Point mutations ppt


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  • 1: particle that binds (ligere = to bind, as in liaison) HORMONAL CHALLENGE: An X-ray structure of genistein bound to the Estrogen Receptor-b ligand1-binding domain demonstrates the difficulty that faced ER-b drug developers:
  • 1 – insertion  frame shift 2 deletion  frame shift
  • Source: http://www.sciencemag.org/cgi/content/full/315/5811/466/F1
  • Walker et al. (1999) Nature 402, 313-320
  • 1: cancer
  • Temperature affects expression of the gene for black fur pigment. This gene is expressed only below a certain temperature threshold
  • 1: genes for making dark pigment are switched on at cold temperatures and switched off at warm temperatures. That explains the color pattern of the rabbit.
  • Campbell p. 437, fig. 23.8
  • Source: http://www.sciencemag.org/cgi/content/full/310/5755/1754a
  • Quoted from: http://www.gnxp.com/blog/2005/12/race-is-skin-deep.php
  • Source: http://www.sciencemag.org/cgi/content/full/310/5755/1754a
  • Source: http://www.sciencemag.org/cgi/content/full/310/5755/1754a
  • It’s a giant German grey
  • Xiaojiang Gao, Ph.D., George W. Nelson, Ph.D., Peter Karacki, B.A., Maureen P. Martin, M.D., John Phair, M.D., Richard Kaslow, M.D., James J. Goedert, M.D., Susan Buchbinder, M.D., Keith Hoots, M.D., David Vlahov, Ph.D., Stephen J. O'Brien, Ph.D., and Mary Carrington, Ph.D. ABSTRACT Background From studies of genetic polymorphisms and the rate of progression from human immunodeficiency virus type 1 (HIV-1) infection to the acquired immunodeficiency syndrome (AIDS), it appears that the strongest susceptibility is conferred by the major-histocompatibility-complex (MHC) class I type HLA-B*35,Cw*04 allele. However, cytotoxic T-lymphocyte responses have been observed against HIV-1 epitopes presented by HLA-B*3501, the most common HLA-B*35 subtype. We examined subtypes of HLA-B*35 in five cohorts and analyzed the relation of structural differences between HLA-B*35 subtypes to the risk of progression to AIDS. Methods Genotyping of HLA class I loci was performed for 850 patients who seroconverted and had known dates of HIV-1 infection. Survival analyses with respect to the rate of progression to AIDS were performed to identify the effects of closely related HLA-B*35 subtypes with different peptide-binding specificities. Results HLA-B*35 subtypes were divided into two groups according to peptide-binding specificity: the HLA-B*35-PY group, which consists primarily of HLA-B*3501 and binds epitopes with proline in position 2 and tyrosine in position 9; and the more broadly reactive HLA-B*35-Px group, which also binds epitopes with proline in position 2 but can bind several different amino acids (not including tyrosine) in position 9. The influence of HLA-B*35 in accelerating progression to AIDS was completely attributable to HLA-B*35-Px alleles, some of which differ from HLA-B*35-PY alleles by only one amino acid residue. Conclusions: This analysis shows that, in patients with HIV-1 infection, a single amino acid change in HLA molecules has a substantial effect on the rate of progression to AIDS. The different consequences of HLA-B*35-PY and HLA-B*35-Px in terms of disease progression highlight the importance of the epitope specificities of closely related class I molecules in the immune defense against HIV-1. And J Virol. 2002 December; 76(24): 12603–12610. doi: 10.1128/JVI.76.24.12603-12610.2002. Copyright © 2002, American Society for Microbiology Human Immunodeficiency Virus Type 1 (HIV-1)-Specific CD8+-T-Cell Responses for Groups of HIV-1-Infected Individuals with Different HLA-B*35 Genotypes Xia Jin,1* Xiaojiang Gao,2 Murugappan Ramanathan, Jr.,3 Geoffrey R. Deschenes,3 George W. Nelson,2 Stephen J. O'Brien,4 James J. Goedert,5 David D. Ho,3 Thomas R. O'Brien,5 and Mary Carrington2
