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4BBY1013 Biochemistry > Protein Synthesis II > Flashcards

Protein Synthesis II Flashcards

1
Q

1) Define the terms triplet codes and degenerate when referring to the genetic code

A
  • Triplet codes: 3 bases code for 1 amino acid
    There are 20 amino acids to be produced so 4^3 = 64 provides a sufficient amount of combinations to form at least 20 amino acids
  • Degenerate: different codons can code for the same amino acid -> there are 3 special termination codons
  • AUG : methionine (start codon)
  • UAG, UGG, UGA (stop codons)
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2
Q

2) Describe the structure of a tRNA molecule

A
  • 75-90 nucleotides
  • cloverleaf structure due to extensive internal base-pairing
  • unusual bases (contain uracil, not thymine)
  • anticodon on central loop which reads the codons on mRNA and forms a complementary codon
  • all tRNA molecules look similar -> only the amino acid they carry changes, some can recognise more than one codon
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3
Q

3) Define the term ‘wobble mechanism’

A
  • the last base on the codon loop of tRNA can form non Watson-Crick base pairs
  • does not alter the amino acid sequence of the protein
  • allows a single tRNA to recognise more than one codon [allows a faster system]
  • e.g. GCC, GCG, GCU and GCA all code for alanine (however there are some exceptions like serine)
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4
Q

4) Name the enzyme which ‘loads’ tRNA molecules with amino acids

A

Aminoacyl-tRNA synthetases (each one is specific)

  • (each tRNA can only accept a single amino acid that is appropriate for its anticodon sequence)
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5
Q

5) State the reaction for the activation of amino acids by binding to tRNA

A

Amino acid + tRNA -> Amino acyl-tRNA
- ATP –> AMP + PPi

-energy for addition provided by ATP

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6
Q

6) How are the 20 different types of tRNA classified?

A
  • Different types of tRNA classified by the amino acid they carry, e.g. tRNA^phe or tRNA^leu
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7
Q

7) How are activated amino acids (bonded with tRNA) named?

A
  • e.g. tRNA^phe bonded to phenylalanine: Phe-tRNA^phe
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8
Q

8) Which enzyme is responsible for ensuring the correct tRNA is bonded to the correct amino acid?

A

tRNA synthetase

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9
Q

9) Describe the ribosome in E.Coli (prokaryote)

A
  • 70s complex
  • two sub-units 50s and 30s are combined so overall surface area is smaller (70) than sum (80)
  • 3 binding sites present on ribosome (EPA for exit, polymerisation and accepting sites)
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10
Q

10) State the 3 stages of translation

A
  • Initiation
  • Elongation
  • Termination
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11
Q

11) Describe the first stage of translation (initiation) in prokaryotes

A
  • 30s subunit binds to 2 initiation factors: IF1 and IF3
  • mRNA binds to the ribosome
  • fmet-tRNA^fmet binds GTP-1F2 (GTP at 5’ end of mRNA) and enters the ‘P’ site of the 30s subunit
  • fmet-tRNA^fmet anticodon loop lines up with AUG initiation codon
  • 50s subunit binds to the 30s subunit (mRNA in between) and GDP + Pi released
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12
Q

12) What is the Shine-Dalgarno sequence and what is its function?

A
  • A sequence on the bacterial mRNA strand which is a ribosomal binding site
  • Upstream of (before) AUG start codon which binds to the 16s rRNA of the ribosome
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13
Q

13) What is the 16s rRNA of a ribosome?

A
  • 16s rRNA is the anchor sequence (e.g. -35, -10 boxes) to the Shine-Dalgarno sequence on the mRNA strand, which ensures in-frame translation -> correct triplet codes translated each time
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14
Q

14) How can several proteins be formed from one mRNA strand?

A
  • several Shine-Dalgarno sequences preceeding several AUG codons
  • the ribosome will move along the strand, its 16s rRNA binding at each SDS, and translation will occur to produce proteins
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15
Q

15) Describe the second stage of translation in prokaryotes (elongation)

A
  • Amino-acyl tRNA binds to an elongation factor (EF) and delivers its amino acid to the ribosome [at A site]
  • Proof-reading pause occurs (GTP hydrolysis provides energy for peptide bond formation)
  • Enzyme peptidyl transferase (in ribosome) causes the tRNA molecule to shift left (to ‘P’ site) and also catalyses the formation of peptide bonds between AAs
  • Translocation : ribosome moves over so A site is empty, and the discharged tRNA^fmet (in ‘E’ site) leaves
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16
Q

16) What happens after the discharged tRNA has exited from the E site of the ribosome?

A

The next amino-acyl tRNA will bind to another elongation factor, bringing the next amino acid to the A site of the ribosome

17
Q

17) Describe the final stage of translation in prokaryotes (termination)

A
  • When a stop codon is reached (UAA, UGA, UAG), a release factor binds to the A site (at the termination codon) and the last tRNA leaves.
  • The amino acid polypeptide then breaks off
18
Q

18) Give 6 differences between prokaryotic and eukaryotic protein synthesis

A
  • P: mRNA is unmodified -> translated as soon as its synthesised while E: immature ‘hnRNA’ is modified by capping/polyadenylation/splicing before translation
  • P: 30s+50s > 70s ribosome, E: 40s+60s ->80s ribosome
  • P: SDS interacts with 16rRNA for ribosome binding while E: interaction between ribosome and cap at 5’ end
  • P: initiator tRNA is fmet-tRNA^fmet, E: met-tRNA^met
  • P: mRNA can code for >1 protein, E: only 1 protein
  • P: free polyribosomes in cytoplasm, E: “ “ & also on RER
19
Q

19) Explain how some antibiotics are selective and give an example

A
  • some kill bacteria by distinguishing between eukaryotic and prokaryotic transcription and translation
  • alpha-aminitin : inhibits RNA polymerase II, involved in eukaryotic protein synthesis
20
Q

20) Why do most antibiotics have minimal effects for eukaryotes?

A
  • few drugs cross the inner mitochondrial membrane and there is a low rate of transcription
21
Q

21) Give 6 examples of antibiotics that affect protein synthesis in prokaryotes and/or eukaryotes

A
  • Actinomycin: binds DNA at transcription initiation complex and prevents elongation by RNA polymerase
  • Rifamycin: inihibition of RNA synthesis, binds to RNA polymerase
  • Streptomycin: affects initiation (30s subunit) and causes misreading of codons
  • Erythromyocin: binds to 50s subunit, prevents relocation of ribosome
  • Chloramphenicol: inhibits peptidyl transferase by binding to the 50s subunit
  • Tetracyclines: inhibits binding of amino acyl-tRNA to the ribosome

4BBY1013 Biochemistry (19 decks)

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