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Biochem 524 > Chapter 6 - How Cells Read the Genome: From DNA to Proteina > Flashcards

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

1
Q

What can happen to RNA that creates incorrect outcome?

A
  1. Can be transported to cytosol prematurely

2. Can become broken or damaged in the cytosol

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2
Q

Tetracycline

A
  1. Acting only on bacteria

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

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3
Q

Streptomycin

A
  1. Acting only on bacteria
  2. Prevents the transition from translation initiation to chain elongation
  3. Also causes miscoding
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4
Q

Chloramphenicol

A
  1. Acting only on bacteria

2. Blocks the peptidyl transferase reaction on ribosome

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5
Q

Erythromycin

A
  1. Acting only on bacteria

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

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6
Q

Rifamycin

A
  1. Acting only on bacteria

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

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7
Q

Puromycin

A
  1. Acting on bacteria and eukaryotes

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

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8
Q

Actinomycin D

A
  1. Acting on bacteria and eukaryotes

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

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9
Q

Cycloheximide

A
  1. Acting only on eukaryotes

2. Blocks the translocation reaction on ribosomes

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10
Q

Anisomycin

A
  1. Acting only on eukaryotes

2. Blocks the peptidyl transferase reaction on ribosome

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11
Q

α-Amanitin

A
  1. Acting only on eukaryotes

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

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12
Q

How do cells avoid translating broken mRNAs?

A

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

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13
Q

nonsense-mediated mRNA decay

A
  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
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14
Q

Where are RNAs processed?

A

In the nucleus

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15
Q

First round of translation

A
  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.
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16
Q

Nonsense-mediated decay may have been especially important in…

A

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.

17
Q

Nonsense mediated decay is also important for…

A
  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
18
Q

Nonsense-mediated surveillance pathway also plays an important role in

A
  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.
19
Q

Proteins bury their…

A

Hydrophobic residues

20
Q

Why do most proteins need chaperones?

A

They become kinetically trapped

21
Q

Molecular chaperones specifically recognize

A
  1. Incorrect, off-pathway configurations
  2. by their exposure of hydrophobic surfaces,
  3. which in correctly folded proteins are typically buried on the inside
22
Q

What are many molecular chaperones called?

A
  1. Heat shock protein (hsp)

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

23
Q

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

A

BIP

24
Q

How do hsp help proteins fold?

A
  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
25
Q

How does hsp70 work?

A
  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
26
Q

How does hsp60 work?

A
  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
27
Q

What is the lid of hsp60?

A

GroES cap

28
Q

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

A
  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
29
Q

Proteasome

A
  1. Protein-destruction machine
  2. ATP-dependent protease
  3. Makes up 1% of cell protein
30
Q

Proteasome core description

A
  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
31
Q

Proteasome ends description

A
  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).
32
Q

How does the proteasome recognize abnormal proteins?

A

Abnormal proteins are marked with ubiquitin on lysine 48.

33
Q

Activation of degradation signal

A
  1. Phosphorylation by protein kinase
  2. Unmasking by protein dissociation
  3. Creation of destabilizing N-terminus (most powerful degradation signal)
34
Q

Activation of ubiquitin ligase

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

Biochem 524 (6 decks)

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