L13: The genetic code

in which direction is a polypeptide created

N to C terminus

what does DNA rep and transcription copy

info between nucleic acids

how are polypeptides written on protein CDS

• codons

• each codon reps one aa

start codon

• translation start site

• AUG for 90% of protein CDS

• at 5’ end

stop codon

• translation stop site

• UAA, UAG, UGA

• rep by a dash in a peptide sequence

• at 3’ end

how to read genetic code

5’ to 3’

reading frames

• a single mRNA can have different translations depending on where the ‘frame’ begins

• in reality has only 1 correct reading frame

how is the reading frame determined

location of AUG

open reading frames (ORFs)

area flanked by the start and the stop codon that are in the same frame

how many ways can a dsDNA be translated

6

how many ways can a single mRNA be translated

3

ORFs in a monocistronic gene

• multiple ORFs occur in all reading frames by chance

• only 1 of them is correct

Implications of a very long ORF

• high chance of being real

• unlikely for a ORF to be super long by chance without getting terminated by a randomly generated stop codon

• likely that it has an important function

first step to finding protein CDS

find a long, uninterupted ORF

how to confirm if a potential protein CDS is real

• check if its accompanied by other features such as promoters

• check if the translated CDS is homologous to already known proteins in the database

• check if CDS is expressed in organism and is functional

genetic code degeneracy

same aa can be coded by more than one codon

why is there genetic code degeneracy

evolved in a way to minimize the effect of single nucleotide mutations in DNA

when does a mutation not cause any changes

• point mutations at the 3rd codon position

• ex. alanine

• usually a silent mutation

point mutation at 2nd codon position

• changes aa residue but preserves polarity 

• increases the chance to preserve its function

codon with 2nd position pyrimidine

codes for np aa

codon with 2nd position purine

codes for polar aa

point mutation at 1st codon position

large aa change

wild type mutation

• sequence of the unaltered protein

• usually most abundant in pop

silent mutation

point mutation does not change aa sequence

missense mutation

point mutation that changes aa

nonsence mutation

• point mutation creates a stop codon

• prematurely stops protein synthesis

frameshift mutation

• insertion or deletion of nucleotide changes the reading frame

• completely changes aa sequence

• huge impact

when does insertion/deletion of nucleotides not cause a frameshift

• inserting/deleting 3 nucleotides

• instead adds/removes an extra aa to the protein