  • Point mutations ppt

    1. 1. Point Mutations Mutations involving a few nucleotides, sometimes as few as a single one (SNPs) 04/19/10
    2. 2. SNPs <ul><li>(Pronounce: snips) S ingle n ucleotide p olymorphisms </li></ul><ul><li>1 nucleotide variations between alleles </li></ul>04/19/10
    3. 3. A Reminder <ul><li>2 SNPs difference between estrogen receptors a and b.  next page </li></ul>04/19/10
    4. 4. Shape and AA Sequence 04/19/10 Genistein, bound to estrogen receptor-b. Only two amino acids (shown) differ between the two estrogen receptors. ( purple : ER-a) ( yellow: ER-b)
    5. 5. Point Mutations <ul><li>The Genome Map </li></ul><ul><li>Lists diseases caused by point mutations by chromosome – with images </li></ul><ul><li>The – more abstract - 1998 update </li></ul><ul><li>The 2002 update </li></ul>04/19/10
    6. 6. Links <ul><li>ThinkQuest Genetics Lab - Mutations </li></ul>04/19/10
    7. 7. Point Mutation <ul><li>We will mutate one codon in several ways. Assume that that codon is, for example, the 15 th codon in a chain of 100 codons in an mRNA. </li></ul>04/19/10
    8. 8. Point Mutations: Mutating a codon – SNP Effects <ul><li>Imagine that this is codon 15 out of 100 codons of a protein gene mRNA. All other codons remain unchanged: </li></ul><ul><li> ATA </li></ul><ul><li> UAU </li></ul><ul><li> tyr </li></ul><ul><li> </li></ul>04/19/10
    9. 9. Point Mutations Mutating a codon – SNP Effects: <ul><li> ATA T TA </li></ul><ul><li> UAU AAU </li></ul><ul><li> tyr asn </li></ul><ul><li>ATT </li></ul><ul><li>UAA </li></ul><ul><li> stop </li></ul>04/19/10 mutation 1 1 AA difference
    10. 10. Point Mutations Mutating a codon – SNP Effects: <ul><li> ATA T TA </li></ul><ul><li> UAU AAU </li></ul><ul><li> tyr asn </li></ul><ul><li> </li></ul><ul><li> </li></ul>04/19/10 mutation 1 <ul><li>Mutation types: </li></ul><ul><li>missense </li></ul>1 AA difference
    11. 11. Point Mutations Mutating a codon – SNP Effects: <ul><li>AT G ATA T TA </li></ul><ul><li>UAC UAU AAU </li></ul><ul><li> tyr tyr asn </li></ul>04/19/10 mutation 1 mutation 2 1 AA difference <ul><li>Mutation types: </li></ul><ul><li>Missense </li></ul><ul><li>Silent </li></ul>Sequence unchanged
    12. 12. Point Mutations: Mutating a codon – Effects of SNPs <ul><li>AT G ATA T TA </li></ul><ul><li>UAC UAU AAU </li></ul><ul><li>tyr tyr asn mutation 3 </li></ul><ul><li>AT T </li></ul><ul><li>UAA </li></ul><ul><li> stop </li></ul>04/19/10 mutation 2 mutation 1
    13. 13. Point Mutations: Mutating a codon <ul><li>AT G ATA T TA </li></ul><ul><li>UAC UAU AAU </li></ul><ul><li>tyr tyr asn 3 </li></ul><ul><li>AT T </li></ul><ul><li>UAA </li></ul><ul><li> stop </li></ul>04/19/10 2 1 <ul><li>Mutation types: </li></ul><ul><li>missense </li></ul><ul><li>silent </li></ul><ul><li>nonsense (stop) – chain is aborted </li></ul>
    14. 14. Point Mutations Can Happen During DNA Repair 04/19/10
    15. 15. SNP Effects – e.g. Frame Shift <ul><li>A cytosine insertion in the NOD2 gene leads to Crohn’s disease (CD). </li></ul><ul><li>CD is a chronic inflammatory gut disorder, thought to be caused by an abnormal inflammatory response to enteric microbes. </li></ul><ul><li>For more info click here </li></ul>04/19/10
    16. 16. How Mutations May Happen <ul><li>Watch this animation and answer the following questions: </li></ul><ul><ul><li>What type of mutation is the result of </li></ul></ul><ul><ul><ul><li>new strand and </li></ul></ul></ul><ul><ul><ul><li>template strand </li></ul></ul></ul><ul><ul><li>slippage? </li></ul></ul>04/19/10
