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S25 Molecular Biology > L12: Translation > Flashcards

L12: Translation Flashcards

(55 cards)

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1
Q

define translation

A

the order of nucleotides in messenger RNA (mRNA) is converted into the linear sequence of amino acids in a protein

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2
Q

what is messenger RNA (mRNA)

A

information contained in the open-reading frame (ORF)

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3
Q

mRNA - what is the open reading frame (ORF)

A

a contiguous, non-overlapping string of codons that specifies protein sequence

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4
Q

Open reading frame (ORF) - what are the start and stop codons

A
  • Start codons: AUG
  • stop codons: UAA, UAG, UGA
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5
Q

what is transfer RNA (tRNA)

A
  • an adapter molecule between codons and amino acids
  • 3’ terminus has a 5’-CCA-3’ sequence that binds cognate amino acids
  • developed by Crick’s Adaptor Hypothesis
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6
Q

tRNA secondary structure

A
  • resembles a clover leaf:
    1. acceptor stem
    2. anticodon loop
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7
Q

tRNA secondary structure - acceptor steam

A

attachment site for amino acid

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8
Q

tRNA secondary structure - anticodon loop

A

contains anticodon which base pairs with the codon

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9
Q

tRNA tertiary structure

A
  • “L” shape
  • is called aminoacyl-tRNA when the RNA is “charged”
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10
Q

tRNA tertiary structure - “charging” of tRNAs

A
  • amino acid is attached to 3’ terminal A nucleotide of tRNA
  • the linkage is a high energy bond between tRNA and amino acid - yields energy when cleaved
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11
Q

tRNA tertiary structure: “charging” of tRNAs - aminoacyl-tRNA synthetase

A
  • enzyme that charges tRNA
  • each amino acid has one dedicated aminoacyl-tRNA synthetase
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12
Q

what are ribosomes

A
  • it is what makes the polypeptide sequence from mRNA
  • its is comprised of both proteins and RNA
  • consists of 2 subunits:
    1. large subunit
    2. small subunit
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13
Q

ribosomes - why is it important for eukaryotes to separate transcription and translation

A

RNA processing and splicing needs to occur after transcription

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14
Q

what are ribosomes - large subunit

A

contains peptidyl transferase center that forms peptide bonds between amino acids

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15
Q

ribosomes: large subunit - how is the peptide bond created

A
  • dehydration reaction - water is kicked out
  • bond is formed between the carboxyl and amino group
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16
Q

ribosomes - small subunit

A

contains decoding center where mRNA codons are read by charged tRNAs

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17
Q

ribosomes - eukaryotes vs prokaryotes

A
  • prokaryotes are smaller and eukaryotes are larger
  • but there are individual ribosomes with differing sizes
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18
Q

rRNA processing

A
  • rRNA begins as a single transcript (pre-rRNA) that is cleaved
  • done so cleaved parts can be incorporated into the ribosome
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19
Q

explain the ribosome cycle

A
  1. ribosome subunits assemble on RNA
  2. mRNA is translated into a polypeptide
  3. ribosome dissociates
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20
Q

ribosome cycle - what is a polysome

A
  • each mRNA can be translated by more than one ribosome simultaneously
  • so a transcript can have many ribosomes on it
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21
Q

what direction is a polypeptide synthesized in?

A
  • amino-to carboxy direction
  • each new amino acid is added to the carboxyl terminus of a growing polypeptide chain
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22
Q

explain peptide bond formation

A
  • called a peptidyl transferase reaction
  • involves:
    1. peptidyl-tRNA
    2. aminoacyl-tRNA
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23
Q

peptide bond formation - peptidyl-tRNA

Study These Flashcards
A
  • attached to a growing polypeptide chain
  • the one already in ribosome
24
Q

