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Biochemistry I > Genetic code + translation > Flashcards

Genetic code + translation Flashcards

1
Q

What are pri-miRNAs?

What is their function?

A

primary transcripts miRNAs transcribed by RNA pol II

  • promoting mRNA degradation
  • stimulating poly-A-tail degradation
  • inhibition of translation
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2
Q

What is a codon?

How many are there?

A

three letter base code w/ 64 possibilities

→ coding for 20 different amino acids

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3
Q

List the 5 features of the genetic code.

A
  • degenerate
  • unambiguous
  • non-overlapping
  • non punctuated
  • universal

DUNo NpU

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4
Q

The genetic code is non-punctuated.

What does it mean?

A

translated continuously until stop codon reached, no bases skipped

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5
Q

The genetic code is non-overlapping.

What does it mean?

A

each nucleotide is part of only 1 codon and only read once

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6
Q

The genetic code is degenerate.

What does it mean?

A

18 of 20 AAs coded by more than 1 codon

only exceptions: Met and Trp

(most are 4-fold degenerate at 3rd position)

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7
Q

The genetic code is almost universal.

What does it mean?

A

most codons code for the same AA in different organism

BUT: not true for mitochondria

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8
Q

The genetic code is unambiguous.

What does it mean?

A

each triplet nucleotide codon in mRNA codes only for 1 specific AA

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9
Q

Which codons code start and stop signals for translation?

A
  • AUG → start signal, codes for Met
  • UAA, UAG, UGA → stop signal to terminate polypeptide translation
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10
Q

There are 2 amino acids which are not directly coded for in the genetic code?

Which amino acids and how are they translated?

A

2 stop codons:

  • UGA → selenocystein
  • UAG → pyrrolysine (not present in humans)

efficiency of translation of those 2 AAs depends on protein that is synthsized in translation initiation factors

just know, wiki says UAG codes for pyrrolyisine, lecture says UGA does

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11
Q

What is the function of tRNA?

A

each tRNA has specific anticodon and carries an AA that is specific for its anticodon

→ use ribosome to bind to complementary codons on mRNA, then transfer their AA to form polypeptide

⇒ at least 20 types of tRNA in each cell

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12
Q

Describe the structure of tRNA.

What are the functions of its structural components?

A

4 arms form cloverleaf-like secondary structure

  • acceptor arm with posttranslationally added CCA 3’-terminal → specific AA binds here
  • TψC contains ψ = pseudouridine →binds to site of protein synth. on ribosome
  • anticodon loop → binds to rRNA
  • D arm often contains dihydrouridine → important for recognition of aminoacyl-tRNA synthetase
  • 5’ terminal phosphate group
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13
Q

What is the function of the CCA tail?

How is it special in eukaryotes?

A

AA specific for tRNA binds here

in eukaryotes added during processing of tRNA, hence not coded by tRNA gene

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14
Q

Some tRNA bases are often modified.

How are they modified and what is their function?

A

often by methylation (or deamidation)

→ affect the tRNA’s interaction with ribosomes

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15
Q

What is the function of aminoacyl-tRNAs?

They are synthesized by which enzyme?

A

tRNA carrying its specific “activated” AA attached to its terminal 3’-OH of CCA

formed by individiual aminoacyl-tRNA synthetases

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16
Q

What is the function of aminoacyl-tRNA synthetase?

A
  1. AA binds to synthetase, activated through the linkage of its -C group directly to AMP → 5’ aminoacyl AMP
    NOTE: driven by hydrolysis of ATP molecule that donates the AMP
  2. tRNA binds to synthetase, AMP-linked -C group on AA then transferred to a -OH group at the 3ʹ of the tRNA acceptor arm → forms aminoacyl-tRNA w/ activated ester linkage

NOTE: irreversible

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17
Q

List some features of the aminoacyl-tRNA synthetase.

A
  • one synthetase for each AA (one AA for each tRNA)
  • high fidelity (1 incorrect AA/104 - 105 reactions) due to proofreading mechanism
  • use identity elements on tRNA to distinguish similar tRNAs
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18
Q

Explain the proofreading mechanism of aminoacyl-tRNA synthetases.

