Molecular Biology Quiz: Protein Synthesis

Stop Codons and Release Factors

• Stop codons are recognized by release factors, not tRNA molecules.
• Release factors are proteins that bind to stop codons and trigger the release of the newly synthesized polypeptide chain from the ribosome.

Start Signal for Protein Synthesis

• Prokaryotes:
  • The initiator tRNA carries formylmethionine (fMet), a modified amino acid.
  • The initiating AUG codon is preceded by the Shine-Dalgarno sequence, which base pairs with a complementary sequence in ribosomal RNA, ensuring proper initiation.
• Eukaryotes:
  • The AUG codon nearest the 5' end of the mRNA is the initiator codon.

Reading Frame

• The reading frame refers to the order of the three non-overlapping nucleotides in an mRNA sequence.
• It is established by the location of the initiator codon, which sets the starting point for translation.

The Genetic Code is Nearly Universal

• The genetic code is highly conserved, meaning most organisms use the same code for translating mRNA into proteins.
• This universality suggests strong selection pressure against deleterious mutations that would alter the code.
• Some exceptions to this universality include:
  • Ciliated protozoa: Certain stop codons in other organisms encode amino acids in ciliated protozoa.
  • Mitochondria: Mitochondrial DNA utilizes variations in the genetic code, likely due to a distinct set of tRNAs that recognize unique codons.

Distinctive Codons of Human Mitochondria

• Human mitochondrial DNA has a few differences in the standard genetic code:
  • UGA is a stop codon in the standard code but encodes tryptophan in human mitochondria.
  • AUA is a leucine codon in the standard code but encodes methionine in human mitochondria.
  • AGA and AGG are arginine codons in the standard code but are stop codons in human mitochondria.

Eukaryotic Genes

• Eukaryotic genes are discontinuous, meaning they contain both coding and non-coding regions.
  • Exons: Coding regions that are translated into protein sequences.
  • Introns: Non-coding regions that are removed during RNA processing.
• The average human gene contains 8 introns, with some having over 100.
• Intron size varies greatly, ranging from 50 to 10,000 nucleotides.

RNA Processing

• Pre-messenger RNA (pre-mRNA) contains both exons and introns.
• During RNA processing, introns are spliced out and exons are joined together, forming mature mRNA.
• Spliceosomes are complex structures composed of proteins and small nuclear RNAs (snRNAs) responsible for splicing.

Spliceosome Recognition

• Spliceosomes recognize specific sequences within introns called splice sites.
• Introns typically begin with GU and end with AG preceded by a pyrimidine-rich tract.

RNA Polymerase

• RNA polymerases are responsible for transcribing DNA into RNA.
• The base composition of newly synthesized RNA is complementary to the DNA template strand.

Transcription Initiation & Termination

• Transcription begins at promoter sites, which are regions along DNA that specifically bind RNA polymerase.
  • Examples of promoter sites in prokaryotes include the Pribnow box and the -35 region.
  • Examples of promoter sites in eukaryotes include the TATA box (Hogness box) and the CAAT box.
• Transcription ends at terminator sites, which are regions that signal RNA polymerase to stop transcribing.
  • In prokaryotes, termination may be caused by a terminator sequence in the DNA or the action of the protein rho.
  • Eukaryotic termination is less well understood.

Transcription Termination in Prokaryotes

• Terminator sequences in prokaryotic genes often form a stem-loop structure followed by a sequence of U residues.
  • The stem-loop structure is formed by base pairing of self-complementary sequences that are rich in G and C.
  • This structure helps to destabilize the RNA polymerase-DNA complex, leading to termination.