Genetics 311 – The genetic code and transcription

A set of questions and answers covering the key concepts from the lecture notes on the genetic code, translation initiation/termination, mutations, and transcription in prokaryotes and eukaryotes.

What is the central dogma of molecular genetics?

The directional flow of genetic information from DNA to RNA to protein.

What is mRNA (messenger RNA) and its role?

mRNA is the intermediate that transfers genetic information from DNA to protein during translation.

How many codons are there and how many amino acids do they encode?

There are 64 codons that code for 20 amino acids.

Why must codons be three nucleotides long?

A three-nucleotide length provides 64 unique combinations, enabling encoding of all 20 amino acids; shorter lengths would not suffice.

Is the genetic code unambiguous?

Yes; each codon specifies only one amino acid.

Is the genetic code degenerate?

Yes; a given amino acid can be specified by more than one codon.

Do codons have start and stop signals?

Yes; start codons initiate translation and stop codons terminate it.

Are codons read with separators (commas) between them?

No; the code is commaless.

Is the genetic code nonoverlapping?

Yes; any single ribonucleotide is part of one codon.

Is the genetic code colinear?

Yes; the sequence of codons corresponds to the sequence of amino acids in the protein.

Is the genetic code nearly universal?

Yes; it is used by viruses, prokaryotes, archaea, and eukaryotes.

What is the initiator codon and what amino acid does it encode?

AUG; encodes methionine (Met); in bacteria, it is often formylated as N-formylmethionine (fMet) on the initiator tRNA.

What is the initiator tRNA in bacteria commonly carrying?

A formylated methionine (fMet) on the initiator tRNA.

What are termination codons and what do they do?

UAG, UAA, and UGA; they do not code for amino acids and signal termination of translation.

What is an Open Reading Frame (ORF)?

A DNA sequence that can be transcribed into RNA and translated into a polypeptide, starting with a start codon and ending with a stop codon.

What special feature can occur with some viral ORFs?

Initiation at different AUG positions out of frame with another AUG can yield distinct polypeptides.

What is a nonsense mutation?

A mutation that creates a premature stop codon, terminating translation and producing a truncated polypeptide.

What is a frameshift mutation?

An insertion or deletion that shifts the reading frame, changing downstream codons and altering the protein.

What is the Wobble Hypothesis?

The first two bases of a codon are often more critical; the third position is less constrained, allowing nonstandard base pairing.

Which amino acid is encoded by AUG and also serves as the start signal?

Methionine (Met); AUG serves as the start codon.

What is the first amino acid sequence of the first ORF in the provided RNA sequence (per the notes)?

Met- Ala- Gly- Trp- Pro- Ser- Thr- Gly

What enzyme directs RNA synthesis using a DNA template in transcription?

RNA polymerase.

What are promoters in transcription?

Specific DNA sequences in the 5′ region upstream of the initial transcription point where RNA polymerase binds to start transcription.

What is the transcription start site and where can it be relative to the ATG?

The location where transcription begins; it can be upstream of the ATG of a gene.

What happens during transcription elongation?

The σ subunit dissociates and the core enzyme elongates the RNA transcript.

How does transcription termination occur in bacteria?

Terminator sequences cause RNA to form a hairpin structure; Rho-dependent termination uses the rho (ρ) factor.

How does eukaryotic transcription differ from prokaryotic transcription?

In eukaryotes, transcription occurs in the nucleus and requires chromatin remodeling, transcription factors, and regulatory elements like enhancers/silencers; mRNA processing is required before translation.

How many RNA polymerases do eukaryotes have and what are their general roles?

Three: RNA Pol I, II, and III; Pol II transcribes mRNA, Pol I rRNA, and Pol III tRNA and others.

What is the role of RNA Pol II core-promoters?

They determine where RNA Pol II binds to DNA.

What are enhancers and silencers?

DNA elements that increase (enhancers) or decrease (silencers) transcription levels, often acting from a distance.

What is the role of transcription factors?

General transcription factors are required for RNA Pol II transcription; activators and repressors modulate the rate of transcription initiation.

What processing steps are applied to eukaryotic mRNA (Cap and Tail)?

Addition of a 5′ cap (7-methylguanosine) and a 3′ poly-A tail; intron removal (splicing) occurs as part of mRNA maturation.

What are introns and exons?

Introns are noncoding regions removed during RNA processing; exons are coding regions retained in the mature mRNA.

What is splicing?

Posttranscriptional removal of introns and joining of exons to produce mature mRNA.

What is a polyribosome?

Multiple ribosomes translating the same mRNA simultaneously, observed in both prokaryotes and eukaryotes.