Genetics Mendelian Genetics Classical Genetics Pea Plants Gregor

Genetics

Mendelian Genetics: Classical Genetics Pea Plants Gregor Mendel: Father of Genetics (1800 s)

Why Pea Plants?

Pea Plants • Easy to grow • Short life cycle • Many traits to follow – Pea color – Pea shape – Pod color – Flower color – Pod shape – Plant size

Mendel’s Laws 1. Law of Dominance Observations: X Pure Short Parent (P) Pure Tall Parent (P) 100% Tall F 1 Generation

Mendel’s Laws X F 2 Short (25%) F 1 Tall F 2 Tall (75%)

What did Mendel NOT know about? • • Chromosomes DNA Genes Meiosis

Mendel’s Laws • We inherit “factors” • Traits that are hidden are “Recessive” • Traits that are Expressed are “Dominant” Law of Dominance: • In a Hybrid, only the dominant trait is seen • No Blending of traits

Mendel’s Laws 2. Law of Segregation Observations: How can you get a yellow from two green parents?

Law of Segregation • Alleles segregate or separate during meiosis and can come together in different pairings

Mendel’s Laws 3. Law of Independent Assortment: • Traits are usually inherited independent of each other (Ex. Blond hair does not always go with blue eyes) – Linked-genes are an exception

Law of Independent Assortment • Random how pairs assort themselves or line up at equator

Gene-Chromosome Theory 1900 s

Gene-Chromosome Theory 1900 s Location of a gene=Locus Different forms of a gene=Alleles Ex. The Height gene can have the tallness or shortness allele We get an allele from Mom and an allele from Dad

Gene-Chromosome Theory 1900 s • Give letter abbreviations for Alleles • The dominant allele wins the letter type and is capitalized • The recessive allele is lowercase Ex. Tall is Dominant over Short T=Tall Allele t=short Allele

Genotypes (Genetic Makeup) of Diploid Organisms • Homozygous Dominant ex. TT • Homozygous Recessive ex. tt • Heterozygous or Hybrid ex. Tt Can’t see in individual!

Phenotypes Appearances and can see! • Tall • Short • Green • Yellow…. .

Mendel’s Laws with Modern View • Law of Dominance: – Tt=T wins • Law of Segregation – Tt becomes T and t during meiosis • Law of Independent Assortment – T and G(green color) will be packaged into gametes independent of each other if they are on different chromosomes and are not “Linked”

Probability Studies • Punnett Square Diagram Tool

Probability Studies • Monohybrid Cross

Probability Studies • Test Cross: – Cross an unknown genotype with a known homozygous recessive

Tracking multiple traits… Yy. Rr x Yy. Rr 1. 2. 3. 4. 5. Treat each trait independently Yy x Yy= YY(1/4), Yy (1/2), yy (1/4) Rr x Rr= RR (1/4), Rr (1/2), rr (1/4) Multiply individual probabilities Chance of YYRR= ¼ x ¼= 1/16

Dihybrid Cross • Phenotypic Ratio – 9: 3: 3: 1 (Dom, Dom): Dom, Rec): (Rec, Dom): (Rec, Rec)

Special Situations in Genetics • Incomplete Dominance – Ex. Japanese four o’clock plant – Cross a red flowered plant with a white flowered plant and get all pink flowered plants – Notations for punnett square: • RR=Red • WW=White • RW=pink

Special Situations in Genetics • Codominance – Both alleles expressed equally – Ex. Roan coat color – Cross Red coat with White coat get Roan – Notations: – RR=Red – WW=White – RW=Roan

Special Situations in Genetics • Multiple Alleles – Blood Group Antigens • • Type A Blood: IAIA or IAi Type B Blood: IBIB or IBi Type AB Blood: IAIB Type O: ii

Special Situations in Genetics • Sex-linkage and Sex Chromosomes – XY and XX – What are the chances from a mating of having a male? Having a female? – What are the chances of having a male first then a female then male?

