic effect.

Question 18

What is the hydrophobic effect

Answer 18

The tendency of hydrophobic residues to aggregate and avoid water.

Question 19

What determines the possibilities of protein folding?

Answer 19

the amount of free energy.

Question 20

What is the molten globule state

Answer 20

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.

Question 21

What structure is the molten state usually in?

Answer 21

secondary

Question 22

What structure lacks in the molten globule?

Answer 22

tertiary

Question 23

What is at the core of the molten globule?

Answer 23

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

Question 24

What is the molten globule state stabilized by?

Answer 24

nonspecific hydrophobic interactions.

Question 25

What is a molten globule?

Answer 25

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

Question 26

What are motifs?

Answer 26

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

Question 27

Can the same peptide sequence exhibit different conformational states?

Answer 27

yes

Question 28

protein folding is a highly __ process

Answer 28

cooperative

Question 29

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

Answer 29

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

Question 30

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

Answer 30

AA sequence

Question 31

What binds are broken during denaturation?

Answer 31

weak bonds in the tertiary structure.

Question 32

What conditions can cause protein denaturation?

Answer 32

heat, pH, agitation and chemicals

Question 33

What are accessory proteins?

Answer 33

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

Question 34

What is an example of an accessory protein?

Answer 34

chaperonin

Question 35

What do chaperones do?

Answer 35

prevent misfolding of proteins.

Question 36

Where are incorrectly folded proteins detected?

Answer 36

the ER

Question 37

What causes the accumulation of misfolded proteins?

Answer 37

an overwhelmingly working proteasome system or a malfunctioning check system.

Question 38

What do normal proteins mostly contain (structurally)?

Answer 38

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

Question 39

What do beta strands often form?

Answer 39

aggregates or amyloid forms

Question 40

How do amyloids progress to amyloid plaques?

Answer 40

seeding (nucleation), fibril formation, or deposit.

Question 41

What can soluble proteins be conformed into?

Answer 41

insoluble amyloid fibrils.

Question 42

What is an amyloid fibril?

Answer 42

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

Question 43

What initiates amyloid fibrillation?

Answer 43

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

Question 44

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

Answer 44

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

Question 45

What are common metals needed for protein folding?

Answer 45

zinc, calcium, iron and copper

Question 46

What do metallochaperones do?

Answer 46

insert the correct metal ion into metal-containing proteins.

Question 47

What are infectious proteins?

Answer 47

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.

Question 48

What are characteristics of infectious proteins?

Answer 48

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

Question 49

What are examples of infectious proteins (plaques)?

Answer 49

prions, amyloid plaques

Question 50

What do amyloid fibrils have in common?

Answer 50

The same core structure

Question 51

What is the core structure enriched in?

Answer 51

beta sheets

Question 52

What do the insoluble fibrils form?

Answer 52

aggregates

Question 53

Are amyloid fibrils disease specific and transmissible?

Answer 53

yes