Understanding Genes & Mutations. John A Phillips III May 16, 2005

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1 Understanding Genes & Mutations John A Phillips III May 16, 2005

2 Learning Objectives Understand gene structure Become familiar with genetic & mutation databases Be able to find information on genetic variation & the phenotype you are studying in the GCRC

3 Gene Components & Structure Promoter 5 Start Transcription Exons DNA Enhancer Transcribed Introns 3 AATAAA polyadenylation signal CAP Site Poly A tail mrna G AUG: Start Translation UAG: Stop Translation AAAAAAAA Translated

4 Gene Structure: Exons & Introns

5 Genetic & Mutation Databases OMIM Human gene mutation database d0.html? Genetic Associations Single nucleotide polymorphisms (SNP)

6 OMIM Genetic Database

8 Genetic Association Database

9 Types of Point Mutations Silent (do not alter codons but??) Missense (amino acid substitutions) Nonsense (premature termination) Frameshift (premature termination) Splicing (create or destroy splice sites; often cause frameshift & premature termination) RNA processing (capping, splicing, polyadenylation & editing)

10 Gene Components & Structure Promoter 5 Start Transcription Exons DNA Enhancer Transcribed Introns 3 AATAAA polyadenylation signal CAP Site Poly A tail mrna G AUG: Start Translation UAG: Stop Translation AAAAAAAA Translated

12 Genetic Code is Composed of Triplets Term Term Met + Start

13 Missense Mutations mrna Protein AUG AAG UUU GGC GCA UUG CAA Met Lys Phe Gly Ala Leu Gln Normal mrna Protein AUG AAG UUU GGU CCA UUG CAA Met Lys Phe Gly Pro Leu Gln Variant Changes in bases 1, 2 & 3 of codon are almost always, always & sometimes missense, respectively Missense changes amino acid sequence ie Ala110Pro The amino acid substitution may be harmful or neutral

15 Nonsense Mutations mrna Protein AUG AAG UUU AAG GCA UUG CAA Met Lys Phe Lys Ala Leu Gln Normal mrna Protein AUG AAG UUU TAG GCA UUG CAA Met Lys Phe Ter Ala Leu Gln Variant Change an amino acid to a premature termination codon (PTC) ie Lys132Ter or Stop Encode a truncated protein PTCs can cause exon skipping or nonsense mediated decay (NMD)

16 Missense &Nonsense Mutations & CF Compound heterozygote: An individual who has two different abnormal alleles at a particular locus, one on each chromosome of a pair; usually refers to individuals affected with an autosomal recessive disorder

17 Frameshift mutation: An insertion or deletion involving a number of base pairs that is not a multiple of 3 & consequently disrupts the triplet reading frame, usually leading to the creation of a premature termination (stop) codon & a truncated protein product

18 Frameshift Mutations mrna Protein AUG AAG UUU GGC GCA UUG AAA Met Lys Phe Gly Ala Leu Lys Normal mrna Protein AUG AAG UUU GGG CAU UGA AA Met Lys Phe Gly His Variant In/del of anything but (3) N bases alters reading frame & amino acid sequence ie 1 bp Del, 185C Usually produces truncated protein

19 Exon 3 ---TCC Intron 3 gtgagtgga-- Normal gtgagcgga-- Mutant DS IVS3 +6 T-C

20 Splicing Mutations Exon 1 Intron Exon 2 Intron Exon 3 Exon 2 Altered mrna Exon 1 Exon 3 Destroy/create a splice site, ISE or ESE Can cause read through, exon skips or activate cryptic splice sites Changing splicing alters RNA sequence & translation product

21 5 & 3 Splice & Branch Point Sequences DNA Exon Intron Exon Intron Transcription Exon mrna

22 mrna Protein Silent Mutations AUG AAG UUU GGC GCA UUG CAA Met Lys Phe Gly Ala Leu Gln Normal mrna Protein AUG AAG UUU GGU GCA UUG CAA Met Lys Phe Gly Ala Leu Gln Variant Do not alter the amino acid sequence ie Gly109Gly Be careful,, they may produce new splice sites or affect ESEs that regulate splice choice

23 Single Nucleotide Polymorphisms (SNPs) TG C / T GC CG G / T AC GT C / T GC AC G / T AC Exon 1 Intron Exon 2 Intron Exon 3 Exon 1 Exon 2 Exon 3 Any single base polymorphic substitution (does not include deletions or insertions) Occur ~1300 bp, there are millions of SNPs Have a population frequency of at least 1% A SNP may or may not affect gene function

24 Summary of Mutations That Cause CF

25 Learning Objectives Understand gene structure Become familiar with genetic & mutation databases Be able to find information on genetic variation & the phenotype you are studying in the GCRC

26 Genetic & Mutation Databases OMIM Human gene mutation database d0.html? Genetic Associations Single nucleotide polymorphisms (SNP)

27 Potential Contribution of Genetic Variation to GCRC Studies Protocols Mendelian (N=42) Complex Disease (N=64) Protocols Drug (N=149) Protocols Protocols18 Organ Systems Studied Susceptibility (N=57) No Genetic (N=26) Circulatory Digestive Endocrine Immune Integument Muscular Nervous Oncology Reproductive Respiratory Skeletal Urinary Protocols

MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

Ch 17 Practice Questions MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question. 1) Garrod hypothesized that "inborn errors of metabolism" such as alkaptonuria