Special Situations in Genetics • Sex-linked Genes – Genes located on sex-chromosomes (mostly on Xchromosome) – Breeding studies don’t follow classical Mendelian genetic probabilities • ex. only male flies develop white eyes Drosophila T. H. Morgan (1900 s)

Why are Fruit Flies so great for genetic studies? • • Small Easy to raise Short reproductive cycle (14 days) Only 4 pairs of chromosomes – Have sex chromosomes and autosomes – XX and XY

What are some sex linked disorders? • Most disorders are on the X chromosome: Ex. : – Colorblindness – Hemophilia – Duchene muscular dystrophy

Genetics of Sex-linkage • Colorblindness (Recessive and Sexlinked): – Diseased Male= Xd. Y – Diseased Female= Xd. Xd – Normal Female= XX – Normal Male= XY – Carrier Female (“Normal”)= Xd. X

Questions • What are the chances of a colorblind man and a normal woman having a daughter that is colorblind? • What are the chances of a normal man and a colorblind woman of having colorblind children?

History of Molecular Genetics • Frederick Griffith (1920 s) – Bacterial transformation with “factors” – Transform S bacteria to R bacteria • Avery, Mac. Leod and Mc. Carty (1944) – The “factor” was DNA • Hershey and Chase (1944) – Worked with viruses (bacteriophages) – DNA carries genetic instructions • Watson and Crick (Rose Franklin)(1953) – DNA Structure

DNA Structure • Double-stranded alpha helix • Monomer: Nucleotide • Nucleotide: Phosphate group, pentose sugar, nitrogenous base

DNA Replication-Make more DNA • • S-Phase of Cycle Helicase DNA Polymerase DNA Ligase Hydrogen bonds break between bases Free nucleotides added to old strands Semiconservative model of replication

DNA Transcription-Make RNA • Happens in Nucleus • DNA code – Codons=three base pairs – Each codon codes for an amino acid • Ex: CAC=Histidine – Start Codons at the beginning of genes – Stop Codons at the ending of genes • Each gene codes for one polypeptide (One Gene -One Polypeptide Hypothesis)

DNA Transcription-Make RNA • Want to make a rough copy (m. RNA) of a specific gene

Events related to RNA Polymerase binding

• m. RNA leaves nucleus and enters cytoplasm • Single-stranded, ribose sugar, Uracil instead of Thymine • m. RNA is processed (--shortens) before meeting a ribosome

DNA Translation Protein Synthesis • Translate m. RNA (which is really DNA code) to protein • Need: – m. RNA – Ribosome – T-RNA – Amino acids

Codons • DNA/m. RNA code – Codons=three base pairs – Each codon codes for an amino acid • Ex: CAC=Histidine – Start Codons at the beginning of genes – Stop Codons at the ending of genes • Each gene codes for one polypeptide (One Gene -One Polypeptide Hypothesis)

Ribosome • • r. RNA (Ribosomal RNA) Protein Large and Small subunits Site of protein synthesis

t-RNA With amino acid anticodon region m. RNA start codon Small subunit of ribosome Large Subunit of ribosome

Polysomes or Polyribosomes • Multiple ribosomes translate in a 5’ to 3’ direction

Protein will have a signal sequence telling ribosome to put it in the ER

Review

Codon Code Book

How is gene expression controlled? • We have all genes in every cell of our body • But why don’t skin cells make insulin? • Why don’t liver cells make keratin?

Let’s look to see how bacteria control genes…. . • E. coli • Lac (Lactose) Operon – Cluster of genes that regulate the production of enzymes that digest lactose – Parts of the Operon • • Regulator Gene Promoter Operator Structural Genes

1 2 3 4 a 4 b 4 c 1. Regulator Gene=codes for a Repressor Protein 2. Promoter=Site for RNA Polymerase binding 3. Operator=On/Off Switch for Structural Genes 4 a-c=Structural Genes=Code for Enzymes to digest Lactose

When Lactose Absent… • Regulator Protein (ie. The Repressor) made and binds to Operator • Repressor turns Operon off 3 No Transcription of Structural Genes RNA Polymerase blocked

When Lactose Present…. • Lactose binds Repressor and prevents Repressor from blocking Operator Lactose Repressor • Now RNA Polymerase can bind Operator and transcribe enzymes genes

Gene Regulation-Higher Organisms • We DO NOT have Operons! • Our genes are NOT clustered • They are spread out amongst our 46 chromosomes

