Transcript Population Genetics - University of Arizona

Genetic Code
The genetic code consists of triplets
• The group of three nucleotides that
together encode one amino acid was
named a codon
The genetic code is non-overlapping
Genetic Code
Remaining questions about the genetic code
• Does the code have codons that are not
translated? (Is the code punctuated?)
• Does each codon specify more than one
amino acid? (Is the code ambiguous?)
• Are the amino acids encoded by more than
one codon? (Is the code degenerate?)
• Is the code the same in all organisms? (Is
the code universal?)
Genetic Code
Deciphering the genetic code
• Synthesized artificial RNA and then
translated them into proteins
Polynuceotide
phosphorylase
NDPs -------------------- RNA + Pi
• Translated the artificial RNAs in a
cell-free protein synthesizing system
Homopolymer was then added to a test tube containing cell-free
translation system, 1 radioactively labeled amino
acid and 19 unlabeled amino acids
Proteins were isolated and checked for radioactivity
Procedure was repeated in 20 tubes, with each tube containing a
different radioactively labeled amino acid
Only one tube contained radioactively labeled protein; the amino
acid that was labeled (phenylalanine) is therefore specified by UUU
Genetic Code
• The first one synthesized was poly U
(UUU)
– Found that the polypeptide only
contained phenylalanine
• AAA = only lysine (poly-lysine)
• CCC = only proline (poly-proline)
• GGG = only glycine (poly-glycine)
Genetic Code
Next synthesized heteropolymers
• The artificial RNA sequence would depend upon
the ratio of the two or more NDPS added
• ADP and CDP in a 1 to 5 ratio
– 1/6 probability of incorporating an A being incorporated
– 5/6 probability of incorporating a C being incorporated
• The resulting RNA molecule would be a collection
of different codons that are made-up of A and C
• The numbers of different codons in the RNA
molecule is a matter of probability
Genetic Code
ADP and CDP added in a 1 to 5 ratio AND if codon is a triplet
Possible
combinations
3A
2A : 1C
1A : 2C
3C
Probability
Possible
codons
Percent
AAA
0.4%
(1/6)2(5/6)
= 2.3%
AAC, ACA,
CAA
6.9%
(1/6)(5/6)2
= 11.6%
ACC, CAC,
CCA
(1/6)3 =
0.4%
(5/6)3 =
57.9%
CCC
(2.3 + 2.3 + 2.3)
34.8%
(11.6 + 11.6 + 11.6)
57.9%
100%
Genetic Code
The poly (AC) RNAs produced proteins containing 6 amino acids
Amino acid
Percent
Possible
codons
Proline
69%
CCC (57.9%)
2C:1A (11.6%)
1A : 2C (11.6%)
2A : 1C (2.3%)
Threonine
14%
Histidine
12%
1A : 2C (11.6%)
Asparagine
2%
2A : 1C (2.3%)
Glutamine
2%
2A : 1C (2.3%)
Lysine
1%
AAA (0.4%)
Genetic Code
Does the code have codons that are not
translated? (Is the code punctuated?)
Yes!
• The code is punctuated with periods, not
commas
– 61 codons code for amino acids
– 3 codons are stop or nonsense codons
• UAG (amber)
• UGA (opal)
• UAA (ochre)
Genetic Code
Does each codon specify more than
one amino acid? (Is the code
ambiguous?)
• NO!!
– Each codon codes for only one amino
acid
Genetic Code
Are the amino acids encoded by more
than one codon? (Is the code
degenerate?)
• YES!!!
• Most amino acids are encoded by
more than one codon
– There are certain patterns of degeneracy
• The first two bases the same, the third one
changes
Genetic Code
Is the code the same in all organisms?
(Is the code universal?)
• At first, YES!!!
• Now we know there are a few
exceptions
– A few different codons in mitochondria
Using the table below, can you translate this nucleotide
sequence?
5’UUCGAUGCCCGGGGUCCUGAAAUUGUUCUAGA 3’
• The first step is to look for the
AUG start codon.
• Next, group the nucleotides into
a reading frame of 3
nucleotides per codons and use
the table to find the amino acid
that corresponds to each codon.
• Stop translating the mRNA
when you reach a stop codon.
• Is this what you got?
Met-Pro-Gly-Val-Leu-Lys-Leu-Phe-Stop