Chapter 6 - How Cells Read the Genome: From DNA to Proteina

Question 1

What can happen to RNA that creates incorrect outcome?

Answer 1

1. Can be transported to cytosol prematurely

2. Can become broken or damaged in the cytosol

Question 2

Tetracycline

Answer 2

1. Acting only on bacteria

2. Blocks binding of aminoacyl-tRNA to the A site of ribosome.

Question 3

Streptomycin

Answer 3

1. Acting only on bacteria
2. Prevents the transition from translation initiation to chain elongation
3. Also causes miscoding

Question 4

Chloramphenicol

Answer 4

1. Acting only on bacteria

2. Blocks the peptidyl transferase reaction on ribosome

Question 5

Erythromycin

Answer 5

1. Acting only on bacteria

2. Binds in the exit channel of ribosome and thereby inhibits elongation of the peptide chain

Question 6

Rifamycin

Answer 6

1. Acting only on bacteria

2. Blocks initiation of RNA chains by binding to RNA polymerase (prevents RNA synthesis).

Question 7

Puromycin

Answer 7

1. Acting on bacteria and eukaryotes

2. Causes the premature release of nascent polypeptide chains by its addition to the growing chain end

Question 8

Actinomycin D

Answer 8

1. Acting on bacteria and eukaryotes

2. Binds the DNA and blocks the movement of RNA polymerase (prevents RNA synthesis)

Question 9

Cycloheximide

Answer 9

1. Acting only on eukaryotes

2. Blocks the translocation reaction on ribosomes

Question 10

Anisomycin

Answer 10

1. Acting only on eukaryotes

2. Blocks the peptidyl transferase reaction on ribosome

Question 11

α-Amanitin

Answer 11

1. Acting only on eukaryotes

2. Blocks mRNA synthesis by binding preferentially to RNA polymerase II

Question 12

How do cells avoid translating broken mRNAs?

Answer 12

The 5’ cap and poly-A tail are recognized by the translation-initiation machinery before translation

Question 13

nonsense-mediated mRNA decay

Answer 13

1. Most powerful mRNA surveillance system
2. Eliminates defective mRNAs before they move away from the nucleus
3. Brought into play when cell determines a nonsense (stop) codon

Question 14

Where are RNAs processed?

Answer 14

In the nucleus

Question 15

First round of translation

Answer 15

1. 5’ end emerges from nuclear pore where a ribosome begins to translate
2. Normally stop codon in last exon
3. If a nonsense codon is found early on translation stop and mRNA degrades quickly
4. First round allows for cells to test fitness of each mRNA as it exists nucleus.

Question 16

Nonsense-mediated decay may have been especially important in…

Answer 16

Evolution - allowing eukaryotic cells to more easily explore new genes formed by DNA rearrangements, mutations or alternative patterns of splicing by selecting only those mRNAs for translation that can produces full-length protein.

Question 17

Nonsense mediated decay is also important for…

Answer 17

1. Cells of developing immune system, where DNA rearrangements that occur often generate premature termination codons.
2. System degrades the mRNA produced thereby avoiding potential toxic effects of truncated proteins

Question 18

Nonsense-mediated surveillance pathway also plays an important role in

Answer 18

1. Mitigating symptoms of many inherited human diseases.
2. If one has a mutated allele and a regular allele, the system allows for the mutated mRNA to be degraded and only allow the regular allele expressed mRNA to continue.
3. This protects cells/organism from worse off symptoms.

Question 19

Proteins bury their…

Answer 19

Hydrophobic residues

Question 20

Why do most proteins need chaperones?

Answer 20

They become kinetically trapped

Question 21

Molecular chaperones specifically recognize

Answer 21

1. Incorrect, off-pathway configurations
2. by their exposure of hydrophobic surfaces,
3. which in correctly folded proteins are typically buried on the inside

Question 22

What are many molecular chaperones called?

Answer 22

1. Heat shock protein (hsp)

2. Because synthesized in dramatically different amounts after a brief exposure of cells to an elevated temperature

Question 23

What is the name of hsp70 that helps fold protein in the cytosol?

Answer 23

BIP

Question 24

How do hsp help proteins fold?

Answer 24

1. They share affinities for the exposed hydrophobic patches on incomplete protein
2. they hydrolyze ATP
3. Often binding and releasing their protein substrates with each ATP hydrolysis cycle

Question 25

How does hsp70 work?

Answer 25

1. Acts early in the life of many proteins (often before protein even leaves the ribosome) 2. With each monomer of hsp70 binding to a string of about four of five hydrophobic amino acids 3. On binding ATP, hsp70 releases the protein into solution allowing it a chance to refold

Question 26

How does hsp60 work?

Answer 26

1. Form large barrel-shaped structures that form large isolation chamber 2. acts after a protein has been fully synthesized. 3. Substrate protein first captured via the hydrophobic entrance to the chamber. 4. Protein is released into the interior of the chamber (lined with hydrophilic surfaces) 5. GroES cap caps the hsp60 6. ATP hydrolyzed, lid pops off and protein escapes (regardless of whether folded correctly or not). 7. Cycle continues until protein properly folded

Question 27

What is the lid of hsp60?

Answer 27

GroES cap

Question 28

What are possible causes of sizable exposed patch of hydrophobic amino acids?

Answer 28

1. Failed to fold correctly after leaving ribosome 2. Suffered an accident that partly unfolded it at a later time 3. Failed to find its normal partner subunit in a larger protein complex

Question 29

Proteasome

Answer 29

1. Protein-destruction machine 2. ATP-dependent protease 3. Makes up 1% of cell protein

Question 30

Proteasome core description

Answer 30

1. Each contain a central hollow cylinder (20S core Proteasome) former from multiple protein subunits that assemble as a stack of four heptameric rings 2. Main active sites are inside he channel

Question 31

Proteasome ends description

Answer 31

1. Each end of the core is normally associated with a large protein complex (19S cap) 2. contains a six subunit protein ring 3. Targets proteins are threaded into the Proteasome core where degraded 4. The threading reaction unfolds the protein exposing them to the proteasome core where they are degraded. 5. Cap proteins are known as unfoldases (AAA protein).

Question 32

How does the proteasome recognize abnormal proteins?

Answer 32

Abnormal proteins are marked with ubiquitin on lysine 48.

Question 33

Activation of degradation signal

Answer 33

1. Phosphorylation by protein kinase 2. Unmasking by protein dissociation 3. Creation of destabilizing N-terminus (most powerful degradation signal)

Question 34

Activation of ubiquitin ligase

Answer 34

1. Phosphorylation by protein kinase 2. Allosteric transition caused by ligand binding 3. Allosteric transition caused by protein subunit addition