Before the technology existed to synthesize RNA molecules of...

Before the technology existed to synthesize RNA molecules of defined sequence like those in Fig. 8.5 similar experiments were performed with synthetic mRNAs of undefined sequence. For example, RNAs consisting only of Us and Gs could be synthesized in vitro, but they would have random sequences. Suppose a pool of random-sequence RNAs was synthesized in a reaction mixture containing three times as much UTP as GTP, and that the resulting RNAs were translated in vitro. a. How many different codons exist in the RNAs? b. How many different amino acids would you find in the polypeptides synthesized? c. Why are your answers to (a) and (b) not the same? d. How often would you expect to find each of the codons in (a)? e. In what proportions would you expect to find each of the amino acids in the polypeptides? f. If you did this experiment-that is, synthesized random-sequence RNAs containing a 3: 1 ratio of U:G, and quantified the amount of each amino acid in the polypeptides produced-prior to knowledge of the genetic code table, what would the results have told you?

Before the technology existed to synthesize RNA molecules of defined sequence like those in Fig. 8.5 similar experiments were performed with synthetic mRNAs of undefined sequence. For example, RNAs consisting only of Us and Gs could be synthesized in vitro, but they would have random sequences. Suppose
a pool of random-sequence RNAs was synthesized in a reaction mixture containing three times as much UTP as GTP, and that the resulting RNAs were translated in vitro.
a. How many different codons exist in the RNAs?
b. How many different amino acids would you find in the polypeptides synthesized?
c. Why are your answers to (a) and (b) not the same?
d. How often would you expect to find each of the codons in (a)?
e. In what proportions would you expect to find each of the amino acids in the polypeptides?
f. If you did this experiment-that is, synthesized random-sequence RNAs containing a 3: 1 ratio of U:G, and quantified the amount of each amino acid in the polypeptides produced-prior to knowledge of the genetic code table, what would the results have told you?

Key Concepts

Codon Formation

A codon is a sequence of three nucleotides that together specify an amino acid during protein synthesis. In any RNA sequence, the number of possible unique codons is determined by the number of nucleotides available; when only two types of nucleotides are used, the total number of possible codons is two raised to the third power, because each codon has three positions.

Genetic Code Degeneracy

The genetic code is degenerate, meaning that multiple codons can code for the same amino acid. This redundancy is important because it leads to situations where fewer unique amino acids are produced than the total number of possible codons. In systems with a limited set of nucleotides, the degeneracy of the code becomes evident when distinct codons result in the same amino acid.

Nucleotide Pool Bias and Codon Frequency

When the relative concentrations of different nucleotides in RNA synthesis are unequal, the probability of incorporating one nucleotide over another changes, thereby affecting the frequency distribution of codons. This bias means that even though all possible codons can be formed, they will not appear with equal frequency in a randomly generated RNA pool if the nucleotide ratios are skewed.

Experimental Inference of the Genetic Code

By translating randomly generated mRNA sequences and analyzing the resulting amino acid composition, one can infer properties of the genetic code. The observed differences between the number of unique codons and the number of amino acids produced (due to degeneracy and nucleotide biases) provide clues about how the genetic code maps codons to amino acids, a concept that would have been central to deducing the code prior to its formal discovery.

Transcript

00:01 That are rna synthesized in a pool of random sequence that contains three times as much utp as gtp.

00:08 There would be 16 different codons.

00:16 So there are four possible nucleotide bases, u, g, a, and c, that can occupy each of the four positions.

00:32 And i only have u and g.

00:40 So there's going to be two times two times two.

00:50 Will be eight different and they will be u -g -u u g -c u -a and u g -a and u g -g will have g u -u -u -g -you -g will have g ucg -u -c -g -g -a and g -u -g.

01:38 Okay so those would be my different there'd be eight okay and then b how many different amino acids, a number of different amino acids.

02:20 Okay, so we have eight possible codons, but there are three code for same amino acid.

02:48 So ugu and ugc, both code for cysteine, with uga as a stop codon.

03:13 That will give me six different amino acids.

03:26 Okay.

03:29 C, why are a and b not the same? i feel like i already answered this.

03:52 It's because multiple codons can code for the same amino acid.

04:16 D, how often would you expect to find each of the codons in a? okay, i'd expect them to find a 3 to 1 ratio of u to g.

05:00 So codons with u in the first and last.

05:12 Let's go first and third positions.

05:27 That would be c, whoopsie, would be three times more frequent than, okay.

06:09 And then e, good heavens, proportion of each amino acid.