The Genetic Code
The Central Dogma: DNA makes RNA
makes protein
In principle: The DNA genotype does not produce the phenotype directly
A DNA gene contains the information
necessary for the production of proteins,
which is expressed biochemically through an
intermediate molecule, RNA,
which functions as a Genetic Code
The Genetic Code ...
is an RNA code
specifies amino acids that make up proteins
Protein expression leads directly (or indirectly) to the phenotype
Allows logical inference of the protein product directly from DNA:
see next section, and lab exercise
was "cracked" before the details of translation were understood:
we can talk about the Code before
describing RNA translation Alternative alleles of genes arise by mutation
which alters the DNA sequence of genes
which may cause amino acid substitutions in proteins
which may affect the function of those proteins
Most genes are highly polymorphic
The Genetic Code is ...
a messenger RNA (mRNA) code
i.e.., the code
is written in RNA
DNA is a coding molecule,
but not the 'genetic code' in the
biochemical sense
in 64 triplets (codons) : 61 for amino acids + 3 'stops' [iG1 7.19]
mRNA codons are read 5'
3'
20 amino acids:
note 1- & 3-letter abbreviations
[more
on
amino
acids
&
proteins
in next section]
For example,
met phe pro lys gly *
M F P K G *
Degenerate: most amino acids are encoded by
more than one codon
first
two
positions
are
critical:
third position can "wobble" [see next section]
if third can be either puRine (R), or either pYrimidine
(Y)
two-fold degeneracy
if third can be any base
four-fold degeneracy
Leucine (leu) has six-fold degeneracy with
six codons in unusual arrangement
|
# codons / amino acid |
|
|
trp, met |
1 @ |
|
ser, arg, leu |
6 @ |
|
ile |
3 @ |
|
14 others |
2 or 4 @ |
Unambiguous: any one triplet codes for only
one amino acid
but not vice versa, because of wobble
'Always' begins with an 'start' or 'initiator'
codon:
AUG
'Always' ends with a 'stop' or 'terminator' codon: UAG, UAA, or UGA
Universal (with some important exceptions)
Five Kingdoms
(animals, plants, algae, fungi, & monera)
use
the same codes for nuclear
DNA (nucDNA)
Organelles (chloroplasts
& mitochondria) have separate genomes:
cpDNA & mitochondrial DNA codes
are evolutionarily modified
e.g., UGA codes for trp
in vertebrate mtDNA code
[iG1
7.Table 2]
Stop codons may be formed by
addition of "A"s to transcript
Lab exercises use mtDNA, so the mtDNA code is
important
Alteration & Variation in the
Genetic Code: Mutations & SNPs
Mutations
- interchanges of
one base type for another
transitions -
alternative pyrimidines [
C
T ]
or purines [ AG ]
transversions -
purine
pyrimidine [C / T A / G]
Recognized in
individuals & populations as SNPs ("snips": single
nucleotide polymorphisms)
[SNPs, Mutations, & Mutants:
a note on terminology & some lessons from
history]
Alternative nucleotide sequences
of a gene
correspond to alternative alleles
or: a single gene occurs
in
variant forms (alleles)
Single-base mutations
Consequences of exon
SNPs depend on position in triplet
3rd position
typically a silent mutation -
if position "wobbles", no change to amino acid
sometimes a mis-sense
mutation -
results in different amino acids
2nd position - always a missense mutation
1st position - almost always a missense
replacement
[Leu codons are major
exception]
stop codon mutations may occur at any position: coding 
non-coding
triplet
non-sense (termination) mutations terminate polypeptides
prematurely
: Identify all
codons one
step away from a termination codon
mutations in non-coding DNA have variable
effects
Ex.: mutations in promoter
regions
mutations at intron / exon
splice junctions
Proteins mutate!
Consequences depend on position of substitution in polypeptide
none: substitution not in active site or binding site
minor: substitution of same type (synonymous substitution)
Allozymes are enzymes arising from allelic variation of enzyme genes
[see Lab Exercise #2]
major: substitution affects structure / function (nonsynonymous substitution)
Ex.: Glu
Val in beta-globin
produces Sickle-cell
hemoglobin (HbS): What is the DNA mutation involved?
Insertion /
Deletion ("indel")
mutations
gain or loss of one or more nucleotides alters the reading
frames
frameshift mutations
(examples)
single & double nucleotide
indel downstream amino acids change
non-sense mutation eventually (quickly) produced
triplet indel - insertion /
deletion of single amino acid
typically milder consequences
multiple triplet insertions produce major effects
Ex.: CGG repeats in "Fragile X" Syndrome
length mutations - very large
indels (102~6 bps)
Genes
are highly
polymorphic (w/ multiple alleles) wrt their SNP variation
[Concept of "wild type" allele is
erroneous]
has 14 exons, encodes 2.4kb mRNA for 452 amino acid protein
Among 68 alleles that affect enzymatic activity of PAH [GenBank List]
68% miss-sense SNPs (many produce Phenylketonuria (PKU))
13% non-sense SNPs (premature termination)
9% indel SNPs (single base
1~5
triplets whole exon)10% splice-site SNPs (including most common variant allele)
Most alleleic variants of the PAH locus are 3rd position silent:
no affect on PAH expression
& therefore undetected
Homework #10:
(1) "What is a Gene?" Write a one-paragraphj essay that that distinguishes Gene, Allele, and Locus
(2) Critique the following statements:
"PAH is the gene for Phenylketonuria (PKU)."
"PKU is a genetic disease caused by absence of the PAH gene."
Text material ©2016 by Steven M. Carr
