L8 The genetic code Flashcards
What does understanding the genetic code allows us to know?
- Infer protein sequences from DNA sequence information.
- Infer protein structure from its sequence
- Infer protein function
- Design tools to study protein function.
Was the genetic code determined before or after techniques developed for the isolation and sequencing of DNA?
Before
How do tRNA adaptor molecules read mRNA sequences?
Through codon/ anti codon interactions.
In what direction are codons read?
Codons are read in a 5’ to 3’ direction and direct the protein synthesis in an N’ to C’ direction.
How are mRNA codons recognised?
They are recognised by base-pairing with anticodon sequences with cognate tRNAs.
What does aminoacylation mean?
The process of adding an amino acid to a tRNA molecule. (Charging tRNA)
What is the role of a charged tRNA?
A charged tRNA carries an amino acid to the ribosome for protein synthesis.
What are the two groups involved in peptide bond formation?
aminoacyl and peptidyl goups.
What are the features of the genetic code?
- Genetic studies by Crick and Brenner showed that the genetic code was based on triplet codon sequences.
- They are nonpunctuated, meaning that all nucleotides have a meaning.
- They are degenerate, meaning multiple codons have the same meaning.
- Almost all codons have a meaning - Universal.
How was the code figured out?
Through in vitro translation and ribosome binding assays
How were cell extracts used to study protein synthesis?
Cell extracts were “programmed” to make protein, using artificial RNAs synthesized with polynucleotide phosphorylase.
What was the significance of poly(U) RNA?
Poly(U) RNA specifically directed the incorporation of phenylalanine into protein.
What codon was deduced to encode phenylalanine?
UUU codon
How was the specificity of tRNA binding to ribosomes determined?
Binding of charged tRNAs to ribosomes in vitro was dependent upon the cognate trinucleotide codon.
What was the key technique used to decipher the genetic code?
The enzymatic synthesis of nearly all 64 trinucleotides.
\What are the start and stop codons?
AUG - Methionine is start
UAG,UGA and UAA - Stop codons
What does synonymous codons mean?
Codons that encode the same amino but tend to differ at the 3rd nucleotide.
What is degeneracy in the genetic code?
Degeneracy refers to the fact that multiple codons can code for the same amino acid.
What are isoacceptor tRNAs?
Isoacceptor tRNAs are different tRNA molecules that can recognize different codons for the same amino acid (synonymous codons)
What is wobble base pairing?
Wobble base pairing is a type of non-standard base pairing that occurs between the third position of the codon and the first position of the anticodon. It allows for flexibility in codon-anticodon recognition.
What is the role of inosine in tRNA?
Inosine can base pair with U, A, and C, which allows for greater flexibility in codon-anticodon recognition.
What is the secondary structure of a tRNA molecule?
- The have a cloverleaf structure.
- The 5’ and 3’ ends are drawn together.
- The amino acid is attached to the 3’ hydroxyl group of the 3’ terminal A nucleotide.
What allows the wobble in tRNA?
Modification of the first positions of the anticodon
When are the specific nucleotides within tRNAs modified?
They are post-transcriptionally modified
About 10% of nucleotides in tRNA are modified
How does coaxial stacking contribute to tRNA stability?
Coaxial stacking of short helices within tRNA increases its thermodynamic stability.
Describe the stacking arrangement of tRNA domains.
The acceptor stem is stacked on the TΨC arm. The anticodon is stacked on the D arm.
Base pairing occurs between the D and TYC loops
Where does base-pairing occur in tRNA?
They occur between between the D and TΨC loops.
What enzymes are responsible for tRNA charging?
Aminoacyl-tRNA synthetases
What is the role of aminoacyl-tRNA synthetases?
They attach the correct amino acid to its corresponding tRNA molecule.
What is the type of bond formed between the amino acid and tRNA?
Ester bond.
How many different aminoacyl tRNA sythetases are there?
There are 20 different ones.
How was the genetic code experimentally determined?
Poly U experiment: They used a system to translate a synthetic RNA molecule consisting entirely of uracil nucleotides
Result: This resulted in the production of a polypeptide chains composed solely of the amino acid phenylalanine. This landmark experiment demonstrated that the RNA codon UUU codes for phenylalanine
How is the same amino acid incorporated into protein when there are multiple codons with the same genetic meaning?
Degeneracy of the Genetic Code: The genetic code is degenerate, meaning multiple codons can code for the same amino
Wobble Base Pairing: At the third position of the codon (the “wobble position”), the base-pairing rules are less strict. This allows a single tRNA molecule to recognize multiple codons that code for the same amino acid.
Inosine (I): Inosine, a modified base found in some tRNAs at the first position of the anticodon, can pair with multiple bases:
I-U
I-A
I-C
List 5 different structural features that are common to all tRNAs.
1) Cloverleaf secondary structure
2) Acceptor stem - 3’ end of tRNA (nucleotide CCA)
3) Anticodon loop
4) L shape - anticodon loop and amino acyl group are positioned at opposite ends of the molecule
5) TΨC arm
Where and how is an amino acid attached to tRNA?
An amino acid is attached to the 3’ end of a tRNA molecule, specifically to the terminal adenosine (A) nucleotide in the CCA sequence. This attachment occurs through a covalent bond between the carboxyl group of the amino acid and the 3’-hydroxyl group of the adenosine.
The process of attaching an amino acid to its corresponding tRNA is called aminoacylation or charging. It is catalyzed by a specific enzyme called aminoacyl-tRNA synthetase. Each amino acid has its own unique aminoacyl-tRNA synthetase, ensuring that the correct amino acid is attached to the correct tRNA.
