Functions and Dysfunctions of Protein Processing

Question 1

What is the difference in the ribosomal structure of prokaryotes and eukaryotes?

Answer 1

Prokaryotes contain a 30S and 50S subunit. Eukaryotes contain a 40S and 60S subunit.

Question 2

Describe the mechanism for the antibiotic Streptomycin.

Answer 2

Binds to 30S subunit and interferes with binding of fmet-tRNA and impairs initiation. Interferes with 30S subunit association with 50S subunit.

Question 3

Describe the mechanism for the antibiotic Clindamycin and erythromycin.

Answer 3

Binds to large 50S subunit, blocking translocation of the ribosome.

Question 4

Describe the mechanism for the antibiotic Tetracycline.

Answer 4

Binds to small 30S subunit, blocks entry of aminoacyl-tRNA to ribosomal complex and impairs elongation.

Question 5

Describe the mechanism for the antibiotic Chloramphenicol.

Answer 5

Inhibits peptidyl transferase activity and impairs peptide bond formation.

Question 6

Describe the mechanism of Shiga toxin and Ricin.

Answer 6

Binds to large 60S subunit (euk.), blocking entry of aminoacyl-tRNA to ribosomal complex.

Question 7

Describe the mechanism of Diphtheria toxin.

Answer 7

Inactivates GTP-bound EF-2, interfering with ribosomal translocation (euk.)

Question 8

Describe the mechanism of Cycloheximide.

Answer 8

Inhibits peptidyl transferase (euk.) and impairs peptide bond formation.

Question 9

Describe the mechanism of Puromycin.

Answer 9

Causes premature chain termination (prok/euk). It resembles the 3’ end of the aminoacylated-tRNA. Leads to premature chain release when attached.

Question 10

Describe the mutation that causes Sickle Cell Anemia and its effect on RBCs.

Answer 10

Arises from a missense mutation that changes Glutamic acid (negatively charged, hydrophilic) to Valine (hydrophobic). The change occurs in HBB, a subunit of hemoglobin. Deforms RBCs into sickle-cell shape, which have poor oxygen capacity and tend to clog capillaries.

Question 11

Describe the mutation that causes Duchenne Muscular Dystrophy (DMD) and its effect on RBCs.

Answer 11

Caused by a large out-of-frame deletion to the dystrophin gene, leading to little/no expression of dystrophin gene. Leads to muscle wasting.

Question 12

What is the difference between Duchenne Muscular Dystrophy (DMD) and Becker Muscular Dystrophy (BMD)?

Answer 12

DMD is an out-of-frame deletion. BMD is a milder version with an in-frame deletion.

Question 13

What sequence signal localizes a protein to the mitochondria?

Answer 13

N-terminal hydrophobic alpha-helix

Question 14

What sequence signal localizes a protein to the nucleus?

Answer 14

A Lysine and Arginine rich sequence

Question 15

What sequence signal localizes a protein to a peroxisome?

Answer 15

Serine, Lysine, and Leucine (SKL)

Question 16

In the secretory pathway, what sequence signal localizes a growing polypeptide and its ribosome to the Rough ER?

Answer 16

1 or 2 basic amino acids (Lys or Arg) near N terminus. Also, an extremely hydrophobic sequence on C terminus of the basic residues.

Question 17

In the secretory pathway, what sequence signal localizes a protein from the Golgi apparatus, back to the Rough ER?

Answer 17

Lysine, Aspartic acid, Glutamic acid, and Leucine (KDEL)

Question 18

In the secretory pathway, what sequence signal localizes a protein to the cell membrane?

Answer 18

N-terminal apolar region

Question 19

In the secretory pathway, what sequence signal localizes a protein to a lysosome?

Answer 19

Mannose-6-phosphate

Question 20

In the secretory pathway, what sequence signal localizes a protein to be secreted?

Answer 20

Tryptophan rich domain

Question 21

What is the purpose of heat shock protein 70 (HSP70)?

