Proteins

Question 1

Levels of structural organization

Answer 1

4

Question 2

Primary structure

Answer 2

amino acid sequence important: peptide bonds

Question 3

secondary structure

Answer 3

alpha- helix beta- sheets important: H- bonds

Question 4

Other secondary structures

Answer 4

loops and coils

Question 5

alpha- helix characteristics

Answer 5

right handed Proline- not found in helical regions “helix breaker”

Question 6

How peptide bonds are connected on an alpha- helix.

Answer 6

Each peptide bond is connected by H- bonds 4 AA residues ahead from it

Question 7

Amino- acids per turn in a helix

Answer 7

3.6

Question 8

Rule (n+4) for the alpha- helix

Answer 8

CO of 1st AA connected to the 4th AA ahead of it or behind of it

Question 9

ß- sheet

Answer 9

H- bonding is bent to form the correct pleated sheet

Question 10

anti- parallel ß-sheet

Answer 10

polypeptide strands run in the opposite direction

Question 11

parallel ß- sheet

Answer 11

polypeptide strands run in the same direction

Question 12

beta sheet arrangement of side chains

Answer 12

projected above and below the plane

Question 13

Bends, loops and turns

Answer 13

non- regular, non- repetitive secondary structures

Question 14

What AA are present in bends and turns?

Answer 14

• Glycine (Gly)
• Proline (Pro)

Question 15

Globular proteins

Answer 15

bends, loops and turns over their surface (rich in Gly and Pro over the surface)

Question 16

Describe globular proteins

Answer 16

a- helices and B- sheets= core of the globular protein bends and turns = surface of the globular protein

Question 17

Tertiary Structure

Answer 17

a- helix, ß- sheet and bends arrange in a regular fashion to form the fundamental functional and 3D structural unit.

Question 18

Describe alpha- helix (secondary structure)

Answer 18

• Right handed
• Hidrogen bonds are the most important
• trans side chains project outward and outward from the helix
• Proline is not found, is a helix breaker because the ring causes a kink an change of direction

Question 19

What is the function of bends, loops and turns?

Answer 19

• Reverse the direction of a polypeptide chain
  *

Question 20

Where are bends, loops and turns found in a globular protein?

Answer 20

• Over the surface

Question 21

What “special bonds” are found in the tertiary structure?

Answer 21

disulfide bonds

Question 22

In a quaternary structure which are the predominant interaction?

Answer 22

Covalent or non covalent between subunits

Question 23

Define quaternary structure

Answer 23

Specific interactions between domains or subunits

Question 24

What is the effect of assembly into a multisubunit

Answer 24

Increases the stability of a protein and improves proteins efficiency

Question 25

Protein Folding

Answer 25

* Can be spontaneous by a trial and error process * Chaperones and chaperonines assist in the process * cis- trans isomerase participates * protein disulfide isomerase participates

Question 26

Most important proteins that assist in protein folding

Answer 26

* chaperones * chaperonines

Question 27

Why proteins are degraded?

Answer 27

misfolding or have accomplished their lifetime

Question 28

How proteins are degraded?

Answer 28

By the Ubiquitin- Proteasome Pathway System * tag with Ubiquitin * 28 subunit proteasome machinery comes and degrades

Question 29

Define pre- fibrils

Answer 29

pre- fibrils are proteins that become misfolded but are succesfully degraded

Question 30

Describe Amyloidosis

Answer 30

* When prefribris (ß- sheets) fail to be degraded, they aggregate together and form amyloid fibrils * Excess degradation * more deposition * Organ dysfunction

Question 31

What process is caused by the accumulation of amyloid repeated ß- sheet structure from partially degraded proteins ?

Answer 31

"seeding" * process of conversion and deposition

Question 32

Congo red dye

Answer 32

deposition of amyloid structures seen red in light microscopy

Question 33

Apple- green birefringence

Answer 33

amyloid structures seen under polarized light

Question 34

Prion disease

Answer 34

* PrP^c normal is a- helix rich with litle or no ß- sheets * PrP^sc turns rich with ß- sheets Diseased is insoluble and becomes accumulated which are resistant to degradation

Question 35

Describe Prion Diseases

Answer 35

* spongiform degeneration * astrocytic gliosis in the CNS * Rapid Brain shrinkage ad deterioration * In humans: Creutzfeld- Jakob Disease * transmissible via Mad cow disease

Question 36

Creutzfeld- Jakob Disease-CJD (Prion disease in humans)

Answer 36

* Type 1:Sporadic (commonest- 85%) * somatic cell mutation OR * Rare spontaneous refolding of PRP^c to PRP^sc * Type 2: Familial CJD

Question 37

Alzheimer disease

Answer 37

* Amyloid accumulation of Aß42 having characteristic ß- pleated sheets, precursor of Aß42 is APP (amyloid precursor protein) * Neurofibrillary tangles

Question 38

Neurofibrillary tangles

Answer 38

* Alzheimers * hyperphosphorylated tau proteins * inside neurons

Question 39

Parkinson's disease

Answer 39

* multifactorial * important defect in ubiquitin proteasome pathway to degrade a- synuclein which leads to its accumulation (bound to ubiquitin)-----\> inclusions (Lewy bodies)

Question 40

Describe Parkinson's Disease

Answer 40

* Face is expressionless * Tremors * pill- rolling tremor * Bradykinesia (slow movement) * Rigid muscles ----\> limited ROM * Shuffling gate * Impaired posture and balance * speech changes