Secondary, tertiary and quaternary protein structure

Question 1

What two secondary structures are found in proteins?

Answer 1

alpha helix and beta sheet

Question 2

What stabilizes the alpha helix?

Answer 2

the interchain hydrogen bonds between the amide backbone and carbonyl groups four residues apart

Question 3

in a right handed helix how many residues are there per turn?

Answer 3

3.6

Question 4

How do the R groups project in an alpha helix?

Answer 4

outward

Question 5

In beta sheets how are the chains connected? How do the R groups come out?

Answer 5

hydrogen bonds between the chains

R groups project from both faces

Question 6

What are the two ways beta sheets can be orientated?

Answer 6

parallel or antiparallel

Question 7

what is a beta bend?

Answer 7

where the polypeptide makes a 180° turn at the protein surface

Question 8

Examples of conformational diseases?

Answer 8

Alzheimers and prions

diabetes (2), parkinsons

Question 9

Alzheimers conformational explanation

Answer 9

human amyloid peptide usually helical transitions to beta sheet which causes nucleation into a giant fibre

Question 10

Prions conformational explanation

Answer 10

normally alpha helixes when converted to beta sheets allows for nucleation

Question 11

What are super secondary structures?

Answer 11

motifs and domains

Question 12

what is a protein motif?

Answer 12

small regions with defined sequence or structure which often serve a common function in different proteins

Question 13

what is a protein domain?

Answer 13

sub regions of single polypeptide chains that can fold and function independently (sometimes correlated with exons)

Question 14

What do you see with a backbone representation of a protein?

Answer 14

Ca per residue

Question 15

what do you see with a wireframe representation of a protein?

Answer 15

every bond and atom

use this if you know catalytic site or mutation

Question 16

what do you see with a space fill representation of a protein?

Answer 16

shows van der waals forces

volume (radii)

Question 17

what do you see with a ribbon representation of a protein?

Answer 17

highlights the secondary structure, which components are alpha helixes or beta sheets

Question 18

What is the native structure stabilized by?

Answer 18

burying the non-polar side chains, hydrophobic effect
optimized hydrogen bonds
any inter chain S-S bonds
maximized side chain packing in interior due to VDW

Question 19

What is the denatured state stabilized by?

Answer 19

increased conformational entropy of the unfolded chain

Question 20

what can cause denaturation?

Answer 20

heat, chemicals, pH extremes, mutations that destabilize N

Question 21

why is denaturation often irreversible?

Answer 21

because of exposure of proteolytic sites and non-polar residues

Question 22

What did the Anfinsen experiment show?

Answer 22

native structure of protein only recovered if urea removed before reducing agent showing that it is not the S-S bonds that dictate protein folding but the primary structure

Question 23

what is the Levinthal paradox?

Answer 23

if explored
randomly, all possible conformtions of
a 100-residue protein would take the age of the universe to sample…yet
proteins often fold within seconds!
because folding is directed by the rapid intial formation of 2° structure elements which prevent other possibilities

Question 24

Some areas of the protein only fold when interacting with binding partners : T or F?

Answer 24

T

Question 25

Some of the intermediates may promote misfolding and aggregation: T or F?

Answer 25

T

Question 26

How is protein folding a free energy funnel?

Answer 26

as get closer the native structure the amount of free energy continually decreases

Question 27

what is chaperon assisted folding?

Answer 27

heat shock proteins (chaperones) help larger molecules fold by providing a safe space allowing it to find the correct formation requires ATP and thus there is a loss of ADP and Pi

Question 28

Quaternary structure is what

Answer 28

multiple polypeptide chains forming a functional protein
nomenclature
homodimer-two identical subunits
heterotetramer-4 different sub units