lec9-Biochemistry Translation Practice Flashcards

Vocabulary flashcards covering the discovery of the genetic code, the components and structure of RNA/ribosomes, and the mechanisms of prokaryotic and eukaryotic translation.

Genetic Code

The system where the sequence of nucleotide bases on a DNA or mRNA strand determines the amino acid sequence of a protein.

Degenerate Code

A property of the genetic code where multiple codons can encode for the same amino acid, specifically $64$ possible permutations for only $20$ amino acids.

Codon

A triplet of nucleotide bases in DNA or RNA that encodes for a specific amino acid.

Matthaei and Nirenberg

Scientists who, around 1962, deciphered the genetic code by using synthetic mRNA in a cell-free system to see which radio-labelled amino acids were incorporated into proteins.

Har Gobind Khorana

A scientist who worked out how to synthesize RNA with specific sequences, which simplified the process of assigning codons to amino acids.

Reading Frame

A specific grouping of nucleotide triplets that determines which amino acids are produced; there are three potential groupings for any given sequence.

Start Codon

The codon $AUG$ which signals the beginning of translation; in prokaryotes, it codes for fMet (formylmethionine), while in eukaryotes, it codes for Met (methionine).

Stop Codons

The three triplets ($UAA$, $UAG$, and $UGA$) that signal the termination of translation and the end of the protein chain.

mRNA

Messenger RNA; the type of RNA that encodes the amino acid sequence of proteins.

rRNA

Ribosomal RNA; serves as both a structural and enzymatic component of the ribosome.

tRNA

Transfer RNA; an adaptor molecule that delivers specific amino acids to the ribosome by linking to mRNA codons through its anticodon.

Anticodon

A triplet of bases on the central loop of a tRNA molecule that is complementary to and hydrogen bonds with an mRNA codon.

Wobble Pairing

A mechanism allowing the third position of a codon to follow non-Watson-Crick base pairing with the tRNA anticodon, allowing a single tRNA to recognize more than one codon.

Aminoacyl-tRNA-synthetase

An enzyme that 'charges' or 'loads' a tRNA molecule with its specific amino acid at the $3'$ end via an ester linkage using ATP.

Activated Amino Acid

A term for a charged tRNA, such as $phe-tRNA^{phe}$, where the amino acid is attached and ready for translation.

70S Ribosome

The prokaryotic ribosome complex consisting of a $30S$ small subunit (containing $16S$ rRNA) and a $50S$ large subunit (containing $23S$ and $5S$ rRNA).

A-site

The Aminoacyl site on the ribosome where the incoming aminoacyl-tRNA binds.

P-site

The Peptidyl site on the ribosome which holds the tRNA covalently linked to the growing polypeptide chain.

E-site

The Exit site on the ribosome where the discharged tRNA is released after its amino acid has been added to the chain.

Shine-Dalgarno Sequence

A sequence found in the $5'$ UTR of prokaryotic mRNA that binds to the $16S$ rRNA to align the $fMet-tRNA^{fMet}$ with the $AUG$ start codon.

Initiation Factors (IFs)

Protein components ($IF1$, $IF2$, and $IF3$) required to assemble the prokaryotic translation initiation complex.

EF-Tu

A prokaryotic elongation factor that, when bound to GTP, delivers the next aminoacyl-tRNA to the ribosomal A-site.

Peptidyl Transferase Process

The reaction where the free $-NH_2$ of the incoming amino acid in the A-site attacks the carbonyl carbon of the previous amino acid to form a peptide bond.

EF-G

An elongation factor that drives the translocation of the ribosome along the mRNA through the hydrolysis of GTP.

Release Factor (RF)

A protein ($RF1$ or $RF2$) that mimics the shape of tRNA and enters the A-site at a stop codon to hydrolyse the finished peptide from the final tRNA.

Polycistronic mRNA

Prokaryotic mRNA that contains coding sequences for more than one protein.

80S Ribosome

The eukaryotic ribosome complex consisting of a $40S$ small subunit and a $60S$ large subunit.

Activation Reaction formula

The chemical equation for charging tRNA: $\text{amino acid} + \text{tRNA} + \text{ATP} \rightarrow \text{aminoacyl-tRNA} + \text{PPi} + \text{AMP}$.