Fundamental Genetics

Lecture 9

The Genetic Code

and Transcription

John Donnie A. Ramos, Ph.D.

Dept. of Biological Sciences
College of Science
University of Santo Tomas

Flow of Genetic Information

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 The Genetic Code
‰ Linear form (mRNA derived from DNA)
‰ Triplet codons (triplets of ribonucleotides coding for 1
amino acid)
‰ Unambiguous (1 codon = 1 amino acid only)
‰ Degenerate ( 1 amino acid can be specified by several
codons)
‰ Contains specific start and stop codons
‰ Commaless (no breaks once translation starts until the
stop codon is reached)
‰ Non-overlapping (single reading frame)
‰ Universal (same ribonucleotide used by all organisms)

The Discovery of the Genetic Code

‰ Francois Jacob and Jacques Monod
(1961) – messenger RNA (mRNA)
‰ Sydney Brenner (1960s) – codon in
triplets (minimal use of the 4 mRNA
bases to specificy 20 aa) (43=64)
‰ Francis Crick – frameshift mutations
alters the codons
‰ Mariane Manago and Severo Ochoa -
polynucleotide phosphorylase
(synthesis of RNA without template)-
paved the way to the production of
RNA polymeres in cell free-systems

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 The Discovery of the Genetic Code
‰ Marshall Nirenberg and J. Heinrich Matthaei (1661) – codons
‰ used cell-free protein synthesizing system and polynucleotide
phosphorylase
‰ RNA Homopolymers (UUUUUU…, AAAAAAA…, CCCCCC…, GGGGG…)
‰ UUU (Phenylalanine)
‰ AAA (Lysine)
‰ CCC (Proline)
‰ RNA Mixed Copolymers

1A:5C (1/6 A: 5/6C)

The Triplet Binding Assay

‰ Developed by M. Nirenberg and P. Leder (1964)
‰ Mimics the in vivo translation of proteins where a mRNA-tRNA-
ribosome complex is formed when all three macromolecules are
allowed to interact.

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 Repeating Copolymers
‰ Developed by Gobind Khorana (1960s)
‰ Synthetic long RNAs with repeating sequences

Results of Repeating Copolymers

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 The Universal Genetic Code

‰ Degeneracy
‰ Wobble
Hypothesis
‰ Start codon
(N-formylmethionine)

‰ Termination
codons
‰ Universal
Viruses
Bacteria
Archaea
Eukaryotes

Exceptions to the Universal Code

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 Transcription
‰ Uses DNA as a template
‰ Catalyzed by RNA polymerase
(holoenzyme of 500 kD)
‰ αββ’σ subunits
‰ Sense strand / template strand –
DNA strand used as a template
for transcription
‰ Promoter region – DNA sequence
recognized by σ factor to initiate
transcription (60 bases).
(upstream of a gene)
‰ TATA box (Pribnow box) –
TATAAT sequence
‰ Sigma factor (σ70, σ28, σ32, σ54)

Transcription
‰ RNA polymerase don’t need
primers
‰ Elongation in 5’ to 3’ direction
‰ Rate in E coli: 50 bases/sec at
37°C
‰ Termination is a function of rho
(ρ) factor – hexameric protein
interacting with the end of a
gene
‰ Polycistronic mRNA – bacterial
mRNA containing information for
the synthesis of proteins of
related function
‰ Monocystronic mRNA –
eukaryotic mRNA containing
information for a single protein.

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 Eukaryotic Transcription
‰ Features of eukaryotic transcription different from prokaryotic
transcription:
‰ Transcription inside the nucleus under the direction of 3 different
RNA polymerases

‰ Presence of protein factors (promoters, enhancers, etc.) binding to

the upstream portion of a gene (cis-acting elements) during
initiation step.
‰ Presence of post-transcriptional regulation.

Cis -acting Elements

‰ TATA Box (Goldberg-Hogness Box)
‰ Located 30 bases upstream from the start of
transcription (-30)
‰ Consensus sequence: TATAAAA
‰ Facilitates denaturation of helix because it is AT-
rich region

‰ CAAT Box
‰ Located 80 bases upstream from the start of
transcription (-80)
‰ Consensus sequence: GGCCAATCT
‰ Influence the efficiency of the promoter

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 Trans -acting Factors
‰ Transcription factors – facilitates template
binding during the initiation of transcription
‰ Example:
‰ TFIID (TATA-binding protein or TBP) – binds to
TATA-box

Post-transcriptional Processing
‰ 7-methylguanosine cap (7mG)
‰ Protection from nucleases
‰ Role mRNA transport across the
nuclear membrane
‰ 3’ cleavage site:
‰ AAUAAA
‰ Failure of 3’ cleavage results to
absence of poly A tail
‰ Split genes – contains intervening
sequences

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 RNA Splicing

‰ Ribozyme – RNA with

catalytic activity
‰ Self-excision process –
process of RNA splicing or
intron removal.
‰ Transesterification –
interaction between
guanosine and the
transcript.
‰ 2 successive
transesterification processes

The Spliceosome

‰ Alternative splicing
‰ Small nuclear ribonucleoproteins
(snRNP or snurps) – bonds to GU
or AG sites of introns
‰ 2 transesterification processes
‰ Snurps form a loop (lariat) in the
branch point region
‰ Produces isoforms of proteins

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 RNA Editing

‰ Substitution editing
‰ changes in the nucleotide bases of a given mRNA
‰ Common in mitochondrial RNA and chloroplast RNA
‰ Example: Apoliprotein B (Apo B) – C to U change CAA
to UAA
‰ Insertion / deletion editing
‰ addition or removal of nucleotide sequences
‰ Common in mitochondrial RNA or guide RNA (gRNA)

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