    17. 17. Point Mutation Types - Overview <ul><li>Panel A shows the normal sequence of DNA from one exon and the protein product it encodes </li></ul><ul><li>Panel B shows a silent mutation, </li></ul><ul><li>Panel C a conservative missense mutation (serine and threonine have very similar structures) </li></ul><ul><li>Panel D a nonconservative missense mutation (serine and proline have very different structures), </li></ul><ul><li>Panel E a nonsense mutation, and </li></ul><ul><li>Panel F a frame-shift mutation. In Panel F, the insertion of a single G throws off the reading frame, so that all amino acids downstream are changed radically. </li></ul>04/19/10 G
    18. 18. Silent Mutations – Not Always Silent <ul><li>Protein folding depends on the speed at which the mRNA moves through the ribosome, since silent translations can alter that speed, they may result in different protein folding </li></ul>04/19/10
    19. 19. Mutations in PIK3CA Where is this gene mutated? 04/19/10
    20. 20. Structure of phosphoinositide 3-kinase gamma <ul><li>Click on a domain in the image in this link for a detailed description of it </li></ul><ul><li>PIK3CAs have several d o m a i ns with different functions </li></ul>04/19/10 A kinase is an enzyme that places a phosphate onto another protein. More specifically, kinases take the gamma (= 3 rd ) phosphate from ATP and place it on a serine, threonine, or tyrosine amino acid of the target substrate.
    21. 21. Mutations in PIK3CA <ul><li>“ Phosphatidylinositol 3-kinases (PI3Ks) are lipid kinases that regulate signaling pathways important for neoplasia 1 , including cell proliferation, adhesion, survival, and motility ( 1 – 3 ). To determine if PI3Ks are genetically altered in tumorigenesis, we sequenced PI3K genes in human cancers and corresponding normal tissue.” </li></ul><ul><li>“ Arrowheads indicate the location of missense mutations, boxes represent functional domains (the p85 binding domain, Ras binding domain, C2 domain, helical domain, and kinase domain). The percentage of mutations detected within each region is indicated below, and the fraction of tumors with mutations is noted above. </li></ul>04/19/10
    22. 22. Why Might Anyone Want to Know This? 04/19/10
    23. 23. PIK3CA A Possible Cancer Treatment? <ul><li>In most of the tumors listed above, the kinase is over-expressed. Inhibiting the kinase may inhibit tumorigenesis. </li></ul>04/19/10
    24. 24. Genes and Environment 04/19/10
    25. 25. Gene Expression And The Environment <ul><li>Russian rabbits have black noses, ears, tails, and paws. </li></ul><ul><li>Yet, the genes for the black pigment are present in ALL their cells. </li></ul><ul><li>Develop a hypothesis to explain the pattern. </li></ul>04/19/10
    26. 26. Genes and Environment <ul><li>If this Russian rabbit has its thigh shaved and is then kept in a cold environment, what will the new fur growth look like? </li></ul>04/19/10
    27. 27. Genes & Environment <ul><li>Plants with the same genes may exhibit dramatically different growth forms, depending on their environment </li></ul>04/19/10 Cuttings from the 7 different plants on the left, grown at different altitudes:
    28. 28. Gene, Smoking Combo Boosts Risk of Elderly Vision Loss <ul><li>Specific mutation raises chances of age-related macular degeneration </li></ul><ul><li>MONDAY, March 20 (HealthDay News) -- A combination of smoking plus a specific gene variant could account for a third of cases of age-related macular degeneration (AMD), researchers say. AMD is the most common cause of visual impairment and legal blindness in older Americans. Interaction between a specific variant of the LOC387715 gene and cigarette smoking greatly increases AMD, say researchers at Duke University Medical Center and Vanderbilt University Medical Center. The finding emphasizes the importance of genetic factors in the onset of AMD, and suggests the potential to reduce the incidence of the disease through smoking prevention and cessation programs. &quot;The most exciting aspect of this research is that it is the combination