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 ...
specifies amino acids that make up proteins
Protein expression leads directly (or indirectly) to the phenotype
was "cracked" before the details of translation were understood:
we can talk about the Code before describing RNA
translation can be used to infer the protein product of a gene directly from DNA:
see next section, and lab exercise
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
As a result, most genes are highly polymorphic
The Genetic Code is ... [iGen3 pp. 106 ff.]
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' [iGen3
06-07]
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"
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
termination codons may be
formed by addition of "A"s to transcript
Lab exercises use mtDNA, so this code is important
Alterations of the Genetic Code:
Mutations
Mutations
- interchanges of
one base type for another
transitions -
alternative pyrimidines [
C
T ]
or purines [ AG ] [iGen3 07-03a,b]
transversions -
purine
pyrimidine [C / T A / G]
Recognized in individuals & populations as SNPs
(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
(MGA2 10-4) [iGen3 07-03cd,fg]
3rd position
typically a silent mutation -
if position "wobbles", no change to amino acid
sometimes a missense
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
nonsense (termination)
mutation terminates polypeptide prematurely [iGen3 07-04]
: Identify all
codons one
step away from a termination codon
[Hint: there are 18]
mutations in non-coding DNA have variable
effects
Ex.: mutations in promoter
regions
mutations at intron / exon
splice junctions
Proteins mutate! Watch your language!
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 minor variants (see laboratory exercise)
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
frameshift mutations
(examples)
single & double nucleotide
indel downstream amino acids change
nonsense 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"
length mutations - larger indels (102~6
bps)
Genes
are highly
polymorphic (w/ multiple alleles) wrt their mutational
variation
has 14 exons, encodes 2.4kb mRNA for 452 amino acid protein
Of 68 alleles known to affect enzymatic activity of PAH [Current GenBank List]
68% miss-sense mutations (many produce Phenylketonuria (PKU))
13% non-sense mutations (premature termination)
9% indel mutations (single base
1~5
triplets whole exon)10% splice-site mutations (including most common variant allele)
Most alleleic variants of the PAH locus are 3rd position silent
no affect on PAH expression
& therefore undetected
Homework:
(1) "What is a Gene?" Write an 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 © 2011 by Steven M. Carr
