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  1. 1. BIOL 350 - Principles of Genetics • Instructors ‣ Dr.Vicki Corbin ‣ Dr. Stuart Macdonald • Textbook ‣ Genetics: Analysis of Genes and Genomes D. L. Hartl & E. W. Jones, 7th Edition • Email ‣ genet350sp09@ku.edu
  2. 2. Chapter 1 Genes, Genomes & Genetic Analysis
  3. 3. Genetics & Genomics • Genetics ‣ The study of biologically inherited traits ‣ Includes classical transmission, molecular, population & quantitative genetics • Genomics ‣ The study of the sequence, organization, and function of genomes
  4. 4. Organism → DNA
  5. 5. DNA is the Genetic Material • Inherited traits are influenced by genes transmitted from parents to offspring • Genes are composed of the chemical deoxyribonucleic acid (DNA) • DNA is the hereditary material in all cellular organisms
  6. 6. Griffiths (1928) Heat-killed S Living R cells + Living S cells Living R cells cells heat-killed S cells Pneumonia Healthy mouse Healthy mouse Pneumonia Only S cells from Only R cells from R and S cells from No cells isolated dead mouse live mouse dead mouse • Substance from dead S cells must be transferred to living R cells, i.e., R bacteria can be transformed into S bacteria
  7. 7. Avery, McLeod & McCarthy (1944) Heat-killed S cells Live R cells Live S cells No live S cells recovered recovered • Only if DNA from S cells is destroyed will mice survive
  8. 8. Properties of DNA 1. Carries blueprint for all parts of a complex organism - DNA must allow diversity 2. Every cell has the same genetic makeup - at every cell division DNA must be faithfully replicated 3. Encodes all proteins made in an organism, and signals when and where they should be made - DNA must have informational content 4. Individuals are not genetically identical - on occasion DNA must be able to change
  9. 9. Structure of DNA • Watson & Crick resolved the 3D structure in 1953 ‣ DNA consists of 2 chains twisted into a double- stranded helix ‣ Helix is right-handed: coils in a clockwise direction ‣ Each strand has polarity
  10. 10. DNA Composition • Each strand of the DNA helix is a linear polymer of nucleotides • Each nucleotide contains a phosphate group, a deoxyribose sugar, and a nitrogenous base • Four DNA bases: Adenine (A) Thymine (T) PURINES PYRIMIDINES Guanine (G) Cytosine (C)
  11. 11. Complementary Base Pairing • Base pairing rules ‣ Adenine pairs with Thymine (A − T) ‣ Cytosine pairs with Guanine (C − G) DNA helix unwind DNA
  12. 12. DNA Replication • Watson-Crick DNA structure suggests a way that DNA can be copied ‣ Strands of the original double- stranded molecule separate ‣ Each original strand serves as a template to create a complementary strand (relying on A-T and G-C base pairing)
  13. 13. Overview Template strand 5′ 3′ 3′ 5′ New strand 5′ 3′ Daughter DNA Parent DNA molecule molecules 3′ 5′ New strand 5′ 3′ 3′ 5′ Template strand
  14. 14. Outcome of DNA Replication • 1 double-stranded parent DNA molecule gives 2 identical daughter copies • Each daughter molecule has 1 parental strand and 1 newly synthesized strand 5’ ATG CCG ATC 3’ 3’ TAC GGC TAG 5’ 5’ ATG CCG ATC 3’ 5’ ATG CCG ATC 3’ 3’ TAC GGC TAG 5’ 3’ TAC GGC TAG 5’
  15. 15. DNA = Information • Sequence of bases (A, C, G, & T) along a DNA molecule encodes genetic information ‣ Huge information potential: a sequence of DNA 10 bases has 410 (> 1 million) possible forms • A DNA molecule can encode vast number of different proteins
  16. 16. Noncoding DNA • Only a fraction of the total DNA in an organism codes for protein • What does noncoding DNA do? ‣ Regulatory DNA sequence - controls when, where, and how much protein-coding genes are expressed (i.e., turned on) ‣ Some DNA is transcribed into RNA molecules that are themselves functional (and are never translated) ‣ Junk DNA - sequence with no known function
  17. 17. DNA → → Protein • DNA sequence provides the information encoding the amino acid sequence of a polypeptide chain (a protein) • BUT this is an indirect process ‣ DNA codes for RNA via transcription ‣ RNA codes for protein via translation
  18. 18. DNA → RNA → Protein • DNA is transcribed into the related molecule ribonucleic acid (RNA) • RNA transcript is processed to form messenger RNA (mRNA) • mRNA translated into an amino acid sequence (a polypeptide) “Central Dogma”
  19. 19. Example • Phenylalanine hydroxylase ‣ The first 21 bases of the gene ‣ The first 7 amino acids in the resulting polypeptide
  20. 20. Transcription (DNA → RNA) • Make an RNA molecule complementary to a single DNA strand ‣ Conceptually similar to DNA replication • RNA transcript often processed to give the mature mRNA ‣ Remove portions of gene not encoding amino acids
  21. 21. RNA Transcript • Transcription begins at an initiation site upstream of the protein-coding region of the gene, and ends at a termination site downstream of the protein-coding region transcription PROTEIN-CODING REGION translation
