General Biology/Genetics/Gene Expression

Flow of genetic information
 * DNA → mRNA → polypeptide
 * Transcription: DNA → mRNA
 * RNA polymerase
 * Nucleus in eukaryotes
 * Transcription also makes rRNA and tRNA
 * Translation: mRNA → polypeptide
 * Ribosomes: protein and rRNA
 * Genetic code and tRNA

The Genetic Code

 * Triplet codon
 * 64 triplet codons (43)
 * Experimentally deciphered in 1961
 * Nearly universal
 * Implies common ancestor to all living things
 * Minor exceptions: certain ciliates, mitochondria, chloroplasts
 * Still evolving

Transcription

 * RNA polymerase
 * NTP substrates
 * Synthesizes single stranded RNA complementary to template strand of DNA
 * New nucleotides to 3’ end
 * Begins at promoter site
 * no primer necessary
 * Ends at terminator site
 * Much posttranscriptional modification in eukaryotes

Transcription bubble
Promoter site
 * Prokaryotes
 * -10 nt, TATA box
 * -35 nt, additional signal
 * Eukayotes
 * -25, TATAAA box
 * Additional signals upstream
 * Promoters may be strong or weak
 * In eukaryotes, access to promoter depends upon state of chromatin coiling

Eukaryote mRNA

 * Synthesized as pre-mRNA, processed in nucleus
 * 5’ end: GTP cap placed in inverted position
 * Essential for ribosome recognition
 * 3’ end: poly-A tail; non-templated addition of ~50-250 A nucleotides; stability
 * Introns: intervening sequences removed

Translation

 * Requires:
 * mRNA
 * tRNA
 * ribosomes
 * translation factors (various proteins)
 * In prokaryotes, takes place on growing mRNA
 * In eukaryotes, in cytoplasm on free ribosomes and RER
 * AUG start codon to stop codon

Translation in bacteria
tRNA
 * Transfer RNA
 * Two important parts
 * Anticodon
 * Hydrogen bonds with mRNA codon
 * 3’ end
 * Accepts amino acid (using energy of ATP)
 * Aminoacyl-tRNA synthetase

Aminoacyl tRNA synthase

 * Enzyme used to bind amino acid from the cytoplasm to tRNA, which then transfers that amino acid to the ribosome for polypeptide formation

Translation

 * Initiation complex
 * Small ribosomal subunit
 * mRNA
 * fMet-tRNA (prokaryotes only; met-tRNA in eukaryotes)
 * Initiation factors
 * Elongation
 * Ribosome
 * mRNA
 * tRNAs
 * Elongation factors

Elongation, translocation

 * incoming tRNA enters the A site
 * rRNA catalyzes peptide bond formation. Note that growing peptide is attached to what was incoming tRNA at P site after translocation.
 * empty tRNA leaves via E site; recycled
 * A site ready for next charged tRNA

Introns/exons

 * In eukaryotes, coding regions of gene may be interrupted by introns, noncoding regions of DNA (RNA)
 * Introns
 * 22- >10,000 nt in length
 * 5’ GU … 3’ AG removal sequence
 * Not essential to genes
 * May constitute >90% of gene
 * removed from pre-mRNA to form mRNA
 * Exon: often codes for functional domain of protein
 * translatable mRNA