Exam 1 Lectures 6

Question 1

the Chou-Fasman method predicts

Answer 1

2ndary structures in proteins

Question 2

Frequency (f) =

Answer 2

part/whole thus (aa in alpha-helix)/(all aa)

Question 3

Propensity (P)=

Answer 3

(propensity)/(natural inclination)

Question 4

spatial arrangement of aa residues that are far apart in the sequence and to the pattern of disulfide (S-S) bonds describes

Answer 4

tertiary structure

Question 5

why is 3’ more compact than 2’

Answer 5

3’ is tightly packed and folded vs 2’ which has alpha helices and beta sheets that are large and big

Question 6

T/F sulfide bonds are highly stable and therefore require high energy to break

Answer 6

true

Question 7

what does PDI stand for and its purpose?

Answer 7

Protein Disulfide Isomerase and it rearranges the polypeptides non-native S-S bonds

Question 8

T/F: when proteins arise from the ribosome, they form by themselves and have errors ie disulfide bridges in wrong places. So PDI aids via -SH group

Answer 8

true

Question 9

PPI helps via

Answer 9

helps to form proper configuration

Question 10

HSP 70 and 40 require _

Answer 10

energy (ATP)

Question 11

HSP 70 and 40 function to _

Answer 11

reverse misfolds, refolding, disaggregation, degradation

Question 12

HSP 90 is for _

Answer 12

signal transduction proteins; integrates signaling functions acting at a late stage of folding substrates

Question 13

mitochondria contain their own HSP 60 and 70 that are distinct and thus have their own _

Answer 13

quality control sys

Question 14

interchain means

Answer 14

disulfide bond in btwn 2 chains ex bovine insulin

Question 15

intrachain means

Answer 15

disulfide bond in same sequence

Question 16

why is protein folding “all or none”

Answer 16

either folded or unfolded. Partially folded = toxic and diseases

Question 17

why is molten globule the rescue step?

Answer 17

an intermediate and very short. Makes sure groups are finding each other and low energy state

Question 18

4’ structure =

Answer 18

spatial arrangement of subunits and nature of their interactions

Question 19

how do 3’ and 4’ structure differ?

Answer 19

3’ = 1 unit whereas 4’ = multiple subunits

Question 20

all proteins have _ structure but only have some _ strucutre

Answer 20

all have 3’ and only some have 4’ structure

Question 21

what are the 3 ways to denature proteins?

Answer 21

physical, chemical, and methods of analysis

Question 22

denaturation means

Answer 22

damaging the protein’s structure

Question 23

physical denaturation includes

Answer 23

Heat: making stable to unstable

pH (extremes) and agitation: both allow for aggregation

Question 24

chemical denaturation includes

Answer 24

Detergent: SDS
Chaotropic agents: urea, guanidine hydrochloride (these interact with hydrophobic groups and messes with non-covalent bonds)
AND
Organic solvents: TCA (disrupts H bonds)

Question 25

methods of analysis denaturation includes:

Answer 25

Turbidity (more hazy=more denatured)
Circular dichroism (lt/rt polarize light differently)
UV absorption (280nm)
Fluorescence (inherited structures ie aromatic absorb light and emit)
Biological activity (receptor proteins bind ligands strongly/lightly

Question 26

molecular chaperons aid via

Answer 26

help proteins go into transient molten state

Question 27

the 2 major classes of chaperones are:

Answer 27

HSP 70 and 90

and Chaperonins=a protein folding container (HSP 60 and 10)

Question 28

T/F: every protein has a lifespan

Answer 28

true

Question 29

Why must the cell remove aged and or damage proteins?

Answer 29

It’s better to recycle, but pathological diseases are associated with protein aggregation

Question 30

what is the proteosome?

Answer 30

protein degradation machinery, large protease complex, and digests ubiquinated tagged proteins

Question 31

in the 26S proteosome, which is the regulatory region and which is the catalytic core region?

19S
20S
19S

Answer 31

the 19S are the regulatory region and 20S is the catalyitc core

Question 32

where do free aas come from and what can it be used for?

Answer 32

free aas come from peptide fragments of ubiquinated proteins. Free aas can be used for biosynthetic rxns.