MIT Department of Biology
7.014 Introductory Biology, Spring 2005
Recitation Section 22
May 2-3, 2005
From Yeast to Humans—Essential Genes on the Evolutionary Continium.
A. CBS protein in yeast and humans
Recall that earlier in the term we considered the human gene CBS and its yeast analog cys4. Recall that these
genes each encode the protein cystathionine β-synthase that is responsible for converting homocysteine into
cystathionine in the cellular pathway of creating cysteine.
1. What is cysteine? Is it important for organism’s survival?
2. What would you expect to be the result of complete absence of the protein product of the yeast CYS4
gene to be? What about the same question for the human CBS protein?
3. Would you expect cells that contain no functional copy of CBS enzyme to accumulate some kind of a
compound? If no, why not? If yes, what kind of a compound would you expect that compound to be?
4. In the experiments we discussed earlier in the term, what was the phenotype of the cys4 mutants on
complete media?
5. As we told you a number of sessions ago, the deficiency in the human analog of CYS4 gene, CBS,
lead to a disease called cysteineurea, resulting in variety of serious conditions, including mental
retardation, heart attack, and stroke. What accounts for such a big difference in phenotype between
CBS protein deficient yeast and humans?
B. Phylogenetic analysis
Below is a figure from a research paper showing alignment of the amino acid sequences of human, rat, yeast,
and E. coli CBS proteins.
Figure removed due to copyright reasons.
Please see:
Kruger, W. D., and D. R. Cox. "A yeast system for expression of human cystathionine beta-synthase:
structuraland functional conservation of the human and yeast genes." Proc Natl Acad Sci USA 91,
no. 14 (July 5, 1994): 6614-8.
1. What do the dashes in the sequence represent?
2. Are the DNA sequences encoding amino acids that are conserved across species above necessarily
the same? Why or why not?
3. What properties of the particular amino acids allow them to be grouped into the conservative
groupings as described in the figure legend above?
4. Look at the genetic code table. Is there a relationship between the codons encoding amino acids in
conservative groupings?
5. Is CBS a good candidate for creating a phylogenetic tree on the basis of its sequence? Why or why
not?
6. Are human disease alleles of CBS likely to help with phylogenetic tree construction? Why or why
not?
7. If constructing a phylogenetic tree on the basis of CBS alignment, would it be more useful to work
with the protein or cDNA sequences? cDNA sequences or DNA sequences? Why?
8. Do you expect the human wild type gene to complement yeast CYS4 deficiency? Why or why not?
9. Is there a way to explore the relationship between human CBS protein and yeast CYS4 protein?
The Genetic Code
U
UUU phe (F)
UUC phe
UUA leu (L)
UUG leu
CUU leu (L)
CUC leu
CUA leu
CUG leu
AUU ile (I)
AUC ile
AUA ile
AUG met (M)
GUU val (V)
GUC val
GUA val
GUG val
U
C
A
G
UCU
UCC
UCA
UCG
CCU
CCC
CCA
CCG
ACU
ACC
ACA
ACG
GCU
GCC
GCA
GCG
C
ser (S)
ser
ser
ser
pro (P)
pro
pro
pro
thr (T)
thr
thr
thr
ala (A)
ala
ala
ala
A
tyr (Y)
tyr
STOP
STOP
his (H)
his
gln (Q)
gln
asn (N)
asn
lys (K)
lys
asp (D)
asp
glu (E)
glu
UAU
UAC
UAA
UAG
CAU
CAC
CAA
CAG
AAU
AAC
AAA
AAG
GAU
GAC
GAA
GAG
STRUCTURES OF AMINO ACIDS
at pH 7.0
O
O
C
H
CH3
H
NH3
+
C
CH2 SH
H
NH3
+
O
H
N
O
+
C
C CH2
NH3
+
N
C
H
H
H
O
S
CH3
H
H
METHIONINE
(met)
C
O
CH2
H
CH3
NH3 OH
+
THREONINE
(thr)
C
CH2
C
H
H
H
H
O
O
NH3
+
C
H
H
C
H
-
O
O
C
C CH2
OH
NH3
+
H
TYROSINE
(tyr)
H
OH
SERINE
(ser)
C
H
CH2
NH3
+
PROLINE
(pro)
H
O
O
H C CH2
CH2
H
N
CH2
+
H
H
N
TRYPTOPHAN
(trp)
O
C
H
CH2CH2CH2CH2
LYSINE
(lys)
O
H
C
NH3
+
CH3
H
O
C
H
C CH3
LEUCINE
(leu)
H
H
C
GLYCINE
(gly)
H
C
PHENYLALANINE
(phe)
O
O
O
C H
NH3
+
O
NH3
+
C CH2
NH3
+
C H
NH2
C
CH2CH3
C
C CH2CH2
C
C
H
O
O
O
O
NH3
+
H
C
C
C
GLUTAMINE
(glN)
O
C H
O
O
CH2CH2
O
ASPARTIC ACID
(asp)
O
C
CH2 C
NH3
+
O
NH3
+
ISOLEUCINE
(ile)
C
H
-
O
NH3 CH3
+
H
HISTIDINE
(his)
O
H
GLUTAMIC ACID
(glu)
C
H
C
NH3
+
CYSTEINE
(cys)
O
CH2CH2
NH2
C
O
C
O
C
H
ASPARAGINE
(asN)
O
C
C
NH3
+
O
O
C
O
CH2 C
C
NH2
+
ARGININE
(arg)
O
H
C
H
NH2
-
O
O
C
H
CH2CH2CH2 N
C
NH3
+
ALANINE
(ala)
O
O
C
C
O
O
O
UGU
UGC
UGA
UGG
CGU
CGC
CGA
CGG
AGU
AGC
AGA
AGG
GGU
GGC
GGA
GGG
H
C
CH3
C
NH3 H
+
CH3
VALINE
(val)
NH3+
G
cys (C)
cys
STOP
trp (W)
arg (R)
arg
arg
arg
ser (S)
ser
arg (R)
arg
gly (G)
gly
gly
gly
U
C
A
G
U
C
A
G
U
C
A
G
U
C
A
G