of the gene and smoking that really puts you at risk,&quot; study senior author Margaret Pericak-Vance, director of the Duke Center for Human Genetics, said in a prepared statement. </li></ul><ul><li>&quot;We demonstrate, for the first time, that a gene variant coupled with a modifiable lifestyle factor such as cigarette smoking confers a significantly higher risk of AMD than either factor alone,&quot; she said. The findings appear in the online edition of the American Journal of Human Genetics , and will be published in the May print issue of the journal. The study included 1,001 people with all forms of AMD and 394 healthy people in a control group. Researchers analyzed 185 variations in the DNA sequence of genes located in a region believed to be associated with susceptibility to AMD. The scientists found that 42 percent of the chromosomes of people with AMD and 26 percent of the people in the control group had a specific variant of LOC387715 statistically associated with the highest risk of developing AMD. In nonsmokers, this genetic variant increased AMD risk twofold. People who had the genetic variant and smoked had an eightfold increased risk of AMD, compared to nonsmokers without the variant. The actual function of the LOC387715 gene in the visual system is unknown, the researchers said. </li></ul><ul><li>-- Robert Preidt SOURCE: Duke University, news release, March 7, 2006 </li></ul>04/19/10
    29. 29. Without the Presence of the Environmental Factor, These Genes Do Not Lead to Disease 04/19/10 Read about: Genetics, race, ethnicity, and health A SAMPLING OF ENVIRONMENTAL GENES Polymorphism Function Environmental exposure Associated disease CYP1A1 Activation Smoking Lung cancer NAT2 Detoxification Smoking Bladder, breast cancer GSTT1 Detoxification Chlorinated solvents Cancer, toxicity Paraoxonase Detoxification Nerve agents, pesticides Nervous system damage HLA-H Nutritional factors Iron in diet Hemochromatosis TGF-alpha Growth factor Maternal smoking Cleft lip & palate Locus on chrom. 17 in mice Immune/inflammatory response Ozone Lung inflammation HLA-DP bet1 marker Immune response Beryllium Chronic beryllium disease (lung disorder) ALAD Biosynthesis Lead Lead poisoning
    30. 30. More about diseases (heart, cancer, diabetes) and environment here (very informative!) 04/19/10
    31. 31. Genes and Skin Color 04/19/10
    32. 32. Genes And Skin Color Findings From Golden Zebra Fish <ul><li>“ Lighter variations of pigmentation in humans are associated with diminished number, size, and density of melanosomes, the pigmented organelles of melanocytes. Here we show that zebrafish golden mutants share these melanosomal changes and that golden encodes a putative cation exchanger slc24a5 (nckx5) that localizes to an intracellular membrane, likely the melanosome or its precursor. </li></ul><ul><li>The human ortholog is highly similar in sequence and functional in zebrafish. The evolutionarily conserved ancestral allele of a human coding polymorphism predominates in African and East Asian populations. In contrast, the variant allele is nearly fixed in European populations, is associated with a substantial reduction in regional heterozygosity , and correlates with lighter skin pigmentation in admixed populations, suggesting a key role for the SLC24A5 gene in human pigmentation. “ </li></ul>04/19/10
    33. 33. Two Primary Alleles for Skin Color Gene <ul><li>Data … show … “that SLC24A5 has two primary alleles, which vary by one amino acid. Nearly all Africans and East Asians have an allele with alanine in a key locus, whereas 98% of Europeans have threonine at that locus.” </li></ul>04/19/10
