Genetic Code and Transcription Quiz

The Genetic Code and Transcription

• Genetic information is stored in DNA and is nearly universal across living organisms.
• The genetic code is transferred from DNA to RNA through transcription, using triplet codons (composed of three ribonucleotides).
• RNA's ribonucleotides form 64 possible three-letter sequences, mostly encoding 20 amino acids in proteins.
• Some codons signal start or stop of protein synthesis.
• Bacterial transcription is simpler than eukaryotic transcription, where initial RNA transcripts require processing before translation.

Learning Objectives

• The genetic code is composed of triplet codons that each specify an amino acid.
• Experimental evidence (using synthetic mRNAs in cell-free systems) supports the triplet nature of the genetic code.
• Changes in nucleotides can alter the amino acid sequence downstream.
• Crick's wobble hypothesis explains how tRNA molecules can recognize multiple codons due to flexible base pairing at the third position in codons.
• Single base changes in DNA can result in specific amino acid substitutions in proteins.
• Mutations can be identified by comparing wild-type and mutant sequences of mRNA or amino acids.
• mRNA codons and tRNA anticodons are complementary; knowing one allows determination of the other.
• Exceptions exist to the universal genetic code in certain species, where specific codons have different meanings.

The Central Dogma

• The central dogma describes the flow of genetic information: DNA → RNA → Protein.
• Transcription involves specific DNA regions and enzymes for initiation, elongation, and termination within bacteria.
• RNA molecules can be traced to their DNA templates, and their sequences predict the resulting amino acids.
• Eukaryotic transcription differs from bacterial transcription due to promoter sequences and additional processing steps.
• Eukaryotic post-transcriptional processing includes 5' capping, 3' polyadenylation, and intron splicing, all affecting mRNA stability.
• mRNA, rRNA, and tRNA have different processing steps.
• RNA splicing removes introns, while RNA editing modifies nucleotide sequences.

The Genetic Code as "Letters"

• The genetic code is linear, using mRNA ribonucleotide bases derived from complementary DNA.
• Each mRNA "word" is a triplet code specifying one amino acid.
• The code is degenerate—many amino acids are coded for by multiple codons.
• Start and stop codons exist to initiate and terminate translation.
• The code is commaless (read sequentially) and non-overlapping (each nucleotide part of only one codon).

Early Studies on the Genetic Code

• Early research initially suggested that DNA directly encoded proteins.
• Subsequent research determined that DNA info is transferred to rRNA for protein synthesis (but this was disproven).
• A messenger RNA (mRNA) intermediate carries genetic information from DNA to proteins.
• The genetic code in mRNA, comprised of four ribonucleotides, specifies 20 amino acids used in protein synthesis.
• The triplet code is necessary because a four-letter code using only two letters per word, offers only 16 possible words, insufficient for 20 amino acids. A triplet code yields 64 unique words which is sufficient for amino acids.
• Experiments using bacteriophages support the triplet nature of the code.
• Frameshift mutations (addition or deletion of one or two nucleotides) shift the reading frame, but if three are involved, the frame is reestablished confirming the triplet code.

The Coding Dictionary and Patterns (64 Codons)

• 61 codons code for amino acids.
• Three codons are termination signals (do not code for amino acids).
• The code is degenerate (multiple codons for one amino acid).
• Certain amino acids have multiple codons (e.g., serine, arginine, leucine have 6 codons each, while tryptophan and methionine have only one).
• Codons often share the first two nucleotides, with the third position varying.
• Crick's wobble hypothesis suggests the first two nucleotides are more critical for binding to tRNA than the third.

Anti-codon Base-Pairing Rules

• The wobble hypothesis explains how a single tRNA anticodon can pair with multiple mRNA codons due to relaxed base-pairing rules at position 3 of the codon.
• Inosine (I), a modified base, can pair with A, U, or C in tRNA.
• Fewer than 30 tRNA species are needed to accommodate the 61 amino acid codons in bacteria and 41-55 in eukaryotes.

Ordered Nature of the Code

• Chemically similar amino acids often share one or two middle bases in their codons.
• The use of chemically similar amino acids for a change helps minimize functional disruption during mutations.

Punctuating the Code (Initiation and Termination Codons)

• Protein synthesis initiates with Methionine, which is formylated in bacteria and unformylated in eukaryotes.
• AUG is the primary initiator codon for methionine.
• GUG and UUG can also sometimes encode methionine.
• Three codons (UAG, UAA, UGA) serve as termination codons, stopping translation.
• Stop codons do not specify any amino acids and are unrecognised by tRNAs.

Transcription and the Genetic Code Is Nearly Universal

• The synthesis of RNA on a DNA template.
• The mRNA sequence is complementary and antiparallel to its DNA template strand (except T → U).
• The core enzyme can synthesise mRNA from a DNA template.

Eukaryotic Transcription Differences from Bacteria

• The use of three different RNA polymerases in eukaryotes vs. one in bacteria.
• Chromatin remodeling in eukaryotes prepares DNA transcription unlike bacteria.
• Multiple general transcription factors and interactions with cis-regulating elements in eukaryotes.
• Specific sequences for termination in eukaryotes.
• Eukaryotic pre-mRNAs are pre-processed into mature mRNAs including the addition of: 5' cap, 3' poly-A tail, and the removal of introns.

RNA Polymerases in Eukaryotes

• Eukaryotic RNA polymerases I, II, and III are responsible for different RNA types (rRNA, tRNA, mRNA).
• RNAP II is involved in mRNA synthesis and regulated by cis-acting elements (promoter, enhancer and silencer).
• Regulatory elements (like promoter, enhancer or silencer) modify the rate of transcription by RNAP II.

Processing Eukaryotic RNA: Caps and Tails

• Eukaryotic mRNAs are processed into mature mRNAs involving the 5' cap, 3' poly-A tail.
• The 5' cap protects mRNA from degradation, aids in nuclear export, and is essential for translation initiation.
• The poly-A tail aids in mRNA stability and translation.

Introns and Exons

• Eukaryotic genes contain non-coding sequences known as introns. These interrupt the protein coding sequence.
• The sequences retained in mature mRNA are known as exons.
• RNA splicing removes introns and joins exons together.
• Introns in eukaryotic genes are identified using a comparison of DNA, mRNA and amino acid sequence.
• Common sequences at intron-exon boundaries can identify introns.
• Some genes have more introns than others and the average number of introns and exons found in a gene.

Splicing Mechanisms: The Spliceosome

• Splicing involves removing introns and joining exons.
• This process is performed using a large complex of protein and RNAs called the spliceosome.
• The spliceosome binds to specific sequence motifs at intron boundaries (donor and acceptor sites)
• Two transesterification reactions excise the intron and join the exons.

RNA Editing

• RNA editing modifies the base sequence of a transcript after transcription in some cases.
• Two types of editing: Substitution (changing a nucleotide) and Insertion/Deletion (adding or removing bases).
• Editing occurs in mitochondrial and chloroplast RNAs in plants in some instances.
• Guide RNA (gRNA) aids with insertion/deletion in trypanosomes.
• Apolipoprotein B (ApoB) mRNA serves as an example of substitution editing.

Test your understanding of the genetic code and the process of transcription. This quiz covers triplet codons, their role in encoding amino acids, and the differences between bacterial and eukaryotic transcription. Dive into the experimental evidence supporting these concepts and explore Crick's wobble hypothesis.