Module 4 Section 4 Flashcards

1
Q

Transfer RNA

A

-relatively small non-coding RNA, single stranded, approx 73-93 nucleotide residues long

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2
Q

tRNA amino acid arm

A
  • has nucleotide sequence 5’-CCA-3’ at 3’ term
  • terminal A residue is where AA attach
  • each tRNA carries specific AA, makes it aminoacylated (AA bound to it)
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3
Q

tRNA anticodon arm

A
  • at opposite end of tRNA to the AA arm

- 3 nucleotide sequence that base pairs complementary to the mRNA

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4
Q

tRNA nomenclature

A
  • Uncharged: tRNA^Leu

- Charged: Leu-tRNA^Leu

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5
Q

“charging” of tRNA

A
  • done by aminoacyl-tRNA synthetases
  • the ribosome does NOT control if tRNA improperly charged
  • different classes of synthetases have different points of contact - some have several, some don’t interact with the anticodon
  • certain nucleotides on the tRNA code for specific synthetases to interact with the tRNA
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6
Q

Wobble base pairing

A
  • would expect 61 tRNA (64-3 STOP codons), is not the case, much fewer due to wobble
  • still pyrimidine-purine, but orientation is slightly off (G-U)
  • 1st and 2nd position of codon ALWAYS have Watson-Crick pairing
  • 3rd codon position can have wobble
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7
Q

Inosine

A
  • wobble nucleotide, converted from adenosine through post-transcriptional modification of tRNA
  • modification aided by ADAR (adenosine deaminase acting on RNA), hydration rxn and removes NH3
  • CAN WOBBLE PAIR WITH A, C or U
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8
Q

Crick’s rules of wobble hypothesis

A
  1. 1st 2 bases of mRNA codon ALWAYS Watson-Crick base pairs with corresponding tRNA anticodon
  2. A) when in 1st base of ANTICODON (in 5’-3’) is C or A, tRNA only recognizes one codon
  3. B) When the 1st base of the ANTICODON (5’-3’) is G or U, tRNA can recognize 2 different codons
  4. C) When the 1st base of the ANTICODON (5’-3’) is I, tRNA can recognize 2 different codons (A, U or C in the complementary position)
  5. codons that differ in 1st 2 bases require different tRNAs
  6. Minimum of 32 tRNAs required to translate all 61 codons
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9
Q

Ribosome

A
  • 60% rRNA, 40% r-protein, rRNA is functional component
  • found free in cytoplasm or attached to endoplasmic reticulum
  • Prok: 70S ribosome, Euk: 80S ribosome
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10
Q

Ribosome subunits

A
  1. Small (30S/40S)
    - contains 16S rRNA
    - 21 proteins: RpS1-RpS21
  2. Large (50S/60S)
    - 5S, 23S rRNA
    - 36 proteins: RpL1-RpL36
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11
Q

Svedberg Units

A
  • S

- rate of sedimentation under a specific G force

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12
Q

Ribosomal functional centers

A
  • A Site: aminoacyl tRNA entry
  • P Site: Peptidyl tRNA - growing peptide chain
  • E Site: Exit site for uncharged tRNAs
  • Decoding center: in small subunit, proofreading of codon-anticodon base pairing
  • Peptidyl transferase center: in large subunit, transfer of polypeptide chain from peptidyl-tRNA in P site to aminoacyl tRNA in A site (no proofreading of charge of tRNA)
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13
Q

Steps of translation (without termination)

A
  1. initiator tRNA charged with methionine
  2. translation initiates with assembly of mRNA and aminoacylated tRNA on the small subunit, large subunit then joins to form active ribosome
  3. polypeptide elongation occurs in successive cycles of aminoacyl-tRNA binding and peptide bond formation
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14
Q

Initiation of translation

A
  • most highly regulated stage of translation
    1. alignment of mRNA on the small ribosomal subunit
  • IF-3 associates with the small subunit to prevent the premature assembly of the ribosome
    2. Association of a charged initiator tRNA with the AUG start codon in the P site
  • tRNA moved to ribosome by IF-2
  • IF-1 blocks A site to ensure correct alignment with AUG
    3. Recruitment of large ribosomal subunit to form complete initiation complex
  • IFs dissociate from the complex (consumes GTP)
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15
Q

tRNAs specific for Methionine

A
  • tRNA^fMet is initiator tRNA, has a formyl group added to amino group of the aminoacyl tRNA
  • N-formylmethionine
  • blocks the Met on its N-terminus so it HAS to be the start, can’t add to carboxyl group
  • tRNA^fMet interacts with IF-2
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16
Q

Charging of tRNA^fMet

A

-2 step process:
-Met-tRNA synthetase charges both tRNA^Met and tRNA^fMet
-transformylase adds formyl group to Met, prevents charged tRNA from participating in elongation
Equivalent system in eukaryotes:
-tRNA^Met vs. tRNAi^Met
-tRNAi^Met interacts with eukaryotic equivalent of IF-2

17
Q

Shine-Dalgarno sequence

A
  • in prokaryotes
  • initiating AUG guided to correct position by Shine-dalgarno sequence
  • 4-9 purines, 8-13 nt upstream of AUG
  • has complementarity to 16S rRNA of small subunit
  • also called ribosomal binding site (RBS)
18
Q

Kozak Sequences

A
  • in eukaryotes
  • consensus sequence surrounding the initiation site, aids in initiation
  • NOT functional equivalent to RBS
  • mRNA contacts the anticodon arm of Met-tRNAi^Met
  • purine nucleotide 3 residues before start codon and G residue immediately following start codon thought to increase translation (through interaction with anticodon arm)
19
Q

Kozak vs. Shine-Dalgarno

A
  • Shine-dalgarno associated with alignment
  • Kozak interacts with anticodon arm of initiator tRNA
  • both are conserved sequences in Prok/Euk but serve slightly different purposes
20
Q

Polycistrinsic mRNA

A
  • multiple proteins from one mRNA
  • ONLY in prokaryotes, Euk: 1mRNA = protein
  • can have overlapping or non-overlapping genes
21
Q

Overlapping Genes

A
  • no new Shine-Dalgarno for realignment
  • open reading frames for the genes overlap, generally have overlapping start/stop codons (ie. AUGA)
  • ribosomes terminating translation of upstream message can initiate downstream message by shifting reading frame
22
Q

Non-Overlapping genes

A
  • the open reading frame for each gene is distinct

- genes have separate Shine-Dalgarno sequences

23
Q

GTP

A
  • energy of translation

- guanosine triphosphate

24
Q

mRNA circularization

A
  • exclusively in eukaryotes
    1. mediates ribosome binding
    2. promotes transcriptional efficiency
    3. Ensures complete processing
  • each mRNA can be translated multiple times
  • 1 mRNA bound by multiple ribosomes = polysome