Gene Regulation-Higher Organisms • Environment and Gene Regulation + Himalayan Rabbit Black Fur

Gene Regulation-Higher Organisms • Environment and Gene Regulation Pollution turning on Oncogenes Cancer

Gene Regulation-Higher Organisms • Differential Coiling of DNA • Different cells have supercoiling in different regions of the DNA Genes in regions that are supercoiled can not be transcribed Regions that are not supercoiled can be transcribed

Gene Regulation-Higher Organisms • Transcription Factors – Molecules that must be in place on DNA for RNA Polymerase to transcribe or not to transcribe DNA

Gene Regulation-Higher Organisms • Differential m. RNA Splicing Exons=Regions that are expressed Introns=Noncoding regions that are sliced out Exons glued back in different orders to produce different m. RNAs and therefore proteins

Alternative Splicing

Gene Regulation-Higher Organisms • Epigenetics – Change in expression of genes without a change in sequence of DNA • Ex. Methylation – 1 -5% of cytosines have A methy group (CH 3) added – Is Inheritable – Strong bond to cytosine But is reversible

Epigenetics • Colorectal Cancer – Oncogenes demethylated – Tumor Suppressor Genes methylated • Environment influences epigenetic changes

Applied Genetics-Mutations • Mutation=change in DNA – Mutations only inherited if they occur in sex cell DNA – Chromosomal Mutations • Change in whole chromosome number or structure – Gene Mutations • Mutation in the sequence of a gene

What causes mutations? • Random errors in DNA copying mechanisms • Mutagens (A Mutagen can also be a Carcinogen) – X-rays – UV light – Chemicals

Chromosomal Mutations • • • Translocations Inversions Additions Deletions Nondisjunction Polyploidy

Translocation FROM A NONHOMOLOGOUS CHROMOSOME!

Inversion

Additions ABCDEFG Normal Chromosome ABCDECDEFG Additional genes came from a HOMOLOGOUS CHROMOSOME

Deletion

Nondisjunction • Chromosomes don’t separate during meiosis • Produces gametes with loss or gain of a whole chromosome

Polyploidy • Offspring with 3 n-5 n chromosomes • Often a nondisjunction event • Occurs in plants • Spray chemical that prevents cell plate formation • Enlarged fruit

Gene Mutations • Point Mutation= single nucleotide change – Deletion (causes Frameshift) – Addition (causes Frameshift) – Substitution • Missense Mutation=altered nucleotide causes for altered codon and altered protein – Ex. Sickle Cell Anemia=Glu to Val switch in Hemoglobin Gene • Nonsense Mutation=altered nucleotide causes for a premature STOP codon • Silent Mutation=No change in protein

FACT • Mutations are rare events. • This is surprising! • Humans inherit 3 x 109 base pairs of DNA from each parent. Just considering singlebase substitutions, this means that each cell has 6 billion (6 x 109) different base pairs that can be the target of a substitution.

Jumping Genes and Mutations • Barbara Mc. Clintock: – Some genes can jump from area to area and jump into and inactivate a gene – Cross-species jumping

Transposons (“Jumping Genes”): Encodes a Transposase to cut and paste Transposon Future Gene Therapy vehicle

Human Genetic Diseases • Tool to track diseases in a family: Pedigree Chart Intercourse Guys are squares Children Girls are circles Shading is disease

Pedigree Chart • Autosomal Dominant (Huntington's)

Pedigree Chart • Autosomal Recessive

Pedigree Charts • X-linked Recessive

Pedigree Charts • X-linked Dominant

Human Genetic Diseases X-Linked Recessive: • Colorblindness • Hemophilia • Duchenne Muscular Dystrophy (muscle breaks down-death by teens)

Human Genetic Diseases. Autosomal Point Mutations • Sickle Cell Anemia – Recessive – Point mutation, Glu to Val switch in Hemoglobin – Carriers resistant to Malaria – Diseased people die early – Affects people of African – No Cure

Human Genetic Diseases. Autosomal Point Mutations • Autosomal Genetic Diseases Phenylketonuria (PKU) – Recessive – Don’t have enzyme that breaks down phenylalanine – Brain damage – Diagnosed from new baby urine – Avoid brain damage with low phenylalanine diet