A

select correct AA by a two-step mechanism

  1. correct AA has highest affinity for the active-site pocket of its synthetase
  2. adenylated AA tried to force into a second editing pocket in the enzyme → excludes correct AA, while allowing access by closely related AAs
    if matching: AA is removed from AMP (or from the tRNA itself if the aminoacyl-tRNA bond has already formed) by hydrolysis

= hydrolytic editing (analogous to the exonucleolytic proofreading by DNA polymerases)

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19
Q

What is wobbling?

A
  • first 2 base pairs of codon-anticodon are Watson-Crick base pairs
  • last base pair can wobble, hence form Hoogsteen base pair

→ main reason for degeneracy of genetic code

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20
Q

Which nucleotides on anticodon can wobble?

List pairs.

A
  • G also w/ U
  • U also w/ G
  • I w/ A, U, C
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21
Q

Where does translation and transcription happen in pro- and eukaryotes?

A
  • in prokaryotes: coupled,
    translation on free ribosomes and polyribosomes
  • in eukaryotes: compartmentalized, transcription in nucleus, translation on free cytoplasmic ribosomes and rER
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22
Q

Describe the general structure of a ribosome.

A

differences in number/size of their rRNA and protein components

  • small subunit: provides framework on which tRNAs are accurately matched to codons of mRNA
  • large subunit: catalyzes the formation of peptide bonds that link AAs together into a polypeptide chain

+ additionally proteins associated w/ subunits on surface

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23
Q

Describe the structure and weight of both ribosomal subunits in pro- and eukaryotes.

A

S refers to Svedberg units, describes weight

  • 70S ribosomes = prokaryotic ribosomes
    • large subunit has 23S and 5S rRNA
      → w/ proteins: 50S rRNA
    • small subunit has 16S
      → w/ proteins: 30S rRNA
  • 80S ribosomes = eukaryotic ribosomes
    • large subunit has 28S and 5S rRNA
      → w/ proteins: 60S rRNA
    • small subunit has 18S
      → w/ proteins: 40S rRNA

​→ eukaryotic ribosomes are heavier due to larger ribosomes + more associated proteins

24
Q

Where are eukaryotic ribosomes synthesized?