peptide bond formation - aminoacyl-tRNA

Study These Flashcards
A
  • the incoming charged tRNA
  • the high energy bond is not broken during the formation of the new peptide bond
25
peptide bond formation - if the high energy bond in aminoacyl-tRNA is not being cleaved, which tRNA is being claved?
- **peptidyl-tRNA** - the high energy bond between the peptidyl-tRNA and polypeptide chain is broken - the released energy drives the formation of a new peptide bond
26
what are the steps of translation?
1. initiation 2. elongation 3. termination
27
initiation of translation - explain the ribosome tRNA binding sites
- A-site - P-site - E-site
28
initiation of translation: ribosome binding site - A-site
binding site for aminoacyl-tRNA
29
initiation of translation: ribosome binding site - P-site
binding site for peptidyl-site
30
initiation of translation: ribosome binding site - E-site
"exiting" site for tRNA released after the peptidyl transferase reaction
31
initiation of translation - what are the three requirements for initiation?
1. ribosome is recruited to the mRNA 2. the charged tRNA is placed at the P-site 2. the ribosome is precisely positioned over the start codon to establish the reading frame
32
initiation of translation - prokaryotic
- they contain a **ribosome binding site (RBS)** termed **Shine-Dalgarno** sequence - this sequence is complementary to a part of the **16S rRNA** in the small subunit. - the 16S rRNA base pairs with the Shine-Dalgarno sequence - this then places the start codon at the P-site - the initiator tRNA (charged with methionine) binds in the P-site of the ribosome
33
initiation of translation - eukaryotes
- translation is initiated by multiple features: 1. 5' cap recruits ribosome to transcript and scans for 1st 5'-AUG-3' 2. **Kozak** sequence surrounds AUG and enhances translation efficiency - the small subunit of the ribosome associates with the initiator tRNA **before** mRNA binding
34
initiation of translation: eukaryotes - Kozak sequence
- 5' - G/A NN **AUG** G - 3' - it interacts with the tRNA, not the ribosome
35
initiation of translation: eukaryotes - why is it important that the small subunit associates with the initiator tRNA before mRNA binding
- the complex is recruited to the 5' cap of the mRNA and it scans in the 5'-3' direction for the first AUG start codon - this start codon is recognized by the initiator tRNA anti-codon - once the start codon is recognized (via the initiator tRNA), the large subunit joins
36
translation elongation - three key events
1. correct aminoacyl-tRNA is loaded into the A-site (dictated by the codon on mRNA) 2. peptidyl transferase reaction occurs between the A-site and P-site polypeptide chain 3. peptidyl-tRNA in the A-site moves to the P-site
37
translation elongation - prokaryotes vs eukaryotes
process is similar for both
38
translation elongation: prokaryotes - elongation factors (EFs)
- EF-Tu - EF-G
39
prokaryotic translation elongation: elongation factors (EFs) - EF-Tu
- it guides the aminoacyl-tRNAs to the ribosome and complexes with GTP - EF-Tu-GTP-aminoacyl-tRNA complex interacts with the **factor-binding center** of large ribosomal subunit - GTP is then hydrolyzed and EF-Tu is released from tRNA and ribosome
40
prokaryotic translation elongation - what happens after EF-Tu is released?
a peptidyl transferase reaction occurs between the A-site amino acid and P-site polypeptide chain
41
prokaryotic translation elongation - after the peptidyl transferase reaction occurs, what must happen to the ribosome?
- translocation: - the P-site tRNA must move to the E-site - the A-site tRNA must move to the P-site - and the mRNA must move by three nucleotides to expose the next codon
42
prokaryotic translation elongation: EF-G - how does it start off?
- required for translocation 1. binds to GTP and associates with the ribosome 2. it contacts the **factor-binding center** of the large subunit and GTP is hydrolyzed
43
prokaryotic translation elongation: EF-G - what happens after the GTP is hydrolyzed?
3. EF-G undergoes conformational change and binds to the A-site 4. tRNA in A-site is pushed into P-site, which forces the P-site tRNA into the E-site
44
prokaryotic translation elongation: EF-G - what happens after the tRNA is pushed to the E-site?
5. base pairing between the tRNAs and mRNA is maintained, which moves the mRNA over by three nucleotides 6. EF-G-GDP and tRNA in the E-site are released and the ribosome is ready for the next amino acid
45
termination of translation
- one of the three stop codons enters the A-site - it is recognized by **release factors (RFs)** that free the polypeptide chain - triggers hydrolysis of the polypeptide chain from the tRNA in the P-site
46
in prokaryotes: how is translation regulated?
- ribosomal proteins repress their own synthesis - ribosomes consists of both RNA and protein - you need an appropriate number of proteins and ribosomal RNA
47
in prokaryotes: translation regulation - what happens when rRNA levels are high
- ribosomal proteins bind to high-affinity binding sites of rRNA - this promotes ribosomal assembly
48
in prokaryotes: translation regulation - what happens when all rRNA molecules are bound by ribosomal protein
- there is no need to make more protein - bc there are no high-affinity binding sites, the ribosomal protein binds to low-affinity binding sites near the RBS
49
in prokaryotes: translation regulation - what happens when the ribosomal protein binds to low-affinity binding sites?
- this prevents translation initiation - and prevents translation of a second ribosomal protein due to the transcript folding back (via intermolecular base pairing)
50
why is it important to have translational-dependent regulation of mRNA?
bc mRNA is susceptible to breaks due to it being single stranded
51
what is an example of translational-dependent regulation of aberrant mRNA?
stalled ribosomes on broken prokaryotic transcripts
52
stalled ribosomes on broken prokaryotic transcripts - how is this dealt with?
- the ribosome reaches the end of the broken transcript before encountering a stop codon - but it doesn't fall off, it is instead rescued by tRNA-mRNA chimera molecule (**tmRNA**) termed **SsrA**
53
stalled ribosomes on broken prokaryotic transcripts - what happens after tmRNA rescues the ribosome
- the tRNA-like 3' structure is charged with Ala and assembles with EF-Tu-GTP - it then binds to the A-site (only fits if the transcript is broken due to its large size) - it then undergoes a peptidyl transferase reaction
54
stalled ribosomes on broken prokaryotic transcripts - what happens after the peptidyl transferase reaction?
- translocation releases the broken transcript - the mRNA component of the tmRNA is translated
55
stalled ribosomes on broken prokaryotic transcripts - how does the ribosome dissociate?
- there are codes for 10 amino acid residues before reaching the stop codon which then allows for dissociation - the 10 amino acids serve as a signal for the cell to degrade the product - degradation prevents detrimental effects of truncated product to cell

S25 Molecular Biology (23 decks)

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