Answer 21

To protect unfolded proteins from degradation prior to entering the mitochondria.

Question 22

Which complexes transport a newly synthesized protein to the mitochondrial intermembrane space and the mitochondrial matrix?

Answer 22

TOM brings the protein into the intermembrane space. TIM brings the protein into the matrix.

Question 23

Describe how the ribosome-mRNA-peptide complex is localized to the Rough ER.

Answer 23

A signal recognition particle (SRP) binds to the ER-targeting signal and the ribosome during translation. SRP tethers the complex to the ER membrane, halting translation temporarily. Translation is resumed when the protein is directed into the ER lumen. Enzymes on the luminal side cleave the signal to release the protein.

Question 24

Describe I-cell disease.

Answer 24

When the tagging of lysosomal proteins with mannose 6P is defective. Leads to high plasma levels of lysosomal enzymes.

Symptoms: failure to thrive, developmental delays, cognitive delays, death by age 7

Question 25

What is the difference between chaperones and chaperonins?

Answer 25

Chaperones protect the protein and help it fold into its proper tertiary structure. Chaperonins have a barrel-shaped compartment that admit unfolded protein and catalyze their folding in an ATP-dependent manner.

Question 26

What is the difference between the two types of Glycosylation?

Answer 26

O-glycosidic links are formed with the hydroxyl groups of Serine and Threonine. N-glycosidic links are always formed with Asparagine. Precursor sugar transferred from phospho Dolichol.

Question 27

Describe the mechanism of Phosphorylation.

Answer 27

Formation of an ester bond between phosphate and OH of an amino acid by using the activity of Serine/Theronine and Tyrosine kinase.

Question 28

What is the role of protein Phosphorylation?

Answer 28

To regulate enzyme activity and protein function. Also in cell growth, proliferation, differentiation, and oncogenesis.

Question 29

Describe the mechanism of Disulfide Bond Formation.

Answer 29

These bonds form between thiol (SH) group of 2 Cysteine residues. Formation and reorganization of these bonds occur in the ER lumen. Facilitated by protein disulfide isomerases.

Question 30

Describe the mechanism of Acetylation.

Answer 30

Proteins are typically acetylated on lysine residues using an Acetyl CoA as the acetyl group donor. Catalyzed by Histone Acetyltransferases (HATs) and Histone deacetylases (HDAC).

Question 31

What cofactor and enzyme is essential for the post-translational modification of Collagen? What kind of symptoms arise from its deficiency?

Answer 31

Ascorbic acid which is needed for the activity of lysyl and prolyl hydroxylases. Deficiency results in skin, bone, and joint disorders.

Question 32

What are the proposed causes of Alzheimer’s Disease (AD)?

Answer 32

1. Misfolding/aggregation of Amyloid Beta Peptide in brain (extracellular) 2. Hyperphosphorylation of Tau, forming neurofibrillary tangles (intracellular)

Question 33

What is the difference between Familial forms and Sporadic forms of neurodegenerative disorders?

Answer 33

Familial forms are typically caused by mutations. Sporadic forms are typically caused by natural brain aging.

Question 34

Describe the mechanism that causes Parkinson’s Disease (PD).

Answer 34

Aggregation of alpha-synuclein (AS) forms insoluble fibrils which deposit as Lewy bodies in dopaminergic neurons in substantia nigra. Leads to reduced availability of dopamine.

Question 35

Describe the mechanism that causes Huntington’s Disease (HD).

Answer 35

Mutation in Huntingtin gene results in expansion of CAG triplet repeats. Results in Polyglutamine repeats in abnormal Huntingtin protein, leading to misfolds and aggregation. Selective death of cells in basal ganglia cause the symptoms.

Question 36

Describe the mechanism that causes Creutzfeldt-Jakob Disease (HD).

Answer 36

Caused by misfolding of prion proteins. It is transmissible; infection by misfolded proteins converts normal proteins to misfolded form. Belongs to Transmissible Spongiform Encephalopathies (TSEs).