A

in the nucleolus

25
Differentiate btw binding sites on ribosomes. Function?
form complex w/ mRNA and tRNA, connect AAs at A site to the growing polypeptide * **mRNA-binding site:** on small subunit * **E site:** transiently holds "used" deacylated tRNA before it **_e_**xits * **P site:** holds tRNA carrying growing **_p_**olypeptide chain * **A site:** holds tRNA w/ next **_A_**A to be added
26
In which direction does translation occur?
mRNA translated in **5'→3'** direction _NOTE:_ **N-terminal** end of a protein is _made first_, then AAs added one by one to the C-terminus of the polypeptide chain
27
In which direction is the anticodon on tRNA read?
**3' → 5'** REMEMBER: left side of tRNA with short P-terminal is 3', hence left base on anticodon read first
28
Explain the general mechanism of translation. What are the 3 basic steps?
1. **initiation:** protein synthesis starting at _AUG codon_ 2. **elongation:** _peptide bonds_ are formed btw 2 adjacent AAs, nascent polypeptide remains attached C-terminally via tRNA to ribosome 3. **termination:** when _stop codon_ reached, ester bonds btw protein and tRNA hydrolytically cleaved
29
What is mono-, polycistronic mRNA? Where do both types usually occur?
* **polycistronic:** mRNA codes for more than protein → common for _prokaryotic_ mRNAs * **monocistronic:** mRNA codes only for one peptide → common for _eukaryotic_ mRNAs
30
What are the _main distinguishing_ features of initiation of translation in prokaryotes?
* **no preinitiation complexes** * use **Shine-Delgarno sequence** * use **fMet** (_formylmethionyl_) instead of Met to bind to AUG start codon * require _much less_ initiation factors (**IFs**) (in eukaryotes those are called eIF) * **not regulated by phosphorylation**
31
Prokaryotic start codons are different than eukaryotic ones.. How?
have **Shine-Delgarno sequence** upstream of _AUG start codon_ on mRNA * untranslated 3 - 9bp sequence * binds to _small subunit_ (16S rRNA) _NOTE:_ ONLY in prokaryotes
32
Explain the stepwise process of prokaryotic initiation.
1. **IF-3 and IF-1** bind to small subunit 2. _small subunit_ associates w/ mRNA 3. **GTP-IF-2** binds to P site of small subunit, then pairs **fMet-tRNA** to AUG codon on mRNA 4. _large subunit_ associates, hydrolyzes GTP to **GDP + Pi** 5. all **IFs are released**, complete _70S initiation complex_ is formed
33
What are the 3 steps of the elongation of translation?
1. binding of **aminoacyl-tRNA to A site** 2. **peptide bond formation** 3. **translocation** + **expulsion** of deacylated tRNA from P- and E-sites
34
Elongation can be divided into 3 basic steps.. What happens in the 1st step _in prokaryotes_, after the 70S complex is formed?
_binding of aminoacyl-tRNA to A site_ 1. ​​complex of **EF-Tu-GTP, aminoacyl-tRNA,** bind to A site, EF-Tu checks if correct aminoacyl-tRNA bound 2. when correct tRNA bound, **EF-Tu hydrolzes GTP** → EF-Tu-GDP and Pi released
35
What is the function of EF-Ts?
_GEF protein_ **releases GDP from EF-Tu,** **rebinds GTP** for new elongation
36
Elongation can be divided into 3 basic steps.. What happens in the 2nd step _in prokaryotes_, after 2 aminoacyl-tRNAs are bound to the ribosome?
_peptide bond formation_ catalyzed by **adenine in peptidyl transferase center** of large ribosomal subunit _nucleophilic attack_ of C-terminal of bound peptidyl-tRNA on P site by ⍺-N group of aminoacyl-tRNA on A site ⇒ attachment of _nascent peptide chain to A site_, deacetylated tRNA remains in P site
37
Elongation can be divided into 3 basic steps.. What happens in the last step _in prokaryotes_, after formation of a new peptide bond?
_translocation + expulsion_ 1. **EF-G-GTP** binds 2. hydrolysis of GTP causes **translocation of ribosome by one codon** → deacylated tRNA now on E site, peptidyl-tRNA on P site, A site empty again 3. EF-G-GDP released, deacetylated tRNA leaves ribosome
38
How is eukaryotic elongation different from prokaryotic?
only different translation factors used * **eEF1A** instead of EF-Tu (association of aminoacyl-tRNA w/ ribosome) * **eEF1B** instead of EF-Ts (GEF) * **eEF2** instead of EF-G (translocation)
39
How is translation terminated in prokaryotes?
1. when _stop codon reached_, RF associates instead of new aminoacyl-tRNA at A site * **RF-1** for UAA, UAG * **RF-2** for UAA, UGA 2. **RF-3-GTP** also binds, hydrolzyes its GTP 3. **RF-1 or 2** now hydrolyzes peptidyl-tRNA, releasing the peptide → ribosome dissociates into subunits, mRNA, tRNA also released
40
How is termination in eukaryotes different from that in prokaryotes?
only different translation factors used * **eRF1** instead of RF-1 or RF-2: _recognizes all 3 stop codons_ * **eRF3** instead of RF-3 (hydrolysis of GTP) * ribosomal subunits dissociate when _new eIFs bind_
41
