CHEM-527 Introductory Biochemistry
Problem Set 8b

Codon Utilization

1. The degeneracy of the genetic code has been viewed as a protective device in that mutations to synonymous codons result in no change in the amino acid sequence of a coded protein. Before nucleotide sequencing became possible, it was commonly hypothesized that there would be no preference among synonymous codons, Now that a large number of genes have been sequenced it is possible to test the hypothesis. Table 1 displays the codon frequencies for the glyceraldehyde-3-phosphate dehydrogenase gene from baker's yeast. In Table 2, the nucleotide sequence for the yeast phosphoglycerate kinase mRNA in yeast is given along with its amino acid sequence.
  a) Tabulate the codon utilization frequency for the phosphoglycerate kinase mRNA. In comparison with the GAPDH mRNA, what patterns in codon utilization do you see?

b) Speculate on the significance of the codon utilization patterns in yeast. What would you predict for other genes in yeast? (Consider that glyceraldehyde 3-phosphate dehydrogenase may constitute several percent of the total soluble protein in a glycolyzing yeast cell.)

c) Bonus for the mathematically inclined: Generate a mathematical expression which will reflect the degree of non-randomness in codon utilization. Ideally when codons are used randomly in a gene the value would be 0 and would range up to 1.0 for gene where only one of several codons was used for each amino acid. Calculate the values of this expression for each of the yeast genes listed.


Table 1. Codon Utilization Table for the Yeast (Saccharomyces cerevisiae) Gene Coding for Glyceraldehyde-3-Phosphate Dehydrogenase


 
Codon Position 2
  
U
C
A
G
AA
 Codon No AA Codon No
AA
 Codon No
AA
 Codon No
C

o

d

o

n
 
 

P

o

s

I

t

I

o

n
 
 

1
U





 

PHE
 UUU 0
 

SER

 

 UCU 13
TYR		 UAU 0
CYS		 UGU 2
U
C

o

d

o

n
 
 

P

o

s

I

t

I

o

n
 
 

3

 
UUC 10 UCC 12 UAC 11 UGC 0
C

 
 
 

LEU

 UUA 0 UCA 0
STOP		 UAA (1) STOP UGA 0
A
UUG 21 UCG 0 UAG 0 TRP UGG 3
G

 

C

 CUU 0
 
 

PRO

 CCU 0
HIS		 CAU 0
 

ARG

 CGU 0
U
CUC 0 CCC 0 CAC 8 CGC 0
C
CUA 0 CCA 12
GLN		 CAA 5 CGA 0
A
CUG 0 CCG 0 CAG 0 CGG 0
G

A

ILE

 AUU 9
 

THR

 ACU 12
ASN		 AAU 0
SER		 AGU 0
U
AUC 11 ACC 12 AAC 12 AGC 0
C
AUA 0 ACA 0
LYS		 AAA 1
ARG		 AGA 11
A
MET
 AUG 7 ACG 0 AAG 25 AGG 0
G

 

G
 

VAL

 GUU 22
 

ALA

 GCU 25 ASP GAU 9
 

GLY

 GGU 25
U
GUC 15 GCC 7 GAC 16 GGC 0
C
GUA 0 GCA 0
GLU		 GAA 12 GGA 1
A
GUG 0 GCG 0 GAG 2 GGG 0
G

Table 2. The Amino Acid Sequence for Yeast Phosphoglycerate Kinase

and the Coding (mRNA) Sequence for its mRNA

 M   S   L   S   S   K   L   S   V   Q   D   L   D   L   K   D   K
AUG-UCU-UUA-UCU-UCA-AAG-UUG-UCU-GUC-CAA-GAU-UUG-GAC-UUG-AAG-GAC-AAG-

 R   V   F   I   R   V   D   F   N   V   P   L   D   G   K   K   I
CGU-GUC-UUC-AUC-AGA-GUU-GAC-UUC-AAC-GUC-CCA-UUG-GAC-GGU-AAG-AAG-AUC-

 T   S   N   Q   R   I   V   A   A   L   P   T   I   K   Y   V   L
ACU-UCU-AAC-CAA-AGA-AUU-GUU-GCU-GCU-UUG-CCA-ACC-AUC-AAG-UAC-GUU-UUG-

 E   H   H   P   R   Y   V   V   L   A   S   H   L   G   R   P   N
GAA-CAC-CAC-CCA-AGA-UAC-GUU-GUC-UUG-GCU-UCU-CAC-UUG-GGU-AGA-CCA-AAC-

 G   E   R   N   E   K   Y   S   L   A   P   V   A   K   E   L   Q
GGU-GAA-AGA-AAC-GAA-AAA-UAC-UCU-UUG-GCU-CCA-GUU-GCU-AAG-GAA-UUG-CAA-

 S   L   L   G   K   D   V   T   F   L   N   D   C   V   G   P   E
UCA-UUG-UUG-GGU-AAG-GAU-GUC-ACC-UUC-UUG-AAC-GAC-UGU-GUC-GGU-CCA-GAA-