  22. 22. RNA • RNA (ribonucleic acid) is structurally similar to DNA ‣ RNA contains a ribose sugar (DNA contains deoxyribose) ‣ RNA is typically single-stranded ‣ RNA contains the base Uracil (U) rather than Thymine (T)
  23. 23. RNA-DNA Base Pairing • In the RNA-DNA duplex formed during transcription, U (in RNA) pairs with A (in DNA)
  24. 24. Role of RNA Intermediate • The mature mRNA transcript serves as a “working copy” of the gene • Increases number of copies of the genetic information in the cell ‣ remember each cell hold just 2 copies of the DNA gene • Provides an additional level of regulation
  25. 25. Translation (RNA → Protein) Process occurs at ribosomes
  26. 26. Stepwise Amino Acid Addition Polypeptide chain elongates until a “stop” codon is found, then is released from the ribosome
  27. 27. 3 Types of RNA Used in Translation • messenger RNA (mRNA) - carries genetic information from the gene • ribosomal RNA (rRNA) - major constituent of ribosomes • transfer RNA (tRNA) - each carries an amino acid and an anticodon (complementary to a mRNA codon sequence)
  28. 28. Triplet Code • A codon = a 3-base DNA triplet in a gene • There are 4 (= 64) possible codons, but just 3 20 amino acids... • Not all of the codons encode an amino acid ‣ Stop (or termination) codons • Some amino acids are encoded by multiple codons ‣ Triplet code is degenerate
  29. 29. The Standard Genetic Code 2nd nucleotide in codon (middle) 3rd nucleotide in codon (3′ end) 1st nucleotide in codon (5′ end) Codon Abbreviations
  30. 30. Start & Stop Codons • AUG (specifies Methionine) is the start codon for polypeptide synthesis ‣ All polypeptide chains start with Met ‣ Met is also used within polypeptide chains • UAA, UAG, UGA are the stop codons ‣ Signal end of translation and release of polypeptide from ribosome ‣ Stop codons are not recognized by tRNA molecules
  31. 31. Universal Code? • Triplet genetic code is almost universal, but there are a few exceptions • For example, the vertebrate mitochondrial DNA genetic code: Codon Standard Vertebrate mtDNA AGA Arg stop AGG Arg stop AUA Ile Met UGA stop Trp
  32. 32. Polypeptide → Protein • Polypeptide resulting from transcription/translation is not the final protein • Protein = folded polypeptide chain • Amino acid sequence helps specify the folding - does not myoglobin completely determine the 3D structure protein 3D structure
  33. 33. Genes Change by Mutation • Mutation = a heritable change in the genome sequence • A mutation gives a mutant gene sequence, which will produce a mutant mRNA and protein, and yield a mutant phenotype ‣ A phenotype is any observable quality, characteristic or trait
  34. 34. Drosophila white Gene Mutation • The product of the white gene operates in the pigment synthesis pathway • Normal, wild-type gene → red eyes • Defective, mutant gene → white eyes WILD-TYPE MUTANT
  35. 35. Phenylketonuria (PKU) • Normal individual ‣ Phenylalanine (an amino acid) in food is converted into tyrosine by the enzyme phenylalanine hydroxylase (PAH) Phenylalanine • Individual with mutant hydroxylase PAH enzyme ‣ Phenylalanine accumulates, and excess is broken down into harmful metabolites
  36. 36. PKU Disease • Individuals with a PAH enzyme mutation have mental retardation • PKU is one of very few diseases that can be controlled by diet (if caught early) ‣ US has tested all newborns since the 1960’s - if positive they are put on a diet low in phenylalanine • Incidence of PKU: ‣ 1 in 10,000 Caucasian children ‣ 1 in 200,000 African-American children
  37. 37. Wild-type PAH Enzyme Production of PAH enzyme in a non-mutant (wildtype) individual
  38. 38. PAH: Start Codon Mutation No PAH enzyme is made because translation cannot be initiated
  39. 39. PAH: Mutation in Middle of Gene Mutant form of PAH protein is produced that cannot properly metabolize phenylalanine
  40. 40. Lots of Mutations Lead to PKU • >100 mutations in the PAH gene result in a malfunctioning enzyme ‣ Most are single base changes (e.g., C → T) in protein- coding regions of the gene (exons) that lead to single amino acid changes ‣ Some are in noncoding gene regions (introns) and impact how the PAH mRNA is processed
  41. 41. Genes & Environment Influence Traits • PKU shows that a single gene can have a major effect on a trait • Also demonstrates that environment is very important ‣ PKU mutations have no effect on individuals that severly restrict their phenylalanine intake • Many traits show this kind of gene-by- environment interaction
  42. 42. Polygenic Traits • PKU is unusual in that only one gene can mutate to give the disease • Most traits are polygenic, and are influenced by many genes (along with environmental factors) ‣ Most human diseases are complex traits
  43. 43. Pleiotropy • Some genes can affect more than one trait - gene said to have pleiotropic effects • Example: 40% of cats with white fur and blue eyes are also deaf ‣ The genetic factor affecting fur and eye color can also lead to deafness