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 and E. coli CBS proteins. Below is a figure from a research paper showing alignment of the amino acid sequences of human, rat, yeast, 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? 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): 6614-8.5. 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 C A G U UUU phe (F) UUC phe UUA leu (L) UUG leu UCU UCC UCA UCG ser (S) ser ser ser UAU tyr (Y) UAC tyr UAA STOP UAG STOP UGU cys (C) UGC cys UGA STOP UGG trp (W) U C A G C CUU leu (L) CUC leu CUA leu CUG leu CCU CCC CCA CCG pro (P) pro pro pro CAU his (H) CAC his CAA gln (Q) CAG gln CGU arg (R) CGC arg CGA arg CGG arg U C A G A AUU ile (I) AUC ile AUA ile AUG met (M) ACU ACC ACA ACG thr (T) thr thr thr AAU asn (N) AAC asn AAA lys (K) AAG lys AGU ser (S) AGC ser AGA arg (R) AGG arg U C A G G GUU val (V) GUC val GUA val GUG val GCU GCC GCA GCG ala (A) ala ala ala GAU asp (D) GAC asp GAA glu (E) GAG glu GGU gly (G) GGC gly GGA gly GGG gly U C A G STRUCTURES OF AMINO ACIDS at pH 7.0 - OO OO OCO OCO H -C OC O C HC CH2 CNH2 H C CH2H C CH3 H C CH2CH2CH2 N C -NH3 ONH3 NH3 NH3 NH2 + + NH2+ + ALANINE ARGININE + ASPARAGINE ASPARTIC ACID (ala) (arg) (asN) (asp) OO OO OCO OCO C O H C CH2 C O C H CCH2CH2C H C HSH H C CH2CH2 - NH3 NH3 O NH3 NH2 NH3 ++ ++ CYSTEINE GLUTAMIC ACID GLUTAMINE GLYCINE (cys) (glu) (glN) (gly) --H OO OO OCO OO C + HC H C HN C +H C C CH2CH3 H C CH2 C CH3 H C CH2CH2CH2CH2 NH3H C CH2 NH3 CH3 NH3 CH3 NH3NH3 CN H++ + + H ISOLEUCINE LEUCINE LYSINE HISTIDINE (ile) (leu) (lys) (his) OCO O OH H OCCO OO C C H C CH2CH2 SCH3 H C CH2 H H CH2 H C CH2 OH CH2 NH3 ++ NH3 NH3 HH N + CH2 + METHIONINE H H (met) PHENYLALANINE PROLINE SERINE (phe) (pro) (ser) -HHOO - OO --C N OO H H OCCH3O C H H CCH2C C H H C CH2 OH HCHCCCH3 NH3 C CH3+ NH3 HNH3NH3 OH ++H THREONINE TRYPTOPHAN H(thr) (trp) H+ HH VALINE TYROSINE
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