 V   E   A   A   V   K   A   S   A   P   G   S   V   I   L   L   E
GUU-GAA-GCC-GCU-GUC-AAG-GCU-UCU-GCC-CCA-GGU-UCC-GUU-AUU-UUG-UUG-GAA-

 N   L   R   Y   H   I   E   E   E   G   S   R   K   V   D   G   Q
AAC-UUG-CGU-UAC-CAC-AUC-GAA-GAA-GAA-GGU-UCC-AGA-AAG-GUC-GAU-GGU-CAA-

 K   V   K   A   S   K   E   D   V   Q   K   F   R   H   E   L   S
AAG-GUC-AAG-GCU-UCC-AAG-GAA-GAU-GUU-CAA-AAG-UUC-AGA-CAC-GAA-UUG-AGC-

 S   L   A   D   V   Y   I   N   D   A   F   G   T   A   H   R   A
UCU-UUG-GCU-GAU-GUU-UAC-AUC-AAC-GAU-GCC-UUC-GGU-ACC-GCU-CAC-AGA-GCU-

 H   S   S   M   V   G   F   D   L   P   Q   R   A   A   G   F   L
CAC-UCU-UCU-AUG-GUC-GGU-UUC-GAC-UUG-CCA-CAA-CGU-GCU-GCC-GGU-UUC-UUG-

 L   E   K   E   L   K   Y   F   G   K   A   L   E   N   P   T   R
UUG-GAA-AAG-GAA-UUG-AAG-UAC-UUC-GGU-AAG-GCU-UUG-GAG-AAC-CCA-ACC-AGA-

 P   F   L   A   I   L   G   G   A   K   V   A   D   K   I   Q   L
CCA-UUC-UUG-GCC-AUC-UUA-GGU-GGU-GCC-AAG-GUU-GCU-GAC-AAG-AUU-CAA-UUG-

 I   D   N   L   L   D   K   V   D   S   I   I   I   G   G   G   M
AUU-GAC-AAC-UUG-UUG-GAC-AAG-GUC-GAC-UCU-AUC-AUC-AUU-GGU-GGU-GGU-AUG-

 A   F   T   F   K   K   V   L   E   N   T   E   I   G   D   S   I
GCU-UUC-ACC-UUC-AAG-AAG-GUU-UUG-GAA-AAC-ACU-GAA-AUC-GGU-GAC-UCC-AUC-

 F   D   K   A   G   A   E   I   V   P   K   L   M   E   K   A   K
UUC-GAC-AAG-GCU-GGU-GCU-GAA-AUC-GUU-CCA-AAG-UUG-AUG-GAA-AAG-GCC-AAG-

 A   K   G   V   E   V   V   L   P   V   D   F   I   I   A   D   A
GCC-AAG-GGU-GUC-GAA-GUC-GUC-UUG-CCA-GUC-GAC-UUC-AUC-AUU-GCU-GAU-GCU-

 F   S   A   D   A   N   T   K   T   V   T   D   K   E   G   I   P
UUC-UCU-GCU-GAU-GCC-AAC-ACC-AAG-ACU-GUC-ACU-GAC-AAG-GAA-GGU-AUU-CCA-

 A   G   W   Q   G   L   D   N   G   P   E   S   R   K   L   F   A
GCU-GGC-UGG-CAA-GGG-UUG-GAC-AAU-GGU-CCA-GAA-UCU-AGA-AAG-UUG-UUU-GCU-

 A   T   V   A   K   A   K   T   I   V   W   N   G   P   P   G   V
GCU-ACU-GUU-GCA-AAG-GCU-AAG-ACC-AUU-GUC-UGG-AAC-GGU-CCA-CCA-GGU-GUU-

 F   E   F   E   K   F   A   A   G   T   K   A   L   L   D   E   V
UUC-GAA-UUC-GAA-AAG-UUC-GCU-GCU-GGU-ACU-AAG-GCU-UUG-UUA-GAC-GAA-GUU-

 V   K   S   S   A   A   G   N   T   V   I   I   G   G   G   D   T
GUC-AAG-AGC-UCU-GCU-GCU-GGU-AAC-ACC-GUC-AUC-AUU-GGU-GGU-GGU-GAC-ACU-

 A   T   V   A   K   K   Y   G   V   T   D   K   I   S   H   V   S
GCC-ACU-GUC-GCU-AAG-AAG-UAC-GGU-GUC-ACU-GAC-AAG-AUC-UCC-CAU-GUC-UCU-

 T   G   G   G   A   S   L   E   L   L   E   G   K   E   L   P   G
ACU-GGU-GGU-GGU-GCU-UCU-UUG-GAA-UUA-UUG-GAA-GGU-AAG-GAA-UUG-CCA-GGU-

 V   A   F   L   S   E   K   K  end
GUU-GCU-UUC-UUA-UCC-GAA-AAG-AAA-UAA


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Last updated: 22 September 1999 by Hal White
Copyright 1999, Department of Chemistry and Biochemistry, University of Delaware, Newark, DE  19716