Human Genetic Diseases. Autosomal Point Mutations • Tay-Sachs – Recessive – Brain damage – Lack enzyme to breakdown lipids in brain – Affects Jewish, Eastern Europe Origin – Death early – No Cure

Human Genetic Diseases. Autosomal Point Mutations • Cystic Fibrosis – Recessive – Glands make thick mucus that builds up in lungs – Affects European Origin – Gene Therapy Cure Target

Human Genetic Diseases. Autosomal Point Mutations • Huntington’s Disease – Dominant!!!!!!! – Progressive breakdown of brain cells and death – Begins in 30 s – Some evidence for protective effect from getting cancer and higher repro potential

Human Genetic Diseases-Whole Chromosome Problems • Down Syndrome – Extra Chromosome #21 – Mental Retardation and Physical abnormalities – From Nondisjunction Mutation

Human Genetic Diseases-Whole Chromosome Problems • Turner’s Syndrome – Female with only one X chromosome (XO) – Undeveloped sexual characteristics

Human Genetic Diseases-Whole Chromosome Problems • Klinefelter’s Syndrome – XXY Genotype – Male with undeveloped sex organs

Detection Methods for Genetic Diseases • Karyotyping – Picture of chromosomes

Detection Methods for Genetic Diseases • Amniocentesis – Extract amniotic fluid – Take sample of shed baby cells – Can do karyotyping – Can detect disease genes – Can be done 1518 weeks

Detection Methods for Genetic Diseases • Chorionic Villus Sampling – Take chorion sample – Probe for disease genes – Can do karyotype – Can be done at 10 -12 weeks

What to do with the genetic knowledge? • Genetic Counseling – Tells of probabilities for offspring to be diseased – Draws pedigree chart

Detection Methods for Abnormalities • Ultrasound – Look for structural abnormalities – Blast soundwaves

Detection Methods for Abnormalities • Fetoscopy – Camera’s look – Can have attachments for sample collection

Genetic Engineering Man’s command over genes 1. Selective Breeding • Mate only genetically desirable animals 2. Inbreeding – Keep desired traits in family of organisms by breeding relatives with each other – High chance of homozygous recessive – Ex. Pure bred dogs

Genetic Engineering 3. Outbreeding – Breed unrelated organisms to introduce beneficial genes – Ex. Hybrid vigor • Dumb male donkey and a female horse=strong, smart mule • Can create organisms resistant to disease from a cross

Genetic Engineering 4. Create mutations – Seedless fruit – Large polyploidy fruit (chemical prevents disjunction) 5. Cloning – Producing organisms that are genetically alike (like what asexual organisms do!) – Dolly the Sheep

How to make Dolly

The future of cloning:

Genetic Engineering 6. Recombinant DNA Technology – Creating altered DNA via gene splicing – Ex. Get Bacteria to make a product of a human gene

How to create Recombinant DNA: • Extract bacterial Plasmid DNA • Cut open using Restriction Enzymes • Insert desired gene • Put back into bacteria • Bacteria replicate in culture (all will be clones)

• Insulin extracted from bacterial culture

Transduction of Bacteria: Ways of putting Recombinant DNA into bacteria:

Vs. Bacterial Transformation

Recombinant DNA and Gene Therapy • Background: – Lytic vs. Lysogenic Life Cycle of virus

Recombinant DNA and Gene Therapy • Let’s use the lysogenic lifecycle to our advantage!

Risks • Random insertion into genome • Cases of leukemia developed in gene therapy patients • Sometimes viruses redevelop repro ability

Epistasis • Multiple genes interacting to produce a given phenotype

Human Height • Height: (80%) Controlled by multiple genes and (20%) environment (ie. Nutrition) • So far over 400 genome locations found related to height

Labrador Retriever Color • Determined by the B and E alleles – B (black pigment), b (brown pigment) – E (get pigment in hair), e (no pigment in hair)

Human Eye Color Blue Recessive but 80% of Icelanders have Blue or Green 2% of world has green Majority of world has type of Brown eyes