    34. 34. A SNP Determines Skin Color in Many People <ul><li>“… polymorphisms within the” SLC24A5 “gene. … the G and A alleles of the single nucleotide polymorphism (SNP) rs1426654 encoded alanine or threonine, respectively, at amino acid 111 in the third exon of SLC24A5 . “ </li></ul><ul><li>“ The allele frequency for the Thr 111 variant ranged from 98.7 to 100% among several European-American population samples, … </li></ul><ul><li>the ancestral alanine allele ( Ala 111 ) had a frequency of 93 to 100% in African, Indigenous American, and East Asian population samples” </li></ul>04/19/10
    35. 35. Gene SLC24A5 <ul><li>… “ the team measured the pigmentation levels of 203 African Americans and 105 African Caribbeans--groups that represent an admixture of African and European ancestry--and compared their SLC24A5 genotypes. </li></ul><ul><li>Subjects homozygous for the threonine allele tended to be lightest skinned , </li></ul><ul><li>those homozygous for the alanine allele were darkest , </li></ul><ul><li>and heterozygotes were in between , as shown by the degree of reflectance of their skin. The team concludes that between 25% and 38% of the skin-color difference between Europeans and Africans can be attributed to SLC24A5 variants ” </li></ul>04/19/10
    36. 36. 04/19/10 Published by AAAS R. L. Lamason et al., Science 310, 1782 -1786 (2005) Fig. 6. Effect of SLC24A5 Genotype on Pigmentation in Admixed Populations
    37. 37. Genes and the Size of a Dog A SNIP in the IGF-1 Gene Determines Dog Size 04/19/10
    38. 38. <ul><li>( B ) … IGF1 haplotypes and mean skeletal size. Haplotypes were inferred for 20 markers spanning the IGF1 gene (chromosome 15: 44,212,792 to 44,278,140, CanFam1). Out of the 720 chromosomes with successful inference, 96% carry one of just two haplotypes, B and I, identical to haplotypes inferred for small and giant dogs, respectively . Data are graphed as a histogram for each genotype: </li></ul><ul><ul><li>B/B (closed triangle, black line) </li></ul></ul><ul><ul><li>B/I (open square, dashed line) </li></ul></ul><ul><ul><li>I/I (closed circle, gray line) </li></ul></ul>04/19/10 Published by AAAS N. B. Sutter et al., Science 316, 112 -115 (2007) Relationships of skeletal size, SNP markers, IGF1 haplotype, and serum levels of the IGF1 protein in dogs <ul><li>(C) Serum levels of IGF1 protein (ng/ml) as a function of haplotype. </li></ul>
    39. 39. This Rabbit Must Have The Large Version 04/19/10
    40. 40. Last Not Least Genes and HIV Progression 04/19/10
    41. 41. Effect of a Single Amino Acid Change in MHC Class I Molecules on the Rate of Progression to AIDS <ul><li>Conclusions: </li></ul><ul><li>This analysis shows that, in patients with HIV-1 infection, a single amino acid change in HLA molecules has a substantial effect on the rate of progression to AIDS. </li></ul><ul><li>… different consequences of HLA-B*35-PY and HLA-B*35-Px in terms of disease progression … </li></ul><ul><li>Human immunodeficiency virus type 1 (HIV-1)-infected individuals with HLA-B*35 allelic variants B*3502/3503/3504/5301 (B*35-Px) progress more rapidly to AIDS than do those with B*3501 (B*35-PY). </li></ul><ul><li>'Indians vulnerable to HIV/Aids' </li></ul><ul><li>India is home to one in seven HIV-positive people: </li></ul><ul><li>Indians infected with the Aids virus are more likely to contract the disease than people in the west, a new study has found. </li></ul>04/19/10
    42. 42. On the Up-Side Eternal Life? 04/19/10
    43. 43. Boosting Gene Extends Mouse Life Span <ul><li>Whereas lab mice can live about 2 years, mice engineered to overproduce a protein called Klotho [Greek goddess who spins life's thread], have celebrated third birthdays, … </li></ul><ul><li>The mutant rodents represent a rare case of a single gene substantially influencing life span in mammals. </li></ul><ul><li>These mice, which overexpress the gene for Klotho, have celebrated their third birthdays. </li></ul>04/19/10
    44. 44. The End 04/19/10