How come, eRF1 (or RF-1/2) able to bind to the mRNA?
due to its structural similarity to tRNA = **molecular mimicry**
42
Eukaryotic initiation is somewhat different from that in prokaryotes. What are the 4 general steps of the initiation here?
1. formation of **43S **_pre_**initiation complex** 2. formation of **48S **_pre_**initiation complex** 3. **scanning** of mRNA 4. formation of **80S initiation complex**​
43
Eukaryotic initiation can be divided into 4 basic steps.. What happens in the 1st step?
_formation of 43S preinitiation complex_ 1. **eIF1, eIF1A and eIF3** bind to small subunit 2. complex of **eIF2, Met-tRNA and GTP** bind to P-site
44
Eukaryotic initiation can be divided into 4 basic steps.. What happens in the 2nd step, after the 43S preinitiation complex has formed?
_formation of 48S preinitiation complex_ **multienzyme complex eIF4** binds to _5' cap_ of mRNA and to **poly-A binding protein I** (_PABP_) which is associated w/ _3' end of poly A tail_ → entire mRNA forms a _closed loop_, ensuring that only intact mRNA is translated
45
Eukaryotic initiation can be divided into 4 basic steps.. What happens in the 3rd step, after the 48S preinitiation complex has formed?
_scanning_ **eIF4** has **helicase activity**, starts unwinding mRNA in 5'→3' until it finds _AUG start codon_/**Kozak sequence** → when found, _Met binds_ to mRNA, _GTP hydrolyzed_, **eIF2-GDP** leaves 48S preinitiation complex
46
What is the Kozak sequence?
typical sequence in _eukaryotes_ **surrounding the AUG start codon** to intiate translation
47
Which factor has the GEF function in eukaryotes to restore eIF2-GTP
**eIF2B**
48
Eukaryotic initiation can be divided into 4 basic steps.. What happens in the 4th step, after the the 48S preinitiation has bind Met to the mRNA?
_formation of 80S initiation complex_ 1. **eIF5-GTP and eIF1A** associate w/ small ribosomal subunit 2. _large ribsomal subunit_ can now bind to 48S preininitiation complex due to eIF5, release of **eIF1 and eIF3** 3. large ribosomal subunit _hydrolyzes eIF5-GTP_, causing it to leave as well → 80S initiation complex is ready for elongation
49
How much energy is required to add 1 AA to the nascent polypeptide chain?
**4 macroergic bonds** (BUT: 1 ATP, 2 GTP) 1. **1 ATP to AMP** needed for charging of tRNA 2. 1 GTP needed for binding of aminoacyl-tRNA on A site 3. 1 GTP needed for translocation of ribosome
50
Only the translation of eukaryotes is regulated. What are the 2 mechanisms?
eIF2 and eIF4 not present in prokaryotes * **eIF2** can be **phosphorylated**, causing _inhibition of translation_ * **eIF4** can be **phosphorylated**, _prerequisite for translation_
51
What is the mechanism behind eIF2 phosphorylation?
eIF2 needs bound GTP to be active can be **phosphorylated at α-subunit**, then **eIF2B (GEF) cannot be released** to exchange GTP w GDP → _remains inactivated_
52
Which 4 enzymes are able to phosphorylate eIF2, hence inactivating translation?
* _**HRI** (heme regulated inhibitor):_ present in erythrocyte precursors, activated in response to heme deficit to switch off translation of globin mRNA as long as deficit persists * **_GCN2_** _(general AA control):_ activated in response to free tRNAs, as a signal when cell is lacking AAs for translation * **_PERK_** _(pancreatic kinase of ER lumen)_ activated when unfolded proteins in ER accumulate * **_PKR_** _(RNA dependent protein kinase)_ activated in response to binding of dsRNA, as can be found in some viral infections
53
Explain how eIF4 contributes to the regulation of translation in eukaryotes.
eIF4 has multiple subunits * **eIF4E** binds _5'cap and eIF4G_ * cannot bind cap if associated w/ **eIF4-BP** (binding protein) * only binds eIF4-BP if _NOT phosphorylated_ * eIF4-BP is phosphorylated by _mTOR_ * _​_**eIF4G** binds to small ribosomal subunit
54
Which signals activate mTOR, which inhibit it?
mTOR (mammalian target of rapamycin) * _activated_ in response to **GFs**, **accumulating AAs** * _inhibited_ by **hypoxia, AMP and rapamycin**
55
How do some viruses trigger the translation of their mRNA once they infected the cell?
_initiate their translation **independent of 5' cap**_ 1. **cleave eIF4G**, suppressing translation of host's mRNA → creates a C-terminal on eIF4G 2. small ribosomal subunit, containing cleaved eIF4G now binds to **IRES** (_internal ribosome entry site_) on viral mRNA
56
List some viruses that have specific IRES, hence are able to translate their mRNA in a cap indpendent manner.
* **picornaviruses** (ex: poliovirus) * **hepatitis c virus** * **encephalomyocarditis virus** (_EMCV_) * **cricket paralysis virus** (_CrPV_)
57
List some antibiotics and their effect on translation.
inhibit translation

Biochemistry I (13 decks)

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